From 28c4aad5e175596f113e596c8a45a1614bca3c8f Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 15:34:20 +0000 Subject: [PATCH 001/268] Updated build-celltype-ref workflow to take only one label based on param --- bin/train_SingleR.R | 44 +++++++++++++++++++++----------------- build-celltype-ref.nf | 2 ++ config/profile_ccdl.config | 3 ++- 3 files changed, 28 insertions(+), 21 deletions(-) diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index 1cb04144..9e4ea813 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -19,14 +19,20 @@ option_list <- list( opt_str = c("--ref_file"), type = "character", help = "path to rds file with reference dataset to use for cell type annotation. - These reference datasets must contain annotations labeled with - `label.main`, `label.fine`, and `label.ont`." + These reference datasets must contain annotations labeled with the given + `label_name` (default 'label.ont')." ), make_option( opt_str = c("--output_file"), type = "character", help = "path to output rds file to store trained model for reference dataset." ), + make_option( + opt_str = c("--label_name"), + type = "character", + default = "label.ont", + help = "name of cell type label to use for training the reference dataset." + ), make_option( opt_str = c("--fry_tx2gene"), type = "character", @@ -72,9 +78,13 @@ if(opt$threads > 1){ # read in model ref_data <- readr::read_rds(opt$ref_file) -# check that ref data contains correct labels -if(!all(c("label.main", "label.fine", "label.ont") %in% colnames(colData(ref_data)))){ - stop("Reference dataset must contain `label.main`, `label.fine`, and `label.ont` in `colData`.") +# check that ref data contains correct labels, and set up label column for later +label_col <- opt$label_name +names(label_col) <- label_col +if(!label_col %in% colnames(colData(ref_data))){ + stop( + glue::glue("Reference dataset must contain `{label_col}` in `colData`.") + ) } # read in tx2gene @@ -91,19 +101,13 @@ if (length(gene_ids) == 0){ # Train models ----------------------------------------------------------------- -label_cols <- c("label.main", "label.fine", "label.ont") -names(label_cols) <- label_cols - -models <- label_cols |> - purrr::map(\(label_col) { - SingleR::trainSingleR( - ref_data, - labels = colData(ref_data)[, label_col], - genes = "de", - # only use genes found in index - restrict = gene_ids, - BPPARAM = bp_param - )}) - +singler_model <- SingleR::trainSingleR( + ref_data, + labels = colData(ref_data)[, label_col], + genes = "de", + # only use genes found in index + restrict = gene_ids, + BPPARAM = bp_param +) # export models -readr::write_rds(models, opt$output_file) +readr::write_rds(singler_model, opt$output_file) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index d03527c4..de8df5b6 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -2,6 +2,7 @@ nextflow.enable.dsl=2 params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv" +params. process train_singler_models { container params.SCPCATOOLS_CONTAINER @@ -20,6 +21,7 @@ process train_singler_models { --ref_file ${celltype_ref} \ --output_file ${celltype_model} \ --fry_tx2gene ${tx2gene} \ + --label_name ${params.label_name} \ --seed ${params.seed} \ --threads ${task.cpus} """ diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index 55958fbe..40902a34 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -12,8 +12,9 @@ params{ // a set of run_ids for testing run_ids = "SCPCR000001,SCPCS000101" - // cell type references + // cell type references and SingleR label of interest celltype_refs_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" + label_name = "label.ont" // Private CCDL containers CELLRANGER_CONTAINER = '589864003899.dkr.ecr.us-east-1.amazonaws.com/scpca-cellranger:6.1.2' From 217d9ae27df0a3489bad5d22bc47b278ce89e6ea Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 15:46:12 +0000 Subject: [PATCH 002/268] add default param for reference rds files --- config/profile_ccdl.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index 40902a34..4c9eed50 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -15,6 +15,10 @@ params{ // cell type references and SingleR label of interest celltype_refs_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" label_name = "label.ont" + + // output directory for cell type references + celltype_ref_dir = "s3://scpca-references/celltype/singler_models" + // Private CCDL containers CELLRANGER_CONTAINER = '589864003899.dkr.ecr.us-east-1.amazonaws.com/scpca-cellranger:6.1.2' From 86372233cc47dc4f4c017cb05e4df8442f698d8a Mon Sep 17 00:00:00 2001 From: Stephanie Date: Mon, 17 Jul 2023 11:59:19 -0400 Subject: [PATCH 003/268] woops typo --- build-celltype-ref.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index de8df5b6..efcb7862 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -2,7 +2,6 @@ nextflow.enable.dsl=2 params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv" -params. process train_singler_models { container params.SCPCATOOLS_CONTAINER From 24115d597a94500a6e97e5a4133a6fbe1dcd0f2f Mon Sep 17 00:00:00 2001 From: Stephanie Date: Mon, 17 Jul 2023 11:59:57 -0400 Subject: [PATCH 004/268] remove new directory addition since i think this might be a diff typo, maybeeee --- config/profile_ccdl.config | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index 4c9eed50..1ccab0d1 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -15,10 +15,7 @@ params{ // cell type references and SingleR label of interest celltype_refs_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" label_name = "label.ont" - - // output directory for cell type references - celltype_ref_dir = "s3://scpca-references/celltype/singler_models" - + // Private CCDL containers CELLRANGER_CONTAINER = '589864003899.dkr.ecr.us-east-1.amazonaws.com/scpca-cellranger:6.1.2' From 5555e6231ed49ada285008bdba41c032182be049 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Mon, 17 Jul 2023 12:03:19 -0400 Subject: [PATCH 005/268] No typos before, just need more clarifying comments --- config/reference_paths.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/reference_paths.config b/config/reference_paths.config index befd5703..8de5ad45 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -7,5 +7,5 @@ ref_rootdir = 's3://scpca-references' barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references -celltype_ref_dir = "${params.ref_rootdir}/celltype/references" -celltype_model_dir = "${params.ref_rootdir}/celltype/singler_models" +celltype_ref_dir = "${params.ref_rootdir}/celltype/references" // original (generally celldex) files themselves +celltype_model_dir = "${params.ref_rootdir}/celltype/singler_models" // models build from original (celldex) files From 3fbae98a8f30e4e879e368085f05a36434f62b7a Mon Sep 17 00:00:00 2001 From: Stephanie Date: Mon, 17 Jul 2023 12:45:07 -0400 Subject: [PATCH 006/268] WIP: update classification script --- bin/classify_SingleR.R | 79 ++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 49 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 9cdb2a67..43503773 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -21,11 +21,17 @@ option_list <- list( help = "path to output rds file to store processed sce object. Must end in .rds" ), make_option( - opt_str = c("--singler_models"), + opt_str = c("--singler_model_file"), type = "character", - help = "list of models generated for use with SingleR. Each input file contains - a list of models generated from a single reference, one each for each label type: - `label.main`, `label.fine`, and `label.ont`." + help = "path to file containing model generated for use with SingleR containing labels + for the given `label_name`." + ), + # TODO: do we even need this? We could check that the label is correct, but maybe unnecessary since only 1 is expected anyways + make_option( + opt_str = c("--label_name"), + type = "character", + default = "label.ont", + help = "name of cell type label to use for annotation in the reference dataset." ), make_option( opt_str = c("--seed"), @@ -53,13 +59,9 @@ if(!file.exists(opt$input_sce_file)){ } # check that references all exist -model_files <- unlist(stringr::str_split(opt$singler_models, ",")) -if(!all(file.exists(model_files))){ - missing_files <- model_files[which(!file.exists(model_files))] - glue::glue(" - Missing model file(s): {missing_files} - ") - stop("Please make sure that all provided SingleR models exist.") +singler_model_file <- opt$singler_model_file +if(!file.exists(singler_model_file)) { + stop(glue::glue("Provided model file {singler_model_file} is missing.")) } # set up multiprocessing params @@ -72,44 +74,23 @@ if(opt$threads > 1){ # read in input rds file sce <- readr::read_rds(opt$input_sce_file) -# read in references as a list of lists -# each file contains a named list of models generated using the same reference dataset -# but unique labels in the reference dataset -model_names <- stringr::str_remove(basename(model_files), "_model.rds") -names(model_files) <- model_names -model_list <- purrr::map(model_files, readr::read_rds) |> - # ensure we have label type before reference name - # example: label.main_HumanPrimaryCellAtlasData - # where `label.main` is the name of the model stored in the file and - # `HumanPrimaryCellAtlasData` is the name of the reference used for each file containing a list of models - purrr::imap(\(model_list, ref_name){ - names(model_list) <- glue::glue("{names(model_list)}_{ref_name}") - model_list - }) |> - purrr::flatten() - -# SingleR classify ------------------------------------------------------------- - -# create a partial function for mapping easily -classify_sce <- purrr::partial(SingleR::classifySingleR, - test = sce, - fine.tune=TRUE, - BPPARAM = bp_param) -# run singleR for all provided models -all_singler_results <- model_list |> - purrr::map(classify_sce) - -# Annotate sce ----------------------------------------------------------------- - -# create a dataframe with a single column of annotations for each model used -all_annotations_df <- all_singler_results |> - purrr::map_dfc(\(result) result$pruned.labels ) |> - DataFrame() - -colData(sce) <- cbind(colData(sce), all_annotations_df) - -# store results in metadata -metadata(sce)$singler_results <- all_singler_results +# read in model +singler_model <- readr::read_rds(singler_model_file) + +# SingleR classify and annotate SCE------------------------------------------------------------- + +singler_results <- SingleR::classifySingleR( + ref = singler_model, + test = sce, + fine.tune = TRUE, + BPPARAM = bp_param +) + +# add annotations to SCE colData, simply +sce$singler_results$pruned.labels + +# store full SingleR results in metadata +metadata(sce)$singler_results <- singler_results # export sce with annotations added readr::write_rds(sce, From 41db7fd91239b6a47dcc346e836809eb2fee835e Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 16:51:26 +0000 Subject: [PATCH 007/268] a little debugging --- bin/classify_SingleR.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 43503773..49a2f4fd 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -80,14 +80,14 @@ singler_model <- readr::read_rds(singler_model_file) # SingleR classify and annotate SCE------------------------------------------------------------- singler_results <- SingleR::classifySingleR( - ref = singler_model, + trained = singler_model, test = sce, fine.tune = TRUE, BPPARAM = bp_param ) # add annotations to SCE colData, simply -sce$singler_results$pruned.labels +sce$pruned.labels <- singler_results$pruned.labels # store full SingleR results in metadata metadata(sce)$singler_results <- singler_results From 4987b43027886d463e4566ae703f96f5f0294d85 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 17:16:03 +0000 Subject: [PATCH 008/268] variable name updates to match 1 model approach --- modules/classify-celltypes.nf | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 8e12893c..0a21dcd7 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -5,23 +5,19 @@ process classify_singleR { label 'cpus_4' publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: - tuple val(meta), path(processed_rds), path(singler_models) + tuple val(meta), path(processed_rds), path(singler_model_file) output: tuple val(meta), path(annotated_rds) script: annotated_rds = "${meta.library_id}_annotated.rds" - singler_list = singler_models in List ? singler_models.join(',') : singler_models """ classify_SingleR.R \ --input_sce_file ${processed_rds} \ --output_sce_file ${annotated_rds} \ - --singler_models ${singler_list} \ + --singler_model_file ${singler_model_file} \ --seed ${params.seed} \ --threads ${task.cpus} - """ - - } workflow annotate_celltypes { @@ -32,9 +28,8 @@ workflow annotate_celltypes { .splitCsv(header: true, sep: '\t') .map{[ project_id = it.scpca_project_id, - singler_model = "${params.celltype_model_dir}/${it.celltype_ref_name}_model.rds" + singler_model_file = "${params.celltype_model_dir}/${it.celltype_ref_name}_model.rds" ]} - .groupTuple(by: 0) // group by project id // create channel with grouped meta, processed sce object, and all references to use grouped_celltype_ch = processed_sce_channel @@ -44,7 +39,7 @@ workflow annotate_celltypes { .map{[ it[0], // meta it[1], // processed rds - it[2] // tuple of reference models + it[2] // reference model file ]} classify_singleR(grouped_celltype_ch) From ad711562f96438b46fd943bf6ceec40424df546f Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 17:20:16 +0000 Subject: [PATCH 009/268] really dont need label_name here, and comment update --- bin/classify_SingleR.R | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 49a2f4fd..c5fa413c 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -23,15 +23,7 @@ option_list <- list( make_option( opt_str = c("--singler_model_file"), type = "character", - help = "path to file containing model generated for use with SingleR containing labels - for the given `label_name`." - ), - # TODO: do we even need this? We could check that the label is correct, but maybe unnecessary since only 1 is expected anyways - make_option( - opt_str = c("--label_name"), - type = "character", - default = "label.ont", - help = "name of cell type label to use for annotation in the reference dataset." + help = "path to file containing a single model generated for SingleR annotation" ), make_option( opt_str = c("--seed"), From 108ee191731cba5c2ec8cb21b2715a6f7e957bb7 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 17 Jul 2023 17:26:33 +0000 Subject: [PATCH 010/268] add test metadata file for PR testing ONLY --- test-celltype-metadata.tsv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 test-celltype-metadata.tsv diff --git a/test-celltype-metadata.tsv b/test-celltype-metadata.tsv new file mode 100644 index 00000000..57e4023b --- /dev/null +++ b/test-celltype-metadata.tsv @@ -0,0 +1,2 @@ +scpca_project_id celltype_ref_name celltype_singler_file +SCPCP000007 test-BlueprintEncodeData celldex-BlueprintEncodeData.rds From 8de6b2cca956f32987619cf442481682a36d7ab9 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 18 Jul 2023 09:20:57 -0400 Subject: [PATCH 011/268] remove name assignment. use ontoProc to obtain and save cell names corresponding to ontology ids in the model object --- bin/train_SingleR.R | 27 ++++++++++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index 9e4ea813..ff7adc37 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -19,7 +19,7 @@ option_list <- list( opt_str = c("--ref_file"), type = "character", help = "path to rds file with reference dataset to use for cell type annotation. - These reference datasets must contain annotations labeled with the given + These reference datasets must contain annotations labeled with the given `label_name` (default 'label.ont')." ), make_option( @@ -80,7 +80,6 @@ ref_data <- readr::read_rds(opt$ref_file) # check that ref data contains correct labels, and set up label column for later label_col <- opt$label_name -names(label_col) <- label_col if(!label_col %in% colnames(colData(ref_data))){ stop( glue::glue("Reference dataset must contain `{label_col}` in `colData`.") @@ -99,7 +98,7 @@ if (length(gene_ids) == 0){ stop("Provided tx2gene tsv file does not contain any genes.") } -# Train models ----------------------------------------------------------------- +# Train model ----------------------------------------------------------------- singler_model <- SingleR::trainSingleR( ref_data, @@ -109,5 +108,27 @@ singler_model <- SingleR::trainSingleR( restrict = gene_ids, BPPARAM = bp_param ) + +# If the label is `label.ont` (default), save corresponding cell label names +if (label_col == "label.ont") { + cl_ont <- ontoProc::getCellOnto() + + # grab ontology ids from singler_model which are stored as + # `original.exprs` names (`original.exprs` itself is an empty list) + ontology_ids <- names(singler_model$original.exprs) + + # grab corresponding cell names + cell_names <- purrr::map( + ontology_ids, + \(cl_id) cl_ont$name[cl_id] + ) |> unlist() + + # save data frame with _matching_ ontology ids and cell names to model object + # use tibble to avoid rownames + singler_model$cell_ontology_df <- tibble::tibble( + ontology_id = names(cell_names), + ontology_cell_names = cell_names + ) +} # export models readr::write_rds(singler_model, opt$output_file) From 4ca7239127e6213b7a5f18ccec237e503237be78 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 18 Jul 2023 09:33:29 -0400 Subject: [PATCH 012/268] Add stub, and clean up a different stub I noticed while I'm here --- modules/classify-celltypes.nf | 5 +++++ modules/sce-processing.nf | 4 ++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 0a21dcd7..69c4d5bb 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -18,6 +18,11 @@ process classify_singleR { --seed ${params.seed} \ --threads ${task.cpus} """ + stub: + annotated_rds = "${meta.library_id}_annotated.rds" + """ + touch "${annotated_rds}" + """ } workflow annotate_celltypes { diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 38b2dcfb..90cbea59 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -25,7 +25,7 @@ process make_unfiltered_sce{ stub: unfiltered_rds = "${meta.library_id}_unfiltered.rds" """ - touch "${meta.library_id}_unfiltered.rds" + touch ${unfiltered_rds} """ } @@ -46,7 +46,7 @@ process make_merged_unfiltered_sce{ // add feature metadata as an element of the main meta object meta['feature_type'] = feature_meta.technology.split('_')[0] meta['feature_meta'] = feature_meta - + // If feature_type is "CITEseq", make it "adt" if (meta['feature_type'] == "CITEseq") { meta['feature_type'] = "adt" From f001d77d9c77b5239e8c31d498419bbbc8e62bcf Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 18 Jul 2023 09:37:36 -0400 Subject: [PATCH 013/268] Update nextflow map and add/update comments --- modules/classify-celltypes.nf | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 69c4d5bb..6d62f6e8 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -36,16 +36,14 @@ workflow annotate_celltypes { singler_model_file = "${params.celltype_model_dir}/${it.celltype_ref_name}_model.rds" ]} - // create channel with grouped meta, processed sce object, and all references to use + // create channel grouped_celltype_ch as: [meta, processed sce object, SingleR reference model] + // input processed_sce_channel is [meta, unfiltered, filtered, processed] grouped_celltype_ch = processed_sce_channel .map{[it[0]["project_id"]] + it} .combine(celltype_ch, by: 0) .map{it.drop(1)} // remove extra project ID - .map{[ - it[0], // meta - it[1], // processed rds - it[2] // reference model file - ]} + // creates [meta, processed, SingleR reference model] + .map{ it[0..2] } classify_singleR(grouped_celltype_ch) From 30a218645d200ac75196a6e7853152260c4fa034 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 18 Jul 2023 15:20:46 -0400 Subject: [PATCH 014/268] Update deprecated function, fix model parsing code, simplify other code --- bin/train_SingleR.R | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index ff7adc37..c1dd3ad3 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -111,17 +111,13 @@ singler_model <- SingleR::trainSingleR( # If the label is `label.ont` (default), save corresponding cell label names if (label_col == "label.ont") { - cl_ont <- ontoProc::getCellOnto() + cl_ont <- ontoProc::getOnto("cellOnto") - # grab ontology ids from singler_model which are stored as - # `original.exprs` names (`original.exprs` itself is an empty list) - ontology_ids <- names(singler_model$original.exprs) + # grab ontology ids from singler_model + ontology_ids <- singler_model$labels$unique # grab corresponding cell names - cell_names <- purrr::map( - ontology_ids, - \(cl_id) cl_ont$name[cl_id] - ) |> unlist() + cell_names <- cl_ont$name[ontology_ids] # save data frame with _matching_ ontology ids and cell names to model object # use tibble to avoid rownames From c12f3ad8e70d46ad4aeb43e3160d89d53031ec6d Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 18 Jul 2023 15:33:51 -0400 Subject: [PATCH 015/268] goodbye test TSV since scpca-admin is now updated --- test-celltype-metadata.tsv | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 test-celltype-metadata.tsv diff --git a/test-celltype-metadata.tsv b/test-celltype-metadata.tsv deleted file mode 100644 index 57e4023b..00000000 --- a/test-celltype-metadata.tsv +++ /dev/null @@ -1,2 +0,0 @@ -scpca_project_id celltype_ref_name celltype_singler_file -SCPCP000007 test-BlueprintEncodeData celldex-BlueprintEncodeData.rds From bd942205cdd2a378b3b18ee479b4f8e8884ddbcc Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 19 Jul 2023 09:47:01 -0400 Subject: [PATCH 016/268] bump scpcaTools container to edge so we can have ontoProc in image --- config/containers.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/containers.config b/config/containers.config index d7db889b..e01373a3 100644 --- a/config/containers.config +++ b/config/containers.config @@ -1,5 +1,5 @@ // Docker container images -SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:v0.2.2' +SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:edge' ALEVINFRY_CONTAINER = 'quay.io/biocontainers/alevin-fry:0.7.0--h9f5acd7_1' BCFTOOLS_CONTAINER = 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' From eb4a0e9690c27576072b93939edf508257ccc5bb Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 19 Jul 2023 17:47:39 -0400 Subject: [PATCH 017/268] Update R code to save reference information during training and add that information to final sce after classification. Update cell typing module to pass in the reference label to R script. Still needs testing --- bin/classify_SingleR.R | 33 ++++++++++++++++++++++++++++++--- bin/train_SingleR.R | 7 ++++++- modules/classify-celltypes.nf | 1 + 3 files changed, 37 insertions(+), 4 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index c5fa413c..ecd6db19 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -25,6 +25,12 @@ option_list <- list( type = "character", help = "path to file containing a single model generated for SingleR annotation" ), + make_option( + opt_str = c("--label_name"), + type = "character", + default = "label.ont", + help = "label used when building the SingleR reference" + ), make_option( opt_str = c("--seed"), type = "integer", @@ -78,11 +84,32 @@ singler_results <- SingleR::classifySingleR( BPPARAM = bp_param ) -# add annotations to SCE colData, simply -sce$pruned.labels <- singler_results$pruned.labels +# add annotations to SCE colData +if (opt$label_name == "label.ont") { + # If ontologies were used, create ontology column and join in the cell names + sce$singler_celltype_ontology <- singler_results$pruned.labels + + colData(sce) <- colData(sce) |> + as.data.frame() |> + dplyr::left_join( + singler_model$cell_ontology_df, + by = c("singler_celltype_ontology" = "ontology_id") + ) |> + # this is the new column that was joined in with the cell names + dplyr::rename(singler_celltype_annotation = ontology_cell_names) |> + DataFrame() + -# store full SingleR results in metadata +} else { + # otherwise, just add cell names + sce$singler_celltype_annotation <- singler_results$pruned.labels +} + +# store full SingleR results in metadata, as well as other SingleR parameters metadata(sce)$singler_results <- singler_results +metadata(sce)$singler_reference <- singler_model$reference_name +metadata(sce)$singler_reference_label <- singler_model$reference_label + # export sce with annotations added readr::write_rds(sce, diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index c1dd3ad3..d02dc5d2 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -123,8 +123,13 @@ if (label_col == "label.ont") { # use tibble to avoid rownames singler_model$cell_ontology_df <- tibble::tibble( ontology_id = names(cell_names), - ontology_cell_names = cell_names + ontology_cell_names = unname(cell_names) ) } + +# Save reference name and label to model object +singler_model$reference_name <- stringr::str_replace(opt$ref_file, "_model.rds$", "") +singler_model$reference_label <- label_col + # export models readr::write_rds(singler_model, opt$output_file) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 6d62f6e8..e14b2141 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -15,6 +15,7 @@ process classify_singleR { --input_sce_file ${processed_rds} \ --output_sce_file ${annotated_rds} \ --singler_model_file ${singler_model_file} \ + --label_name ${params.label_name} \ --seed ${params.seed} \ --threads ${task.cpus} """ From e579b20b37bb5c13564442ed6dd4357695c1f0cb Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 19 Jul 2023 18:36:46 -0400 Subject: [PATCH 018/268] take the reference name from output file, not input file --- bin/train_SingleR.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index d02dc5d2..ea97d803 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -128,7 +128,7 @@ if (label_col == "label.ont") { } # Save reference name and label to model object -singler_model$reference_name <- stringr::str_replace(opt$ref_file, "_model.rds$", "") +singler_model$reference_name <- stringr::str_replace(opt$output_file, "_model.rds$", "") singler_model$reference_label <- label_col # export models From 38849f30bef42599e9ce60da21b994f47f9dd892 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 20 Jul 2023 11:09:50 -0400 Subject: [PATCH 019/268] retain rownames after modifying colData --- bin/classify_SingleR.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index ecd6db19..870081c8 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -97,7 +97,8 @@ if (opt$label_name == "label.ont") { ) |> # this is the new column that was joined in with the cell names dplyr::rename(singler_celltype_annotation = ontology_cell_names) |> - DataFrame() + # make sure we keep rownames + DataFrame(row.names = colData(sce)$barcodes) } else { From dd635298f61e275c76688476a4ee61f063366bca Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 20 Jul 2023 11:16:34 -0500 Subject: [PATCH 020/268] move reference metadata and add process for saving celldex --- bin/save_celldex_refs.R | 33 ++++++++++++++ build-celltype-ref.nf | 52 +++++++++++++++++++--- config/profile_ccdl.config | 2 +- config/reference_paths.config | 5 ++- modules/classify-celltypes.nf | 2 +- references/celltype-reference-metadata.tsv | 8 ++++ 6 files changed, 91 insertions(+), 11 deletions(-) create mode 100644 bin/save_celldex_refs.R create mode 100644 references/celltype-reference-metadata.tsv diff --git a/bin/save_celldex_refs.R b/bin/save_celldex_refs.R new file mode 100644 index 00000000..1b2bce25 --- /dev/null +++ b/bin/save_celldex_refs.R @@ -0,0 +1,33 @@ +#!/usr/bin/env Rscript + +# this script is used to download celldex references and save them as RDS files + +library(optparse) +library(celldex) + +option_list <- list( + make_option( + opt_str = c("--ref_name"), + type = "character", + help = "name associated with celldex reference, e.g., HumanPrimaryCellAtlasData" + ), + make_option( + opt_str = c("--ref_file"), + type = "character", + help = "path to save reference file" + ) +) + +# Parse options +opt <- parse_args(OptionParser(option_list = option_list)) + +# check that provided ref name is in celldex package +if(! opt$ref_name %in% ls("package:celldex")){ + stop(glue::glue("Provided `ref_name` `{opt$ref_name}` does not match a celldex dataset.")) +} + +# get a reference library from celldex: +ref <- do.call(`::`, args = list("celldex", opt$ref_name))(ensembl = TRUE) + +# export ref data +readr::write_rds(ref, opt$ref_file, compress = "gz") diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index efcb7862..717fd043 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -3,13 +3,31 @@ nextflow.enable.dsl=2 params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv" +process save_singler_refs { + container params.SCPCATOOLS_CONTAINER + publishDir "${params.celltype_ref_dir}/singler_references" + label 'mem_8' + input: + tuple val(ref_name), val(ref_database) + output: + path ref_file + script: + ref_file = "${ref_database}-${ref_name}.rds" + """ + save_singler_refs.R \ + --ref_name ${ref_name} \ + --ref_file ${ref_file} + """ + +} + process train_singler_models { container params.SCPCATOOLS_CONTAINER - publishDir "${params.celltype_model_dir}" + publishDir "${params.celltype_ref_dir}/singler_models" label 'cpus_4' label 'mem_16' input: - tuple path(celltype_ref), val(ref_name) + tuple val(ref_name), path(ref_file) path tx2gene output: path celltype_model @@ -29,16 +47,36 @@ process train_singler_models { workflow build_celltype_ref { // create channel of cell type ref files and names - celltype_refs_ch = Channel.fromPath(params.celltype_refs_metafile) + celltype_refs_ch = Channel.fromPath(params.celltype_ref_metadata) .splitCsv(header: true, sep: '\t') + .branch{ + singler: it.celltype_method == "SingleR" + cellassign: it.celltype_method == "CellAssign" + } + + // singler refs to download and train + singler_refs_ch = celltype_refs_ch.singler .map{[ - celltype_ref_file = "${params.celltype_ref_dir}/${it.celltype_singler_file}", - ref_name = it.celltype_ref_name + ref_name: it.celltype_ref_name, + ref_database: it.celltype_ref_database ]} - .unique() // remove any duplicates + + // download and save reference files + save_singler_refs(singler_refs_ch) // train cell type references using SingleR - train_singler_models(celltype_refs_ch, params.t2g_3col_path) + train_singler_models(save_singler_refs.out, params.t2g_3col_path) + + // cellassign refs + cellassign_refs_ch = celltype_refs_ch.cellassign + // create a channel with ref_name, database, organs + .map{[ + ref_name: it.celltype_ref_name, + ref_database: it.celltype_ref_database, + organs: it.organs + ]} + + generate_cellassign_refs(cellassign_refs_ch, params.panglao_marker_genes) } workflow { diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index 1ccab0d1..d3f35313 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -13,7 +13,7 @@ params{ run_ids = "SCPCR000001,SCPCS000101" // cell type references and SingleR label of interest - celltype_refs_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" + celltype_project_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" label_name = "label.ont" diff --git a/config/reference_paths.config b/config/reference_paths.config index 8de5ad45..a990c0d1 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -7,5 +7,6 @@ ref_rootdir = 's3://scpca-references' barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references -celltype_ref_dir = "${params.ref_rootdir}/celltype/references" // original (generally celldex) files themselves -celltype_model_dir = "${params.ref_rootdir}/celltype/singler_models" // models build from original (celldex) files +celltype_ref_dir = "${params.ref_rootdir}/celltype" +celltype_ref_metadata = "${projectDir}/references/celltype-ref-metadata.tsv" +panglao_marker_genes = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" \ No newline at end of file diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index e14b2141..0fb7918c 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -30,7 +30,7 @@ workflow annotate_celltypes { take: processed_sce_channel main: // channel with celltype model and project ids - celltype_ch = Channel.fromPath(params.celltype_refs_metafile) + celltype_ch = Channel.fromPath(params.celltype_project_metafile) .splitCsv(header: true, sep: '\t') .map{[ project_id = it.scpca_project_id, diff --git a/references/celltype-reference-metadata.tsv b/references/celltype-reference-metadata.tsv new file mode 100644 index 00000000..8ac944fc --- /dev/null +++ b/references/celltype-reference-metadata.tsv @@ -0,0 +1,8 @@ +celltype_ref_name celltype_ref_database celltype_method organs +BlueprintEncodeData celldex SingleR NA +DatabaseImmuneCellExpressionData celldex SingleR NA +HumanPrimaryCellAtlasData celldex SingleR NA +MonacoImmuneData celldex SingleR NA +blood PanglaoDB CellAssign Blood, Bone, Immune system +muscle PanglaoDB CellAssign Connective tissue, Immune system, Skeletal muscle, Smooth muscle +brain PanglaoDB CellAssign Brain, Immune system From 85cc4bd7f182229f19d6007d714178a37ea8d0eb Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 20 Jul 2023 12:03:22 -0500 Subject: [PATCH 021/268] add stubs --- add-celltypes.nf | 4 ++-- bin/{save_celldex_refs.R => save_singler_refs.R} | 0 build-celltype-ref.nf | 14 +++++++++++--- config/reference_paths.config | 2 +- 4 files changed, 14 insertions(+), 6 deletions(-) rename bin/{save_celldex_refs.R => save_singler_refs.R} (100%) mode change 100644 => 100755 diff --git a/add-celltypes.nf b/add-celltypes.nf index 35bf5542..8a641a06 100644 --- a/add-celltypes.nf +++ b/add-celltypes.nf @@ -11,8 +11,8 @@ if (!file(params.run_metafile).exists()) { param_error = true } -if (!file(params.celltype_refs_metafile).exists()) { - log.error("The 'celltype_refs_metafile' file '${params.celltype_refs_metafile}' can not be found.") +if (!file(params.celltype_project_metafile).exists()) { + log.error("The 'celltype_project_metafile' file '${params.celltype_project_metafile}' can not be found.") param_error = true } diff --git a/bin/save_celldex_refs.R b/bin/save_singler_refs.R old mode 100644 new mode 100755 similarity index 100% rename from bin/save_celldex_refs.R rename to bin/save_singler_refs.R diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 717fd043..a7877cea 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -18,6 +18,11 @@ process save_singler_refs { --ref_name ${ref_name} \ --ref_file ${ref_file} """ + stub: + ref_file = "${ref_database}-${ref_name}.rds" + """ + touch ${ref_file} + """ } @@ -27,7 +32,7 @@ process train_singler_models { label 'cpus_4' label 'mem_16' input: - tuple val(ref_name), path(ref_file) + tuple val(ref_name), path(celltype_ref) path tx2gene output: path celltype_model @@ -42,6 +47,11 @@ process train_singler_models { --seed ${params.seed} \ --threads ${task.cpus} """ + stub: + celltype_model = "${ref_name}_model.rds" + """ + touch ${celltype_model} + """ } workflow build_celltype_ref { @@ -75,8 +85,6 @@ workflow build_celltype_ref { ref_database: it.celltype_ref_database, organs: it.organs ]} - - generate_cellassign_refs(cellassign_refs_ch, params.panglao_marker_genes) } workflow { diff --git a/config/reference_paths.config b/config/reference_paths.config index a990c0d1..e1b9be0a 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -8,5 +8,5 @@ barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references celltype_ref_dir = "${params.ref_rootdir}/celltype" -celltype_ref_metadata = "${projectDir}/references/celltype-ref-metadata.tsv" +celltype_ref_metadata = "${projectDir}/references/celltype-reference-metadata.tsv" panglao_marker_genes = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" \ No newline at end of file From 654bac7681f9b69bb2b4abb8992904a33acdf87a Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 20 Jul 2023 12:19:04 -0500 Subject: [PATCH 022/268] add panglao file --- references/PanglaoDB_markers_27_Mar_2020.tsv | 8287 ++++++++++++++++++ 1 file changed, 8287 insertions(+) create mode 100644 references/PanglaoDB_markers_27_Mar_2020.tsv diff --git a/references/PanglaoDB_markers_27_Mar_2020.tsv b/references/PanglaoDB_markers_27_Mar_2020.tsv new file mode 100644 index 00000000..9c0c3a37 --- /dev/null +++ b/references/PanglaoDB_markers_27_Mar_2020.tsv @@ -0,0 +1,8287 @@ +species official gene symbol cell type nicknames ubiquitousness index product description gene type canonical marker germ layer organ sensitivity_human sensitivity_mouse specificity_human specificity_mouse +Mm Hs CTRB1 Acinar cells CTRB 0.017 chymotrypsinogen B1 protein-coding gene 1 Endoderm Pancreas 1.0 0.957143 0.000628931 0.0159201 +Mm Hs KLK1 Acinar cells Klk6 0.013 kallikrein 1 protein-coding gene 1 Endoderm Pancreas 0.833333 0.314286 0.00503145 0.0128263 +Mm Hs RBPJL Acinar cells RBP-L|SUHL|RBPSUHL 0.001 recombination signal binding protein for immunoglobulin kappa J region like protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs PTF1A Acinar cells PTF1-p48|bHLHa29 0.001 pancreas associated transcription factor 1a protein-coding gene 1 Endoderm Pancreas 0.0 0.157143 0.000628931 0.000773445 +Mm TRY4 Acinar cells NA 0.007 trypsin 4 protein coding gene 1 Endoderm Pancreas NA NA NA NA +Mm Hs CELA3A Acinar cells ELA3|ELA3A 0.001 chymotrypsin like elastase family member 3A protein-coding gene 1 Endoderm Pancreas 0.833333 0.128571 0.0 0.0 +Mm Hs PRSS1 Acinar cells TRY1 0.002 serine protease 1 protein-coding gene 1 Endoderm Pancreas 1.0 0.0285714 0.00597484 0.0 +Mm AMY2A2 Acinar cells NA 0.001 amylase 2a2 protein coding gene NA Endoderm Pancreas 0.0 0.157143 0.0 0.0 +Mm Hs SPINK1 Acinar cells Spink3|PCTT|PSTI|TATI 0.029 serine peptidase inhibitor, Kazal type 1 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0352201 0.0 +Mm Hs ZG16 Acinar cells hZG16|JCLN1|ZG16A|JCLN 0.013 zymogen granule protein 16 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0144654 0.0 +Mm Hs CEL Acinar cells BSSL|MODY8 0.002 carboxyl ester lipase protein-coding gene 1 Endoderm Pancreas 0.166667 0.442857 0.0 0.000837899 +Mm Hs CELA2A Acinar cells ELA2A 0.005 chymotrypsin like elastase family member 2A protein-coding gene 1 Endoderm Pancreas 0.333333 0.628571 0.0 0.00290042 +Mm AMY2A3 Acinar cells NA 0.001 amylase 2a3 protein coding gene 1 Endoderm Pancreas 0.0 0.342857 0.0 0.000128908 +Mm Hs CPB1 Acinar cells NA 0.005 carboxypeptidase B1 protein-coding gene 1 Endoderm Pancreas 0.833333 0.5 0.00786164 0.00232034 +Mm Hs CELA1 Acinar cells ELA1 0.017 chymotrypsin like elastase family member 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.814286 0.0 0.017467 +Mm AMY2A5 Acinar cells NA 0.002 amylase 2a5 protein coding gene 1 Endoderm Pancreas 0.0 0.414286 0.0 0.00051563 +Mm Hs RNASE1 Acinar cells RAC1|RNS1 0.022 ribonuclease A family member 1, pancreatic protein-coding gene 1 Endoderm Pancreas 0.75 0.0 0.0877358 0.0 +Mm Hs AMY2B Acinar cells NA 0.003 amylase, alpha 2B (pancreatic) protein-coding gene 1 Endoderm Pancreas 0.0833333 0.528571 0.0 0.00148244 +Mm Hs CPA2 Acinar cells NA 0.004 carboxypeptidase A2 protein-coding gene 1 Endoderm Pancreas 0.916667 0.457143 0.0 0.00277151 +Mm Hs CPA1 Acinar cells CPA 0.006 carboxypeptidase A1 protein-coding gene 1 Endoderm Pancreas 0.833333 0.585714 0.0 0.00438286 +Mm Hs CELA3B Acinar cells CBPP|ELA3B 0.007 chymotrypsin like elastase family member 3B protein-coding gene 1 Endoderm Pancreas 0.75 0.8 0.00125786 0.00502739 +Mm Hs PNLIP Acinar cells NA 0.005 pancreatic lipase protein-coding gene 1 Endoderm Pancreas 0.833333 0.585714 0.000314465 0.00354496 +Hs CTRB2 Acinar cells NA 0.001 chymotrypsinogen B2 protein-coding gene 1 Endoderm Pancreas 0.916667 0.0 0.00125786 0.0 +Mm Hs PLA2G1B Acinar cells PLA2|PPLA2|PLA2A 0.007 phospholipase A2 group IB protein-coding gene 1 Endoderm Pancreas 0.833333 0.228571 0.00157233 0.00638092 +Mm Hs PRSS2 Acinar cells TRY2 0.01 serine protease 2 protein-coding gene 1 Endoderm Pancreas 1.0 0.7 0.0103774 0.00696101 +Mm Hs CLPS Acinar cells NA 0.021 colipase protein-coding gene 1 Endoderm Pancreas 0.583333 0.957143 0.000314465 0.0215276 +Hs REG1A Acinar cells PSPS|PSPS1|REG 0.005 regenerating family member 1 alpha protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0273585 0.0 +Mm Hs SYCN Acinar cells SYL|FLJ27441|INSSA1 0.008 syncollin protein-coding gene 1 Endoderm Pancreas 0.833333 0.0 0.00157233 0.0 +Mm Hs PNLIPRP1 Acinar cells PLRP1 0.008 pancreatic lipase related protein 1 protein-coding gene 1 Endoderm Pancreas 0.5 0.628571 0.0 0.00663874 +Mm Hs CTRC Acinar cells CLCR|ELA4 0.003 chymotrypsin C protein-coding gene 1 Endoderm Pancreas 0.833333 0.414286 0.0 0.00135353 +Mm Hs REG3A Acinar cells REG-III|REG3|PBCGF 0.005 regenerating family member 3 alpha protein-coding gene 1 Endoderm Pancreas 0.916667 0.0 0.0106918 0.0 +Hs SERPINA3 Acinar cells AACT 0.0 serpin family A member 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000314465 0.0 +Mm Hs PRSS3 Acinar cells TRY4|PRSS4 0.006 serine protease 3 protein-coding gene 1 Endoderm Pancreas 0.833333 0.0285714 0.0289308 0.0 +Hs REG1B Acinar cells PSPS2|REGH|REGI-BETA 0.002 regenerating family member 1 beta protein-coding gene 1 Endoderm Pancreas 0.916667 0.0 0.0110063 0.0 +Mm Hs CFB Acinar cells H2-Bf|BFD|BF 0.001 complement factor B protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00154689 +Mm Hs GDF15 Acinar cells PLAB|MIC-1|PDF|NAG-1|PTGFB 0.014 growth differentiation factor 15 protein-coding gene 1 Endoderm Pancreas 0.833333 0.0 0.054088 0.00309378 +Mm Hs MUC1 Acinar cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Endoderm Pancreas 0.916667 0.185714 0.0295597 0.0117306 +Hs C15ORF48 Acinar cells NMES1|MIR147BHG 0.018 chromosome 15 open reading frame 48 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.109119 0.0 +Mm Hs DUOXA2 Acinar cells NA 0.0 dual oxidase maturation factor 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.000128908 +Hs AKR1C3 Acinar cells KIAA0119|DDX|HAKRB|PGFS|HSD17B5 0.007 aldo-keto reductase family 1 member C3 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0389937 0.0 +Mm Hs OLFM4 Acinar cells OlfD|GW112 0.013 olfactomedin 4 protein-coding gene 1 Endoderm Pancreas 0.583333 0.0 0.0132075 0.0126974 +Mm Hs GSTA1 Acinar cells NA 0.012 glutathione S-transferase alpha 1 protein-coding gene 1 Endoderm Pancreas 0.916667 0.0 0.0267296 0.00837899 +Mm Hs LGALS2 Acinar cells HL14 0.032 galectin 2 protein-coding gene 1 Endoderm Pancreas 0.916667 0.0142857 0.0345912 0.0308733 +Mm Hs PDZK1IP1 Acinar cells DD96|MAP17|SPAP 0.025 PDZK1 interacting protein 1 protein-coding gene 1 Endoderm Pancreas 1.0 0.114286 0.0396226 0.0228166 +Mm Hs RARRES2 Acinar cells TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0751572 0.0 +Mm Hs CXCL17 Acinar cells Dcip1|UNQ473|VCC1 0.007 C-X-C motif chemokine ligand 17 protein-coding gene 1 Endoderm Pancreas 0.75 0.0 0.0248428 0.00367386 +Mm Hs UBD Acinar cells FAT10 0.0 ubiquitin D protein-coding gene 1 Endoderm Pancreas NA NA NA NA +Mm Hs GSTA2 Acinar cells GST2 0.007 glutathione S-transferase alpha 2 protein-coding gene 1 Endoderm Pancreas 0.916667 0.0142857 0.00628931 0.00650983 +Mm Hs ANPEP Acinar cells gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Endoderm Pancreas 0.75 0.0714286 0.0100629 0.0166291 +Hs LYZ Acinar cells NA 0.008 lysozyme protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0408805 0.0 +Mm Hs ANGPTL4 Acinar cells pp1158|PGAR|ARP4|HFARP|FIAF 0.031 angiopoietin like 4 protein-coding gene 1 Endoderm Pancreas 0.166667 0.0 0.0295597 0.0329359 +Mm Hs ALDOB Acinar cells NA 0.031 aldolase, fructose-bisphosphate B protein-coding gene 1 Endoderm Pancreas 0.583333 0.0428571 0.00408805 0.0370609 +Mm Hs CEBPA Adipocyte progenitor cells C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0299647 +Mm Hs EGFR Adipocyte progenitor cells ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0222431 0.0127687 +Mm Hs FGF10 Adipocyte progenitor cells NA 0.001 fibroblast growth factor 10 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000626566 0.00173244 +Mm Hs GSC Adipocyte progenitor cells NA 0.001 goosecoid homeobox protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.000769971 +Mm Hs MMP3 Adipocyte progenitor cells STMY1|STMY 0.003 matrix metallopeptidase 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00219298 0.00301572 +Mm Hs PPARG Adipocyte progenitor cells PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0109649 0.00461983 +Mm Hs TWIST2 Adipocyte progenitor cells DERMO1|Dermo-1|bHLHa39 0.012 twist family bHLH transcription factor 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00689223 0.0 +Mm Hs GATA3 Adipocyte progenitor cells HDR 0.03 GATA binding protein 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0200501 0.0297722 +Mm Hs GLI1 Adipocyte progenitor cells GLI 0.0 GLI family zinc finger 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.000192493 +Mm Hs SMO Adipocyte progenitor cells FZD11|SMOH 0.005 smoothened, frizzled class receptor protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs STAB1 Adipocyte progenitor cells KIAA0246|STAB-1|FEEL-1|CLEVER-1|FELE-1|FEX1|SCARH2 0.018 stabilin 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00250627 0.0 +Mm Hs WISP2 Adipocyte progenitor cells CTGF-L|CCN5 0.005 WNT1 inducible signaling pathway protein 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00657895 0.0 +Mm Hs WT1 Adipocyte progenitor cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0225564 0.0 +Mm Hs SCARA5 Adipocyte progenitor cells FLJ23907|MGC45780|NET33 0.007 scavenger receptor class A member 5 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0115915 0.0 +Mm Hs HOXC8 Adipocyte progenitor cells HOX3A 0.005 homeobox C8 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00313283 0.00532563 +Mm Hs TCF7L1 Adipocyte progenitor cells TCF3 0.009 transcription factor 7 like 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00845865 0.0 +Mm Hs HOXC9 Adipocyte progenitor cells HOX3B 0.007 homeobox C9 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0159774 0.00494065 +Mm Hs HOXC6 Adipocyte progenitor cells HOX3C 0.004 homeobox C6 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00595238 0.00429901 +Mm Hs HOXC4 Adipocyte progenitor cells HOX3E 0.002 homeobox C4 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.00275906 +Hs ZNF521 Adipocyte progenitor cells EHZF|Evi3 0.002 zinc finger protein 521 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0103383 0.0 +Mm Hs SULT1E1 Adipocyte progenitor cells STE 0.002 sulfotransferase family 1E member 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00595238 0.0 +Mm Hs EBF2 Adipocyte progenitor cells FLJ11500|COE2 0.006 early B cell factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125313 0.00705807 +Mm Hs NRG4 Adipocyte progenitor cells NA 0.001 neuregulin 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00156642 0.000320821 +Mm Hs SLC36A2 Adipocytes PAT2|tramdorin|TRAMD1 0.003 solute carrier family 36 member 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs P2RX5 Adipocytes P2X5 0.0 purinergic receptor P2X 5 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00188383 0.0 +Mm Hs LEP Adipocytes OBS 0.0 leptin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs UCP1 Adipocytes SLC25A7|UCP 0.0 uncoupling protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs CIDEA Adipocytes CIDE-A 0.004 cell death-inducing DFFA-like effector a protein-coding gene 1 Mesoderm Connective tissue 0.0 0.5 0.0 0.0046864 +Mm Hs PRDM16 Adipocytes MEL1|PFM13|KIAA1675|MGC166915|KMT8F 0.001 PR/SET domain 16 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125589 0.000962958 +Mm Hs LHX8 Adipocytes Lhx7 0.001 LIM homeobox 8 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.00154073 +Mm Hs EPSTI1 Adipocytes BRESI1|MGC29634 0.041 epithelial stromal interaction 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0291994 0.0431405 +Mm Hs MC2R Adipocytes ACTHR 0.0 melanocortin 2 receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs FFAR2 Adipocytes FFA2R|GPR43 0.01 free fatty acid receptor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.0 0.0121975 +Mm Hs PIKFYVE Adipocytes MGC40423|KIAA0981|PIKfyve|PIP5K|p235|ZFYVE29|FAB1|PIP5K3 0.003 phosphoinositide kinase, FYVE-type zinc finger containing protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00345369 0.00295307 +Mm Hs CYP11B2 Adipocytes CYP11BL|P-450C18|P450aldo|ALDOS 0.0 cytochrome P450 family 11 subfamily B member 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs TLR2 Adipocytes TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000941915 0.0 +Mm Hs TLR4 Adipocytes hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000313972 0.0 +Mm Hs ADRB1 Adipocytes ADRB1R 0.002 adrenoceptor beta 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0021978 0.0023753 +Mm Hs ADRB2 Adipocytes ADRBR|B2AR|ADRB2R 0.016 adrenoceptor beta 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0100471 0.0181678 +Mm Hs ADRB3 Adipocytes NA 0.0 adrenoceptor beta 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.0 0.000577775 +Mm Hs FABP4 Adipocytes A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 1.0 0.0103611 0.0327406 +Mm Hs TNFRSF9 Adipocytes CD137|4-1BB|ILA 0.003 TNF receptor superfamily member 9 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00345369 0.0 +Mm Hs TBX1 Adipocytes VCF 0.003 T-box 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000941915 0.0 +Mm Hs TMEM26 Adipocytes MGC35010|Em:AC068892.1 0.002 transmembrane protein 26 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs TCF21 Adipocytes POD1|bHLHa23 0.014 transcription factor 21 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00596546 0.0 +Mm Hs ADIPOQ Adipocytes ACRP30|AdipoQ|apM1|GBP28|adiponectin|ACDC 0.004 adiponectin, C1Q and collagen domain containing protein-coding gene 1 Mesoderm Connective tissue 0.0 1.0 0.0 0.00404442 +Mm Hs CFD Adipocytes ADN|DF|PFD 0.018 complement factor D protein-coding gene 1 Mesoderm Connective tissue 0.0 0.75 0.0989011 0.000770367 +Mm Hs ACVR1C Adipocytes ALK7|ACVRLK7 0.002 activin A receptor type 1C protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.00282575 0.00147654 +Mm Hs SLC2A4 Adipocytes GLUT4 0.001 solute carrier family 2 member 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00251177 0.0 +Mm Hs LPIN1 Adipocytes KIAA0188 0.012 lipin 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.0260597 0.0091802 +Mm Hs PLIN1 Adipocytes PLIN 0.0 perilipin 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.5 0.0 0.000192592 +Mm Hs PCK1 Adipocytes PEPCK-C 0.008 phosphoenolpyruvate carboxykinase 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.5 0.0156986 0.00725429 +Mm Hs PPARG Adipocytes PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.010989 0.00442961 +Mm Hs RETN Adipocytes FIZZ3|ADSF|RETN1 0.001 resistin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00533752 0.0 +Mm Hs MEST Adipocytes PEG1 0.039 mesoderm specific transcript protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.103925 0.0207357 +Mm Hs ADM2 Adipocytes AM2|FLJ21135 0.0 adrenomedullin 2 protein-coding gene 1 Mesoderm Connective tissue 0.142857 0.0 0.0 0.000128394 +Mm Hs STAT6 Adipocytes D12S1644|IL-4-STAT 0.01 signal transducer and activator of transcription 6 protein-coding gene 1 Mesoderm Connective tissue 0.714286 0.0 0.00659341 0.0 +Mm Hs TFE3 Adipocytes TFEA|bHLHe33 0.005 transcription factor binding to IGHM enhancer 3 protein-coding gene 1 Mesoderm Connective tissue 0.714286 0.0 0.00345369 0.0 +Mm Hs CPPED1 Adipocytes CSTP1|FLJ11151 0.008 calcineurin like phosphoesterase domain containing 1 protein-coding gene 1 Mesoderm Connective tissue 0.428571 0.125 0.010989 0.00731848 +Mm Hs APPL2 Adipocytes FLJ10659|DIP13B 0.011 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2 protein-coding gene NA Mesoderm Connective tissue 0.714286 0.0 0.0043956 0.012711 +Mm Hs APOL6 Adipocytes APOL-VI|APOLVI 0.003 apolipoprotein L6 protein-coding gene NA Mesoderm Connective tissue 0.714286 0.0 0.0172684 0.0 +Mm Hs PXMP2 Adipocytes PMP22 0.007 peroxisomal membrane protein 2 protein-coding gene NA Mesoderm Connective tissue 0.571429 0.125 0.022606 0.0023753 +Hs CAVIN1 Adipocytes cavin-1|CGL4|PTRF 0.023 caveolae associated protein 1 protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.129356 0.0 +Mm Hs AGT Adipocytes SERPINA8 0.02 angiotensinogen protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.0160126 0.0212493 +Mm Hs SLC1A5 Adipocytes AAAT|ASCT2|RDRC|M7V1 0.038 solute carrier family 1 member 5 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0464678 0.0 +Mm Hs ACSL1 Adipocytes LACS|ACS1|LACS1|FACL1|FACL2 0.022 acyl-CoA synthetase long chain family member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.0191523 0.0231752 +Mm CAR3 Adipocytes NA 0.007 carbonic anhydrase 3 protein coding gene 1 Mesoderm Connective tissue 0.0 1.0 0.0 0.00783206 +Mm Hs BCAT2 Adipocytes BCAM|BCT2 0.021 branched chain amino acid transaminase 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.0144427 0.0202221 +Mm Hs PNPLA2 Adipocytes desnutrin|TTS-2.2|ATGL|FP17548|iPLA2zeta 0.02 patatin like phospholipase domain containing 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.875 0.0160126 0.0202863 +Mm Hs CIDEC Adipocytes CIDE-3|FLJ20871|Fsp27 0.002 cell death inducing DFFA like effector c protein-coding gene 1 Mesoderm Connective tissue 0.0 0.75 0.0 0.00218271 +Mm Hs CDO1 Adipocytes NA 0.036 cysteine dioxygenase type 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.5 0.0119309 0.0415998 +Mm Hs APOC1 Adipocytes NA 0.047 apolipoprotein C1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.75 0.078179 0.0360146 +Mm Hs MMP2 Adipocytes TBE-1|CLG4|CLG4A 0.045 matrix metallopeptidase 2 protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.0656201 0.0385825 +Mm Hs POSTN Adipocytes OSF-2|PN|periostin 0.033 periostin protein-coding gene 1 Mesoderm Connective tissue 0.285714 0.0 0.022606 0.0347307 +Mm Hs LOX Adipocytes NA 0.017 lysyl oxidase protein-coding gene 1 Mesoderm Connective tissue 0.285714 0.25 0.0144427 0.0167555 +Mm Hs COL6A2 Adipocytes NA 0.056 collagen type VI alpha 2 chain protein-coding gene 1 Mesoderm Connective tissue 1.0 0.25 0.101413 0.0441035 +Mm Hs ZBTB16 Adipocytes PLZF|ZNF145 0.007 zinc finger and BTB domain containing 16 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0119309 0.0 +Mm Hs GULP1 Adipocytes CED6|CED-6|GULP 0.01 GULP, engulfment adaptor PTB domain containing 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0298273 0.0046222 +Mm Hs FZD4 Adipocytes CD344 0.007 frizzled class receptor 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.000627943 0.00847403 +Mm Hs TRIP10 Adipocytes HSTP|CIP4|STOT 0.007 thyroid hormone receptor interactor 10 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00502355 0.0 +Mm Hs FGF7 Adipocytes KGF 0.005 fibroblast growth factor 7 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.011303 0.00423702 +Mm Hs MAOB Adipocytes NA 0.009 monoamine oxidase B protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.00973312 0.00937279 +Mm Hs SOCS1 Adipocytes SOCS-1|SSI-1|JAB|TIP3|Cish1 0.012 suppressor of cytokine signaling 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0197802 0.0 +Mm Hs ARNT Adipocytes HIF-1beta|bHLHe2 0.005 aryl hydrocarbon receptor nuclear translocator protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.000627943 0.00590614 +Mm Hs SULT1A1 Adipocytes P-PST|STP1 0.012 sulfotransferase family 1A member 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0204082 0.0 +Mm Hs NNMT Adipocytes NA 0.017 nicotinamide N-methyltransferase protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.0605965 0.00770367 +Mm Hs AOC3 Adipocytes VAP1|HPAO|VAP-1 0.004 amine oxidase, copper containing 3 protein-coding gene 1 Mesoderm Connective tissue 0.142857 0.25 0.00251177 0.00430121 +Mm Hs H6PD Adipocytes NA 0.005 hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.00125589 0.00558516 +Mm Hs CYP27A1 Adipocytes CTX|CYP27 0.006 cytochrome P450 family 27 subfamily A member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0150706 0.00391603 +Mm Hs EBF2 Adipocytes FLJ11500|COE2 0.006 early B cell factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125589 0.00706169 +Mm Hs MNDA Adipocytes PYHIN3 0.019 myeloid cell nuclear differentiation antigen protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0461538 0.0130962 +Mm Hs HSD11B1 Adipocytes SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.00973312 0.0244591 +Mm Hs AR Adipocytes AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.00188383 0.0158567 +Mm Hs GDF10 Adipocytes BMP-3b 0.005 growth differentiation factor 10 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000313972 0.00654812 +Mm Hs CYP1B1 Adipocytes CP1B|GLC3A 0.016 cytochrome P450 family 1 subfamily B member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.0492936 0.00885922 +Mm Hs COL5A3 Adipocytes NA 0.006 collagen type V alpha 3 chain protein-coding gene NA Mesoderm Connective tissue 0.0 0.125 0.000941915 0.00731848 +Mm Hs STEAP4 Adipocytes FLJ23153|TIARP|STAMP2|SchLAH|TNFAIP9 0.007 STEAP4 metalloreductase protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00596546 0.0 +Mm Hs CCL11 Adipocytes eotaxin|MGC22554|SCYA11 0.008 C-C motif chemokine ligand 11 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00313972 0.00969378 +Mm Hs NR1H3 Adipocytes LXR-a|RLD-1|LXRa 0.008 nuclear receptor subfamily 1 group H member 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.125 0.00973312 0.00751107 +Mm Hs DEPTOR Adipocytes DEP.6|FLJ12428|DEPDC6 0.012 DEP domain containing MTOR interacting protein protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.00282575 0.0139308 +Mm Hs CYTH3 Adipocytes GRP1|ARNO3|cytohesin-3|PSCD3 0.01 cytohesin 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00627944 0.0112345 +None TUSC5 Adipocytes NA 0.005 NA NA 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs FMO1 Adipocytes NA 0.012 flavin containing monooxygenase 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.375 0.000313972 0.0140592 +Mm Hs ACADSB Adipocytes SBCAD|ACAD7 0.01 acyl-CoA dehydrogenase short/branched chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.00188383 0.0122617 +Mm Hs XDH Adipocytes XOR|XO 0.011 xanthine dehydrogenase protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00502355 0.0 +Mm Hs RSPO3 Adipocytes FLJ14440|THSD2 0.009 R-spondin 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.010675 0.0 +Mm Hs PTGES Adipocytes MGST-IV|PIG12|MGST1-L1|TP53I12|MGST1L1 0.013 prostaglandin E synthase protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0043956 0.0134814 +Mm Hs CREB3L1 Adipocytes OASIS 0.015 cAMP responsive element binding protein 3 like 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00973312 0.0167555 +Mm Hs ANGPTL2 Adipocytes NA 0.013 angiopoietin like 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00596546 0.0148938 +Mm Hs ADAM12 Adipocytes MCMPMltna|MLTN 0.007 ADAM metallopeptidase domain 12 protein-coding gene NA Mesoderm Connective tissue 0.0 0.125 0.00627944 0.00757527 +Mm ADH1 Adipocytes NA 0.017 alcohol dehydrogenase 1 (class I) protein coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.0 0.0216345 +Mm Hs LBP Adipocytes BPIFD2 0.017 lipopolysaccharide binding protein protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.00156986 0.0197727 +Mm Hs NMB Adipocytes MGC2277|MGC3936|MGC17211 0.013 neuromedin B protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0257457 0.00796045 +Mm Hs RARRES2 Adipocytes TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0788069 0.0 +Mm Hs FST Adipocytes NA 0.02 follistatin protein-coding gene NA Mesoderm Connective tissue 0.285714 0.25 0.0351648 0.0152147 +Mm Hs EGFR Adipocytes ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.022292 0.0127752 +Mm Hs CPXM1 Adipocytes CPX-1|CPX1|CPXM 0.018 carboxypeptidase X, M14 family member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0273155 0.0163703 +Mm Hs C3 Adipocytes CPAMD1|ARMD9|C3a|C3b 0.037 complement C3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.0389325 0.0376196 +Mm Hs ADAMTS5 Adipocytes ADMP-2|ADAMTS11 0.016 ADAM metallopeptidase with thrombospondin type 1 motif 5 protein-coding gene 1 Mesoderm Connective tissue 0.142857 0.125 0.0141287 0.0167555 +Hs MT2A Adipocytes MT2 0.061 metallothionein 2A protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.326217 0.0 +Mm Hs TIMP1 Adipocytes TIMP|CLGI 0.097 TIMP metallopeptidase inhibitor 1 protein-coding gene NA Mesoderm Connective tissue 1.0 0.0 0.408477 0.0 +Mm Hs METRN Adipocytes MGC2601|C16orf23 0.015 meteorin, glial cell differentiation regulator protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.0533752 0.00044938 +Mm Hs METRNL Adipocytes NA 0.037 meteorin like, glial cell differentiation regulator protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.0147567 0.0424344 +Mm Hs MYO1C Adipocytes myr2 0.026 myosin IC protein-coding gene 1 Mesoderm Connective tissue 1.0 0.125 0.033595 0.0223406 +Mm Hs NQO1 Adipocytes DHQU|QR1|NMOR1|DIA4 0.024 NAD(P)H quinone dehydrogenase 1 protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.0728414 0.00802465 +Mm Hs SYAP1 Adipocytes FLJ14495|PRO3113 0.051 synapse associated protein 1 protein-coding gene NA Mesoderm Connective tissue 1.0 0.0 0.109262 0.0 +Mm Hs CRNDE Adipocytes LOC643911|LINC00180|CRNDEP 0.027 colorectal neoplasia differentially expressed other NA Mesoderm Connective tissue 1.0 0.0 0.109262 0.00192592 +Mm Hs AQP5 Adipocytes NA 0.018 aquaporin 5 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0420722 0.013995 +Mm Hs TSPO Adipocytes PBR|MBR|PKBS|mDRC|DBI|pk18|BZRP 0.283 translocator protein protein-coding gene 1 Mesoderm Connective tissue 1.0 0.0 0.340345 0.0 +Mm Hs AZGP1 Adipocytes ZA2G|ZAG 0.008 alpha-2-glycoprotein 1, zinc-binding protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0376766 0.00199011 +Mm Hs LRP1 Adipocytes CD91|LRP1A|APOER|A2MR|IGFBP3R1 0.071 LDL receptor related protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.714286 0.375 0.0339089 0.0772292 +Mm Hs PDE3B Adipocytes HcGIP1 0.01 phosphodiesterase 3B protein-coding gene 1 Mesoderm Connective tissue 0.0 0.125 0.0188383 0.0092444 +Mm Hs LGALS12 Adipocytes NA 0.0 galectin 12 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.000385183 +Mm Hs SERPINF1 Adipocytes EPC-1|PIG35|PEDF 0.057 serpin family F member 1 protein-coding gene 1 Mesoderm Connective tissue 0.142857 0.0 0.105808 0.0 +Mm Hs CPT1B Adipocytes M-CPT1|CPT1-M 0.001 carnitine palmitoyltransferase 1B protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00533752 0.0 +Mm Hs ELOVL3 Adipocytes CIG-30 0.001 ELOVL fatty acid elongase 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.000770367 +Mm Hs PPARGC1A Adipocytes PGC1|PGC1A|PGC-1alpha|PPARGC1 0.01 PPARG coactivator 1 alpha protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00408163 0.0118765 +Mm Hs MPZL1 Adipocytes PZR|FLJ21047 0.097 myelin protein zero like 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.0505495 0.107209 +Mm Hs CITED1 Adipocytes MSG1 0.023 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0160126 0.0245875 +Mm Hs DPT Adipocytes NA 0.021 dermatopontin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00596546 0.0243307 +Mm Hs HOXC9 Adipocytes HOX3B 0.007 homeobox C9 protein-coding gene 1 Mesoderm Connective tissue 0.714286 0.0 0.0144427 0.00494319 +Hs ZNF423 Adipocytes KIAA0760|hOAZ|Ebfaz|Zfp104|NPHP14|JBTS19 0.004 zinc finger protein 423 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0238619 0.0 +Mm Hs ESM1 Adipocytes NA 0.006 endothelial cell specific molecule 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.25 0.0122449 0.00475059 +Mm Hs TH Adrenergic neurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs DDC Adrenergic neurons AADC 0.014 dopa decarboxylase protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00469925 0.0165554 +Mm Hs DBH Adrenergic neurons DBM 0.001 dopamine beta-hydroxylase protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.000770021 +Mm Hs PNMT Adrenergic neurons PENT 0.0 phenylethanolamine N-methyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.000320842 +Mm Hs SLC18A2 Adrenergic neurons SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs NPFF Adrenergic neurons FMRFAL 0.0 neuropeptide FF-amide peptide precursor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC12A7 Adrenergic neurons KCC4|DKFZP434F076 0.006 solute carrier family 12 member 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00281955 0.0 +Mm Hs SYT1 Adrenergic neurons SVP65 0.093 synaptotagmin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.02099 0.0 +Mm Hs AQP1 Airway epithelial cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0178571 0.0424767 +Mm Hs ADH7 Airway epithelial cells ADH-4 0.006 alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00438596 0.0062881 +Mm Hs CDH1 Airway epithelial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0416667 0.0572345 +Mm Hs SEC14L3 Airway epithelial cells TAP2 0.006 SEC14 like lipid binding 3 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs MUC5B Airway goblet cells MG1 0.002 mucin 5B, oligomeric mucus/gel-forming protein-coding gene 1 Mesoderm Lungs 0.0 0.25 0.0093985 0.000385183 +Mm Hs MUC16 Airway goblet cells FLJ14303 0.001 mucin 16, cell surface associated protein-coding gene 1 Mesoderm Lungs 0.0 0.25 0.00219298 0.000834564 +Mm Hs LTF Airway goblet cells HLF2 0.016 lactotransferrin protein-coding gene NA Mesoderm Lungs 0.0 1.0 0.00626566 0.0178468 +Mm Hs SCGB3A1 Airway goblet cells UGRP2|HIN-1|HIN1|LU105|PnSP-2 0.006 secretoglobin family 3A member 1 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0115915 0.0 +Mm DCPP1 Airway goblet cells NA 0.001 demilune cell and parotid protein 1 protein coding gene NA Mesoderm Lungs 0.0 0.875 0.0 0.000641972 +Mm Hs DMBT1 Airway goblet cells GP340|muclin|SALSA|Gp-340|hensin|vomeroglandin 0.01 deleted in malignant brain tumors 1 protein-coding gene NA Mesoderm Lungs 0.0 0.5 0.00281955 0.0107851 +Mm WFDC18 Airway goblet cells NA 0.007 WAP four-disulfide core domain 18 protein coding gene NA Mesoderm Lungs NA NA NA NA +Mm DCPP3 Airway goblet cells NA 0.001 demilune cell and parotid protein 3 protein coding gene NA Mesoderm Lungs 0.0 1.0 0.0 0.000256789 +Mm Hs LIPF Airway goblet cells NA 0.001 lipase F, gastric type protein-coding gene NA Mesoderm Lungs 0.0 1.0 0.0 0.000320986 +Mm DCPP2 Airway goblet cells NA 0.001 demilune cell and parotid protein 2 protein coding gene NA Mesoderm Lungs 0.0 1.0 0.0 0.000385183 +Mm Hs MSLN Airway goblet cells MPF 0.004 mesothelin protein-coding gene NA Mesoderm Lungs 0.0 0.5 0.00125313 0.00507158 +Mm Hs AGR2 Airway goblet cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene NA Mesoderm Lungs 0.0 0.625 0.0733083 0.0121975 +Mm Hs GP2 Airway goblet cells ZAP75 0.001 glycoprotein 2 protein-coding gene NA Mesoderm Lungs 0.0 0.5 0.000626566 0.000641972 +Mm Hs PIGR Airway goblet cells NA 0.031 polymeric immunoglobulin receptor protein-coding gene NA Mesoderm Lungs 0.0 0.5 0.0441729 0.0288887 +Mm Hs TFF2 Airway goblet cells SML1 0.002 trefoil factor 2 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.000313283 0.0 +Mm Hs AQP5 Airway goblet cells NA 0.018 aquaporin 5 protein-coding gene NA Mesoderm Lungs 0.0 0.625 0.0419799 0.013674 +Mm CBR2 Airway goblet cells NA 0.027 carbonyl reductase 2 protein coding gene NA Mesoderm Lungs 0.0 0.625 0.0 0.0330616 +Mm Hs QSOX1 Airway goblet cells QSCN6 0.029 quiescin sulfhydryl oxidase 1 protein-coding gene NA Mesoderm Lungs 0.0 0.375 0.0441729 0.0262567 +Mm Hs FXYD3 Airway goblet cells MAT-8|PLML 0.043 FXYD domain containing ion transport regulator 3 protein-coding gene NA Mesoderm Lungs 0.0 0.625 0.12594 0.0238172 +Mm Hs SEC23B Airway goblet cells CDA-II|CDAII|HEMPAS|CDAN2 0.02 Sec23 homolog B, coat complex II component protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.0238095 0.0 +Mm Hs CEACAM1 Airway goblet cells BGP1|CD66a|BGP 0.024 carcinoembryonic antigen related cell adhesion molecule 1 protein-coding gene NA Mesoderm Lungs 0.0 0.25 0.0191103 0.0258073 +Mm Hs GOLPH3 Airway goblet cells GPP34|GOPP1|MIDAS|Vps74 0.069 golgi phosphoprotein 3 protein-coding gene NA Mesoderm Lungs 0.0 0.375 0.0294486 0.0779996 +Mm Hs GGH Airway goblet cells NA 0.069 gamma-glutamyl hydrolase protein-coding gene NA Mesoderm Lungs 0.0 0.375 0.108396 0.0568145 +Mm Hs GALNT5 Airway goblet cells GalNAc-T5 0.001 polypeptide N-acetylgalactosaminyltransferase 5 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.00344612 0.000641972 +Mm Hs GALNT6 Airway goblet cells GalNAc-T6 0.007 polypeptide N-acetylgalactosaminyltransferase 6 protein-coding gene 1 Mesoderm Lungs 0.0 0.125 0.00093985 0.00815305 +Mm Hs MUC5AC Airway goblet cells NA 0.0 mucin 5AC, oligomeric mucus/gel-forming protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.000313283 0.000577775 +Mm Hs MUC4 Airway goblet cells NA 0.005 mucin 4, cell surface associated protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.016604 0.00263209 +Mm Hs MUC20 Airway goblet cells FLJ14408|KIAA1359 0.0 mucin 20, cell surface associated protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0 0.000128394 +Mm Hs SPDEF Airway goblet cells PDEF|bA375E1.3 0.004 SAM pointed domain containing ETS transcription factor protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.00971178 0.0 +Mm Hs DUSP4 Airway goblet cells HVH2|MKP-2|TYP 0.011 dual specificity phosphatase 4 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0413534 0.00385183 +Mm Hs NOG Airway smooth muscle cells SYNS1 0.002 noggin protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00501253 0.00121912 +Mm Hs ACTA2 Airway smooth muscle cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0194236 0.0388835 +Mm Hs FOXF1 Airway smooth muscle cells FREAC1|FKHL5 0.008 forkhead box F1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00845865 0.00814886 +Mm Hs GATA5 Airway smooth muscle cells bB379O24.1|GATAS 0.002 GATA binding protein 5 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00125313 0.00128329 +Mm Hs GCG Alpha cells GLP2|GRPP 0.024 glucagon protein-coding gene 1 Endoderm Pancreas 0.83871 0.75 0.0439734 0.0180766 +Mm Hs TTR Alpha cells HsT2651|CTS|PALB|CTS1 0.055 transthyretin protein-coding gene 1 Endoderm Pancreas 0.83871 0.0 0.065802 0.0 +Mm Hs GLP1R Alpha cells GLP-1R 0.0 glucagon like peptide 1 receptor protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.0 0.000385976 +Mm Hs ARX Alpha cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Endoderm Pancreas 0.129032 0.35 0.000949067 0.0227726 +Mm Hs POU3F4 Alpha cells BRN4|OTF9|DFNX2|DFN3 0.004 POU class 3 homeobox 4 protein-coding gene NA Endoderm Pancreas 0.0 0.275 0.00221449 0.00379543 +Mm Hs NKX2-2 Alpha cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene NA Endoderm Pancreas 0.290323 0.075 0.00759253 0.000450306 +Mm Hs RESP18 Alpha cells NA 0.062 regulated endocrine specific protein 18 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs PYY Alpha cells PYY1 0.016 peptide YY protein-coding gene 1 Endoderm Pancreas 0.0 0.925 0.00126542 0.0179479 +Mm Hs PCSK2 Alpha cells SPC2|NEC2 0.032 proprotein convertase subtilisin/kexin type 2 protein-coding gene 1 Endoderm Pancreas 0.83871 0.85 0.0167668 0.0327436 +Mm Hs SLC38A5 Alpha cells SN2|JM24 0.02 solute carrier family 38 member 5 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.023094 0.0 +Mm Hs TM4SF4 Alpha cells il-TMP 0.017 transmembrane 4 L six family member 4 protein-coding gene 1 Endoderm Pancreas 0.806452 0.0 0.0132869 0.0 +Mm Hs CRYBA2 Alpha cells NA 0.009 crystallin beta A2 protein-coding gene 1 Endoderm Pancreas 0.967742 0.975 0.0113888 0.00488903 +Mm Hs NKX6-1 Alpha cells Nkx6.1|NKX6A 0.006 NK6 homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0322581 0.3 0.0101234 0.00450306 +Mm Hs KCNK16 Alpha cells K2p16.1|TALK-1|TALK1 0.007 potassium two pore domain channel subfamily K member 16 protein-coding gene NA Endoderm Pancreas 0.225806 0.875 0.0056944 0.00443873 +Mm Hs PCSK1 Alpha cells PC1|NEC1 0.008 proprotein convertase subtilisin/kexin type 1 protein-coding gene NA Endoderm Pancreas 0.0645161 0.225 0.00885796 0.00791251 +Mm Hs PRRG2 Alpha cells PRGP2 0.009 proline rich and Gla domain 2 protein-coding gene NA Endoderm Pancreas 0.0645161 0.475 0.000316356 0.0100354 +Mm Hs IRX2 Alpha cells NA 0.012 iroquois homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.0967742 0.275 0.00537805 0.0124799 +Mm Hs ALDH1A1 Alpha cells RALDH1|PUMB1|ALDH1 0.039 aldehyde dehydrogenase 1 family member A1 protein-coding gene 1 Endoderm Pancreas 0.903226 0.0 0.080038 0.0288196 +Mm Hs PEMT Alpha cells PEMPT|PEMT2 0.013 phosphatidylethanolamine N-methyltransferase protein-coding gene 1 Endoderm Pancreas 0.709677 0.0 0.0385954 0.00276616 +Mm Hs CHGA Alpha cells NA 0.057 chromogranin A protein-coding gene 1 Endoderm Pancreas 0.967742 1.0 0.0287884 0.0598263 +4 DEPP1 Alpha cells DEPP|Fseg|C10orf10 0.0 DEPP1, autophagy regulator protein-coding gene 1 Endoderm Pancreas NA NA NA NA +Mm Hs SMIM24 Alpha cells HSPC323|C19orf77 0.037 small integral membrane protein 24 protein-coding gene 1 Endoderm Pancreas 0.741935 0.0 0.0281556 0.0 +Mm Hs F10 Alpha cells NA 0.011 coagulation factor X protein-coding gene 1 Endoderm Pancreas 0.645161 0.0 0.00917431 0.00836282 +Mm Hs SCGN Alpha cells SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Endoderm Pancreas 0.83871 0.0 0.0218285 0.0 +Mm Hs SLC30A8 Alpha cells ZnT-8 0.005 solute carrier family 30 member 8 protein-coding gene 1 Endoderm Pancreas 0.677419 0.0 0.00885796 0.0 +Mm Hs SH3GL2 Alpha cells SH3P4|SH3D2A|CNSA2|EEN-B1 0.025 SH3 domain containing GRB2 like 2, endophilin A1 protein-coding gene 1 Endoderm Pancreas 0.0322581 0.0 0.00221449 0.0 +Hs SCGB2A1 Alpha cells UGB3|LPHC|MGC71973|MGB2 0.003 secretoglobin family 2A member 1 protein-coding gene 1 Endoderm Pancreas 0.806452 0.0 0.00980702 0.0 +Mm Hs FAP Alpha cells NA 0.006 fibroblast activation protein alpha protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00253084 0.0065616 +Mm Hs DPP4 Alpha cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0132869 0.0213574 +Mm Hs GPR119 Alpha cells hGPCR2|GPCR2 0.0 G protein-coupled receptor 119 protein-coding gene 1 Endoderm Pancreas 0.0 0.1 0.0 0.000128659 +Mm Hs MAFB Alpha cells KRML 0.053 MAF bZIP transcription factor B protein-coding gene 1 Endoderm Pancreas 0.709677 0.7 0.0528314 0.0512062 +Mm Hs PAX6 Alpha cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Endoderm Pancreas 0.258065 0.85 0.0120215 0.0569315 +Mm Hs NEUROD1 Alpha cells BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Endoderm Pancreas 0.806452 1.0 0.0155014 0.0405275 +Mm Hs LOXL4 Alpha cells FLJ21889|LOXC 0.0 lysyl oxidase like 4 protein-coding gene 1 Endoderm Pancreas 0.129032 0.0 0.0 0.000321647 +Mm Hs PLCE1 Alpha cells KIAA1516|NPHS3 0.005 phospholipase C epsilon 1 protein-coding gene 1 Endoderm Pancreas 0.0322581 0.0 0.00822525 0.00456739 +Mm Hs GC Alpha cells VDBP|hDBP 0.009 GC, vitamin D binding protein protein-coding gene 1 Endoderm Pancreas 0.774194 0.375 0.00664347 0.00694757 +Mm Hs KLHL41 Alpha cells SARCOSIN|Krp1|KBTBD10 0.001 kelch like family member 41 protein-coding gene 1 Endoderm Pancreas 0.0322581 0.0 0.000316356 0.000514635 +Mm Hs FEV Alpha cells Pet-1 0.003 FEV, ETS transcription factor protein-coding gene 1 Endoderm Pancreas 0.16129 0.475 0.00189813 0.00225153 +Mm Hs PTGER3 Alpha cells EP3 0.001 prostaglandin E receptor 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00126542 0.00128659 +Mm Hs RFX6 Alpha cells MGC33442|dJ955L16.1|RFXDC1 0.001 regulatory factor X6 protein-coding gene 1 Endoderm Pancreas 0.225806 0.0 0.00126542 0.0 +Mm Hs SMARCA1 Alpha cells NURF140|SWI|hSNF2L|SNF2L1|SNF2L 0.015 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 protein-coding gene 1 Endoderm Pancreas 0.0967742 0.0 0.0408099 0.0 +Mm Hs PGR Alpha cells NR3C3 0.003 progesterone receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00664347 0.00192988 +Mm Hs LDB2 Alpha cells LDB1 0.019 LIM domain binding 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0246757 0.0190415 +Mm Hs IRX1 Alpha cells IRX-5 0.009 iroquois homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.125 0.0 0.01055 +Mm Hs UCP2 Alpha cells SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Endoderm Pancreas 0.16129 0.0 0.00347991 0.0 +Mm Hs FXYD5 Alpha cells OIT2 0.213 FXYD domain containing ion transport regulator 5 protein-coding gene 1 Endoderm Pancreas 0.741935 0.0 0.374881 0.173882 +Mm Hs RGS4 Alpha cells SCZD9 0.052 regulator of G protein signaling 4 protein-coding gene 1 Endoderm Pancreas 0.387097 0.0 0.0056944 0.0 +Mm Hs GLS Alpha cells KIAA0838|GLS1 0.061 glutaminase protein-coding gene 1 Endoderm Pancreas 0.0967742 0.25 0.0189813 0.0718559 +Mm CHIL3 Alveolar macrophages NA 0.022 chitinase-like 3 protein coding gene NA Mesoderm Lungs 0.0 0.913043 0.0 0.0208481 +Mm Hs PLET1 Alveolar macrophages C11orf34 0.018 placenta expressed transcript 1 protein-coding gene NA Mesoderm Lungs 0.0 0.793478 0.0 0.01775 +Mm Hs IL1B Alveolar macrophages IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene NA Mesoderm Lungs 0.0 0.369565 0.0253759 0.025689 +Mm WFDC21 Alveolar macrophages NA 0.02 WAP four-disulfide core domain 21 protein coding gene NA Mesoderm Lungs NA NA NA NA +Mm BGLAP3 Alveolar macrophages NA 0.002 bone gamma-carboxyglutamate protein 3 protein coding gene NA Mesoderm Lungs 0.0 0.0652174 0.0 0.00212999 +Mm Hs CCL3 Alveolar macrophages G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene NA Mesoderm Lungs 0.0 0.217391 0.00783208 0.0415026 +Mm Hs G0S2 Alveolar macrophages NA 0.04 G0/G1 switch 2 protein-coding gene NA Mesoderm Lungs 0.0 0.141304 0.0454261 0.0371781 +Mm Hs CXCL2 Alveolar macrophages SCYB2|GROb|MIP-2a|MGSA-b|CINC-2a|GRO2 0.041 C-X-C motif chemokine ligand 2 protein-coding gene NA Mesoderm Lungs 0.0 0.619565 0.0567043 0.0346608 +Mm Hs MCEMP1 Alveolar macrophages MGC132456|C19orf59 0.022 mast cell expressed membrane protein 1 protein-coding gene NA Mesoderm Lungs 0.0 0.826087 0.0018797 0.0212354 +Mm Hs KLHDC4 Alveolar macrophages DKFZp434G0522 0.008 kelch domain containing 4 protein-coding gene NA Mesoderm Lungs 0.0 0.521739 0.0109649 0.00438908 +Mm BCL2A1D Alveolar macrophages NA 0.028 B cell leukemia/lymphoma 2 related protein A1d protein coding gene NA Mesoderm Lungs 0.0 0.75 0.0 0.0294326 +Mm Hs GDA Alveolar macrophages NA 0.039 guanine deaminase protein-coding gene NA Mesoderm Lungs 0.0 0.673913 0.0018797 0.0440199 +Mm Hs CLEC7A Alveolar macrophages dectin-1|hDectin-1|CD369|SCARE2|CLECSF12 0.03 C-type lectin domain containing 7A protein-coding gene NA Mesoderm Lungs 0.0 0.934783 0.0466792 0.0196863 +Mm BCL2A1B Alveolar macrophages NA 0.043 B cell leukemia/lymphoma 2 related protein A1b protein coding gene NA Mesoderm Lungs 0.0 0.684783 0.0 0.0477635 +Mm Hs ITGAX Alveolar macrophages CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Lungs 0.0 0.434783 0.0162907 0.0027109 +Mm Hs TNFAIP2 Alveolar macrophages B94|EXOC3L3 0.027 TNF alpha induced protein 2 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.0404135 0.0 +Mm Hs CD36 Alveolar macrophages SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene NA Mesoderm Lungs 0.0 0.48913 0.0344612 0.0415026 +Mm Hs GAL Alveolar macrophages GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene NA Mesoderm Lungs 0.0 0.0869565 0.0184837 0.0107791 +Mm CAR4 Alveolar macrophages NA 0.032 carbonic anhydrase 4 protein coding gene NA Mesoderm Lungs 0.0 0.478261 0.0 0.0373072 +Mm EAR2 Alveolar macrophages NA 0.009 eosinophil-associated, ribonuclease A family, member 2 protein coding gene 1 Mesoderm Lungs 0.0 0.902174 0.0 0.00548635 +Mm Hs TLR2 Alveolar macrophages TIL4|CD282 0.014 toll like receptor 2 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.00093985 0.0 +Mm Hs GPNMB Alveolar macrophages NMB|HGFIN 0.013 glycoprotein nmb protein-coding gene NA Mesoderm Lungs 0.0 0.195652 0.0297619 0.00832634 +Mm Hs MRC1 Alveolar macrophages CLEC13D|CD206|bA541I19.1|CLEC13DL|MRC1L1 0.029 mannose receptor C-type 1 protein-coding gene 1 Mesoderm Lungs 0.0 0.869565 0.00971178 0.0297554 +Mm LYZ1 Alveolar macrophages NA 0.031 lysozyme 1 protein coding gene NA Mesoderm Lungs 0.0 0.543478 0.0 0.034919 +Mm Hs MARCO Alveolar macrophages SCARA2|SR-A6 0.003 macrophage receptor with collagenous structure protein-coding gene 1 Mesoderm Lungs 0.0 0.23913 0.00407268 0.00174272 +Mm Hs CSF2RB Alveolar macrophages IL5RB|CD131|betaGMR|IL3RB 0.018 colony stimulating factor 2 receptor beta common subunit protein-coding gene NA Mesoderm Lungs 0.0 0.521739 0.00281955 0.0184599 +Mm Hs MPP1 Alveolar macrophages PEMP|DXS552E 0.043 membrane palmitoylated protein 1 protein-coding gene NA Mesoderm Lungs 0.0 0.217391 0.0473058 0.041309 +Mm Hs TRIM25 Alveolar macrophages EFP|RNF147|ZNF147 0.027 tripartite motif containing 25 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.0184837 0.0 +Mm EAR1 Alveolar macrophages NA 0.003 eosinophil-associated, ribonuclease A family, member 1 protein coding gene 1 Mesoderm Lungs 0.0 0.608696 0.0 0.000193636 +Mm Hs OLR1 Alveolar macrophages LOX-1|SCARE1|CLEC8A 0.004 oxidized low density lipoprotein receptor 1 protein-coding gene NA Mesoderm Lungs 0.0 0.478261 0.00845865 0.000193636 +Mm Hs S100A4 Alveolar macrophages P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.371241 0.0 +Mm Hs GNGT2 Alveolar macrophages GNG9 0.054 G protein subunit gamma transducin 2 protein-coding gene 1 Mesoderm Lungs 0.0 0.630435 0.000313283 0.0623507 +Mm SIGLECF Alveolar macrophages NA 0.002 sialic acid binding Ig-like lectin F protein coding gene 1 Mesoderm Lungs NA NA NA NA +Mm Hs AGA Anterior pituitary gland cells ASRG 0.02 aspartylglucosaminidase protein-coding gene NA Ectoderm Brain 0.0 0.714286 0.0109649 0.021148 +Mm Hs ANGPT1 Anterior pituitary gland cells KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene NA Ectoderm Brain 0.0 0.107143 0.0018797 0.0122132 +Mm Hs CHGA Anterior pituitary gland cells NA 0.057 chromogranin A protein-coding gene NA Ectoderm Brain 0.0 0.642857 0.0379073 0.0611943 +Mm Hs CPEB4 Anterior pituitary gland cells KIAA1673 0.018 cytoplasmic polyadenylation element binding protein 4 protein-coding gene NA Ectoderm Brain 0.0 0.0357143 0.0322682 0.0162628 +None DDX26B Anterior pituitary gland cells NA 0.006 NA NA NA Ectoderm Brain 0.0 0.142857 0.0 0.00681365 +Mm GH Anterior pituitary gland cells NA 0.005 growth hormone protein coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00437102 +Mm Hs IGSF1 Anterior pituitary gland cells KIAA0364|IGDC1|IGCD1|INHBP|MGC75490|PGSF2 0.003 immunoglobulin superfamily member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.535714 0.000626566 0.00244263 +Mm Hs MEST Anterior pituitary gland cells PEG1 0.039 mesoderm specific transcript protein-coding gene NA Ectoderm Brain 0.0 0.5 0.103697 0.0198624 +Mm Hs NKTR Anterior pituitary gland cells p104 0.071 natural killer cell triggering receptor protein-coding gene NA Ectoderm Brain 0.0 0.107143 0.133459 0.0559234 +Mm Hs NUCB2 Anterior pituitary gland cells NEFA 0.066 nucleobindin 2 protein-coding gene NA Ectoderm Brain 0.0 0.642857 0.243734 0.022755 +Mm Hs PITX2 Anterior pituitary gland cells IGDS|Brx1|Otlx2|IRID2|IHG2|RIEG|RIEG1|RGS 0.01 paired like homeodomain 2 protein-coding gene NA Ectoderm Brain 0.0 0.428571 0.0109649 0.00790641 +Mm Hs POU1F1 Anterior pituitary gland cells GHF-1|POU1F1a|PIT-1|PIT1 0.001 POU class 1 homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.678571 0.0 0.000192839 +Mm Hs PRL Anterior pituitary gland cells NA 0.004 prolactin protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0106516 0.00160699 +Mm Hs RAB27A Anterior pituitary gland cells RAB27|HsT18676 0.011 RAB27A, member RAS oncogene family protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0222431 0.0 +Mm Hs RCN3 Anterior pituitary gland cells RLP49 0.071 reticulocalbin 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0153509 0.0 +Mm Hs SEZ6L2 Anterior pituitary gland cells PSK-1|FLJ90517 0.045 seizure related 6 homolog like 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0253759 0.0 +Mm Hs SIX6 Anterior pituitary gland cells Six9|OPTX2 0.004 SIX homeobox 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs TBRG1 Anterior pituitary gland cells FLJ14621|TB-5|NIAM 0.06 transforming growth factor beta regulator 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0325815 0.0 +Mm Hs TMEM130 Anterior pituitary gland cells DKFZp761L1417|FLJ42643 0.04 transmembrane protein 130 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs POMC Anterior pituitary gland cells POC|ACTH|NPP|LPH 0.008 proopiomelanocortin protein-coding gene 1 Ectoderm Brain 0.0 0.821429 0.0238095 0.00353539 +Mm Hs GMPPA Anterior pituitary gland cells NA 0.013 GDP-mannose pyrophosphorylase A protein-coding gene NA Ectoderm Brain 0.0 0.25 0.00657895 0.0133702 +Mm TRIM30B Anterior pituitary gland cells NA 0.003 tripartite motif-containing 30B protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs GNB3 Anterior pituitary gland cells NA 0.005 G protein subunit beta 3 protein-coding gene NA Ectoderm Brain 0.0 0.464286 0.00093985 0.00565662 +Mm Hs HEPACAM2 Anterior pituitary gland cells FLJ38683 0.012 HEPACAM family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.214286 0.0112782 0.0121489 +Mm Hs ASB4 Anterior pituitary gland cells ASB-4 0.005 ankyrin repeat and SOCS box containing 4 protein-coding gene NA Ectoderm Brain 0.0 0.107143 0.0 0.00642797 +Mm Hs RAX Anterior pituitary gland cells RX 0.006 retina and anterior neural fold homeobox protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs NKX2-1 Anterior pituitary gland cells TTF-1|TTF1|NKX2A|BCH|TITF1 0.01 NK2 homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0714286 0.00532581 0.0113132 +Mm Hs FGF10 Anterior pituitary gland cells NA 0.001 fibroblast growth factor 10 protein-coding gene NA Ectoderm Brain 0.0 0.0714286 0.000626566 0.00160699 +Mm Hs FSHB Anterior pituitary gland cells NA 0.0 follicle stimulating hormone subunit beta protein-coding gene 1 Ectoderm Brain 0.0 0.142857 0.0 0.0 +Mm Hs PCSK1 Anterior pituitary gland cells PC1|NEC1 0.008 proprotein convertase subtilisin/kexin type 1 protein-coding gene 1 Ectoderm Brain 0.0 0.107143 0.0093985 0.00829209 +Mm Hs GNRHR Anterior pituitary gland cells LHRHR|GRHR 0.0 gonadotropin releasing hormone receptor protein-coding gene 1 Ectoderm Brain 0.0 0.107143 0.0 0.000385678 +Mm Hs PITX1 Anterior pituitary gland cells POTX|BFT 0.009 paired like homeodomain 1 protein-coding gene NA Ectoderm Brain 0.0 0.0714286 0.00657895 0.00899916 +Hs GH1 Anterior pituitary gland cells GH-N|GHN|GH|hGH-N 0.0 growth hormone 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs TSHB Anterior pituitary gland cells NA 0.001 thyroid stimulating hormone beta protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PAX7 Anterior pituitary gland cells Hup1 0.001 paired box 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.000899916 +Mm Hs LHB Anterior pituitary gland cells LSH-B|CGB4|hLHB 0.001 luteinizing hormone beta polypeptide protein-coding gene 1 Ectoderm Brain 0.0 0.142857 0.0 0.000835637 +Mm Hs S100B Astrocytes S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0313873 0.0 +Mm Hs SLC1A2 Astrocytes GLT-1|EAAT2 0.071 solute carrier family 1 member 2 protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.00878845 0.0 +Mm Hs GFAP Astrocytes FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 1.0 0.344262 0.00376648 0.00837696 +Mm Hs BYSL Astrocytes Enp1 0.013 bystin like protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109856 0.0137435 +Mm Hs ALDH1L1 Astrocytes 10-fTHF|FTHFD 0.008 aldehyde dehydrogenase 1 family member L1 protein-coding gene 1 Ectoderm Brain 0.0 0.140984 0.00156937 0.00765707 +Mm Hs CD40 Astrocytes Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0131827 0.0110602 +Mm Hs SLC1A3 Astrocytes EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.00910232 0.0 +Mm Hs FGFR3 Astrocytes CEK2|JTK4|CD333|ACH 0.021 fibroblast growth factor receptor 3 protein-coding gene 1 Ectoderm Brain 1.0 0.681967 0.00910232 0.0106675 +Mm Hs GJB6 Astrocytes EDH|CX30|ED2 0.013 gap junction protein beta 6 protein-coding gene 1 Ectoderm Brain 0.0 0.534426 0.000313873 0.00562827 +Mm Hs AQP4 Astrocytes MIWC 0.024 aquaporin 4 protein-coding gene 1 Ectoderm Brain 1.0 0.878689 0.00408035 0.0124346 +Mm Hs HTRA1 Astrocytes HtrA|IGFBP5-protease|ARMD7|PRSS11 0.065 HtrA serine peptidase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.84918 0.0338983 0.0572644 +Mm Hs S100A8 Astrocytes P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0800377 0.0 +Mm Hs CLDN10 Astrocytes OSP-L|CPETRL3 0.028 claudin 10 protein-coding gene 1 Ectoderm Brain 0.0 0.718033 0.0238544 0.0164921 +Mm Hs ITIH3 Astrocytes H3P 0.009 inter-alpha-trypsin inhibitor heavy chain 3 protein-coding gene 1 Ectoderm Brain 0.0 0.360656 0.00345261 0.0039267 +Mm Hs NKAIN4 Astrocytes bA261N11.2|FAM77A|C20orf58 0.036 sodium/potassium transporting ATPase interacting 4 protein-coding gene 1 Ectoderm Brain 0.166667 0.668852 0.00878845 0.0295812 +Mm Hs ACSL6 Astrocytes KIAA0837|LACS5|FACL6 0.022 acyl-CoA synthetase long chain family member 6 protein-coding gene NA Ectoderm Brain 0.0 0.832787 0.0144382 0.0078534 +Mm Hs ACSBG1 Astrocytes BGM|FLJ30320|MGC14352|BG1|KIAA0631|hBG1|hsBG 0.023 acyl-CoA synthetase bubblegum family member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.796721 0.0 0.0132853 +Mm Hs TRIL Astrocytes KIAA0644 0.023 TLR4 interactor with leucine rich repeats protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00345261 0.0 +Mm Hs AGT Astrocytes SERPINA8 0.02 angiotensinogen protein-coding gene 1 Ectoderm Brain 0.833333 0.622951 0.0144382 0.00942408 +Mm Hs GPR37L1 Astrocytes ETBR-LP-2 0.041 G protein-coupled receptor 37 like 1 protein-coding gene 1 Ectoderm Brain 1.0 0.977049 0.00251099 0.032199 +Mm Hs SLC4A4 Astrocytes NBC1|HNBC1|NBC2|pNBC|hhNMC|SLC4A5 0.033 solute carrier family 4 member 4 protein-coding gene 1 Ectoderm Brain 0.166667 0.0 0.0119272 0.0 +Mm Hs NTSR2 Astrocytes NTR2 0.019 neurotensin receptor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.977049 0.0 0.00503927 +Mm Hs SLC6A11 Astrocytes GAT3 0.02 solute carrier family 6 member 11 protein-coding gene 1 Ectoderm Brain 0.833333 0.0 0.000313873 0.0 +Mm Hs HSPA2 Astrocytes NA 0.03 heat shock protein family A (Hsp70) member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.121311 0.0430006 0.0270942 +Mm Hs SLC16A2 Astrocytes XPCT|MCT8|DXS128|AHDS|MRX22 0.023 solute carrier family 16 member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00345261 0.0 +Mm Hs SYNE1 Astrocytes SYNE-1B|KIAA0796|8B|Nesprin-1|enaptin|MYNE1|CPG2|dJ45H2.2|SCAR8|ARCA1|Nesp1|C6orf98 0.05 spectrin repeat containing nuclear envelope protein 1 protein-coding gene 1 Ectoderm Brain 0.666667 0.0 0.0141243 0.0 +Mm Hs DIO2 Astrocytes TXDI2|SelY 0.003 iodothyronine deiodinase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0491803 0.00564972 0.00137435 +Mm Hs SLC7A10 Astrocytes asc-1 0.005 solute carrier family 7 member 10 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000627746 0.0 +Mm Hs ENTPD2 Astrocytes NTPDase-2|CD39L1 0.012 ectonucleoside triphosphate diphosphohydrolase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.108197 0.00094162 0.0126963 +Mm Hs HSPB6 Astrocytes FLJ32389|Hsp20|PPP1R91 0.005 heat shock protein family B (small) member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.00327869 0.00188324 0.00621728 +Mm Hs PLXNB1 Astrocytes KIAA0407|PLXN5 0.006 plexin B1 protein-coding gene 1 Ectoderm Brain 0.833333 0.0688525 0.000627746 0.00556283 +Mm Hs LCAT Astrocytes NA 0.005 lecithin-cholesterol acyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.213115 0.000313873 0.00170157 +Mm Hs PLA2G7 Astrocytes LDL-PLA2 0.048 phospholipase A2 group VII protein-coding gene 1 Ectoderm Brain 0.0 0.908197 0.0116133 0.0393979 +Mm Hs CMTM5 Astrocytes FLJ37521|CKLFSF5 0.044 CKLF like MARVEL transmembrane domain containing 5 protein-coding gene 1 Ectoderm Brain 0.0 0.537705 0.00784683 0.0431283 +Mm Hs S1PR1 Astrocytes edg-1|D1S3362|CD363 0.044 sphingosine-1-phosphate receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0112994 0.0 +Mm Hs SLC39A12 Astrocytes FLJ30499 0.007 solute carrier family 39 member 12 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs LUZP2 Astrocytes NA 0.037 leucine zipper protein 2 protein-coding gene 1 Ectoderm Brain 0.0 0.508197 0.0047081 0.0363874 +Mm Hs GSTA4 Astrocytes NA 0.063 glutathione S-transferase alpha 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0786885 0.0596359 0.0625654 +Mm Hs SLC25A28 Astrocytes MRS3/4|MRS4L 0.007 solute carrier family 25 member 28 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0229127 0.0 +Mm Hs SLC25A46 Astrocytes NA 0.045 solute carrier family 25 member 46 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0263653 0.0 +Mm Hs WNT3 Astrocytes MGC131950|MGC138321|MGC138323 0.003 Wnt family member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000627746 0.0 +Mm Hs FZD2 Astrocytes NA 0.012 frizzled class receptor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.101639 0.00784683 0.0103403 +Mm Hs TEAD1 Astrocytes TEF-1|TCF13|AA 0.027 TEA domain transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0238544 0.0 +Mm Hs RLBP1 Astrocytes CRALBP 0.028 retinaldehyde binding protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ALDOC Astrocytes NA 0.078 aldolase, fructose-bisphosphate C protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00094162 0.0787304 +Mm Hs GJA1 Astrocytes CX43|ODOD|SDTY3|ODDD|GJAL 0.1 gap junction protein alpha 1 protein-coding gene 1 Ectoderm Brain 1.0 0.993443 0.0615191 0.0894634 +Mm Hs APOE Astrocytes AD2 0.343 apolipoprotein E protein-coding gene 1 Ectoderm Brain 0.833333 1.0 0.131199 0.377225 +Mm Hs LCN2 Astrocytes NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.056811 0.0426047 +Mm Hs SOX9 Astrocytes SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0323289 0.0 +Mm Hs VIM Astrocytes NA 0.427 vimentin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.591651 0.0 +Mm Hs CCR7 Astrocytes BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.042059 0.0116492 +Mm Hs AANAT Astrocytes SNAT 0.0 aralkylamine N-acetyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs FABP7 Astrocytes B-FABP|BLBP 0.142 fatty acid binding protein 7 protein-coding gene 1 Ectoderm Brain 0.0 0.688525 0.0144382 0.164202 +Mm Hs SOCS3 Astrocytes SSI-3|CIS3|SOCS-3|Cish3 0.081 suppressor of cytokine signaling 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0944758 0.0 +Mm Hs SYNM Astrocytes KIAA0353|DMN 0.017 synemin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00094162 0.0 +Mm Hs HMG20A Astrocytes HMGX1|FLJ10739|HMGXB1 0.008 high mobility group 20A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00784683 0.00890052 +Mm Hs NFATC3 Astrocytes NFAT4|NFATX 0.002 nuclear factor of activated T cells 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00627746 0.00143979 +Mm Hs SRR Astrocytes ILV1 0.001 serine racemase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC1A6 Astrocytes EAAT4 0.003 solute carrier family 1 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313873 0.0 +Mm Hs ETS1 Astrocytes FLJ10768|ETS-1 0.095 ETS proto-oncogene 1, transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0389203 0.111322 +Mm Hs SLIT1 Astrocytes slit1|MEGF4|Slit-1|SLIT3|SLIL1 0.001 slit guidance ligand 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313873 0.0 +Mm Hs SNPH Astrocytes bA314N13.5 0.004 syntaphilin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs IL23A Astrocytes SGRF|IL23P19|IL-23|IL-23A|P19 0.002 interleukin 23 subunit alpha protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00690521 0.00104712 +Mm Hs CD2 B cells NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.213178 0.0958466 0.0265544 +Mm Hs CD5 B cells NA 0.004 CD5 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00415335 0.00450186 +Mm Hs MS4A1 B cells Bp35|MS4A2|CD20 0.014 membrane spanning 4-domains A1 protein-coding gene 1 Mesoderm Immune system 0.483871 0.620155 0.0111821 0.00156586 +Mm Hs CR2 B cells CD21|C3DR 0.001 complement C3d receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0483871 0.0348837 0.0 0.0 +Mm Hs CD22 B cells SIGLEC-2|SIGLEC2 0.003 CD22 molecule protein-coding gene 1 Mesoderm Immune system 0.0967742 0.127907 0.00127796 0.000195733 +Hs FCER2 B cells CLEC4J|CD23|CD23A|FCE2 0.002 Fc fragment of IgE receptor II protein-coding gene 1 Mesoderm Immune system 0.016129 0.0 0.00191693 0.0 +Mm Hs CD40 B cells Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Immune system 0.112903 0.0 0.0111821 0.0110263 +Mm Hs CD69 B cells CLEC2C 0.024 CD69 molecule protein-coding gene NA Mesoderm Immune system 0.725806 0.0930233 0.0990415 0.00593723 +Mm Hs CD70 B cells CD27L|CD27LG|TNFSF7 0.002 CD70 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00255591 0.000130489 +Mm Hs CD79A B cells MB-1|IGA 0.024 CD79a molecule protein-coding gene 1 Mesoderm Immune system 0.983871 0.914729 0.0246006 0.00339271 +Mm Hs CD79B B cells IGB 0.028 CD79b molecule protein-coding gene 1 Mesoderm Immune system 0.919355 0.926357 0.0255591 0.00835128 +Mm Hs CD80 B cells B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000195733 +Mm Hs CD86 B cells B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0232558 0.0124601 0.0292947 +Mm Hs TNFRSF9 B cells CD137|4-1BB|ILA 0.003 TNF receptor superfamily member 9 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00351438 0.0 +Mm Hs SDC1 B cells CD138|syndecan|SYND1|SDC 0.046 syndecan 1 protein-coding gene NA Mesoderm Immune system 0.016129 0.0 0.0469649 0.0 +Mm Hs TNFSF4 B cells OX-40L|gp34|CD252|TXGP1 0.0 TNF superfamily member 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000958466 0.0 +Mm Hs TNFRSF13B B cells TACI|CD267|IGAD2 0.016 TNF receptor superfamily member 13B protein-coding gene NA Mesoderm Immune system 0.0806452 0.0 0.00383387 0.0 +Mm Hs TNFRSF13C B cells BAFFR|CD268 0.008 TNF receptor superfamily member 13C protein-coding gene 1 Mesoderm Immune system 0.451613 0.0 0.0105431 0.0 +Mm Hs PDCD1 B cells CD279|hSLE1|PD-1|SLEB2 0.003 programmed cell death 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00479233 0.00254453 +Mm Hs IGHD B cells FLJ00382|FLJ46727|MGC29633 0.008 immunoglobulin heavy constant delta other 1 Mesoderm Immune system 0.177419 0.406977 0.00543131 0.000782932 +Mm Hs IGHM B cells NA 0.078 immunoglobulin heavy constant mu other 1 Mesoderm Immune system 0.83871 0.968992 0.0396166 0.0677236 +Mm Hs RASGRP3 B cells KIAA0846|GRP3|CalDAG-GEFIII 0.025 RAS guanyl releasing protein 3 protein-coding gene NA Mesoderm Immune system 0.0322581 0.0 0.00894569 0.0 +Hs HLA-DRA B cells HLA-DRA1 0.039 major histocompatibility complex, class II, DR alpha protein-coding gene 1 Mesoderm Immune system 0.935484 0.0 0.198083 0.0 +Mm Hs LTB B cells TNFSF3|TNFC 0.065 lymphotoxin beta protein-coding gene NA Mesoderm Immune system 0.612903 0.453488 0.154313 0.0385594 +Hs HLA-DQA1 B cells HLA-DQA 0.01 major histocompatibility complex, class II, DQ alpha 1 protein-coding gene NA Mesoderm Immune system 0.258065 0.0 0.0472843 0.0 +Mm Hs FLI1 B cells SIC-1 0.036 Fli-1 proto-oncogene, ETS transcription factor protein-coding gene NA Mesoderm Immune system 0.016129 0.127907 0.0057508 0.0422131 +Mm Hs CD14 B cells NA 0.051 CD14 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.00387597 0.0271566 0.0563711 +Mm Hs SEMA6D B cells KIAA1479|FLJ11598 0.026 semaphorin 6D protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00159744 0.0 +Mm Hs LAIR1 B cells CD305 0.027 leukocyte associated immunoglobulin like receptor 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0232558 0.0162939 0.0302734 +Mm Hs IFIT3 B cells ISG60|RIG-G|CIG-49|IFI60|GARG-49|IRG2|IFIT4 0.014 interferon induced protein with tetratricopeptide repeats 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0155039 0.0223642 0.0113525 +Mm Hs IGLL1 B cells IGVPB|IGL5|14.1|CD179B|IGLL 0.007 immunoglobulin lambda like polypeptide 1 protein-coding gene NA Mesoderm Immune system 0.435484 0.0697674 0.027476 0.000978665 +Mm Hs DNTT B cells TDT 0.007 DNA nucleotidylexotransferase protein-coding gene NA Mesoderm Immune system 0.241935 0.0426357 0.00223642 0.00554577 +Mm Hs MME B cells CALLA|CD10 0.017 membrane metalloendopeptidase protein-coding gene 1 Mesoderm Immune system 0.0967742 0.0 0.0255591 0.0152672 +Mm Hs SPN B cells LSN|CD43|GPL115 0.029 sialophorin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0517572 0.0 +Mm Hs CD19 B cells NA 0.007 CD19 molecule protein-coding gene 1 Mesoderm Immune system 0.129032 0.356589 0.00543131 0.000195733 +Hs CD24 B cells CD24A 0.039 CD24 molecule protein-coding gene 1 Mesoderm Immune system 0.370968 0.0 0.188498 0.0 +Mm Hs CD27 B cells S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene 1 Mesoderm Immune system 0.112903 0.0 0.0210863 0.0160501 +Mm Hs B3GAT1 B cells GlcAT-P|HNK-1|NK-1|CD57|LEU7 0.014 beta-1,3-glucuronyltransferase 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0028754 0.017094 +Mm Hs CD72 B cells LYB2|CD72b 0.003 CD72 molecule protein-coding gene 1 Mesoderm Immune system 0.0967742 0.0581395 0.0 0.00189209 +Mm Hs MUM1 B cells MUM-1|EXPAND1 0.02 melanoma associated antigen (mutated) 1 protein-coding gene NA Mesoderm Immune system 0.0 0.00387597 0.0207668 0.0206825 +Mm Hs PAX5 B cells BSAP 0.003 paired box 5 protein-coding gene 1 Mesoderm Immune system 0.0483871 0.182171 0.000638978 0.000521955 +Mm Hs JCHAIN B cells IGCJ|JCH|IGJ 0.017 joining chain of multimeric IgA and IgM protein-coding gene NA Mesoderm Immune system 0.306452 0.251938 0.0444089 0.0039799 +Mm Hs MZB1 B cells MGC29506|HSPC190|pERp1|MEDA-7 0.025 marginal zone B and B1 cell specific protein protein-coding gene NA Mesoderm Immune system 0.580645 0.844961 0.027476 0.00704639 +Mm Hs LY6D B cells E48 0.03 lymphocyte antigen 6 family member D protein-coding gene 1 Mesoderm Immune system 0.0 0.906977 0.00127796 0.0216611 +Mm H2-DMB2 B cells NA 0.013 histocompatibility 2, class II, locus Mb2 protein coding gene 1 Mesoderm Immune system 0.0 0.542636 0.0 0.00730737 +Mm Hs FCMR B cells TOSO|FAIM3 0.009 Fc fragment of IgM receptor protein-coding gene 1 Mesoderm Immune system 0.112903 0.406977 0.0115016 0.000913421 +Mm Hs BANK1 B cells BANK|FLJ20706 0.006 B cell scaffold protein with ankyrin repeats 1 protein-coding gene 1 Mesoderm Immune system 0.225806 0.232558 0.00415335 0.00130489 +Mm Hs EDEM1 B cells KIAA0212|EDEM 0.038 ER degradation enhancing alpha-mannosidase like protein 1 protein-coding gene NA Mesoderm Immune system 0.0 0.232558 0.00798722 0.0410387 +Mm Hs VPREB3 B cells 8HS20 0.011 V-set pre-B cell surrogate light chain 3 protein-coding gene 1 Mesoderm Immune system 0.629032 0.0 0.00479233 0.0 +Mm H2-OB B cells NA 0.007 histocompatibility 2, O region beta locus protein coding gene 1 Mesoderm Immune system 0.0 0.391473 0.0 0.00274026 +Mm Hs POU2AF1 B cells OBF1|BOB1 0.01 POU class 2 associating factor 1 protein-coding gene 1 Mesoderm Immune system 0.0967742 0.51938 0.0057508 0.000521955 +Mm Hs CRELD2 B cells MGC11256 0.065 cysteine rich with EGF like domains 2 protein-coding gene NA Mesoderm Immune system 0.0483871 0.232558 0.0984026 0.0533699 +Mm Hs DERL3 B cells FLJ43842|MGC71803|derlin-3|IZP6|C22orf14 0.01 derlin 3 protein-coding gene NA Mesoderm Immune system 0.0483871 0.186047 0.0335463 0.00137013 +Mm SIGLECG B cells NA 0.002 sialic acid binding Ig-like lectin G protein coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs RALGPS2 B cells FLJ10244|FLJ25604 0.048 Ral GEF with PH domain and SH3 binding motif 2 protein-coding gene NA Mesoderm Immune system 0.0483871 0.0 0.0226837 0.0 +Mm Hs FCHSD2 B cells KIAA0769|SH3MD3 0.003 FCH and double SH3 domains 2 protein-coding gene NA Mesoderm Immune system 0.0 0.00387597 0.00159744 0.002936 +Mm Hs POLD4 B cells POLDS 0.065 DNA polymerase delta 4, accessory subunit protein-coding gene NA Mesoderm Immune system 0.0 0.48062 0.0 0.0724865 +Mm CMAH B cells NA 0.003 cytidine monophospho-N-acetylneuraminic acid hydroxylase protein coding gene NA Mesoderm Immune system 0.0 0.0852713 0.0 0.00287075 +Mm Hs TNFRSF17 B cells BCM|CD269|TNFRSF13A|BCMA 0.005 TNF receptor superfamily member 17 protein-coding gene NA Mesoderm Immune system 0.0483871 0.0 0.00926518 0.0 +Mm Hs HVCN1 B cells MGC15619|Hv1|VSOP 0.014 hydrogen voltage gated channel 1 protein-coding gene NA Mesoderm Immune system 0.0645161 0.290698 0.0115016 0.00919945 +Mm TRP53INP1 B cells NA 0.014 transformation related protein 53 inducible nuclear protein 1 protein coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs FCRLA B cells MGC4595|FCRLc2|FCRLb|FCRLc1|FCRLd|FCRLe|FCRL|FCRLa|FREB|FCRLX|FCRLM1 0.012 Fc receptor like A protein-coding gene NA Mesoderm Immune system 0.112903 0.55814 0.000958466 0.00254453 +Mm Hs EDEM2 B cells FLJ10783|bA4204.1|C20orf49|C20orf31 0.037 ER degradation enhancing alpha-mannosidase like protein 2 protein-coding gene NA Mesoderm Immune system 0.016129 0.22093 0.0057508 0.0386246 +Mm Hs BLNK B cells SLP65|Ly57|SLP-65|BLNK-s|BASH|bca 0.017 B cell linker protein-coding gene NA Mesoderm Immune system 0.016129 0.387597 0.000319489 0.0135056 +Mm H2-OA B cells NA 0.006 histocompatibility 2, O region alpha locus protein coding gene NA Mesoderm Immune system 0.0 0.174419 0.0 0.00424088 +Mm Hs TXNDC11 B cells EFP1 0.011 thioredoxin domain containing 11 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00543131 0.0 +Mm Hs BTLA B cells BTLA1|CD272 0.001 B and T lymphocyte associated protein-coding gene NA Mesoderm Immune system 0.0 0.0348837 0.000319489 0.000978665 +Mm Hs SMAP2 B cells SMAP1L 0.053 small ArfGAP2 protein-coding gene NA Mesoderm Immune system 0.0483871 0.0 0.0325879 0.0 +Mm SCD1 B cells NA 0.036 stearoyl-Coenzyme A desaturase 1 protein coding gene NA Mesoderm Immune system NA NA NA NA +None FAM46C B cells NA 0.02 NA NA NA Mesoderm Immune system 0.016129 0.178295 0.0408946 0.0137666 +Mm Hs FKBP11 B cells FKBP19 0.031 FK506 binding protein 11 protein-coding gene NA Mesoderm Immune system 0.0806452 0.162791 0.028754 0.0282508 +Mm Hs SEC61A1 B cells NA 0.04 Sec61 translocon alpha 1 subunit protein-coding gene NA Mesoderm Immune system 0.0322581 0.0 0.0693291 0.0 +Mm Hs SPCS3 B cells FLJ22649|SPC22/23|YLR066W|PRO3567 0.069 signal peptidase complex subunit 3 protein-coding gene NA Mesoderm Immune system 0.0645161 0.0 0.158147 0.0 +Mm Hs SPIB B cells SPI-B 0.01 Spi-B transcription factor protein-coding gene NA Mesoderm Immune system 0.0967742 0.0 0.00702875 0.0 +Mm Hs EAF2 B cells BM040|TRAITS 0.009 ELL associated factor 2 protein-coding gene NA Mesoderm Immune system 0.0967742 0.189922 0.029393 0.000260977 +Mm Hs CXCR4 B cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.83871 0.0620155 0.185623 0.00789457 +Mm Hs BIRC3 B cells cIAP2|hiap-1|MIHC|RNF49|MALT2|c-IAP2|API2 0.026 baculoviral IAP repeat containing 3 protein-coding gene NA Mesoderm Immune system 0.177419 0.0658915 0.0814696 0.0140275 +Mm Hs IGLC2 B cells NA 0.022 immunoglobulin lambda constant 2 other 1 Mesoderm Immune system 0.612903 0.771318 0.0338658 0.00195733 +Mm Hs IGLC3 B cells NA 0.02 immunoglobulin lambda constant 3 (Kern-Oz+ marker) other 1 Mesoderm Immune system 0.33871 0.806202 0.0204473 0.00371893 +Mm Hs IGLC1 B cells NA 0.008 immunoglobulin lambda constant 1 other NA Mesoderm Immune system 0.0 0.48062 0.0 0.0017616 +Mm Hs IL21R B cells CD360 0.013 interleukin 21 receptor protein-coding gene NA Mesoderm Immune system 0.0 0.0426357 0.0 0.0155934 +Mm Hs IGKC B cells HCAK1 0.072 immunoglobulin kappa constant other NA Mesoderm Immune system 0.83871 0.976744 0.149521 0.0379722 +Mm IGLV1 B cells 1810027O01Rik 0.003 immunoglobulin lambda variable 1 NA NA Mesoderm Immune system 0.0 0.244186 0.0 6.52443e-05 +Mm Hs VPREB1 B cells VpreB|CD179A 0.003 V-set pre-B cell surrogate light chain 1 protein-coding gene 1 Mesoderm Immune system 0.419355 0.0 0.000958466 0.0 +Mm VPREB2 B cells NA 0.001 pre-B lymphocyte gene 2 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs LRMP B cells JAW1 0.015 lymphoid restricted membrane protein protein-coding gene 1 Mesoderm Immune system 0.0806452 0.22093 0.000958466 0.0125922 +Mm Hs KLHL6 B cells FLJ00029 0.014 kelch like family member 6 protein-coding gene 1 Mesoderm Immune system 0.0322581 0.135659 0.000319489 0.0140928 +Mm Hs SLAMF6 B cells KALI|NTBA|KALIb|Ly108|SF2000|NTB-A|CD352 0.003 SLAM family member 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs FAM129C B cells FLJ39802|BCNP1 0.003 family with sequence similarity 129 member C protein-coding gene 1 Mesoderm Immune system 0.145161 0.135659 0.00511182 6.52443e-05 +Mm Hs BST1 B cells CD157 0.008 bone marrow stromal cell antigen 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0155039 0.00638978 0.00854701 +Mm Hs MSH5 B cells G7 0.0 mutS homolog 5 protein-coding gene NA Mesoderm Immune system 0.0 0.0116279 0.0 0.000326222 +Mm Hs DOK3 B cells FLJ22570 0.017 docking protein 3 protein-coding gene NA Mesoderm Immune system 0.0 0.248062 0.000319489 0.0161154 +Mm Hs BACH2 B cells BTBD25 0.003 BTB domain and CNC homolog 2 protein-coding gene 1 Mesoderm Immune system 0.0322581 0.100775 0.000958466 0.00189209 +Mm FCER2A B cells NA 0.002 Fc receptor, IgE, low affinity II, alpha polypeptide protein coding gene 1 Mesoderm Immune system 0.0 0.120155 0.0 0.0 +Mm Hs PXK B cells FLJ20335|Slob 0.012 PX domain containing serine/threonine kinase like protein-coding gene 1 Mesoderm Immune system 0.016129 0.0813954 0.0111821 0.0111568 +Mm Hs IGHG1 B cells NA 0.006 immunoglobulin heavy constant gamma 1 (G1m marker) other NA Mesoderm Immune system 0.129032 0.0852713 0.0159744 6.52443e-05 +Mm Hs IGHG3 B cells NA 0.005 immunoglobulin heavy constant gamma 3 (G3m marker) other NA Mesoderm Immune system 0.112903 0.116279 0.013099 0.000195733 +Hs IGHG4 B cells NA 0.002 immunoglobulin heavy constant gamma 4 (G4m marker) other NA Mesoderm Immune system 0.0967742 0.0 0.0105431 0.0 +Mm IGHA B cells IgA|Igh-2 0.007 immunoglobulin heavy constant alpha NA NA Mesoderm Immune system 0.0 0.193798 0.0 0.00626346 +Mm Hs CD38 B cells NA 0.016 CD38 molecule protein-coding gene 1 Mesoderm Immune system 0.145161 0.0775194 0.0115016 0.0150714 +Mm Hs PTPRC B cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Immune system 0.209677 0.341085 0.216294 0.102238 +Mm Hs EBF1 B cells COE1|EBF 0.105 early B cell factor 1 protein-coding gene 1 Mesoderm Immune system 0.354839 0.70155 0.028115 0.114439 +Mm Hs BCL11A B cells BCL11A-XL|BCL11A-L|BCL11A-S|CTIP1|HBFQTL5|ZNF856|EVI9 0.134 B cell CLL/lymphoma 11A protein-coding gene 1 Mesoderm Immune system 0.66129 0.104651 0.102556 0.143277 +Mm Hs CCR7 B cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.016129 0.251938 0.042492 0.00737261 +Mm Hs CD55 B cells TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Immune system 0.0483871 0.197674 0.127476 0.0167026 +Mm Hs CD74 B cells DHLAG 0.169 CD74 molecule protein-coding gene 1 Mesoderm Immune system 0.983871 0.94186 0.351438 0.111437 +Mm Hs CD52 B cells HE5|EDDM5|CDW52 0.181 CD52 molecule protein-coding gene 1 Mesoderm Immune system 0.870968 0.930233 0.266134 0.146865 +Mm Hs TLR9 B cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SWAP70 B cells KIAA0640|SWAP-70 0.019 switching B cell complex subunit SWAP70 protein-coding gene 1 Mesoderm Immune system 0.0967742 0.0 0.0178914 0.0 +Mm Hs HMGA1 B cells HMGIY 0.084 high mobility group AT-hook 1 protein-coding gene 1 Mesoderm Immune system 0.274194 0.0542636 0.295208 0.0266197 +Mm Hs CD38 B cells memory NA 0.016 CD38 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0140977 0.0161052 +Mm Hs CD80 B cells memory B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000192493 +Mm Hs CD84 B cells memory SLAMF5|hCD84|mCD84 0.023 CD84 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0093985 0.0272698 +Mm Hs CD86 B cells memory B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.012218 0.0291947 +Mm Hs NT5E B cells memory CD73|eN|eNT|CALJA|NT5 0.005 5'-nucleotidase ecto protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00720551 0.00372153 +Mm Hs PAX5 B cells memory BSAP 0.003 paired box 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.00352903 +Mm Hs PTPRC B cells memory T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.216165 0.106192 +Mm Hs SPIB B cells memory SPI-B 0.01 Spi-B transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00877193 0.0 +Mm Hs ADAM28 B cells memory eMDCII|MDC-Lm|MDC-Ls|ADAM23 0.004 ADAM metallopeptidase domain 28 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0172306 0.00147578 +Mm Hs AIM2 B cells memory PYHIN4 0.002 absent in melanoma 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.00173244 +Mm Hs ALOX5 B cells memory 5-LOX 0.006 arachidonate 5-lipoxygenase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00313283 0.00641643 +Mm Hs BACH2 B cells memory BTBD25 0.003 BTB domain and CNC homolog 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.00352903 +Mm Hs BANK1 B cells memory BANK|FLJ20706 0.006 B cell scaffold protein with ankyrin repeats 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00845865 0.00513314 +Mm Hs BLK B cells memory MGC10442 0.005 BLK proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00250627 0.00423484 +Mm Hs CCR6 B cells memory CKR-L3|GPR-CY4|CMKBR6|GPR29|DRY-6|DCR2|BN-1|CD196|STRL22 0.001 C-C motif chemokine receptor 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00186076 +Mm Hs CD180 B cells memory RP105|Ly78|LY64 0.012 CD180 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00093985 0.0142445 +Mm Hs CD19 B cells memory NA 0.007 CD19 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00783208 0.0060956 +Hs CD1C B cells memory NA 0.001 CD1c molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00501253 0.0 +Mm Hs CD22 B cells memory SIGLEC-2|SIGLEC2 0.003 CD22 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00313283 0.00230991 +Mm Hs CD27 B cells memory S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0228697 0.0157844 +Mm Hs CD37 B cells memory TSPAN26 0.116 CD37 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.215852 0.0949631 +Mm Hs CD69 B cells memory CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.111216 0.00737889 +Mm Hs CD72 B cells memory LYB2|CD72b 0.003 CD72 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0018797 0.00282323 +Mm Hs CD79A B cells memory MB-1|IGA 0.024 CD79a molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0432331 0.0184793 +Mm Hs CD79B B cells memory IGB 0.028 CD79b molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0429198 0.0235483 +Hs CLCA3P B cells memory CLCA3 0.0 chloride channel accessory 3, pseudogene pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs CR2 B cells memory CD21|C3DR 0.001 complement C3d receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00093985 0.000577478 +Mm Hs CXCR5 B cells memory MDR15|CD185|BLR1 0.001 C-X-C motif chemokine receptor 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00102663 +Mm Hs DENND5B B cells memory MGC24039 0.013 DENN domain containing 5B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00595238 0.0151428 +Mm Hs FCGR2B B cells memory CD32B 0.031 Fc fragment of IgG receptor IIb protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00469925 0.0360603 +Hs FCRL2 B cells memory FCRH2|IRTA4|CD307b|SPAP1 0.0 Fc receptor like 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs FRK B cells memory RAK|PTK5 0.005 fyn related Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00720551 0.00417068 +Mm Hs GNG7 B cells memory FLJ00058 0.009 G protein subunit gamma 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0260025 0.00481232 +Hs GPR18 B cells memory NA 0.001 G protein-coupled receptor 18 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00689223 0.0 +Hs GUSBP11 B cells memory NA 0.0 glucuronidase, beta pseudogene 11 pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs HHEX B cells memory HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0228697 0.0395893 +Hs HLA-DOB B cells memory NA 0.001 major histocompatibility complex, class II, DO beta protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00501253 0.0 +Hs IFNA10 B cells memory IFN-alphaC 0.0 interferon alpha 10 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs IGHD B cells memory FLJ00382|FLJ46727|MGC29633 0.008 immunoglobulin heavy constant delta other 1 Mesoderm Immune system 0.0 0.0 0.00877193 0.00750722 +Mm Hs IGHM B cells memory NA 0.078 immunoglobulin heavy constant mu other 1 Mesoderm Immune system 0.0 0.0 0.0551378 0.0826436 +Mm Hs IGKC B cells memory HCAK1 0.072 immunoglobulin kappa constant other 1 Mesoderm Immune system 0.0 0.0 0.162907 0.053513 +Hs IGLL3P B cells memory 16.1|IGLL3 0.0 immunoglobulin lambda like polypeptide 3, pseudogene pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs IL7 B cells memory IL-7 0.007 interleukin 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0093985 0.0069939 +Mm Hs IRF8 B cells memory IRF-8|ICSBP|ICSBP1 0.069 interferon regulatory factor 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0272556 0.075008 +Mm Hs LTB B cells memory TNFSF3|TNFC 0.065 lymphotoxin beta protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.163221 0.0454283 +Mm Hs LY86 B cells memory MD-1|dJ80N2.1 0.07 lymphocyte antigen 86 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0272556 0.0782804 +Mm Hs MBL2 B cells memory COLEC1 0.002 mannose binding lectin 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000626566 0.00256657 +Mm Hs MS4A1 B cells memory Bp35|MS4A2|CD20 0.014 membrane spanning 4-domains A1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0203634 0.0118062 +Mm Hs NMBR B cells memory BB1R 0.0 neuromedin B receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs NPIPB15 B cells memory LOC440348|NPIPL2 0.002 nuclear pore complex interacting protein family member B15 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0103383 0.0 +Mm Hs P2RX5 B cells memory P2X5 0.0 purinergic receptor P2X 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0018797 0.0 +Mm Hs PNOC B cells memory PPNOC|N/OFQ|NOP 0.009 prepronociceptin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00093985 0.00994546 +Mm Hs PTPRCAP B cells memory CD45-AP 0.072 protein tyrosine phosphatase, receptor type C associated protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0865576 +Mm Hs RALGPS2 B cells memory FLJ10244|FLJ25604 0.048 Ral GEF with PH domain and SH3 binding motif 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.023183 0.0 +Mm Hs RASGRP2 B cells memory CALDAG-GEFI 0.066 RAS guanyl releasing protein 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0238095 0.0 +Mm Hs SIK1 B cells memory msk|SNF1LK 0.029 salt inducible kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SIT1 B cells memory SIT 0.003 signaling threshold regulating transmembrane adaptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00971178 0.0 +Mm Hs SLC12A1 B cells memory NKCC2 0.001 solute carrier family 12 member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000626566 0.0 +Mm Hs SP140 B cells memory LYSP100-B|LYSP100-A 0.014 SP140 nuclear body protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0037594 0.0 +Mm Hs STAP1 B cells memory STAP-1|BRDG1 0.004 signal transducing adaptor family member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00281955 0.0 +Mm Hs TMEM156 B cells memory FLJ23235 0.001 transmembrane protein 156 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00501253 0.0 +Mm Hs TNFRSF13B B cells memory TACI|CD267|IGAD2 0.016 TNF receptor superfamily member 13B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00532581 0.0 +Mm Hs TNFRSF17 B cells memory BCM|CD269|TNFRSF13A|BCMA 0.005 TNF receptor superfamily member 17 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0100251 0.0 +Mm Hs TRAF4 B cells memory MLN62|RNF83 0.062 TNF receptor associated factor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs VPREB3 B cells memory 8HS20 0.011 V-set pre-B cell surrogate light chain 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0169173 0.0 +Mm Hs ZBTB32 B cells memory TZFP|FAZF|FAXF|Rog|ZNF538 0.004 zinc finger and BTB domain containing 32 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0150376 0.0 +Mm Hs CD19 B cells naive NA 0.007 CD19 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00786906 0.0060956 +Mm Hs CD2 B cells naive NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0944287 0.0296439 +Mm Hs CD72 B cells naive LYB2|CD72b 0.003 CD72 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00188857 0.00282323 +Mm Hs IL2RA B cells naive IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0201448 0.00673725 +Mm Hs MME B cells naive CALLA|CD10 0.017 membrane metalloendopeptidase protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0270696 0.0150144 +Mm Hs ABCB4 B cells naive MDR2|PFIC-3|GBD1|PGY3|MDR3 0.002 ATP binding cassette subfamily B member 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0026949 +Mm Hs ADAM28 B cells naive eMDCII|MDC-Lm|MDC-Ls|ADAM23 0.004 ADAM metallopeptidase domain 28 protein-coding gene 1 Mesoderm Immune system 0.333333 0.0 0.0157381 0.00147578 +Mm Hs BACH2 B cells naive BTBD25 0.003 BTB domain and CNC homolog 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00157381 0.00352903 +Mm Hs BANK1 B cells naive BANK|FLJ20706 0.006 B cell scaffold protein with ankyrin repeats 1 protein-coding gene 1 Mesoderm Immune system 0.533333 0.0 0.00598048 0.00513314 +Mm Hs BCL7A B cells naive BCL7 0.078 BCL tumor suppressor 7A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0141643 0.0946423 +Mm Hs BEND5 B cells naive FLJ11588|C1orf165 0.007 BEN domain containing 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00157381 0.00821303 +Mm Hs BLK B cells naive MGC10442 0.005 BLK proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.00220334 0.00423484 +Mm Hs BRAF B cells naive BRAF1 0.025 B-Raf proto-oncogene, serine/threonine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0160529 0.0277831 +Mm Hs CD180 B cells naive RP105|Ly78|LY64 0.012 CD180 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000944287 0.0142445 +Hs CD1C B cells naive NA 0.001 CD1c molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0050362 0.0 +Mm Hs CD22 B cells naive SIGLEC-2|SIGLEC2 0.003 CD22 molecule protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.00283286 0.00230991 +Mm Hs CD37 B cells naive TSPAN26 0.116 CD37 molecule protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.21215 0.0949631 +Mm Hs CD69 B cells naive CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.666667 0.0 0.108593 0.00737889 +Mm Hs CD79A B cells naive MB-1|IGA 0.024 CD79a molecule protein-coding gene 1 Mesoderm Immune system 0.933333 0.0 0.0390305 0.0184793 +Mm Hs CD79B B cells naive IGB 0.028 CD79b molecule protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.038401 0.0235483 +Mm Hs CR2 B cells naive CD21|C3DR 0.001 complement C3d receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000944287 0.000577478 +Mm Hs CXCR5 B cells naive MDR15|CD185|BLR1 0.001 C-X-C motif chemokine receptor 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00102663 +Mm Hs EAF2 B cells naive BM040|TRAITS 0.009 ELL associated factor 2 protein-coding gene 1 Mesoderm Immune system 0.133333 0.0 0.0302172 0.00340071 +Hs FCER2 B cells naive CLEC4J|CD23|CD23A|FCE2 0.002 Fc fragment of IgE receptor II protein-coding gene 1 Mesoderm Immune system 0.4 0.0 0.000314762 0.0 +Mm Hs FCGR2B B cells naive CD32B 0.031 Fc fragment of IgG receptor IIb protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00472144 0.0360603 +Hs FCRL2 B cells naive FCRH2|IRTA4|CD307b|SPAP1 0.0 Fc receptor like 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs FRK B cells naive RAK|PTK5 0.005 fyn related Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00723953 0.00417068 +Hs GPR18 B cells naive NA 0.001 G protein-coupled receptor 18 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00692477 0.0 +Hs GUSBP11 B cells naive NA 0.0 glucuronidase, beta pseudogene 11 pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs HHEX B cells naive HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0229777 0.0395893 +Hs HLA-DOB B cells naive NA 0.001 major histocompatibility complex, class II, DO beta protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0050362 0.0 +Mm Hs IGHD B cells naive FLJ00382|FLJ46727|MGC29633 0.008 immunoglobulin heavy constant delta other 1 Mesoderm Immune system 0.866667 0.0 0.00472144 0.00750722 +Mm Hs IGHM B cells naive NA 0.078 immunoglobulin heavy constant mu other 1 Mesoderm Immune system 1.0 0.0 0.0506767 0.0826436 +Mm Hs IGKC B cells naive HCAK1 0.072 immunoglobulin kappa constant other 1 Mesoderm Immune system 1.0 0.0 0.158955 0.053513 +Hs IGLL3P B cells naive 16.1|IGLL3 0.0 immunoglobulin lambda like polypeptide 3, pseudogene pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs IL4R B cells naive CD124 0.002 interleukin 4 receptor protein-coding gene 1 Mesoderm Immune system 0.4 0.0 0.00849858 0.0 +Mm Hs IRF8 B cells naive IRF-8|ICSBP|ICSBP1 0.069 interferon regulatory factor 8 protein-coding gene 1 Mesoderm Immune system 0.2 0.0 0.02644 0.075008 +Mm Hs LTB B cells naive TNFSF3|TNFC 0.065 lymphotoxin beta protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.15927 0.0454283 +Mm Hs LY86 B cells naive MD-1|dJ80N2.1 0.07 lymphocyte antigen 86 protein-coding gene 1 Mesoderm Immune system 0.2 0.0 0.02644 0.0782804 +Mm Hs MEP1A B cells naive PPHA 0.004 meprin A subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000944287 0.00551813 +Mm Hs MICAL3 B cells naive KIAA0819 0.02 microtubule associated monooxygenase, calponin and LIM domain containing 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0100724 0.0223292 +Mm Hs MS4A1 B cells naive Bp35|MS4A2|CD20 0.014 membrane spanning 4-domains A1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0157381 0.0118062 +Mm Hs NMBR B cells naive BB1R 0.0 neuromedin B receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs P2RX5 B cells naive P2X5 0.0 purinergic receptor P2X 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00188857 0.0 +Mm Hs P2RY14 B cells naive KIAA0001|GPR105 0.012 purinergic receptor P2Y14 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00346239 0.0141803 +Mm Hs PNOC B cells naive PPNOC|N/OFQ|NOP 0.009 prepronociceptin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000944287 0.00994546 +Hs PSG2 B cells naive PSGGB|PSG1|PSBG2 0.0 pregnancy specific beta-1-glycoprotein 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs PTPRCAP B cells naive CD45-AP 0.072 protein tyrosine phosphatase, receptor type C associated protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0865576 +Mm Hs RALGPS2 B cells naive FLJ10244|FLJ25604 0.048 Ral GEF with PH domain and SH3 binding motif 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0232924 0.0 +Mm Hs RASGRP2 B cells naive CALDAG-GEFI 0.066 RAS guanyl releasing protein 2 protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.0236072 0.0 +Mm Hs SELL B cells naive LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene 1 Mesoderm Immune system 0.533333 0.0 0.0579163 0.0 +Mm Hs SIK1 B cells naive msk|SNF1LK 0.029 salt inducible kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SLC12A1 B cells naive NKCC2 0.001 solute carrier family 12 member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000629525 0.0 +Mm Hs SPIB B cells naive SPI-B 0.01 Spi-B transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00881335 0.0 +Mm Hs STAP1 B cells naive STAP-1|BRDG1 0.004 signal transducing adaptor family member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00283286 0.0 +Hs TCL1A B cells naive TCL1 0.003 T cell leukemia/lymphoma 1A protein-coding gene 1 Mesoderm Immune system 0.733333 0.0 0.0116462 0.0 +Mm Hs UGT1A8 B cells naive UGT1H 0.0 UDP glucuronosyltransferase family 1 member A8 other 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs VPREB3 B cells naive 8HS20 0.011 V-set pre-B cell surrogate light chain 3 protein-coding gene 1 Mesoderm Immune system 0.533333 0.0 0.0144791 0.0 +Hs ZNF286A B cells naive KIAA1874|ZNF286 0.0 zinc finger protein 286A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000944287 0.0 +Mm Hs TNFSF8 B cells naive CD153|CD30LG 0.001 TNF superfamily member 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs FOXP1 B cells naive QRF1|12CC4|HSPC215|hFKH1B 0.174 forkhead box P1 protein-coding gene 1 Mesoderm Immune system 0.8 0.0 0.229777 0.16163 +Mm Hs MITF B cells naive MI|bHLHe32|WS2A|WS2 0.004 melanogenesis associated transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00598048 0.00340071 +Mm Hs CD52 B cells naive HE5|EDDM5|CDW52 0.181 CD52 molecule protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.274473 0.159833 +Hs HLA-DQB1 B cells naive HLA-DQB 0.012 major histocompatibility complex, class II, DQ beta 1 protein-coding gene 1 Mesoderm Immune system 0.866667 0.0 0.0610639 0.0 +Mm Hs TNFRSF13C B cells naive BAFFR|CD268 0.008 TNF receptor superfamily member 13C protein-coding gene 1 Mesoderm Immune system 0.933333 0.0 0.0147938 0.0 +Hs LINC00926 B cells naive NA 0.003 long intergenic non-protein coding RNA 926 non-coding RNA 1 Mesoderm Immune system 0.933333 0.0 0.0113314 0.0 +Mm Hs STAG3 B cells naive NA 0.006 stromal antigen 3 protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.0182562 0.0 +Mm Hs BIRC3 B cells naive cIAP2|hiap-1|MIHC|RNF49|MALT2|c-IAP2|API2 0.026 baculoviral IAP repeat containing 3 protein-coding gene 1 Mesoderm Immune system 0.533333 0.0 0.0812087 0.0148861 +Mm Hs CD74 B cells naive DHLAG 0.169 CD74 molecule protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.360718 0.125184 +Mm Hs KRT5 Basal cells KRT5A|EBS2 0.019 keratin 5 protein-coding gene 1 Mesoderm Epithelium 0.66 1.0 0.0141354 0.0150154 +Mm Hs KRT17 Basal cells PCHC1 0.025 keratin 17 protein-coding gene NA Mesoderm Epithelium 0.793333 0.0 0.039119 0.0157213 +Mm Hs BCL2 Basal cells Bcl-2|PPP1R50 0.043 BCL2, apoptosis regulator protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00164366 0.0516555 +Mm Hs KRT14 Basal cells EBS3|EBS4 0.019 keratin 14 protein-coding gene 1 Mesoderm Epithelium 0.293333 0.0 0.00624589 0.0191863 +Hs TP63 Basal cells SHFM4|EEC3|p63|p73L|OFC8|KET|p73H|p53CP|TP73L|TP53L|TP53CP 0.001 tumor protein p63 protein-coding gene 1 Mesoderm Epithelium 0.12 0.0 0.0 0.0 +Mm Hs CDH3 Basal cells CDHP|PCAD 0.006 cadherin 3 protein-coding gene NA Mesoderm Epithelium 0.193333 0.0 0.00230112 0.0038501 +Mm Hs KRT6B Basal cells KRTL1 0.004 keratin 6B protein-coding gene 1 Mesoderm Epithelium 0.24 0.0 0.00230112 0.00205339 +Mm Hs METTL5 Basal cells HSPC133 0.032 methyltransferase like 5 protein-coding gene NA Mesoderm Epithelium 0.42 0.0 0.105851 0.00635267 +Mm Hs ANXA11 Basal cells ANX11 0.038 annexin A11 protein-coding gene NA Mesoderm Epithelium 0.666667 1.0 0.163379 0.00173255 +Mm Hs TMEM14A Basal cells PTD011|C6orf73 0.03 transmembrane protein 14A protein-coding gene NA Mesoderm Epithelium 0.366667 0.0 0.086785 0.0 +Mm Hs BNIP3 Basal cells Nip3 0.042 BCL2 interacting protein 3 protein-coding gene NA Mesoderm Epithelium 0.433333 1.0 0.149244 0.00660934 +Mm Hs TYMP Basal cells MNGIE|ECGF1 0.011 thymidine phosphorylase protein-coding gene NA Mesoderm Epithelium 0.18 0.0 0.0519395 0.0 +Mm Hs DPP7 Basal cells DPPII|DPP2 0.038 dipeptidyl peptidase 7 protein-coding gene NA Mesoderm Epithelium 0.32 0.0 0.165023 0.00474846 +Mm Hs OPTN Basal cells FIP2|HYPL|FIP-2|TFIIIA-INTP|HIP7|GLC1E 0.025 optineurin protein-coding gene NA Mesoderm Epithelium 0.32 1.0 0.0825115 0.00949692 +Mm Hs PLAU Basal cells URK 0.01 plasminogen activator, urokinase protein-coding gene NA Mesoderm Epithelium 0.533333 0.0 0.0197239 0.00250257 +Mm Hs CAPN1 Basal cells muCANP|muCL|CANPL1 0.018 calpain 1 protein-coding gene NA Mesoderm Epithelium 0.333333 1.0 0.0338593 0.010652 +Mm Hs BACE2 Basal cells CEAP1|DRAP|ALP56|AEPLC 0.018 beta-secretase 2 protein-coding gene NA Mesoderm Epithelium 0.34 1.0 0.0351742 0.0115503 +Mm Hs CTNNB1 Basal cells beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene NA Mesoderm Epithelium 0.433333 1.0 0.201512 0.0113578 +Mm Hs ILK Basal cells NA 0.026 integrin linked kinase protein-coding gene NA Mesoderm Epithelium 0.306667 1.0 0.0802104 0.00744353 +Mm Hs PKP3 Basal cells NA 0.021 plakophilin 3 protein-coding gene NA Mesoderm Epithelium 0.253333 1.0 0.0177515 0.0191222 +Mm Hs ITGA3 Basal cells CD49c|VLA3a|VCA-2|GAP-B3|MSK18 0.012 integrin subunit alpha 3 protein-coding gene NA Mesoderm Epithelium 0.266667 1.0 0.00756082 0.00898357 +Hs MT1L Basal cells MTF|MT1R 0.003 metallothionein 1L, pseudogene pseudogene NA Mesoderm Epithelium 0.146667 0.0 0.0108481 0.0 +Mm Hs SRSF4 Basal cells SRP75|SFRS4 0.031 serine and arginine rich splicing factor 4 protein-coding gene NA Mesoderm Epithelium 0.506667 0.0 0.117686 0.0 +Mm Hs RAB38 Basal cells NY-MEL-1 0.014 RAB38, member RAS oncogene family protein-coding gene NA Mesoderm Epithelium 0.14 0.0 0.0042735 0.0 +Mm Hs ALKBH7 Basal cells MGC10974|SPATA11 0.072 alkB homolog 7 protein-coding gene NA Mesoderm Epithelium 0.393333 0.0 0.295858 0.0170046 +Mm Hs DNPH1 Basal cells rcl|dJ330M21.3|C6orf108 0.051 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 protein-coding gene NA Mesoderm Epithelium 0.406667 0.0 0.160092 0.0171971 +Mm Hs KRT23 Basal cells K23|DKFZP434G032|HAIK1|CK23|MGC26158 0.014 keratin 23 protein-coding gene NA Mesoderm Epithelium 0.506667 1.0 0.035503 0.00545431 +Mm Hs SLC16A3 Basal cells NA 0.033 solute carrier family 16 member 3 protein-coding gene NA Mesoderm Epithelium 0.293333 0.0 0.0499671 0.0 +Mm Hs GYPC Basal cells GPC|GYPD|Ge|CD236|CD236R 0.049 glycophorin C (Gerbich blood group) protein-coding gene NA Mesoderm Epithelium 0.166667 0.0 0.234057 0.00654517 +Mm Hs DUSP23 Basal cells FLJ20442|DUSP25 0.023 dual specificity phosphatase 23 protein-coding gene NA Mesoderm Epithelium 0.42 0.0 0.0851414 0.00417094 +Mm Hs RARRES1 Basal cells LXNL 0.01 retinoic acid receptor responder 1 protein-coding gene NA Mesoderm Epithelium 0.193333 0.0 0.0262985 0.0 +Mm Hs ITGA2 Basal cells CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene NA Mesoderm Epithelium 0.666667 1.0 0.0144642 0.00301591 +Mm Hs SLC25A37 Basal cells MSCP|MFRN|MFRN1|HT015 0.032 solute carrier family 25 member 37 protein-coding gene NA Mesoderm Epithelium 0.353333 0.0 0.110454 0.0 +Hs GAPDHP1 Basal cells GAPDP1|GAPDHL2|GAPDL2 0.012 glyceraldehyde-3-phosphate dehydrogenase pseudogene 1 pseudogene NA Mesoderm Epithelium 0.233333 0.0 0.0512821 0.0 +Mm Hs ITGB6 Basal cells NA 0.007 integrin subunit beta 6 protein-coding gene NA Mesoderm Epithelium 0.1 1.0 0.0230112 0.00340092 +Mm Hs ITGB4 Basal cells CD104 0.013 integrin subunit beta 4 protein-coding gene NA Mesoderm Epithelium 0.213333 1.0 0.0042735 0.0136037 +Mm Hs SPHK1 Basal cells SPHK 0.016 sphingosine kinase 1 protein-coding gene NA Mesoderm Epithelium 0.26 0.0 0.0259698 0.0 +Mm Hs ACTG2 Basal cells ACTSG|ACTL3|ACTA3 0.011 actin, gamma 2, smooth muscle, enteric protein-coding gene NA Mesoderm Epithelium 0.1 0.0 0.0167653 0.00956109 +Mm Hs IRF6 Basal cells OFC6|VWS|LPS 0.015 interferon regulatory factor 6 protein-coding gene NA Mesoderm Epithelium 0.413333 1.0 0.0095332 0.0136037 +Mm Hs RAB13 Basal cells NA 0.058 RAB13, member RAS oncogene family protein-coding gene NA Mesoderm Epithelium 0.553333 0.0 0.217949 0.0 +Mm Hs LAMB3 Basal cells nicein-125kDa|kalinin-140kDa|BM600-125kDa|LAMNB1 0.017 laminin subunit beta 3 protein-coding gene 1 Mesoderm Epithelium 0.633333 1.0 0.0249836 0.00936858 +Mm Hs ACADVL Basal cells VLCAD|LCACD|ACAD6 0.05 acyl-CoA dehydrogenase very long chain protein-coding gene NA Mesoderm Epithelium 0.76 1.0 0.213018 0.00603183 +Mm Hs MMP7 Basal cells PUMP-1|MPSL1 0.007 matrix metallopeptidase 7 protein-coding gene NA Mesoderm Epithelium 0.18 0.0 0.0174227 0.0036576 +Mm Hs HEBP2 Basal cells SOUL|C6orf34 0.042 heme binding protein 2 protein-coding gene NA Mesoderm Epithelium 0.82 0.0 0.139053 0.00583932 +Mm Hs FBXO32 Basal cells MAFbx|ATROGIN1|Fbx32 0.011 F-box protein 32 protein-coding gene NA Mesoderm Epithelium 0.273333 0.0 0.0147929 0.00686602 +Hs MT1E Basal cells MTD 0.021 metallothionein 1E protein-coding gene NA Mesoderm Epithelium 0.486667 0.0 0.109467 0.0 +Hs MT2P1 Basal cells NA 0.013 metallothionein 2 pseudogene 1 pseudogene NA Mesoderm Epithelium 0.393333 0.0 0.0529257 0.0 +Mm Hs SERINC2 Basal cells FKSG84|PRO0899|TDE2L 0.027 serine incorporator 2 protein-coding gene NA Mesoderm Epithelium 0.48 0.0 0.0585141 0.0 +Mm Hs NNMT Basal cells NA 0.017 nicotinamide N-methyltransferase protein-coding gene NA Mesoderm Epithelium 0.166667 0.0 0.0552268 0.00789271 +Mm Hs KRT15 Basal cells K15|CK15|K1CO 0.022 keratin 15 protein-coding gene 1 Mesoderm Epithelium 0.633333 1.0 0.0190664 0.0172613 +Mm Hs PLP2 Basal cells A4-LSB|MGC126187 0.049 proteolipid protein 2 protein-coding gene NA Mesoderm Epithelium 0.78 1.0 0.169297 0.0100744 +Hs MT1X Basal cells MT-1l 0.021 metallothionein 1X protein-coding gene NA Mesoderm Epithelium 0.546667 0.0 0.0884287 0.0 +Mm Hs S100A14 Basal cells BCMP84 0.03 S100 calcium binding protein A14 protein-coding gene NA Mesoderm Epithelium 0.733333 0.0 0.0654175 0.0 +Mm Hs LAMC2 Basal cells nicein-100kDa|kalinin-105kDa|BM600-100kDa|EBR2|LAMB2T|LAMNB2|EBR2A 0.012 laminin subunit gamma 2 protein-coding gene 1 Mesoderm Epithelium 0.36 1.0 0.00591716 0.0100103 +Mm Hs BMP7 Basal cells OP-1 0.01 bone morphogenetic protein 7 protein-coding gene 1 Mesoderm Epithelium 0.0133333 1.0 0.00558843 0.00917608 +Mm Hs MYLK Basal cells smMLCK|MYLK1|MLCK1 0.047 myosin light chain kinase protein-coding gene 1 Mesoderm Epithelium 0.193333 0.0 0.0486522 0.0467787 +Mm Hs CD69 Basophils CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.466667 0.111216 0.00693642 +Mm Hs IL3RA Basophils CD123 0.008 interleukin 3 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.6 0.0 0.00732177 +Mm Hs CCR3 Basophils CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0014772 +Mm Hs ENPP3 Basophils PD-IBETA|gp130RB13-6|B10|CD203c|PDNP3 0.002 ectonucleotide pyrophosphatase/phosphodiesterase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00211946 +Mm Hs FCER1A Basophils FCE1A 0.004 Fc fragment of IgE receptor Ia protein-coding gene 1 Mesoderm Immune system 0.0 0.866667 0.0184837 0.000834939 +Mm Hs TLR4 Basophils hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.0 +Mm Hs LTC4S Basophils MGC33147 0.037 leukotriene C4 synthase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00783208 0.044894 +Mm Hs CPA3 Basophils NA 0.009 carboxypeptidase A3 protein-coding gene 1 Mesoderm Immune system 0.0 0.933333 0.00845865 0.00757868 +Mm Hs ITGAL Basophils CD11A 0.013 integrin subunit alpha L protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.00407268 0.014772 +Mm Hs ITGAM Basophils CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.00313283 0.0302505 +Mm Hs ITGAX Basophils CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0162907 0.00526654 +Hs IL4R Basophils CD124 0.002 interleukin 4 receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0103383 0.0 +Mm Hs ITGB7 Basophils NA 0.031 integrin subunit beta 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.8 0.0 0.0373796 +Mm Hs IL4 Basophils BSF1|IL-4|BCGF1|BCGF-1|MGC79402 0.002 interleukin 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.6 0.0 0.00211946 +Mm MCPT8 Basophils NA 0.004 mast cell protease 8 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.00398202 +Mm PRSS34 Basophils NA 0.003 protease, serine 34 protein coding gene 1 Mesoderm Immune system 0.0 0.666667 0.0 0.00282595 +Mm Hs MS4A2 Basophils MS4A1|FCER1B|APY 0.003 membrane spanning 4-domains A2 protein-coding gene 1 Mesoderm Immune system 0.0 0.933333 0.0018797 0.00224791 +Mm Hs MS4A3 Basophils HTM4|CD20L 0.013 membrane spanning 4-domains A3 protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.00313283 0.0144509 +Mm Hs HDC Basophils NA 0.019 histidine decarboxylase protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00156642 0.0219011 +Mm Hs GATA2 Basophils NFE1B 0.02 GATA binding protein 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.933333 0.0134712 0.0209377 +Mm Hs CCL3 Basophils G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00783208 0.0416185 +Mm Hs CD33 Basophils SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0125313 0.0172768 +Mm Hs CD44 Basophils IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.133333 0.300439 0.0877328 +Mm Hs CDH1 Basophils uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.0416667 0.057097 +Mm Hs HTR1B Basophils 5-HT1B|HTR1D2|5-HT1DB 0.002 5-hydroxytryptamine receptor 1B protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0 0.00237636 +Mm Hs IGFBP7 Basophils MAC25|IGFBP-7|FSTL2 0.172 insulin like growth factor binding protein 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.239035 0.163198 +Mm MRGPRA6 Basophils NA 0.0 MAS-related GPR, member A6 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs DNASE2B Basophils DLAD 0.001 deoxyribonuclease 2 beta protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00093985 0.000513809 +Mm Hs FADS2 Basophils FADSD6|D6D|TU13|DES6|SLL0262|LLCDL2 0.008 fatty acid desaturase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.02099 0.00430315 +Mm Hs GPC4 Basophils K-glypican 0.01 glypican 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0075188 0.0113038 +Mm Hs GRM6 Basophils GPRC1F|mGlu6|MGLUR6|CSNB1B 0.003 glutamate metabotropic receptor 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0 0.0032113 +Mm Hs ACSS2 Basophils ACSA|AceCS|dJ1161H23.1|ACAS2 0.006 acyl-CoA synthetase short chain family member 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.00595238 0.00674374 +Mm Hs ADORA2B Basophils NA 0.004 adenosine A2b receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.133333 0.00438596 0.00398202 +Mm ALOX8 Basophils NA 0.0 arachidonate 8-lipoxygenase protein coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0 0.0 +Mm Hs AQP9 Basophils SSC1|HsT17287 0.003 aquaporin 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.533333 0.00313283 0.00289017 +Mm Hs BACE1 Basophils BACE 0.022 beta-secretase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0037594 0.0259473 +Mm Hs BMP4 Basophils BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0241228 0.0166346 +Mm Hs CABLES1 Basophils HsT2563|FLJ35924 0.001 Cdk5 and Abl enzyme substrate 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.000770713 +Mm Hs CCL4 Basophils MIP-1-beta|Act-2|AT744.1|SCYA4 0.049 C-C motif chemokine ligand 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.933333 0.0557644 0.0481053 +Mm CCL9 Basophils NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Mesoderm Immune system 0.0 0.933333 0.0 0.0432884 +Mm Hs CEBPA Basophils C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.533333 0.0 0.0294798 +Mm DEFB40 Basophils NA 0.0 defensin beta 40 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs E2F8 Basophils FLJ23311 0.002 E2F transcription factor 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0029544 +Mm Hs FADS1 Basophils D5D|FADSD5|TU12|FADS6|LLCDL1 0.05 fatty acid desaturase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0770677 0.0378292 +Mm Hs FAR2 Basophils FLJ10462|SDR10E2|MLSTD1 0.004 fatty acyl-CoA reductase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0103383 0.00263327 +Mm Hs FBXO9 Basophils FBX9|NY-REN-57 0.059 F-box protein 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.4 0.0388471 0.0625562 +Mm Hs GABBR1 Basophils hGB1a|GPRC3A 0.14 gamma-aminobutyric acid type B receptor subunit 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0018797 0.175851 +4 GM9895 Basophils NA 0.0 predicted gene 9895 lncRNA gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs GPR183 Basophils EBI2 0.019 G protein-coupled receptor 183 protein-coding gene 1 Mesoderm Immune system 0.0 0.266667 0.0488722 0.0123314 +None GPR97 Basophils NA 0.0 NA NA 1 Mesoderm Immune system NA NA NA NA +Mm Hs HGF Basophils F-TCF|HGFB|HPTA|DFNB39 0.002 hepatocyte growth factor protein-coding gene 1 Mesoderm Immune system 0.0 0.533333 0.0075188 6.42261e-05 +Mm Hs HIST1H1D Basophils H1.3|H1d|H1s-2|H1F3 0.006 histone cluster 1 H1 family member d protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0200501 0.00308285 +Mm Hs HIST1H2AC Basophils H2AFL 0.01 histone cluster 1 H2A family member c protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0316416 0.00404624 +Mm Hs IFITM1 Basophils 9-27|CD225|DSPA2a|IFI17 0.059 interferon induced transmembrane protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0322682 0.0639692 +Mm Hs INF2 Basophils MGC13251|C14orf151|C14orf173 0.015 inverted formin, FH2 and WH2 domain containing protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.0175439 0.0152216 +Mm Hs JAZF1 Basophils TIP27|DKFZp761K2222|ZNF802 0.002 JAZF zinc finger 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0075188 0.00134875 +Mm Hs L1CAM Basophils CD171|HSAS1|SPG1|HSAS|MIC5 0.018 L1 cell adhesion molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.0213873 +Mm Hs LAMA5 Basophils NA 0.008 laminin subunit alpha 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.012218 0.00777136 +Mm Hs MBOAT1 Basophils MGC44669|dJ434O11.1|LPEAT1|OACT1 0.006 membrane bound O-acyltransferase domain containing 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.333333 0.0 0.00712909 +Mm Hs NFIL3 Basophils E4BP4|NFIL3A|NF-IL3A|IL3BP1 0.014 nuclear factor, interleukin 3 regulated protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.00313283 0.0160565 +Mm Hs NPL Basophils NPL1|DHDPS1|C1orf13 0.017 N-acetylneuraminate pyruvate lyase protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.018797 0.0176622 +Mm NT5C3 Basophils NA 0.068 5'-nucleotidase, cytosolic III protein coding gene 1 Mesoderm Immune system 0.0 0.666667 0.0 0.0842646 +Mm Hs OSBPL5 Basophils KIAA1534|ORP5|OBPH1 0.003 oxysterol binding protein like 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00372511 +Mm Hs OTUB2 Basophils FLJ21916|MGC3102|C14orf137 0.006 OTU deubiquitinase, ubiquitin aldehyde binding 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0140977 0.00513809 +Mm Hs P2RY1 Basophils P2Y1|SARCC 0.003 purinergic receptor P2Y1 protein-coding gene 1 Mesoderm Immune system 0.0 0.133333 0.00219298 0.00301863 +Mm Hs PDK3 Basophils NA 0.015 pyruvate dehydrogenase kinase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00595238 0.0170841 +Mm Hs PDZD4 Basophils KIAA1444|LU1|FLJ34125|PDZRN4L|LNX5|PDZK4 0.005 PDZ domain containing 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00635838 +Mm Hs PERP Basophils PIGPC1|dJ496H19.1|KCP1|THW|KRTCAP1 0.077 PERP, TP53 apoptosis effector protein-coding gene 1 Mesoderm Immune system 0.0 0.133333 0.167607 0.0518947 +Hs PIGY Basophils MGC14156 0.0 phosphatidylinositol glycan anchor biosynthesis class Y protein-coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs PLEKHG5 Basophils KIAA0720|Syx|GEF720|Tech 0.003 pleckstrin homology and RhoGEF domain containing G5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0666667 0.000626566 0.00404624 +Mm Hs PLG Basophils NA 0.001 plasminogen protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.0017341 +Mm Hs RNF39 Basophils HZFw1|LIRF 0.001 ring finger protein 39 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00219298 0.0 +Mm Hs SLC26A3 Basophils DRA|CLD 0.003 solute carrier family 26 member 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.012218 0.0 +Mm Hs SLC26A8 Basophils NA 0.003 solute carrier family 26 member 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0119048 0.0 +Mm Hs SNCAIP Basophils SYPH1 0.002 synuclein alpha interacting protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0056391 0.0 +Mm Hs ST6GALNAC5 Basophils MGC3184|ST6GalNAcV|SIAT7E 0.007 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.0 +Hs SUPT3H Basophils SPT3|SPT3L 0.004 SPT3 homolog, SAGA and STAGA complex component protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0191103 0.0 +Mm Hs TULP3 Basophils TUBL3 0.007 tubby like protein 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0119048 0.0 +Mm Hs TEC Basophils PSCTK4 0.001 tec protein tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs UNC93A Basophils dJ366N23.2|dJ366N23.1 0.0 unc-93 homolog A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs WRN Basophils RECQL2|RECQ3 0.004 Werner syndrome RecQ like helicase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00595238 0.0 +Mm Hs ID1 Basophils dJ857M17.1.2|bHLHb24 0.149 inhibitor of DNA binding 1, HLH protein protein-coding gene 1 Mesoderm Immune system 0.0 0.266667 0.209586 0.128324 +Mm Hs GFAP Bergmann glia FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.0149532 +Mm Hs GDF10 Bergmann glia BMP-3b 0.005 growth differentiation factor 10 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.000313283 0.00635348 +Mm Hs GJB6 Bergmann glia EDH|CX30|ED2 0.013 gap junction protein beta 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.01598 +Mm Hs GRIA4 Bergmann glia GluA4|GLURD|GLUR4 0.014 glutamate ionotropic receptor AMPA type subunit 4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00344612 0.016365 +Mm Hs GRM3 Bergmann glia GPRC1C|mGlu3|MGLUR3 0.002 glutamate metabotropic receptor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0037594 0.0019253 +Mm Hs NTSR2 Bergmann glia NTR2 0.019 neurotensin receptor 2 protein-coding gene NA Ectoderm Brain 0.0 0.333333 0.0 0.0240021 +Mm Hs ITIH3 Bergmann glia H3P 0.009 inter-alpha-trypsin inhibitor heavy chain 3 protein-coding gene 1 Ectoderm Brain 0.0 0.666667 0.00344612 0.0107817 +Mm Hs A2M Bergmann glia FWP007|S863-7|CPAMD5 0.012 alpha-2-macroglobulin protein-coding gene 1 Ectoderm Brain 0.0 0.333333 0.0623434 0.00160442 +Mm Hs PTCH1 Bergmann glia BCNS|NBCCS|PTCH 0.012 patched 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0191103 0.0108458 +Mm Hs CDC42EP4 Bergmann glia KAIA1777|BORG4|MGC3740|MGC17125 0.027 CDC42 effector protein 4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0184837 0.0304197 +Mm Hs BTBD17 Bergmann glia LGALS3BPL|BTBD17A|TANGO10A 0.022 BTB domain containing 17 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00093985 0.0272109 +Mm Hs AQP4 Bergmann glia MIWC 0.024 aquaporin 4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00595238 0.0292004 +Mm Hs SLC4A4 Bergmann glia NBC1|HNBC1|NBC2|pNBC|hhNMC|SLC4A5 0.033 solute carrier family 4 member 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.012218 0.0 +Mm Hs HOPX Bergmann glia LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.091792 0.0220768 +Mm Hs GPR37L1 Bergmann glia ETBR-LP-2 0.041 G protein-coupled receptor 37 like 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00438596 0.050507 +Mm Hs ACSBG1 Bergmann glia BGM|FLJ30320|MGC14352|BG1|KIAA0631|hBG1|hsBG 0.023 acyl-CoA synthetase bubblegum family member 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.0284302 +Mm Hs ALDH1L1 Bergmann glia 10-fTHF|FTHFD 0.008 aldehyde dehydrogenase 1 family member L1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0102683 +Mm Hs SLC1A3 Bergmann glia EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109649 0.0 +Mm Hs SLC1A2 Bergmann glia GLT-1|EAAT2 0.071 solute carrier family 1 member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0 +Mm Hs S100B Bergmann glia S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.033208 0.0 +Mm Hs VIM Bergmann glia NA 0.427 vimentin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.590539 0.0 +Mm Hs FABP7 Bergmann glia B-FABP|BLBP 0.142 fatty acid binding protein 7 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.014411 0.174304 +Mm Hs TTC21B Bergmann glia FLJ11457|JBTS11|NPHP12|IFT139B|THM1 0.001 tetratricopeptide repeat domain 21B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs HEPACAM Bergmann glia FLJ25530|hepaCAM|GLIALCAM 0.033 hepatic and glial cell adhesion molecule protein-coding gene 1 Ectoderm Brain 0.0 0.666667 0.0 0.0412656 +Mm Hs ZEB2 Bergmann glia KIAA0569|ZFHX1B 0.144 zinc finger E-box binding homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.085213 0.0 +Mm Hs UFL1 Bergmann glia NLBP|Maxer|RCAD|KIAA0776 0.003 UFM1 specific ligase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs NRXN3 Bergmann glia KIAA0743|C14orf60 0.093 neurexin 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00783208 0.115454 +Mm Hs ATP7A Bergmann glia MNK 0.001 ATPase copper transporting alpha protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0019253 +Mm Hs BICD2 Bergmann glia KIAA0699 0.014 BICD cargo adaptor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00877193 0.0155307 +Mm Hs GJA1 Bergmann glia CX43|ODOD|SDTY3|ODDD|GJAL 0.1 gap junction protein alpha 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0632832 0.106982 +Mm Hs METRN Bergmann glia MGC2601|C16orf23 0.015 meteorin, glial cell differentiation regulator protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0554511 0.000449236 +Mm Hs P2RX7 Bergmann glia P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00877193 0.00346554 +Mm Hs EGFR Bergmann glia ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0222431 0.0127711 +Mm Hs GRIA1 Bergmann glia GluA1|GLURA|GLUR1 0.056 glutamate ionotropic receptor AMPA type subunit 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00156642 0.0694391 +Mm Hs P2RY1 Bergmann glia P2Y1|SARCC 0.003 purinergic receptor P2Y1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.00314465 +Mm Hs GRIN2B Bergmann glia GluN2B|NMDAR2B 0.076 glutamate ionotropic receptor NMDA type subunit 2B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00501253 0.0946605 +Mm Hs GRIN3A Bergmann glia GluN3A 0.006 glutamate ionotropic receptor NMDA type subunit 3A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00782955 +Mm Hs SEPT4 Bergmann glia CE5B3|hucep-7|ARTS|hCDCREL-2|MART|PNUTL2 0.081 septin 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0169173 0.0 +Mm Hs DAO Bergmann glia DAMOX|DAAO 0.001 D-amino acid oxidase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00128353 +Mm Hs ITGB1 Bergmann glia CD29|GPIIA|FNRB|MSK12|MDF2 0.276 integrin subunit beta 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.168546 0.302079 +Mm Hs KIF1BP Bergmann glia DKFZP586B0923|TTC20|KBP|KIAA1279 0.023 KIF1 binding protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.027981 +Mm Hs GCGR Beta cells GGR 0.001 glucagon receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.000836389 +Mm Hs JPH3 Beta cells JP-3|CAGL237|HDL2|JP3|TNRC22 0.024 junctophilin 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000315457 0.030303 +Mm Hs CD40 Beta cells Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0132492 0.0108731 +Mm Hs HAMP Beta cells LEAP-1|HEPC|HFE2B|LEAP1 0.002 hepcidin antimicrobial peptide protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00410095 0.00231616 +Mm Hs EZH1 Beta cells KIAA0388|KMT6B 0.002 enhancer of zeste 1 polycomb repressive complex 2 subunit protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000946372 0.00238049 +Mm Hs NTRK1 Beta cells TRKA|MTC 0.004 neurotrophic receptor tyrosine kinase 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00476099 +Mm Hs PDX1 Beta cells IDX-1|STF-1|PDX-1|MODY4|IPF1 0.005 pancreatic and duodenal homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.681818 0.690476 0.00126183 0.00289519 +Mm Hs SLC2A2 Beta cells GLUT2 0.007 solute carrier family 2 member 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00189274 0.0 +Mm Hs NKX6-2 Beta cells NKX6B|GTX|NKX6.1 0.024 NK6 homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000630915 0.030303 +Mm INS1 Beta cells NA 0.018 insulin I protein coding gene 1 Endoderm Pancreas 0.0 1.0 0.0 0.0201377 +Mm INS2 Beta cells NA 0.02 insulin II protein coding gene 1 Endoderm Pancreas 0.0 0.833333 0.0 0.0226468 +Mm Hs FXYD2 Beta cells MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene 1 Endoderm Pancreas 0.363636 0.0 0.00189274 0.0306891 +Mm Hs NPY Beta cells PYY4 0.015 neuropeptide Y protein-coding gene NA Endoderm Pancreas 0.136364 0.238095 0.00473186 0.0164704 +Hs INS Beta cells IDDM2 0.009 insulin protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0470032 0.0 +Mm Hs RIMS1 Beta cells KIAA0340|RIM1|RAB3IP2|CORD7 0.01 regulating synaptic membrane exocytosis 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00126183 0.0 +Mm Hs MAFA Beta cells RIPE3b1|hMafA 0.002 MAF bZIP transcription factor A protein-coding gene 1 Endoderm Pancreas 0.5 0.666667 0.000315457 0.000193013 +Mm Hs EFNA5 Beta cells AF1|LERK7|EPLG7 0.029 ephrin A5 protein-coding gene 1 Endoderm Pancreas 0.0 0.0238095 0.0249211 0.0299813 +Mm Hs LMX1A Beta cells LMX1.1|LMX1 0.003 LIM homeobox transcription factor 1 alpha protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000630915 0.0034099 +Mm Hs NKX2-2 Beta cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.727273 0.119048 0.00536278 0.000321688 +Mm Hs NKX6-1 Beta cells Nkx6.1|NKX6A 0.006 NK6 homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.772727 0.785714 0.00504732 0.00315254 +Mm Hs PAX4 Beta cells MODY9 0.001 paired box 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0010294 +Mm Hs IAPP Beta cells AMYLIN 0.023 islet amyloid polypeptide protein-coding gene 1 Endoderm Pancreas 1.0 1.0 0.0353312 0.0179502 +Mm Hs PCSK2 Beta cells SPC2|NEC2 0.032 proprotein convertase subtilisin/kexin type 2 protein-coding gene 1 Endoderm Pancreas 0.909091 0.857143 0.018612 0.0326192 +Mm Hs G6PC2 Beta cells IGRP 0.004 glucose-6-phosphatase catalytic subunit 2 protein-coding gene 1 Endoderm Pancreas 0.863636 0.785714 0.00536278 0.000128675 +Mm Hs SLC30A8 Beta cells ZnT-8 0.005 solute carrier family 30 member 8 protein-coding gene 1 Endoderm Pancreas 0.909091 0.0 0.00914827 0.0 +Mm ERO1LB Beta cells NA 0.007 ERO1-like beta (S. cerevisiae) protein coding gene 1 Endoderm Pancreas 0.0 0.785714 0.0 0.00714148 +Mm Hs PCSK1 Beta cells PC1|NEC1 0.008 proprotein convertase subtilisin/kexin type 1 protein-coding gene 1 Endoderm Pancreas 0.818182 0.785714 0.00378549 0.00636943 +Mm Hs GJD2 Beta cells CX36|GJA9 0.005 gap junction protein delta 2 protein-coding gene 1 Endoderm Pancreas 0.590909 0.452381 0.00189274 0.00379592 +Mm Hs SCGN Beta cells SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0230284 0.0 +Mm Hs IGF2 Beta cells FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene 1 Endoderm Pancreas 0.0454545 0.0 0.0463722 0.000900727 +Mm Hs SYT13 Beta cells KIAA1427 0.029 synaptotagmin 13 protein-coding gene 1 Endoderm Pancreas 0.590909 0.0 0.00283912 0.0 +Mm Hs FFAR2 Beta cells FFA2R|GPR43 0.01 free fatty acid receptor 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.428571 0.0 0.0111304 +Mm Hs NPTX2 Beta cells NA 0.008 neuronal pentraxin 2 protein-coding gene 1 Endoderm Pancreas 0.818182 0.0 0.0126183 0.00688413 +Mm Hs PFKFB2 Beta cells NA 0.001 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 protein-coding gene 1 Endoderm Pancreas 0.272727 0.0714286 0.00315457 0.000193013 +Mm Hs EDARADD Beta cells NA 0.001 EDAR associated death domain protein-coding gene 1 Endoderm Pancreas 0.0454545 0.0 0.0022082 0.000900727 +Mm Hs HOPX Beta cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Endoderm Pancreas 0.863636 0.333333 0.0864353 0.0214244 +Mm Hs SH3GL2 Beta cells SH3P4|SH3D2A|CNSA2|EEN-B1 0.025 SH3 domain containing GRB2 like 2, endophilin A1 protein-coding gene 1 Endoderm Pancreas 0.0454545 0.0 0.0022082 0.0 +Mm Hs ADCYAP1 Beta cells NA 0.003 adenylate cyclase activating polypeptide 1 protein-coding gene 1 Endoderm Pancreas 0.772727 0.0 0.000946372 0.00257351 +Hs SCGB2A1 Beta cells UGB3|LPHC|MGC71973|MGB2 0.003 secretoglobin family 2A member 1 protein-coding gene 1 Endoderm Pancreas 0.818182 0.0 0.0119874 0.0 +Mm Hs CASR Beta cells FHH|NSHPT|GPRC2A|HHC|HHC1 0.001 calcium sensing receptor protein-coding gene 1 Endoderm Pancreas 0.272727 0.0952381 0.000315457 0.000257351 +Mm Hs MAFB Beta cells KRML 0.053 MAF bZIP transcription factor B protein-coding gene 1 Endoderm Pancreas 0.772727 0.357143 0.0542587 0.0520492 +Mm Hs PAX6 Beta cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Endoderm Pancreas 0.909091 0.785714 0.00820189 0.0570032 +Mm Hs NEUROD1 Beta cells BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Endoderm Pancreas 0.909091 0.785714 0.0170347 0.0409831 +Mm Hs ISL1 Beta cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.681818 0.738095 0.00883281 0.0294666 +Mm Hs TGFBR3 Beta cells betaglycan|BGCAN 0.019 transforming growth factor beta receptor 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0164038 0.0 +Mm Hs SMAD9 Beta cells SMAD8|SMAD8/9|MADH9 0.002 SMAD family member 9 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00851735 0.0 +Mm Hs SIX3 Beta cells HPE2 0.014 SIX homeobox 3 protein-coding gene 1 Endoderm Pancreas 0.0454545 0.0 0.00283912 0.0 +Mm Hs SIX2 Beta cells NA 0.001 SIX homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00189274 0.0 +Mm Hs BMP5 Beta cells NA 0.002 bone morphogenetic protein 5 protein-coding gene 1 Endoderm Pancreas 0.0909091 0.0 0.00599369 0.000772052 +Mm Hs PIR Beta cells NA 0.011 pirin protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0160883 0.00920028 +Mm Hs STXBP5 Beta cells tomosyn|LLGL3 0.004 syntaxin binding protein 5 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00283912 0.0 +Mm Hs DLK1 Beta cells FA1|pG2|Pref-1|ZOG|Delta1 0.055 delta like non-canonical Notch ligand 1 protein-coding gene 1 Endoderm Pancreas 0.681818 0.333333 0.0416404 0.0572605 +Mm Hs MEG3 Beta cells GTL2|NCRNA00023|LINC00023|onco-lncRNA-83 0.288 maternally expressed 3 non-coding RNA 1 Endoderm Pancreas 0.909091 0.833333 0.109779 0.333591 +Mm Hs RGS16 Beta cells A28-RGS14|RGS-r 0.01 regulator of G protein signaling 16 protein-coding gene 1 Endoderm Pancreas 0.136364 0.0 0.0195584 0.0 +Mm Hs RELN Cajal-Retzius cells RL|PRO1598 0.018 reelin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs DIABLO Cajal-Retzius cells SMAC|DIABLO-S|FLJ25049|FLJ10537|DFNA64 0.026 diablo IAP-binding mitochondrial protein protein-coding gene NA Ectoderm Brain 0.0 0.882023 0.0 0.0231713 +Mm Hs ST3GAL5 Cajal-Retzius cells ST3GalV|SIATGM3S|SIAT9 0.04 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0128446 0.0 +Mm Hs ISOC1 Cajal-Retzius cells CGI-111 0.022 isochorismatase domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0505618 0.0200501 0.0216785 +Mm Hs SMOC2 Cajal-Retzius cells SMAP2 0.026 SPARC related modular calcium binding 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0178571 0.0 +Mm Hs DYNC1I1 Cajal-Retzius cells DNCIC1|DNCI1 0.022 dynein cytoplasmic 1 intermediate chain 1 protein-coding gene NA Ectoderm Brain 0.0 0.780899 0.00250627 0.0182385 +Mm Hs NHLH2 Cajal-Retzius cells bHLHa34|HEN2 0.021 nescient helix-loop-helix 2 protein-coding gene NA Ectoderm Brain 0.0 0.904494 0.00156642 0.0159019 +Mm Hs CLSTN2 Cajal-Retzius cells CSTN2|CS2|FLJ39113|CDHR13 0.014 calsyntenin 2 protein-coding gene NA Ectoderm Brain 0.0 0.848315 0.00219298 0.00798338 +Mm Hs TMEM163 Cajal-Retzius cells DKFZP566N034|SV31 0.027 transmembrane protein 163 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs CACNA2D2 Cajal-Retzius cells KIAA0558 0.027 calcium voltage-gated channel auxiliary subunit alpha2delta 2 protein-coding gene NA Ectoderm Brain 0.0 0.938202 0.00125313 0.0238852 +Mm Hs CIB2 Cajal-Retzius cells DFNB48|USH1J 0.021 calcium and integrin binding family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.320225 0.0018797 0.022652 +Mm LHX1OS Cajal-Retzius cells NA 0.013 LIM homeobox 1, opposite strand lincRNA gene NA Ectoderm Brain 0.0 0.893258 0.0 0.00636075 +Mm Hs NDNF Cajal-Retzius cells FLJ23191|C4orf31 0.017 neuron derived neurotrophic factor protein-coding gene NA Ectoderm Brain 0.0 0.910112 0.00626566 0.0102551 +Mm Hs LINGO1 Cajal-Retzius cells FLJ14594|LERN1|LRRN6A 0.019 leucine rich repeat and Ig domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0505618 0.0018797 0.0231713 +Mm Hs LNPK Cajal-Retzius cells Ul|LNP1|KIAA1715 0.031 lunapark, ER junction formation factor protein-coding gene NA Ectoderm Brain 0.0 0.0505618 0.0238095 0.0333615 +Mm Hs RNF138 Cajal-Retzius cells STRIN|NARF 0.053 ring finger protein 138 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0742481 0.0 +Mm Hs TMEM170B Cajal-Retzius cells NA 0.027 transmembrane protein 170B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ABCC5 Cajal-Retzius cells MRP5|SMRP|EST277145|MOAT-C 0.044 ATP binding cassette subfamily C member 5 protein-coding gene NA Ectoderm Brain 0.0 0.219101 0.00438596 0.0520543 +Mm Hs CNRIP1 Cajal-Retzius cells DKFZP566K1924|CRIP1|CRIP1a|CRIP1b|C2orf32 0.031 cannabinoid receptor interacting protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0786517 0.0228697 0.0328422 +Mm Hs EBF3 Cajal-Retzius cells COE3|DKFZp667B0210 0.012 early B cell factor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.308989 0.000626566 0.0118777 +Mm Hs FUT9 Cajal-Retzius cells Fuc-TIX 0.039 fucosyltransferase 9 protein-coding gene NA Ectoderm Brain 0.0 0.0674157 0.0018797 0.0478354 +Mm Hs PABPN1 Cajal-Retzius cells PAB2|OPMD 0.05 poly(A) binding protein nuclear 1 protein-coding gene NA Ectoderm Brain 0.0 0.0337079 0.10307 0.0345947 +Mm Hs GNL3L Cajal-Retzius cells FLJ10613|GNL3B 0.053 G protein nucleolar 3 like protein-coding gene NA Ectoderm Brain 0.0 0.174157 0.000313283 0.0649056 +Mm Hs NUDT2 Cajal-Retzius cells APAH1 0.03 nudix hydrolase 2 protein-coding gene NA Ectoderm Brain 0.0 0.106742 0.0366541 0.0253132 +Mm Hs SLC25A46 Cajal-Retzius cells NA 0.045 solute carrier family 25 member 46 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0263158 0.0 +Mm Hs NSMCE3 Cajal-Retzius cells HCA4|MAGEG1|MAGEL3|NSE3|NDNL2 0.048 NSE3 homolog, SMC5-SMC6 complex component protein-coding gene NA Ectoderm Brain 0.0 0.0842697 0.0222431 0.0534173 +Mm Hs DACH1 Cajal-Retzius cells DACH 0.013 dachshund family transcription factor 1 protein-coding gene NA Ectoderm Brain 0.0 0.286517 0.0275689 0.00798338 +Mm Hs FAM69B Cajal-Retzius cells MGC20262|C9orf136 0.034 family with sequence similarity 69 member B protein-coding gene NA Ectoderm Brain 0.0 0.146067 0.000626566 0.0416045 +Mm Hs HOMER2 Cajal-Retzius cells CPD|Cupidin|Vesl-2|HOMER-2B|HOMER-2|HOMER-2A|DFNA68 0.022 homer scaffold protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.241573 0.0100251 0.0222626 +Mm Hs MAP9 Cajal-Retzius cells ASAP|FLJ21159 0.037 microtubule associated protein 9 protein-coding gene NA Ectoderm Brain 0.0 0.140449 0.0335213 0.0378399 +Mm Hs DNM3 Cajal-Retzius cells KIAA0820 0.043 dynamin 3 protein-coding gene NA Ectoderm Brain 0.0 0.151685 0.00313283 0.0525086 +Mm Hs LZTFL1 Cajal-Retzius cells BBS17 0.026 leucine zipper transcription factor like 1 protein-coding gene NA Ectoderm Brain 0.0 0.0224719 0.0181704 0.0287532 +Mm Hs FSD1 Cajal-Retzius cells MGC3213|MIR1 0.015 fibronectin type III and SPRY domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.157303 0.0175439 0.0122022 +Mm Hs TCEAL1 Cajal-Retzius cells pp21|SIIR|WEX9 0.017 transcription elongation factor A like 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0178571 0.0 +Mm Hs RAB11FIP2 Cajal-Retzius cells KIAA0941|nRip11|Rab11-FIP2 0.04 RAB11 family interacting protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00219298 0.0 +Mm Hs BARHL2 Cajal-Retzius cells NA 0.004 BarH like homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.168539 0.0 0.00331018 +Mm Hs TRIM44 Cajal-Retzius cells DIPB|MC7 0.055 tripartite motif containing 44 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0679825 0.0 +Mm Hs SLC17A6 Cajal-Retzius cells DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs B3GALT1 Cajal-Retzius cells beta3Gal-T1 0.005 beta-1,3-galactosyltransferase 1 protein-coding gene NA Ectoderm Brain 0.0 0.106742 0.00313283 0.00376452 +Mm Hs SLITRK5 Cajal-Retzius cells bA364G4.2|KIAA0918|LRRC11 0.009 SLIT and NTRK like family member 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ERC2 Cajal-Retzius cells CAST1|KIAA0378|SPBC110|Spc110|ELKSL 0.03 ELKS/RAB6-interacting/CAST family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.325843 0.000313283 0.0340754 +Mm Hs NBEA Cajal-Retzius cells KIAA1544|BCL8B|FLJ10197|LYST2 0.032 neurobeachin protein-coding gene NA Ectoderm Brain 0.0 0.0393258 0.00469925 0.0387486 +Mm Hs SLC25A36 Cajal-Retzius cells FLJ10618|PNC2 0.059 solute carrier family 25 member 36 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0755013 0.0 +Mm Hs ZDBF2 Cajal-Retzius cells FLJ45338|KIAA1571|Slx9 0.018 zinc finger DBF-type containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs MAPK8 Cajal-Retzius cells JNK|JNK1|SAPK1|PRKM8 0.023 mitogen-activated protein kinase 8 protein-coding gene NA Ectoderm Brain 0.0 0.393258 0.0194236 0.0207049 +Mm Hs GDF5 Cajal-Retzius cells CDMP1|BMP14 0.004 growth differentiation factor 5 protein-coding gene NA Ectoderm Brain 0.0 0.483146 0.0 0.0 +Mm Hs ACHE Cajal-Retzius cells YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene NA Ectoderm Brain 0.0 0.410112 0.00469925 0.0150581 +Mm Hs CCM2 Cajal-Retzius cells MGC4607|OSM|C7orf22 0.052 CCM2 scaffold protein protein-coding gene NA Ectoderm Brain 0.0 0.292135 0.0435464 0.0477705 +Mm Hs WRAP73 Cajal-Retzius cells WDR8 0.01 WD repeat containing, antisense to TP73 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00657895 0.0 +None FAM65B Cajal-Retzius cells NA 0.006 NA NA NA Ectoderm Brain 0.0 0.157303 0.0 0.00590641 +Mm Hs NRG1 Cajal-Retzius cells HRG|NDF|GGF|NRG1-IT2 0.012 neuregulin 1 protein-coding gene NA Ectoderm Brain 0.0 0.191011 0.0128446 0.0106445 +Mm Hs ATP13A2 Cajal-Retzius cells HSA9947|CLN12|PARK9 0.034 ATPase cation transporting 13A2 protein-coding gene NA Ectoderm Brain 0.0 0.775281 0.00469925 0.0326475 +Mm Hs CNTNAP2 Cajal-Retzius cells Caspr2|KIAA0868 0.037 contactin associated protein like 2 protein-coding gene NA Ectoderm Brain 0.0 0.629214 0.0238095 0.0338807 +Mm Hs PNOC Cajal-Retzius cells PPNOC|N/OFQ|NOP 0.009 prepronociceptin protein-coding gene NA Ectoderm Brain 0.0 0.280899 0.00093985 0.00681508 +Mm Hs LHX1 Cajal-Retzius cells LIM-1 0.011 LIM homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.752809 0.00657895 0.00402414 +Mm Hs LINGO2 Cajal-Retzius cells LERN3|LRRN6C 0.019 leucine rich repeat and Ig domain containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.735955 0.00219298 0.0154475 +Mm Hs FAT3 Cajal-Retzius cells KIAA1989|CDHF15|CDHR10 0.009 FAT atypical cadherin 3 protein-coding gene NA Ectoderm Brain 0.0 0.544944 0.00250627 0.0046732 +Mm Hs SRGAP3 Cajal-Retzius cells KIAA0411|MEGAP|WRP|ARHGAP14|SRGAP2 0.018 SLIT-ROBO Rho GTPase activating protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0100251 0.0 +Mm Hs CDH4 Cajal-Retzius cells NA 0.017 cadherin 4 protein-coding gene NA Ectoderm Brain 0.0 0.814607 0.000313283 0.0112287 +Mm Hs FLRT3 Cajal-Retzius cells NA 0.027 fibronectin leucine rich transmembrane protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.831461 0.0153509 0.0210294 +Mm Hs EDIL3 Cajal-Retzius cells DEL1 0.045 EGF like repeats and discoidin domains 3 protein-coding gene NA Ectoderm Brain 0.0 0.713483 0.0222431 0.0432271 +Mm CAR10 Cajal-Retzius cells NA 0.021 carbonic anhydrase 10 protein coding gene NA Ectoderm Brain 0.0 0.764045 0.0 0.0179139 +Mm Hs ZCCHC12 Cajal-Retzius cells FLJ16123|SIZN|SIZN1|PNMA7A 0.038 zinc finger CCHC-type containing 12 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs RALGPS2 Cajal-Retzius cells FLJ10244|FLJ25604 0.048 Ral GEF with PH domain and SH3 binding motif 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.023183 0.0 +Mm Hs FAM196A Cajal-Retzius cells NA 0.009 family with sequence similarity 196, member A protein coding gene NA Ectoderm Brain 0.0 0.803371 0.0 0.00259622 +Mm Hs SMAD1 Cajal-Retzius cells MADR1|JV4-1|MADH1 0.036 SMAD family member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0153509 0.0 +Mm Hs TBR1 Cajal-Retzius cells NA 0.018 T-box, brain 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs KCNH7 Cajal-Retzius cells Kv11.3|HERG3|erg3 0.012 potassium voltage-gated channel subfamily H member 7 protein-coding gene NA Ectoderm Brain 0.0 0.814607 0.000626566 0.0058415 +Mm Hs LHX5 Cajal-Retzius cells NA 0.01 LIM homeobox 5 protein-coding gene NA Ectoderm Brain 0.0 0.848315 0.00219298 0.00240151 +Mm Hs CALB2 Cajal-Retzius cells CAL2 0.03 calbindin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.882023 0.00281955 0.0277147 +Mm Hs EMX2 Cajal-Retzius cells NA 0.027 empty spiracles homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.865169 0.0112782 0.022003 +Mm Hs ZIC2 Cajal-Retzius cells HPE5 0.01 Zic family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0119048 0.0 +Mm Hs WNT7B Cajal-Retzius cells NA 0.008 Wnt family member 7B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs AATF Cajal-Retzius cells DED|CHE-1|BFR2 0.018 apoptosis antagonizing transcription factor protein-coding gene NA Ectoderm Brain 0.0 0.0168539 0.0469925 0.0101253 +Mm Hs NANOS1 Cajal-Retzius cells NOS1|ZC2HC12A 0.002 nanos C2HC-type zinc finger 1 protein-coding gene NA Ectoderm Brain 0.0 0.0337079 0.0 0.00168754 +Mm Hs TBCK Cajal-Retzius cells MGC16169|HSPC302 0.006 TBC1 domain containing kinase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs RGMB Cajal-Retzius cells FLJ90406|DRAGON 0.009 repulsive guidance molecule BMP co-receptor b protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00626566 0.0 +Mm Hs DACT1 Cajal-Retzius cells DAPPER1|THYEX3|HDPR1|DAPPER|FRODO 0.003 dishevelled binding antagonist of beta catenin 1 protein-coding gene NA Ectoderm Brain 0.0 0.00561798 0.00783208 0.00266113 +Mm TRP73 Cajal-Retzius cells NA 0.008 transformation related protein 73 protein coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs EOMES Cajal-Retzius cells TBR2 0.021 eomesodermin protein-coding gene 1 Ectoderm Brain 0.0 0.00561798 0.00219298 0.0263517 +Mm Hs CNR1 Cajal-Retzius cells CB1K5|CB-R|CB1|CANN6|CB1A|CNR 0.065 cannabinoid receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.140449 0.00250627 0.0806127 +Hs HAR1A Cajal-Retzius cells HAR1F|NCRNA00064|LINC00064 0.0 highly accelerated region 1A non-coding RNA 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs MYH6 Cardiac stem and precursor cells NA 0.003 myosin heavy chain 6 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0 0.00346487 +Mm Hs WT1 Cardiac stem and precursor cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0225564 0.0 +Mm Hs TBX18 Cardiac stem and precursor cells NA 0.004 T-box 18 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.000313283 0.0 +Mm Hs FUT4 Cardiac stem and precursor cells FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0 0.000705807 +Hs KITLG Cardiac stem and precursor cells SCF|Kitl|KL-1|FPH2|SLF|DFNA69 0.001 KIT ligand protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00626566 0.0 +Mm Hs NKX2-5 Cardiac stem and precursor cells CSX1|NKX2.5|NKX4-1|CSX|NKX2E 0.003 NK2 homeobox 5 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.000313283 0.00166827 +Mm Hs ISL1 Cardiac stem and precursor cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0134712 0.0313763 +Mm Hs GATA4 Cardiac stem and precursor cells NA 0.008 GATA binding protein 4 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00469925 0.00795637 +Mm Hs ETV2 Cardiac stem and precursor cells ER71 0.002 ETS variant 2 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0137845 0.0 +Mm Hs KIT Cardiac stem and precursor cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00250627 0.0185435 +Mm Hs ABCG2 Cardiac stem and precursor cells EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00469925 0.0467116 +Mm Hs MESP1 Cardiac stem and precursor cells MGC10676|bHLHc5 0.005 mesoderm posterior bHLH transcription factor 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00689223 0.00494065 +Mm Hs BMP4 Cardiac stem and precursor cells BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0241228 0.0166185 +Mm Hs ADGRL2 Cardiac stem and precursor cells KIAA0786|LEC1|LPHH1|LPHN2 0.021 adhesion G protein-coupled receptor L2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00407268 0.025409 +Mm Hs TBX3 Cardiac stem and precursor cells TBX3-ISO|XHL|UMS 0.024 T-box 3 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0303885 0.0 +Mm Hs TBX4 Cardiac stem and precursor cells NA 0.0 T-box 4 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs WNT5A Cardiac stem and precursor cells hWNT5A 0.015 Wnt family member 5A protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00814536 0.0 +Mm Hs ANKRD1 Cardiac stem and precursor cells C-193|ALRP|CVARP|MCARP 0.007 ankyrin repeat domain 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00783208 0.00660892 +Mm Hs TNNC1 Cardiomyocytes TNNC 0.005 troponin C1, slow skeletal and cardiac type protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00093985 0.0 +Mm Hs ADM Cardiomyocytes AM 0.026 adrenomedullin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0635965 0.0177778 +Mm Hs ALCAM Cardiomyocytes CD166|MEMD 0.0 activated leukocyte cell adhesion molecule protein-coding gene 1 Mesoderm Heart NA NA NA NA +Mm Hs NPPA Cardiomyocytes ANP|PND 0.0 natriuretic peptide A protein-coding gene 1 Mesoderm Heart 0.0 0.0833333 0.0 0.0 +Mm Hs FGF2 Cardiomyocytes FGFB 0.004 fibroblast growth factor 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0178571 0.000966184 +Mm Hs NPPB Cardiomyocytes NA 0.003 natriuretic peptide B protein-coding gene 1 Mesoderm Heart 0.0 0.35 0.0018797 0.00109501 +Mm Hs TNNI3 Cardiomyocytes TNNC1|CMH7|CMD2A 0.01 troponin I3, cardiac type protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0106516 0.0 +Mm Hs TNNT2 Cardiomyocytes CMH2|CMD1D 0.011 troponin T2, cardiac type protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0103383 0.0 +Mm Hs ANKRD1 Cardiomyocytes C-193|ALRP|CVARP|MCARP 0.007 ankyrin repeat domain 1 protein-coding gene 1 Mesoderm Heart 0.0 0.8 0.00783208 0.00354267 +Mm Hs NPPC Cardiomyocytes CNP 0.003 natriuretic peptide C protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.000626566 0.00309179 +Mm Hs DES Cardiomyocytes CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Heart 0.0 0.783333 0.0093985 0.0203543 +Mm Hs HAND2 Cardiomyocytes dHand|Thing2|Hed|bHLHa26 0.004 heart and neural crest derivatives expressed 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0166667 0.0093985 0.00193237 +Mm Hs HAND1 Cardiomyocytes eHand|Thing1|Hxt|bHLHa27 0.005 heart and neural crest derivatives expressed 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.014411 0.00193237 +Mm Hs GATA4 Cardiomyocytes NA 0.008 GATA binding protein 4 protein-coding gene 1 Mesoderm Heart 0.0 0.05 0.00469925 0.00779388 +Mm Hs GATA6 Cardiomyocytes NA 0.019 GATA binding protein 6 protein-coding gene 1 Mesoderm Heart 0.0 0.316667 0.00469925 0.0199678 +Mm Hs MYL2 Cardiomyocytes CMH10 0.005 myosin light chain 2 protein-coding gene 1 Mesoderm Heart 0.0 0.916667 0.0 0.00302738 +Mm Hs NKX2-5 Cardiomyocytes CSX1|NKX2.5|NKX4-1|CSX|NKX2E 0.003 NK2 homeobox 5 protein-coding gene NA Mesoderm Heart 0.0 0.35 0.000313283 0.000322061 +Mm Hs PNMT Cardiomyocytes PENT 0.0 phenylethanolamine N-methyltransferase protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00093985 0.000322061 +Mm Hs ACTA1 Cardiomyocytes NEM3|ACTA 0.004 actin, alpha 1, skeletal muscle protein-coding gene 1 Mesoderm Heart 0.0 0.0333333 0.00250627 0.00405797 +Mm Hs CD36 Cardiomyocytes SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Heart 0.0 0.716667 0.0344612 0.0415459 +Mm Hs RBM20 Cardiomyocytes NA 0.002 RNA binding motif protein 20 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs VLDLR Cardiomyocytes CARMQ1|CHRMQ1|VLDLRCH 0.025 very low density lipoprotein receptor protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0037594 0.0 +Mm Hs ALPK3 Cardiomyocytes MAK|KIAA1330|Midori 0.0 alpha kinase 3 protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.000626566 0.000257649 +Mm Hs RBM24 Cardiomyocytes FLJ30829|dJ259A10.1|RNPC6 0.005 RNA binding motif protein 24 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs FABP4 Cardiomyocytes A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Heart 0.0 0.466667 0.0103383 0.031562 +Mm Hs CKMT2 Cardiomyocytes SMTCK 0.002 creatine kinase, mitochondrial 2 protein-coding gene 1 Mesoderm Heart 0.0 0.4 0.00093985 0.000708535 +Mm Hs SPEG Cardiomyocytes MGC12676|KIAA1297|SPEGalpha|SPEGbeta|BPEG|APEG1 0.005 SPEG complex locus protein-coding gene NA Mesoderm Heart 0.0 0.0 0.000313283 0.0 +Mm Hs MYH7B Cardiomyocytes KIAA1512|dJ756N5.1|MYH14|MHC14 0.0 myosin heavy chain 7B protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.0 0.0 +Mm Hs MYOM2 Cardiomyocytes NA 0.004 myomesin 2 protein-coding gene 1 Mesoderm Heart 0.0 0.483333 0.0172306 0.000193237 +Mm Hs MYOM1 Cardiomyocytes NA 0.003 myomesin 1 protein-coding gene NA Mesoderm Heart 0.0 0.616667 0.000626566 0.00167472 +Mm COX8B Cardiomyocytes NA 0.004 cytochrome c oxidase subunit 8B protein coding gene NA Mesoderm Heart 0.0 0.85 0.0 0.00115942 +Mm Hs PDLIM5 Cardiomyocytes LIM|Enh 0.041 PDZ and LIM domain 5 protein-coding gene 1 Mesoderm Heart 0.0 0.75 0.0858396 0.0294364 +Mm Hs MYH7 Cardiomyocytes CMD1S|CMH1|MPD1 0.001 myosin heavy chain 7 protein-coding gene 1 Mesoderm Heart 0.0 0.383333 0.000313283 0.000257649 +Mm Hs PLN Cardiomyocytes CMD1P 0.006 phospholamban protein-coding gene 1 Mesoderm Heart 0.0 0.833333 0.0134712 0.00154589 +Mm Hs TCAP Cardiomyocytes T-cap|TELE|telethonin|CMD1N|LGMD2G 0.003 titin-cap protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs SORBS2 Cardiomyocytes ARGBP2|KIAA0777 0.046 sorbin and SH3 domain containing 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0203634 0.0 +Mm Hs RYR2 Cardiomyocytes ARVC2|VTSIP|ARVD2 0.008 ryanodine receptor 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs OBSCN Cardiomyocytes KIAA1556|UNC89|KIAA1639|ARHGEF30 0.002 obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF protein-coding gene NA Mesoderm Heart 0.0 0.683333 0.000313283 6.44122e-05 +Mm Hs ACTC1 Cardiomyocytes CMD1R|ACTC 0.011 actin, alpha, cardiac muscle 1 protein-coding gene 1 Mesoderm Heart 0.0 1.0 0.0134712 0.00463768 +Mm Hs MYL3 Cardiomyocytes CMH8|VLC1|MLC1V|MLC1SB 0.008 myosin light chain 3 protein-coding gene 1 Mesoderm Heart 0.0 0.933333 0.0 0.00599034 +Mm Hs CORO6 Cardiomyocytes FLJ14871 0.001 coronin 6 protein-coding gene NA Mesoderm Heart 0.0 0.183333 0.000313283 0.000644122 +Mm Hs PDE4D Cardiomyocytes DPDE3 0.021 phosphodiesterase 4D protein-coding gene 1 Mesoderm Heart 0.0 0.15 0.0153509 0.0214493 +Mm Hs NEXN Cardiomyocytes nexilin|NELIN 0.014 nexilin F-actin binding protein protein-coding gene 1 Mesoderm Heart 0.0 0.733333 0.0169173 0.0100483 +Mm MHRT Cardiomyocytes Myheart 0.001 myosin heavy chain associated RNA transcript non-coding RNA 1 Mesoderm Heart 0.0 0.233333 0.0 0.00057971 +Mm Hs FHL2 Cardiomyocytes SLIM3|DRAL 0.043 four and a half LIM domains 2 protein-coding gene 1 Mesoderm Heart 0.0 0.85 0.10401 0.0254428 +Mm Hs MYBPC3 Cardiomyocytes MYBP-C|CMH4 0.003 myosin binding protein C, cardiac protein-coding gene 1 Mesoderm Heart 0.0 0.833333 0.00093985 0.000128824 +Mm Hs MYH6 Cardiomyocytes NA 0.003 myosin heavy chain 6 protein-coding gene 1 Mesoderm Heart 0.0 0.883333 0.0 6.44122e-05 +Mm Hs TTN Cardiomyocytes CMPD4|FLJ32040|TMD|CMH9|LGMD2J|MYLK5|CMD1G 0.007 titin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0112782 0.0 +Mm Hs GPIHBP1 Cardiomyocytes LOC338328|GPI-HBP1 0.017 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.00469925 0.0194525 +Mm Hs AQP1 Cardiomyocytes CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.0178571 0.0423833 +Mm Hs DMD Cardiomyocytes DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85 0.012 dystrophin protein-coding gene NA Mesoderm Heart 0.0 0.116667 0.00469925 0.013913 +Mm Hs MFN2 Cardiomyocytes CPRP1|KIAA0214|MARF|CMT2A2 0.016 mitofusin 2 protein-coding gene 1 Mesoderm Heart 0.0 0.416667 0.0075188 0.0162963 +Mm Hs ASB2 Cardiomyocytes ASB-2 0.005 ankyrin repeat and SOCS box containing 2 protein-coding gene 1 Mesoderm Heart 0.0 0.366667 0.00344612 0.00483092 +Mm Hs ART3 Cardiomyocytes NA 0.021 ADP-ribosyltransferase 3 protein-coding gene 1 Mesoderm Heart 0.0 0.25 0.016604 0.0222222 +Mm Hs RRAD Cardiomyocytes REM3|RAD 0.007 RRAD, Ras related glycolysis inhibitor and calcium channel regulator protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00532581 0.0 +Mm Hs ADPRHL1 Cardiomyocytes NA 0.002 ADP-ribosylhydrolase like 1 protein-coding gene NA Mesoderm Heart 0.0 0.516667 0.000626566 0.000193237 +Mm Hs JPH2 Cardiomyocytes JP-2 0.002 junctophilin 2 protein-coding gene 1 Mesoderm Heart 0.0 0.333333 0.0 0.00186795 +Mm Hs PYGM Cardiomyocytes NA 0.002 glycogen phosphorylase, muscle associated protein-coding gene NA Mesoderm Heart 0.0 0.333333 0.000313283 0.00161031 +Mm Hs HSPB7 Cardiomyocytes cvHSP 0.004 heat shock protein family B (small) member 7 protein-coding gene 1 Mesoderm Heart 0.0 0.683333 0.00438596 0.00109501 +Mm Hs MYOZ2 Cardiomyocytes FATZ-2|C4orf5 0.002 myozenin 2 protein-coding gene 1 Mesoderm Heart 0.0 0.666667 0.0 0.000128824 +Mm Hs ENO3 Cardiomyocytes NA 0.01 enolase 3 protein-coding gene 1 Mesoderm Heart 0.0 0.766667 0.000313283 0.00779388 +Mm Hs TRDN Cardiomyocytes NA 0.004 triadin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00845865 0.0 +Mm Hs ACTN2 Cardiomyocytes NA 0.005 actinin alpha 2 protein-coding gene 1 Mesoderm Heart 0.0 0.7 0.0 0.00380032 +Mm Hs TNNI1 Cardiomyocytes NA 0.009 troponin I1, slow skeletal type protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00908521 0.0 +Mm Hs SMPX Cardiomyocytes DFNX4|DFN6 0.006 small muscle protein X-linked protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs MYL7 Cardiomyocytes MYLC2A|MYL2A 0.009 myosin light chain 7 protein-coding gene 1 Mesoderm Heart 0.0 0.566667 0.0100251 0.00470209 +Mm Hs TBX20 Cardiomyocytes NA 0.004 T-box 20 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs TRIM63 Cardiomyocytes MURF-1|IRF|SMRZ|RNF28 0.002 tripartite motif containing 63 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs MB Cardiomyocytes PVALB 0.001 myoglobin protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.00156642 6.44122e-05 +Mm Hs CTGF Cardiomyocytes IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Mesoderm Heart 0.0 0.05 0.0996241 0.0123027 +Mm Hs MYL4 Cardiomyocytes AMLC|GT1|PRO1957 0.016 myosin light chain 4 protein-coding gene 1 Mesoderm Heart 0.0 0.416667 0.0291353 0.00856683 +Mm Hs LOX Cardiomyocytes NA 0.017 lysyl oxidase protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0150376 0.0169404 +Mm Hs CTNNB1 Cardiomyocytes beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0333333 0.212406 0.0113366 +Mm Hs CPT1A Cardiomyocytes CPT1-L|L-CPT1 0.011 carnitine palmitoyltransferase 1A protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00971178 0.0117874 +Mm Hs SOX18 Cardiomyocytes NA 0.012 SRY-box 18 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0197368 0.0 +Mm Hs NOTCH1 Cardiomyocytes TAN1 0.007 notch 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00469925 0.00766506 +Mm Hs SLN Cardiomyocytes MGC12301|MGC125854|MGC125855 0.003 sarcolipin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00219298 0.0 +Mm Hs CSRP3 Cardiomyocytes CMD1M 0.005 cysteine and glycine rich protein 3 protein-coding gene 1 Mesoderm Heart 0.0 0.916667 0.0 0.00289855 +Mm Hs TXLNB Cardiomyocytes DKFZp451A175|MDP77|dJ522B19.2|C6orf198 0.001 taxilin beta protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs ATP2A2 Cardiomyocytes SERCA2|ATP2B|DAR 0.144 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 protein-coding gene 1 Mesoderm Heart 0.0 0.85 0.0473058 0.162383 +Mm Hs CKM Cardiomyocytes CKMM 0.003 creatine kinase, M-type protein-coding gene 1 Mesoderm Heart 0.0 0.766667 0.00219298 0.000386473 +Mm Hs CKB Cardiomyocytes CKBB 0.469 creatine kinase B protein-coding gene 1 Mesoderm Heart 0.0 0.05 0.232143 0.524638 +Mm Hs CXCR4 Cardiomyocytes LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.198308 0.00882448 +Hs IL11RA Cardiomyocytes NA 0.004 interleukin 11 receptor subunit alpha protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0197368 0.0 +Mm Hs MITF Cardiomyocytes MI|bHLHe32|WS2A|WS2 0.004 melanogenesis associated transcription factor protein-coding gene 1 Mesoderm Heart 0.0 0.0333333 0.00595238 0.00328502 +Mm Hs ZFPM2 Cardiomyocytes FOG2|hFOG-2|ZNF89B|ZC2HC11B 0.0 zinc finger protein, FOG family member 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00313283 0.0 +Mm Hs BDNF Cardiomyocytes NA 0.012 brain derived neurotrophic factor protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0018797 0.0146216 +Mm Hs GJA5 Cardiomyocytes CX40 0.002 gap junction protein alpha 5 protein-coding gene 1 Mesoderm Heart 0.0 0.15 0.00156642 0.00109501 +Mm Hs FMOD Cardiomyocytes SLRR2E 0.009 fibromodulin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00595238 0.00914654 +Mm Hs MTTP Cardiomyocytes MTP 0.014 microsomal triglyceride transfer protein protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00908521 0.0151369 +Mm Hs SLC5A1 Cardiomyocytes D22S675|NAGT|SGLT1 0.011 solute carrier family 5 member 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00219298 0.0 +Mm Hs ADIPOQ Cardiomyocytes ACRP30|AdipoQ|apM1|GBP28|adiponectin|ACDC 0.004 adiponectin, C1Q and collagen domain containing protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.00457327 +Mm Hs TRPV1 Cardiomyocytes NA 0.001 transient receptor potential cation channel subfamily V member 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 0.0 +Mm Hs HAMP Cardiomyocytes LEAP-1|HEPC|HFE2B|LEAP1 0.002 hepcidin antimicrobial peptide protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00407268 0.00231884 +Mm Hs SGPL1 Cardiomyocytes SPL 0.034 sphingosine-1-phosphate lyase 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0460526 0.0 +Mm Hs HMGB2 Cardiomyocytes HMG2 0.279 high mobility group box 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0666667 0.325501 0.262866 +Mm Hs STC1 Cardiomyocytes STC 0.005 stanniocalcin 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0178571 0.0 +Mm Hs FGF23 Cardiomyocytes NA 0.0 fibroblast growth factor 23 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0 6.44122e-05 +Mm Hs STRN Cardiomyocytes PPP2R6A|STRN1 0.018 striatin protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.00093985 0.0 +Mm Hs HEY2 Cardiomyocytes bHLHb32|HERP1|HESR2 0.004 hes related family bHLH transcription factor with YRPW motif 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0150376 0.00154589 +Mm Hs ADIPOR1 Cardiomyocytes PAQR1|ACDCR1 0.206 adiponectin receptor 1 protein-coding gene 1 Mesoderm Heart 0.0 0.316667 0.113722 0.222093 +Mm Hs ADIPOR2 Cardiomyocytes PAQR2|ACDCR2 0.034 adiponectin receptor 2 protein-coding gene 1 Mesoderm Heart 0.0 0.0333333 0.0213033 0.0351047 +Mm Hs PDE1A Cardiomyocytes NA 0.018 phosphodiesterase 1A protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0216165 0.0177134 +Mm Hs BMP4 Cardiomyocytes BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.0241228 0.0166828 +Mm Hs CASQ2 Cardiomyocytes PDIB2 0.003 calsequestrin 2 protein-coding gene 1 Mesoderm Heart 0.0 0.483333 0.000313283 0.0021256 +Mm Hs TPM1 Cardiomyocytes C15orf13|CMH3 0.253 tropomyosin 1 protein-coding gene 1 Mesoderm Heart 0.0 0.0 0.179198 0.0 +Mm Hs SSTR2 Cholangiocytes NA 0.028 somatostatin receptor 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0118704 0.0 +Mm Hs SLC4A2 Cholangiocytes HKB3|BND3L|NBND3|EPB3L1 0.007 solute carrier family 4 member 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs SCTR Cholangiocytes NA 0.0 secretin receptor protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs KRT7 Cholangiocytes CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Endoderm Liver 0.32 1.0 0.0959256 0.0472951 +Mm Hs KCNN2 Cholangiocytes KCa2.2|hSK2 0.003 potassium calcium-activated channel subfamily N member 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000320821 0.00436373 +Mm Hs ITGB4 Cholangiocytes CD104 0.013 integrin subunit beta 4 protein-coding gene 1 Endoderm Liver 0.0533333 0.0 0.0131537 0.0136687 +Mm Hs GGT6 Cholangiocytes FLJ90165 0.003 gamma-glutamyltransferase 6 protein-coding gene 1 Endoderm Liver 0.12 0.0 0.00481232 0.00211769 +Mm Hs CFTR Cholangiocytes ABC35|TNR-CFTR|CFTR/MRP|CF|ABCC7 0.003 cystic fibrosis transmembrane conductance regulator protein-coding gene 1 Endoderm Liver 0.12 0.0 0.00384986 0.00288776 +Mm Hs CCKBR Cholangiocytes NA 0.0 cholecystokinin B receptor protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000641643 0.000128345 +Mm Hs AQP4 Cholangiocytes MIWC 0.024 aquaporin 4 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0060956 0.029391 +Mm Hs AQP1 Cholangiocytes CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Endoderm Liver 0.04 0.0 0.0173244 0.0424822 +Mm Hs PIGR Cholangiocytes NA 0.031 polymeric immunoglobulin receptor protein-coding gene 1 Endoderm Liver 0.706667 1.0 0.0282323 0.029006 +Mm Hs GGT1 Cholangiocytes D22S672|D22S732|CD224 0.01 gamma-glutamyltransferase 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00192493 0.0121928 +Mm Hs JAG1 Cholangiocytes AHD|AWS|HJ1|CD339|AGS|JAGL1 0.027 jagged 1 protein-coding gene 1 Endoderm Liver 0.04 0.0 0.02342 0.0284284 +Mm Hs GPBAR1 Cholangiocytes BG37|TGR5|M-BAR|GPCR19|GPR131|MGC40597 0.001 G protein-coupled bile acid receptor 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00352903 0.0 +Mm Hs GGT7 Cholangiocytes D20S101|dJ18C9.2|GGTL5|GGTL3 0.007 gamma-glutamyltransferase 7 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000320821 0.00847077 +Mm Hs KRT19 Cholangiocytes K19|CK19|K1CS|MGC15366 0.088 keratin 19 protein-coding gene 1 Endoderm Liver 0.92 1.0 0.152711 0.0653276 +Mm Hs ONECUT2 Cholangiocytes OC-2 0.012 one cut homeobox 2 protein-coding gene 1 Endoderm Liver 0.0 0.5 0.00352903 0.0130912 +Mm Hs ALPL Cholangiocytes TNSALP|TNALP|TNAP|HOPS 0.009 alkaline phosphatase, liver/bone/kidney protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00417068 0.0105243 +Mm Hs HNF1B Cholangiocytes LFB3|VHNF1|HNF1beta|MODY5|TCF2 0.005 HNF1 homeobox B protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00962464 0.00462042 +Mm Hs ALB Cholangiocytes NA 0.008 albumin protein-coding gene 1 Endoderm Liver 0.0133333 0.0 0.0282323 0.00378618 +Mm Hs AGR2 Cholangiocytes XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene 1 Endoderm Liver 0.866667 0.5 0.0542188 0.0124495 +Mm MUC3 Cholangiocytes NA 0.01 mucin 3, intestinal protein coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0125136 +Mm Hs TFF3 Cholangiocytes HITF|ITF 0.022 trefoil factor 3 protein-coding gene 1 Endoderm Liver 0.56 0.0 0.0327238 0.0 +Mm Hs TFF1 Cholangiocytes D21S21|pS2|pNR-2|HP1.A|BCEI 0.006 trefoil factor 1 protein-coding gene 1 Endoderm Liver 0.253333 0.0 0.0147578 0.0 +Mm Hs SOX9 Cholangiocytes SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Endoderm Liver 0.12 0.0 0.0301572 0.0 +Mm Hs EPCAM Cholangiocytes Ly74|TROP1|GA733-2|EGP34|EGP40|EGP-2|KSA|CD326|Ep-CAM|HEA125|KS1/4|MK-1|MH99|MOC31|323/A3|17-1A|TACST-1|CO-17A|M4S1|MIC18|TACSTD1 0.117 epithelial cell adhesion molecule protein-coding gene 1 Endoderm Liver 0.653333 1.0 0.157202 0.104088 +Mm Hs CLDN4 Cholangiocytes CPE-R|WBSCR8|hCPE-R|CPETR|CPETR1 0.047 claudin 4 protein-coding gene 1 Endoderm Liver 0.88 0.5 0.110363 0.0286209 +Mm Hs MMP7 Cholangiocytes PUMP-1|MPSL1 0.007 matrix metallopeptidase 7 protein-coding gene 1 Endoderm Liver 0.2 0.0 0.0208534 0.00365783 +Mm Hs TFF2 Cholangiocytes SML1 0.002 trefoil factor 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000320821 0.0 +Mm Hs SCGB3A1 Cholangiocytes UGRP2|HIN-1|HIN1|LU105|PnSP-2 0.006 secretoglobin family 3A member 1 protein-coding gene 1 Endoderm Liver 0.173333 0.0 0.00769971 0.0 +Mm Hs FXYD2 Cholangiocytes MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0044915 0.0306103 +Mm Hs DEFB1 Cholangiocytes HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene 1 Endoderm Liver 0.08 0.0 0.0247032 0.00532632 +Hs CD24 Cholangiocytes CD24A 0.039 CD24 molecule protein-coding gene 1 Endoderm Liver 0.64 0.0 0.181264 0.0 +Mm Hs LCN2 Cholangiocytes NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Endoderm Liver 0.506667 0.0 0.0458774 0.0417763 +Mm Hs CXCL1 Cholangiocytes SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Endoderm Liver 0.32 0.0 0.0391402 0.0305461 +Hs CXCL6 Cholangiocytes GCP-2|CKA-3|SCYB6 0.001 C-X-C motif chemokine ligand 6 protein-coding gene 1 Endoderm Liver 0.0533333 0.0 0.00352903 0.0 +Mm Hs LGALS2 Cholangiocytes HL14 0.032 galectin 2 protein-coding gene 1 Endoderm Liver 0.133333 1.0 0.0356112 0.0306745 +Mm Hs TACSTD2 Cholangiocytes TROP2|GA733-1|EGP-1|M1S1 0.033 tumor associated calcium signal transducer 2 protein-coding gene 1 Endoderm Liver 0.346667 0.0 0.0923965 0.0 +Mm Hs ELF3 Cholangiocytes ESE-1|ERT|ESX 0.048 E74 like ETS transcription factor 3 protein-coding gene 1 Endoderm Liver 0.893333 1.0 0.0978505 0.0333697 +Mm Hs SPP1 Cholangiocytes BSPI|ETA-1|BNSP|OPN 0.057 secreted phosphoprotein 1 protein-coding gene 1 Endoderm Liver 0.04 0.0 0.0535772 0.0 +Mm Hs MUC5B Cholangiocytes MG1 0.002 mucin 5B, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm Liver 0.213333 0.0 0.0044915 0.00051338 +Mm Hs LGALS4 Cholangiocytes GAL4 0.032 galectin 4 protein-coding gene 1 Endoderm Liver 0.613333 1.0 0.0247032 0.0306103 +Mm Hs CHAT Cholinergic neurons NA 0.001 choline O-acetyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00160411 +Mm Hs SLC18A3 Cholinergic neurons VACHT 0.002 solute carrier family 18 member A3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs ACHE Cholinergic neurons YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.0195701 +Mm Hs SLC5A7 Cholinergic neurons hCHT|CHT1 0.002 solute carrier family 5 member 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs TAC1 Cholinergic neurons NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs BRCA1 Cholinergic neurons RNF53|PPP1R53|FANCS 0.007 BRCA1, DNA repair associated protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0297619 0.00121912 +Mm Hs ACLY Cholinergic neurons ATPCL|CLATP|ACL 0.087 ATP citrate lyase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0595238 0.0922682 +Mm Hs PRG4 Chondrocytes JCAP|SZP|HAPO|bG174L6.2|FLJ32635|CACP 0.004 proteoglycan 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.3 0.00156642 0.00385728 +Mm Hs TNC Chondrocytes MGC167029|HXB|DFNA56 0.033 tenascin C protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0128446 0.0 +Mm Hs CRTAC1 Chondrocytes FLJ10320|CEP-68|ASPIC1 0.005 cartilage acidic protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125313 0.00655738 +Mm Hs CREB3L2 Chondrocytes BBF2H7|TCAG_1951439 0.025 cAMP responsive element binding protein 3 like 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.166667 0.0238095 0.0234651 +Mm Hs RUNX2 Chondrocytes AML3|PEBP2A1|PEBP2aA1|CCD|CBFA1|CCD1 0.008 runt related transcription factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00877193 0.0 +Mm Hs ACAN Chondrocytes CSPGCP|CSPG1|AGC1 0.002 aggrecan protein-coding gene 1 Mesoderm Connective tissue 0.0 0.766667 0.000313283 0.000450016 +Mm Hs COL2A1 Chondrocytes STL1|SEDC|AOM 0.009 collagen type II alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.966667 0.0119048 0.00514304 +Mm Hs COMP Chondrocytes THBS5|PSACH|EDM1|EPD1 0.005 cartilage oligomeric matrix protein protein-coding gene 1 Mesoderm Connective tissue 0.0 0.933333 0.00657895 0.00302154 +Mm Hs MATN3 Chondrocytes EDM5|HOA 0.001 matrilin 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.4 0.00093985 0.0 +Mm Hs RUNX3 Chondrocytes AML2|PEBP2A3|CBFA3 0.018 runt related transcription factor 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0206767 0.0 +Mm Hs SOX6 Chondrocytes NA 0.017 SRY-box 6 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0225564 0.0 +Mm Hs BMP2 Chondrocytes BMP2A 0.008 bone morphogenetic protein 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.266667 0.00845865 0.00726455 +Mm Hs CTNNB1 Chondrocytes beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0333333 0.212406 0.011379 +Mm Hs FGF18 Chondrocytes FGF-18|ZFGF5 0.001 fibroblast growth factor 18 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000626566 0.000707168 +Mm Hs GLI3 Chondrocytes PAP-A|PAPA1|PAPB|ACLS|PPDIV|GCPS|PHS 0.003 GLI family zinc finger 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0056391 0.00218579 +Mm Hs PBX3 Chondrocytes NA 0.009 PBX homeobox 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0037594 0.00874317 +Mm Hs PTHLH Chondrocytes PTHRP 0.002 parathyroid hormone like hormone protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00250627 0.00244294 +Mm Hs SMO Chondrocytes FZD11|SMOH 0.005 smoothened, frizzled class receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs STAT1 Chondrocytes STAT91|ISGF-3 0.034 signal transducer and activator of transcription 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0567043 0.0 +Mm Hs MMP13 Chondrocytes CLG3 0.003 matrix metallopeptidase 13 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.00334298 +Mm Hs VEGFA Chondrocytes VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0247494 0.0 +Mm Hs MATN1 Chondrocytes CRTM|CMP 0.0 matrilin 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.3 0.0 6.4288e-05 +Mm Hs COL9A1 Chondrocytes NA 0.006 collagen type IX alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.866667 0.00657895 0.00469302 +Mm Hs COL10A1 Chondrocytes NA 0.0 collagen type X alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0666667 0.0 0.0 +Mm Hs IGF2 Chondrocytes FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0463659 0.000900032 +Mm Hs MIA Chondrocytes CD-RAP 0.003 MIA SH3 domain containing protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0333333 0.0 0.0043073 +Mm Hs SDC3 Chondrocytes N-syndecan|SYND3 0.007 syndecan 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125313 0.0 +Mm Hs EMP1 Chondrocytes TMP|CL-20 0.076 epithelial membrane protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.766667 0.112782 0.067631 +Mm Hs COL6A1 Chondrocytes NA 0.063 collagen type VI alpha 1 chain protein-coding gene NA Mesoderm Connective tissue 0.0 0.8 0.0902256 0.0541305 +Mm Hs CYTL1 Chondrocytes C17|C4orf4 0.012 cytokine like 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.933333 0.0278822 0.00623594 +Mm Hs LCN2 Chondrocytes NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0666667 0.0567043 0.0417229 +None AC159092.1 Chondrocytes NA 0.031 NA NA NA Mesoderm Connective tissue 0.0 0.833333 0.0 0.0372228 +Mm Hs LUM Chondrocytes SLRR2D|LDC 0.051 lumican protein-coding gene 1 Mesoderm Connective tissue 0.0 0.666667 0.0870927 0.0415301 +Mm Hs GADD45B Chondrocytes GADD45BETA|DKFZP566B133|MYD118 0.108 growth arrest and DNA damage inducible beta protein-coding gene 1 Mesoderm Connective tissue 0.0 0.766667 0.194236 0.0899389 +Mm Hs SCRG1 Chondrocytes SCRG-1 0.037 stimulator of chondrogenesis 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0172306 0.0 +Mm Hs HAPLN1 Chondrocytes CRTL1 0.009 hyaluronan and proteoglycan link protein 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.966667 0.0256892 0.0032144 +Mm Hs COL11A1 Chondrocytes STL2|CO11A1|COLL6 0.009 collagen type XI alpha 1 chain protein-coding gene NA Mesoderm Connective tissue 0.0 1.0 0.00971178 0.00681453 +Mm Hs S100A9 Chondrocytes MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.103383 0.0 +Mm Hs CHAD Chondrocytes SLRR4A 0.002 chondroadherin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.833333 0.0 0.00135005 +Mm Hs COL9A3 Chondrocytes EDM3|FLJ90759|DJ885L7.4.1 0.019 collagen type IX alpha 3 chain protein-coding gene NA Mesoderm Connective tissue 0.0 0.933333 0.0125313 0.0181292 +Mm Hs DLK1 Chondrocytes FA1|pG2|Pref-1|ZOG|Delta1 0.055 delta like non-canonical Notch ligand 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.533333 0.0460526 0.0570878 +Mm Hs S100A8 Chondrocytes P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0798872 0.0 +Mm Hs CHODL Chondrocytes FLJ12627|PRED12|MT75|C21orf68 0.004 chondrolectin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125313 0.0043073 +Mm Hs ATF4 Chondrocytes TAXREB67|CREB-2|TXREB 0.35 activating transcription factor 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.9 0.385025 0.337512 +Hs SHOX Chondrocytes PHOG|GCFX|SHOXY 0.0 short stature homeobox protein-coding gene 1 Mesoderm Connective tissue NA NA NA NA +Mm Hs MGP Chondrocytes NA 0.082 matrix Gla protein protein-coding gene 1 Mesoderm Connective tissue 0.0 1.0 0.116541 0.071424 +Mm Hs TCF4 Chondrocytes SEF2-1B|ITF2|bHLHb19|E2-2 0.394 transcription factor 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.169486 0.0 +Mm Hs VDR Chondrocytes NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00250627 0.0 +Mm Hs ATRX Chondrocytes XH2|XNP|RAD54|JMS|MRX52 0.408 ATRX, chromatin remodeler protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0333333 0.2099 0.454195 +Mm Hs NOG Chondrocytes SYNS1 0.002 noggin protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00501253 0.00122147 +Mm Hs AGER Chondrocytes SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00125313 0.0135648 +Mm Hs IL10RA Chondrocytes HIL-10R|CDW210A|CD210a|CD210|IL10R 0.011 interleukin 10 receptor subunit alpha protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0075188 0.0120861 +Mm Hs TTR Choroid plexus cells HsT2651|CTS|PALB|CTS1 0.055 transthyretin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0733083 0.0 +Mm Hs KL Choroid plexus cells NA 0.004 klotho protein-coding gene 1 Ectoderm Brain 0.0 0.956522 0.0 0.00334147 +Mm Hs SOSTDC1 Choroid plexus cells DKFZp564D206|USAG1|DAND7 0.009 sclerostin domain containing 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs CLIC6 Choroid plexus cells CLIC5|CLIC1L 0.008 chloride intracellular channel 6 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.000626566 0.00835368 +Mm Hs SLC4A10 Choroid plexus cells NBCn2|NCBE 0.009 solute carrier family 4 member 10 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs HTR2C Choroid plexus cells 5-HT2C|5HTR2C|HTR1C 0.002 5-hydroxytryptamine receptor 2C protein-coding gene NA Ectoderm Brain 0.0 0.913043 0.0 0.000963886 +Mm Hs AQP1 Choroid plexus cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Ectoderm Brain 0.0 0.869565 0.0178571 0.0412543 +Mm Hs SLC16A2 Choroid plexus cells XPCT|MCT8|DXS128|AHDS|MRX22 0.023 solute carrier family 16 member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs SLC4A2 Choroid plexus cells HKB3|BND3L|NBND3|EPB3L1 0.007 solute carrier family 4 member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC4A5 Choroid plexus cells NBC4 0.002 solute carrier family 4 member 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC31A1 Choroid plexus cells hCTR1|CTR1|COPT1 0.052 solute carrier family 31 member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0112782 0.0 +Mm CAR12 Choroid plexus cells NA 0.004 carbonic anhydrase 12 protein coding gene 1 Ectoderm Brain 0.0 0.913043 0.0 0.00385555 +Mm Hs CLDN2 Choroid plexus cells NA 0.009 claudin 2 protein-coding gene NA Ectoderm Brain 0.0 0.782609 0.00281955 0.00931757 +Mm Hs SLC13A4 Choroid plexus cells SUT-1|SUT1 0.004 solute carrier family 13 member 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs SLC29A4 Choroid plexus cells FLJ34923|ENT4 0.006 solute carrier family 29 member 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0093985 0.0 +Mm Hs PRLR Choroid plexus cells NA 0.013 prolactin receptor protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.0106516 0.012659 +Mm Hs CLDN1 Choroid plexus cells SEMP1|ILVASC 0.01 claudin 1 protein-coding gene NA Ectoderm Brain 0.0 0.565217 0.0285088 0.00481943 +Mm Hs SLC2A12 Choroid plexus cells GLUT12 0.001 solute carrier family 2 member 12 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs WFIKKN2 Choroid plexus cells WFIKKNRP|WFDC20B 0.0 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC23A2 Choroid plexus cells SVCT2|KIAA0238|YSPL2|SLC23A1 0.007 solute carrier family 23 member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs SLC26A11 Choroid plexus cells NA 0.0 solute carrier family 26 member 11 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs CHMP1A Choroid plexus cells KIAA0047|CHMP1|Vps46A|PRSM1|PCOLN3 0.094 charged multivesicular body protein 1A protein-coding gene 1 Ectoderm Brain 0.0 0.0869565 0.0560777 0.100244 +Mm Hs SLC26A4 Chromaffin cells PDS|DFNB4 0.001 solute carrier family 26 member 4 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00093985 0.0 +Mm Hs AGRP Chromaffin cells Agrt|ART|ASIP2 0.001 agouti related neuropeptide protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0 0.00160411 +Mm Hs IGF2 Chromaffin cells FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0463659 0.0008983 +Mm Hs SNAP25 Chromaffin cells SNAP-25|RIC-4|RIC4|SEC9|bA416N4.2|dJ1068F16.2|SNAP 0.112 synaptosome associated protein 25 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0222431 0.0 +Mm Hs SLC18A2 Chromaffin cells SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00125313 0.0 +Mm Hs SNAPIN Chromaffin cells BLOC1S7|BORCS3|SNAPAP 0.056 SNAP associated protein protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0592105 0.0 +Mm Hs PNMT Chromaffin cells PENT 0.0 phenylethanolamine N-methyltransferase protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00093985 0.000320821 +Mm Hs RAPGEF2 Chromaffin cells PDZ-GEF1|RA-GEF|DKFZP586O1422|KIAA0313|PDZGEF1 0.003 Rap guanine nucleotide exchange factor 2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00250627 0.0 +Mm Hs SERPINE1 Chromaffin cells PAI|PLANH1|PAI1 0.014 serpin family E member 1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0388471 0.0 +Mm Hs GJD2 Chromaffin cells CX36|GJA9 0.005 gap junction protein delta 2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00595238 0.00500481 +Mm Hs CACNA1D Chromaffin cells Cav1.3|CACH3|CACN4|CCHL1A2|CACNL1A2 0.004 calcium voltage-gated channel subunit alpha1 D protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.000626566 0.00494065 +Mm Hs PIK3C2A Chromaffin cells PI3K-C2alpha 0.006 phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0191103 0.00243824 +Mm Hs NCS1 Chromaffin cells NCS-1|FREQ 0.122 neuronal calcium sensor 1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00689223 0.152198 +Mm Hs PLD1 Chromaffin cells NA 0.004 phospholipase D1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00219298 0.00468399 +Mm Hs PLD2 Chromaffin cells NA 0.0 phospholipase D2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0 0.000384986 +Mm Hs DOC2B Chromaffin cells DOC2BL 0.002 double C2 domain beta protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00093985 0.00186076 +Mm Hs UNC13A Chromaffin cells KIAA1032|Munc13-1 0.0 unc-13 homolog A protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0 0.0 +Mm Hs SLC18A1 Chromaffin cells CGAT|VMAT1|VAT1 0.001 solute carrier family 18 member A1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.000313283 0.0 +Mm Hs STX1A Chromaffin cells HPC-1|p35-1|STX1 0.013 syntaxin 1A protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00657895 0.0 +Mm Hs NPY Chromaffin cells PYY4 0.015 neuropeptide Y protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0056391 0.0170677 +Mm Hs NTRK1 Chromaffin cells TRKA|MTC 0.004 neurotrophic receptor tyrosine kinase 1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0 0.00474816 +Mm Hs P2RY1 Chromaffin cells P2Y1|SARCC 0.003 purinergic receptor P2Y1 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.00219298 0.00314405 +Mm Hs SLC12A2 Chromaffin cells NKCC1|BSC|BSC2|PPP1R141 0.074 solute carrier family 12 member 2 protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0501253 0.0 +Mm Hs CHGA Chromaffin cells NA 0.057 chromogranin A protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.0379073 0.0622393 +Mm Hs PLAT Chromaffin cells NA 0.057 plasminogen activator, tissue type protein-coding gene 1 Mesoderm Adrenal glands 0.0 0.0 0.035401 0.0638434 +Mm Hs SEC14L3 Ciliated cells TAP2 0.006 SEC14 like lipid binding 3 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs CCDC153 Ciliated cells LOC283152 0.006 coiled-coil domain containing 153 protein-coding gene NA Endoderm Lungs 0.0 1.0 0.00156642 0.00763702 +Mm DYNLT1C Ciliated cells NA 0.008 dynein light chain Tctex-type 1C protein coding gene NA Endoderm Lungs 0.0 0.0 0.0 0.0107175 +Mm Hs FAM161A Ciliated cells FLJ13305|RP28 0.009 FAM161A, centrosomal protein protein-coding gene NA Endoderm Lungs 0.0 1.0 0.0194236 0.00699525 +Mm Hs TMEM212 Ciliated cells FLJ23172 0.006 transmembrane protein 212 protein-coding gene NA Endoderm Lungs 0.0 0.0 0.000313283 0.0 +Mm Hs USMG5 Ciliated cells NA 0.022 upregulated during skeletal muscle growth 5 protein coding gene NA Endoderm Lungs 0.0 0.0 0.023183 0.0 +Mm Hs CCDC181 Ciliated cells FLJ25846|C1orf114 0.013 coiled-coil domain containing 181 protein-coding gene NA Endoderm Lungs 0.0 0.666667 0.0297619 0.00981902 +Mm CES1D Ciliated cells NA 0.016 carboxylesterase 1D protein coding gene NA Endoderm Lungs 0.0 1.0 0.0 0.0198948 +Mm Hs FOXJ1 Ciliated cells HFH-4|HFH4|FKHL13 0.01 forkhead box J1 protein-coding gene 1 Endoderm Lungs 0.0 0.666667 0.00877193 0.0112309 +Mm Hs CCDC17 Ciliated cells FLJ33084 0.001 coiled-coil domain containing 17 protein-coding gene NA Endoderm Lungs 0.0 0.666667 0.0018797 0.000834296 +Mm Hs CCDC39 Ciliated cells DKFZp434A128|CILD14|FAP59 0.007 coiled-coil domain containing 39 protein-coding gene NA Endoderm Lungs 0.0 1.0 0.0156642 0.00500578 +Mm FAM177A Ciliated cells NA 0.0 family with sequence similarity 177, member A protein coding gene NA Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs ODF3B Ciliated cells NA 0.009 outer dense fiber of sperm tails 3B protein-coding gene NA Endoderm Lungs 0.0 0.666667 0.0219298 0.00725196 +Mm Hs CYP2S1 Ciliated cells NA 0.004 cytochrome P450 family 2 subfamily S member 1 protein-coding gene NA Endoderm Lungs 0.0 1.0 0.0056391 0.00429983 +Mm Hs LRRC23 Ciliated cells B7|LRPB7 0.008 leucine rich repeat containing 23 protein-coding gene NA Endoderm Lungs 0.0 0.0 0.0100251 0.00834296 +Mm Hs SCGB1A1 Ciliated cells CC10|CCSP|CC16|UGB 0.028 secretoglobin family 1A member 1 protein-coding gene NA Endoderm Lungs 0.0 0.0 0.0109649 0.0 +Mm Hs APPL2 Ciliated cells FLJ10659|DIP13B 0.011 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2 protein-coding gene NA Endoderm Lungs 0.0 0.333333 0.00595238 0.0126428 +Mm Hs TUBB4B Ciliated cells Beta2|TUBB2C 0.276 tubulin beta 4B class IVb protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.338346 0.0 +Mm Hs SYT2 Clara cells NA 0.002 synaptotagmin 2 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs CYP2E1 Clara cells CYP2E 0.003 cytochrome P450 family 2 subfamily E member 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00439009 0.00341099 +Mm Hs SCGB1A1 Clara cells CC10|CCSP|CC16|UGB 0.028 secretoglobin family 1A member 1 protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.0100345 0.0 +Mm Hs FOXM1 Clara cells HFH-11|trident|HNF-3|INS-1|MPP2|MPHOSPH2|TGT3|FKHL16 0.001 forkhead box M1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.00167332 +Mm CYP2F2 Clara cells NA 0.008 cytochrome P450, family 2, subfamily f, polypeptide 2 protein coding gene 1 Endoderm Lungs 0.0 0.87234 0.0 0.00682198 +Mm Hs CTSE Clara cells NA 0.009 cathepsin E protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00878018 0.00901017 +Mm Hs MUC5B Clara cells MG1 0.002 mucin 5B, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm Lungs 0.0 0.12766 0.00940734 0.000128717 +Mm Hs SCGB3A2 Clara cells UGRP1|LU103|PNSP1 0.008 secretoglobin family 3A member 2 protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.0084666 0.0 +Mm Hs SFTPC Clara cells SP-C|PSP-C|SMDP2|BRICD6|SFTP2 0.029 surfactant protein C protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.022264 0.0 +Mm Hs MUC1 Clara cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Endoderm Lungs 0.666667 0.340426 0.0322985 0.0115201 +Mm Hs CYP4B1 Clara cells NA 0.018 cytochrome P450 family 4 subfamily B member 1 protein-coding gene 1 Endoderm Lungs 0.666667 0.659574 0.0122295 0.0171837 +Mm Hs ALDH1A1 Clara cells RALDH1|PUMB1|ALDH1 0.039 aldehyde dehydrogenase 1 family member A1 protein-coding gene 1 Endoderm Lungs 0.0 0.851064 0.0881154 0.0262582 +Mm Hs BPIFA1 Clara cells LUNX|bA49G10.5|SPLUNC1|PLUNC 0.006 BPI fold containing family A member 1 protein-coding gene 1 Endoderm Lungs 0.0 0.319149 0.00407651 0.00572789 +Mm Hs SCGB3A1 Clara cells UGRP2|HIN-1|HIN1|LU105|PnSP-2 0.006 secretoglobin family 3A member 1 protein-coding gene 1 Endoderm Lungs 0.666667 0.0 0.0109752 0.0 +Mm Hs MUC4 Clara cells NA 0.005 mucin 4, cell surface associated protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0166196 0.00263869 +Mm Hs AHR Clara cells bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Endoderm Lungs 0.0 0.0638298 0.0112888 0.00675763 +Mm Hs MMP28 Clara cells MMP-25|MM28|EPILYSIN|MMP-28 0.0 matrix metallopeptidase 28 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00188147 6.43583e-05 +Mm Hs LEPR Clara cells OBR|CD295 0.005 leptin receptor protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00783945 0.00431201 +Mm Hs ERN1 Clara cells IRE1|IRE1P 0.002 endoplasmic reticulum to nucleus signaling 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00595798 0.00122281 +Mm Hs SFTPA1 Clara cells SP-A|SP-A1|COLEC4|SFTP1 0.015 surfactant protein A1 protein-coding gene 1 Endoderm Lungs 0.666667 0.0 0.0172468 0.0 +Mm Hs CARM1 Clara cells PRMT4 0.0 coactivator associated arginine methyltransferase 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.000450508 +Mm CYP2B10 Clara cells NA 0.004 cytochrome P450, family 2, subfamily b, polypeptide 10 protein coding gene 1 Endoderm Lungs 0.0 0.0212766 0.0 0.00456944 +Mm Hs RAB3D Clara cells RAB16|D2-2|RAD3D|GOV 0.015 RAB3D, member RAS oncogene family protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs SFTPD Clara cells SP-D|COLEC7|SFTP4 0.01 surfactant protein D protein-coding gene 1 Endoderm Lungs 0.333333 0.0 0.00407651 0.0 +Mm Hs KCNE3 Crypt cells MiRP2 0.01 potassium voltage-gated channel subfamily E regulatory subunit 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.0121912 +Mm Hs KCNQ1 Crypt cells Kv7.1|KCNA8|KVLQT1|JLNS1|LQT1|LQT|KCNA9 0.004 potassium voltage-gated channel subfamily Q member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00093985 0.00532563 +Mm Hs OLFM4 Crypt cells OlfD|GW112 0.013 olfactomedin 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0153509 0.0126404 +Mm Hs PROM1 Crypt cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00720551 0.0241899 +Mm Hs LGR5 Crypt cells HG38|FEX|GPR67|GPR49 0.002 leucine rich repeat containing G protein-coupled receptor 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313283 0.00198909 +Mm Hs EPHB2 Crypt cells Hek5|Tyro5|DRT|EPHT3 0.002 EPH receptor B2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00469925 0.00198909 +Mm Hs ASCL2 Crypt cells HASH2|bHLHa45 0.005 achaete-scute family bHLH transcription factor 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0075188 0.00481232 +Mm Hs BMI1 Crypt cells RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00532581 0.00930382 +Mm Hs HOPX Crypt cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.091792 0.022265 +Mm Hs LRIG1 Crypt cells LIG-1|DKFZP586O1624|LIG1 0.004 leucine rich repeats and immunoglobulin like domains 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00156642 0.00442733 +Mm Hs TERT Crypt cells TRT|TCS1|hEST2|EST2 0.0 telomerase reverse transcriptase protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs MSI1 Crypt cells NA 0.022 musashi RNA binding protein 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0253759 0.0216234 +Mm Hs SMOC2 Crypt cells SMAP2 0.026 SPARC related modular calcium binding 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0178571 0.0 +Mm Hs TNFRSF19 Crypt cells TAJ-alpha|TROY|TAJ|TRADE 0.017 TNF receptor superfamily member 19 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00156642 0.0 +Mm Hs SLC12A2 Crypt cells NKCC1|BSC|BSC2|PPP1R141 0.074 solute carrier family 12 member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0501253 0.0 +Mm Hs AXIN2 Crypt cells MGC126582|DKFZp781B0869 0.006 axin 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00802053 +Mm Hs XCL1 Decidual cells LPTN|ATAC|SCM-1a|SCM-1|LTN|SCYC1 0.006 X-C motif chemokine ligand 1 protein-coding gene NA NA Reproductive 1.0 0.0 0.00971482 0.0 +Mm Hs IGFBP1 Decidual cells IGF-BP25|AFBP|hIGFBP-1|PP12 0.004 insulin like growth factor binding protein 1 protein-coding gene NA NA Reproductive 1.0 0.0 0.0166092 0.00121928 +Hs XCL2 Decidual cells SCM-1b|SCYC2 0.002 X-C motif chemokine ligand 2 protein-coding gene NA NA Reproductive 1.0 0.0 0.0103416 0.0 +Mm Hs CTSW Decidual cells NA 0.026 cathepsin W protein-coding gene NA NA Reproductive 1.0 1.0 0.0614228 0.0193159 +Hs IL32 Decidual cells NK4|TAIF|TAIFb|TAIFd 0.036 interleukin 32 protein-coding gene NA NA Reproductive 1.0 0.0 0.204638 0.0 +Mm Hs TRDC Decidual cells NA 0.011 T cell receptor delta constant other NA NA Reproductive 1.0 0.0 0.0253839 0.0 +Mm Hs KLRC1 Decidual cells NKG2-A|NKG2-B|CD159a|NKG2 0.004 killer cell lectin like receptor C1 protein-coding gene NA NA Reproductive 1.0 0.0 0.0084613 0.00275942 +Mm Hs PRL Decidual cells NA 0.004 prolactin protein-coding gene NA NA Reproductive 1.0 0.0 0.0103416 0.00340114 +Mm Hs CST7 Decidual cells NA 0.028 cystatin F protein-coding gene NA NA Reproductive 0.0 1.0 0.0692573 0.01861 +Mm Hs AREG Decidual cells SDGF|AREGB 0.031 amphiregulin protein-coding gene NA NA Reproductive 1.0 1.0 0.100282 0.0143105 +Mm Hs PDX1 Delta cells IDX-1|STF-1|PDX-1|MODY4|IPF1 0.005 pancreatic and duodenal homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.125 0.7 0.00565327 0.00430177 +Mm Hs FFAR4 Delta cells PGR4|GPR129|GPR120|O3FAR1 0.005 free fatty acid receptor 4 protein-coding gene 1 Endoderm Pancreas 0.25 0.9 0.00408291 0.00430177 +Mm Hs SST Delta cells SMST 0.027 somatostatin protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0452261 0.0 +Mm Hs PCSK9 Delta cells NARC-1|FH3|HCHOLA3 0.005 proprotein convertase subtilisin/kexin type 9 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00031407 0.0059069 +Mm Hs RBP4 Delta cells NA 0.032 retinol binding protein 4 protein-coding gene 1 Endoderm Pancreas 0.875 0.0 0.03549 0.0 +Mm Hs PAX4 Delta cells MODY9 0.001 paired box 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00102729 +Mm Hs RESP18 Delta cells NA 0.062 regulated endocrine specific protein 18 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs HHEX Delta cells HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Endoderm Pancreas 1.0 1.0 0.0204146 0.0389727 +Mm Hs ISL1 Delta cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Endoderm Pancreas 1.0 1.0 0.0109925 0.0307544 +Mm Hs SCGN Delta cells SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Endoderm Pancreas 0.875 0.0 0.0276382 0.0 +Mm Hs KCNK16 Delta cells K2p16.1|TALK-1|TALK1 0.007 potassium two pore domain channel subfamily K member 16 protein-coding gene 1 Endoderm Pancreas 0.125 1.0 0.00753769 0.00603531 +Mm Hs IAPP Delta cells AMYLIN 0.023 islet amyloid polypeptide protein-coding gene 1 Endoderm Pancreas 0.75 1.0 0.040201 0.0199679 +Mm Hs FXYD2 Delta cells MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00439698 0.030626 +Mm Hs NPTX2 Delta cells NA 0.008 neuronal pentraxin 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0182161 0.00686998 +Hs GPC5-AS1 Delta cells NA 0.001 GPC5 antisense RNA 1 non-coding RNA 1 Endoderm Pancreas 0.5 0.0 0.00282663 0.0 +Mm Hs UCP2 Delta cells SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Endoderm Pancreas 0.125 0.0 0.00471106 0.0 +Mm Hs LEPR Delta cells OBR|CD295 0.005 leptin receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00785176 0.00430177 +Mm Hs BAIAP3 Delta cells BAP3|KIAA0734 0.003 BAI1 associated protein 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.1 0.0 0.00423756 +Hs MS4A8 Delta cells CD20L5|MS4A8B 0.001 membrane spanning 4-domains A8 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00376884 0.0 +Mm Hs CASR Delta cells FHH|NSHPT|GPRC2A|HHC|HHC1 0.001 calcium sensing receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.1 0.00219849 0.000449438 +Mm Hs BCHE Delta cells CHE2 0.003 butyrylcholinesterase protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0053392 0.00243981 +Mm Hs GABRB3 Delta cells NA 0.025 gamma-aminobutyric acid type A receptor beta3 subunit protein-coding gene 1 Endoderm Pancreas 0.125 0.2 0.00408291 0.0303692 +Mm Hs UNC5B Delta cells UNC5H2|p53RDL1 0.002 unc-5 netrin receptor B protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs EDN3 Delta cells ET3 0.003 endothelin 3 protein-coding gene 1 Endoderm Pancreas 0.125 0.0 0.00219849 0.00378812 +Mm Hs PRG4 Delta cells JCAP|SZP|HAPO|bG174L6.2|FLJ32635|CACP 0.004 proteoglycan 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00157035 0.00443018 +Mm Hs GHSR Delta cells NA 0.0 growth hormone secretagogue receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs FRZB Delta cells FRZB-PEN|FRZB1|SRFP3|FRP-3|SFRP3|FRE|FRITZ|FRZB-1|FZRB|hFIZ 0.012 frizzled related protein protein-coding gene 1 Endoderm Pancreas 0.125 0.8 0.0301508 0.00744783 +Mm Hs PCSK1 Delta cells PC1|NEC1 0.008 proprotein convertase subtilisin/kexin type 1 protein-coding gene 1 Endoderm Pancreas 0.75 0.4 0.00753769 0.0082183 +Mm Hs GABRG2 Delta cells NA 0.024 gamma-aminobutyric acid type A receptor gamma2 subunit protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00125628 0.0297271 +Mm Hs POU3F1 Delta cells OCT6|SCIP|OTF6 0.013 POU class 3 homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00031407 0.0167576 +Mm Hs BHLHE41 Delta cells DEC2|SHARP-1|SHARP1|bHLHe41|BHLHB3 0.031 basic helix-loop-helix family member e41 protein-coding gene 1 Endoderm Pancreas 0.0 0.1 0.00753769 0.0371108 +Mm Hs EHF Delta cells ESE3|ESEJ 0.024 ETS homologous factor protein-coding gene 1 Endoderm Pancreas 0.0 0.4 0.0515075 0.019069 +Mm Hs LCORL Delta cells MLR1|FLJ30696 0.015 ligand dependent nuclear receptor corepressor like protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0113065 0.0157303 +Mm Hs ETV1 Delta cells ER81 0.037 ETS variant 1 protein-coding gene 1 Endoderm Pancreas 0.125 0.8 0.00785176 0.0445586 +Mm Hs IL6 Dendritic cells IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0141215 0.0064981 +Mm Hs CD86 Dendritic cells B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.204082 0.642857 0.00295567 0.0275365 +Mm Hs CD83 Dendritic cells HB15|BL11 0.045 CD83 molecule protein-coding gene 1 Mesoderm Immune system 0.44898 0.857143 0.0187192 0.045358 +Hs CD1A Dendritic cells NA 0.0 CD1a molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs CR2 Dendritic cells CD21|C3DR 0.001 complement C3d receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000985222 0.000579039 +Mm Hs TLR9 Dendritic cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs CD1C Dendritic cells NA 0.001 CD1c molecule protein-coding gene 1 Mesoderm Immune system 0.0952381 0.0 0.000656814 0.0 +Hs CD209 Dendritic cells DC-SIGN|CDSIGN|DC-SIGN1|CLEC4L 0.0 CD209 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs LAMP3 Dendritic cells TSC403|DC-LAMP|DCLAMP|CD208 0.008 lysosomal associated membrane protein 3 protein-coding gene 1 Mesoderm Immune system 0.0340136 0.0 0.0124795 0.00688413 +Hs CD1B Dendritic cells NA 0.0 CD1b molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TREM2 Dendritic cells TREM-2|Trem2a|Trem2b|Trem2c 0.042 triggering receptor expressed on myeloid cells 2 protein-coding gene 1 Mesoderm Immune system 0.0272109 0.0 0.00558292 0.0 +Mm Hs FABP4 Dendritic cells A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Immune system 0.0340136 0.0238095 0.0091954 0.0332626 +Mm Hs S100A9 Dendritic cells MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Immune system 0.517007 0.0 0.0834154 0.0 +Mm Hs ARG1 Dendritic cells NA 0.007 arginase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00361248 0.00720582 +Hs HLA-DRA Dendritic cells HLA-DRA1 0.039 major histocompatibility complex, class II, DR alpha protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.174384 0.0 +Hs HLA-DQA1 Dendritic cells HLA-DQA 0.01 major histocompatibility complex, class II, DQ alpha 1 protein-coding gene NA Mesoderm Immune system 0.55102 0.0 0.0272578 0.0 +Hs HLA-DMB Dendritic cells D6S221E|RING7 0.009 major histocompatibility complex, class II, DM beta protein-coding gene 1 Mesoderm Immune system 0.482993 0.0 0.0229885 0.0 +Hs HLA-DMA Dendritic cells D6S222E|RING6 0.022 major histocompatibility complex, class II, DM alpha protein-coding gene 1 Mesoderm Immune system 0.809524 0.0 0.090312 0.0 +Hs HLA-DQB1 Dendritic cells HLA-DQB 0.012 major histocompatibility complex, class II, DQ beta 1 protein-coding gene 1 Mesoderm Immune system 0.632653 0.0 0.0374384 0.0 +Mm Hs CLEC10A Dendritic cells HML2|HML|CD301|CLECSF14 0.01 C-type lectin domain containing 10A protein-coding gene 1 Mesoderm Immune system 0.238095 0.0 0.000985222 0.00971498 +Hs HLA-DRB1 Dendritic cells HLA-DR1B 0.033 major histocompatibility complex, class II, DR beta 1 protein-coding gene 1 Mesoderm Immune system 0.986395 0.0 0.141215 0.0 +Hs HLA-DPA1 Dendritic cells HLA-DP1A 0.031 major histocompatibility complex, class II, DP alpha 1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.130706 0.0 +Hs HLA-DPB1 Dendritic cells HLA-DP1B 0.032 major histocompatibility complex, class II, DP beta 1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.137603 0.0 +Mm Hs DNASE1L3 Dendritic cells DNAS1L3|LSD 0.015 deoxyribonuclease 1 like 3 protein-coding gene 1 Mesoderm Immune system 0.0952381 0.571429 0.00591133 0.0147333 +Mm Hs CLEC9A Dendritic cells UNQ9341|HEEE9341|CD370|DNGR-1 0.002 C-type lectin domain containing 9A protein-coding gene 1 Mesoderm Immune system 0.0612245 0.452381 0.00131363 0.000193013 +Hs LILRB2 Dendritic cells LIR-2|ILT4|MIR-10|LIR2|CD85d|MIR10 0.002 leukocyte immunoglobulin like receptor B2 protein-coding gene NA Mesoderm Immune system 0.190476 0.0 0.000985222 0.0 +Mm Hs ETV6 Dendritic cells TEL 0.015 ETS variant 6 protein-coding gene 1 Mesoderm Immune system 0.251701 0.238095 0.0394089 0.00720582 +Mm Hs CD163 Dendritic cells MM130|SCARI1 0.005 CD163 molecule protein-coding gene 1 Mesoderm Immune system 0.0952381 0.0 0.00295567 0.00431062 +Mm Hs CXCR4 Dendritic cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.455782 0.047619 0.185878 0.00868558 +Hs CXCL8 Dendritic cells SCYB8|LUCT|LECT|MDNCF|TSG-1|IL-8|NAP-1|3-10C|MONAP|AMCF-I|LYNAP|NAF|b-ENAP|GCP-1|K60|GCP1|IL8 0.02 C-X-C motif chemokine ligand 8 protein-coding gene 1 Mesoderm Immune system 0.360544 0.0 0.107061 0.0 +Mm Hs VSIG4 Dendritic cells Z39IG 0.005 V-set and immunoglobulin domain containing 4 protein-coding gene 1 Mesoderm Immune system 0.204082 0.0 0.00426929 0.0 +Mm Hs NR4A3 Dendritic cells CSMF|MINOR 0.01 nuclear receptor subfamily 4 group A member 3 protein-coding gene 1 Mesoderm Immune system 0.102041 0.214286 0.00788177 0.00900727 +Mm Hs CCR7 Dendritic cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.0544218 0.428571 0.0413793 0.010294 +Mm Hs TRAF1 Dendritic cells EBI6 0.01 TNF receptor associated factor 1 protein-coding gene 1 Mesoderm Immune system 0.0204082 0.0 0.00525452 0.0 +Mm Hs RELB Dendritic cells REL-B 0.015 RELB proto-oncogene, NF-kB subunit protein-coding gene 1 Mesoderm Immune system 0.0612245 0.0 0.0144499 0.0 +Mm Hs BATF3 Dendritic cells JUNDM1|SNFT 0.008 basic leucine zipper ATF-like transcription factor 3 protein-coding gene 1 Mesoderm Immune system 0.0612245 0.904762 0.00656814 0.00469665 +Mm Hs CCL22 Dendritic cells STCP-1|ABCD-1|DC/B-CK|A-152E5.1|MGC34554|SCYA22 0.002 C-C motif chemokine ligand 22 protein-coding gene 1 Mesoderm Immune system 0.00680272 0.452381 0.000656814 0.000900727 +Mm Hs SLAMF7 Dendritic cells CRACC|19A|CS1|CD319 0.013 SLAM family member 7 protein-coding gene 1 Mesoderm Immune system 0.0204082 0.0 0.00689655 0.0 +Mm Hs XCR1 Dendritic cells GPR5|CCXCR1 0.001 X-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0136054 0.0 0.0 0.0 +Mm H2-DMA Dendritic cells NA 0.065 histocompatibility 2, class II, locus DMa protein coding gene 1 Mesoderm Immune system 0.0 0.714286 0.0 0.0754681 +Mm Hs CXCL16 Dendritic cells SR-PSOX|CXCLG16|SRPSOX 0.048 C-X-C motif chemokine ligand 16 protein-coding gene 1 Mesoderm Immune system 0.265306 0.904762 0.0561576 0.0431706 +Mm Hs SCIMP Dendritic cells DTFT5783|UNQ5783|FLJ32580|MGC163426|MGC163428|C17orf87 0.008 SLP adaptor and CSK interacting membrane protein protein-coding gene 1 Mesoderm Immune system 0.0136054 0.0 0.000985222 0.0 +Mm Hs FCGR2B Dendritic cells CD32B 0.031 Fc fragment of IgG receptor IIb protein-coding gene 1 Mesoderm Immune system 0.0748299 0.404762 0.00131363 0.035064 +Mm Hs FGD2 Dendritic cells ZFYVE4 0.017 FYVE, RhoGEF and PH domain containing 2 protein-coding gene NA Mesoderm Immune system 0.176871 0.47619 0.00361248 0.0171782 +Mm Hs RAB7B Dendritic cells MGC9726|MGC16212 0.013 RAB7B, member RAS oncogene family protein-coding gene 1 Mesoderm Immune system 0.0272109 0.0 0.000985222 0.0 +Mm Hs NAAA Dendritic cells ASAHL 0.025 N-acylethanolamine acid amidase protein-coding gene 1 Mesoderm Immune system 0.217687 0.5 0.00426929 0.0266358 +Mm Hs HCK Dendritic cells JTK9 0.031 HCK proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.401361 0.595238 0.0045977 0.0322332 +Mm Hs CD180 Dendritic cells RP105|Ly78|LY64 0.012 CD180 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.333333 0.000985222 0.0133822 +Mm RETNLA Dendritic cells NA 0.004 resistin like alpha protein coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs HFE Dendritic cells HLA-H 0.017 homeostatic iron regulator protein-coding gene NA Mesoderm Immune system 0.0 0.452381 0.000328407 0.020202 +Mm Hs CCR2 Dendritic cells CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.452381 0.0 0.025156 +Mm Hs RYR1 Dendritic cells RYR|PPP1R137|MHS|MHS1|CCO 0.002 ryanodine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00164204 0.0 +Mm Hs ITGAE Dendritic cells CD103|HUMINAE 0.033 integrin subunit alpha E protein-coding gene 1 Mesoderm Immune system 0.047619 0.238095 0.132677 0.00514701 +Mm Hs SEMA4A Dendritic cells SemB|FLJ12287|CORD10|SEMAB 0.013 semaphorin 4A protein-coding gene 1 Mesoderm Immune system 0.047619 0.0 0.00229885 0.0 +Mm Hs DPP4 Dendritic cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.428571 0.0137931 0.020202 +Mm Hs SLAMF8 Dendritic cells BLAME|SBBI42|CD353 0.003 SLAM family member 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00197044 0.0 +Mm Hs CXCR3 Dendritic cells CKR-L2|CMKAR3|IP10-R|MigR|CD183|GPR9 0.005 C-X-C motif chemokine receptor 3 protein-coding gene NA Mesoderm Immune system 0.0 0.285714 0.00558292 0.00398893 +Mm Hs BTLA Dendritic cells BTLA1|CD272 0.001 B and T lymphocyte associated protein-coding gene 1 Mesoderm Immune system 0.0 0.357143 0.000328407 0.000579039 +Mm Hs FLT3 Dendritic cells FLK2|CD135 0.009 fms related tyrosine kinase 3 protein-coding gene 1 Mesoderm Immune system 0.0136054 0.761905 0.000328407 0.00720582 +Mm Hs TLR3 Dendritic cells CD283 0.003 toll like receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00755337 0.0 +Mm H2-M2 Dendritic cells NA 0.002 histocompatibility 2, M region locus 2 protein coding gene 1 Mesoderm Immune system 0.0 0.285714 0.0 0.00173712 +Mm Hs ITGAX Dendritic cells CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.183673 0.166667 0.00821018 0.00482532 +Mm Hs GPR132 Dendritic cells G2A 0.009 G protein-coupled receptor 132 protein-coding gene 1 Mesoderm Immune system 0.00680272 0.595238 0.0 0.00920028 +Mm Hs ADAM19 Dendritic cells MLTNB 0.013 ADAM metallopeptidase domain 19 protein-coding gene 1 Mesoderm Immune system 0.122449 0.238095 0.0190476 0.0107444 +None AMICA1 Dendritic cells NA 0.015 NA NA 1 Mesoderm Immune system 0.0 0.47619 0.0 0.0167921 +Mm Hs AP1S3 Dendritic cells NA 0.003 adaptor related protein complex 1 subunit sigma 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.166667 0.00361248 0.00225182 +Mm Hs ASS1 Dendritic cells CTLN1|ASS 0.048 argininosuccinate synthase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.52381 0.0426929 0.0472882 +Mm Hs ADGRG5 Dendritic cells PGR27|GPR114 0.0 adhesion G protein-coupled receptor G5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000328407 0.000193013 +Mm Hs GPR68 Dendritic cells OGR1 0.0 G protein-coupled receptor 68 protein-coding gene 1 Mesoderm Immune system 0.0 0.0238095 0.0 0.000128675 +Mm H2-EB2 Dendritic cells NA 0.0 histocompatibility 2, class II antigen E beta2 protein coding gene 1 Mesoderm Immune system 0.0 0.142857 0.0 0.000193013 +Mm Hs KIT Dendritic cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0714286 0.00262726 0.0184006 +Mm KLRI1 Dendritic cells NA 0.0 killer cell lectin-like receptor family I member 1 protein coding gene 1 Mesoderm Immune system 0.0 0.0238095 0.0 6.43376e-05 +Mm Hs KMO Dendritic cells NA 0.004 kynurenine 3-monooxygenase protein-coding gene 1 Mesoderm Immune system 0.0 0.119048 0.000328407 0.004954 +Mm Hs P2RY10 Dendritic cells P2Y10 0.004 P2Y receptor family member 10 protein-coding gene 1 Mesoderm Immune system 0.0 0.261905 0.000656814 0.00411761 +Mm Hs RAB30 Dendritic cells NA 0.002 RAB30, member RAS oncogene family protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00394089 0.0 +Mm Hs SEPT6 Dendritic cells KIAA0128|SEPT2|MGC16619|MGC20339 0.06 septin 6 protein-coding gene 1 Mesoderm Immune system 0.190476 0.0 0.120854 0.0 +Mm Hs ZBTB46 Dendritic cells FLJ13502|BZEL|ZNF340|BTBD4 0.0 zinc finger and BTB domain containing 46 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000328407 0.0 +Mm Hs S100A4 Dendritic cells P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.836735 0.0 0.348768 0.0 +Mm Hs CLEC7A Dendritic cells dectin-1|hDectin-1|CD369|SCARE2|CLECSF12 0.03 C-type lectin domain containing 7A protein-coding gene 1 Mesoderm Immune system 0.62585 0.0238095 0.0187192 0.0250917 +Mm Hs AIF1 Dendritic cells IRT-1|AIF-1|Em:AF129756.17|IBA1 0.085 allograft inflammatory factor 1 protein-coding gene 1 Mesoderm Immune system 0.884354 0.880952 0.0945813 0.0742456 +Mm Hs LST1 Dendritic cells B144|D6S49E 0.082 leukocyte specific transcript 1 protein-coding gene 1 Mesoderm Immune system 0.877551 0.166667 0.0689655 0.0752107 +Mm Hs CTSS Dendritic cells NA 0.129 cathepsin S protein-coding gene 1 Mesoderm Immune system 0.911565 1.0 0.0968801 0.124236 +Mm CD209A Dendritic cells NA 0.003 CD209a antigen protein coding gene 1 Mesoderm Immune system 0.0 0.047619 0.0 0.00386026 +Mm CD209B Dendritic cells NA 0.0 CD209b antigen protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 6.43376e-05 +Mm Hs IRF8 Dendritic cells IRF-8|ICSBP|ICSBP1 0.069 interferon regulatory factor 8 protein-coding gene 1 Mesoderm Immune system 0.183673 0.904762 0.0197044 0.0727659 +Mm H2-AB1 Dendritic cells NA 0.087 histocompatibility 2, class II antigen A, beta 1 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.10146 +Mm Hs ADGRE1 Dendritic cells TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene 1 Mesoderm Immune system 0.00680272 0.0238095 0.000328407 0.0413691 +Mm Hs CCL17 Dendritic cells TARC|ABCD-2|SCYA17 0.002 C-C motif chemokine ligand 17 protein-coding gene 1 Mesoderm Immune system 0.0 0.190476 0.0 0.00160844 +Mm Hs CD14 Dendritic cells NA 0.051 CD14 molecule protein-coding gene 1 Mesoderm Immune system 0.278912 0.119048 0.0144499 0.0553304 +Mm Hs CD207 Dendritic cells Langerin|CLEC4K 0.001 CD207 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0238095 0.0 0.00141543 +Mm Hs CD8A Dendritic cells CD8 0.01 CD8a molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0714286 0.0167488 0.00842823 +Mm Hs CX3CR1 Dendritic cells CMKDR1|V28|GPR13|CMKBRL1 0.039 C-X3-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0408163 0.047619 0.000328407 0.0482532 +Mm H2-EB1 Dendritic cells NA 0.066 histocompatibility 2, class II antigen E beta protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0768835 +Mm Hs ITGAM Dendritic cells CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.00680272 0.0 0.00295567 0.0303674 +Mm Hs LY75 Dendritic cells DEC-205|CLEC13B|CD205 0.003 lymphocyte antigen 75 protein-coding gene 1 Mesoderm Immune system 0.0 0.0952381 0.0 0.00418195 +Mm Hs PDCD1LG2 Dendritic cells PD-L2|Btdc|PDL2|bA574F11.2|CD273|B7-DC 0.0 programmed cell death 1 ligand 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0238095 0.0 0.0 +Mm Hs PTPRC Dendritic cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Immune system 0.782313 0.690476 0.188834 0.104613 +Mm Hs SIRPA Dendritic cells SHPS1|SIRP|MYD-1|BIT|SHPS-1|SIRPalpha|CD172a|SIRPalpha2|MFR|SIRP-ALPHA-1|PTPNS1 0.074 signal regulatory protein alpha protein-coding gene 1 Mesoderm Immune system 0.0340136 0.0 0.00492611 0.0 +Hs FCGR3A Dendritic cells CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene 1 Mesoderm Immune system 0.326531 0.0 0.0213465 0.0 +Hs FTL Dendritic cells MGC71996|NBIA3 0.178 ferritin light chain protein-coding gene 1 Mesoderm Immune system 0.993197 0.0 0.935961 0.0 +Hs SERPINA1 Dendritic cells AAT|A1A|PI1|alpha-1-antitrypsin|A1AT|alpha1AT|PI 0.016 serpin family A member 1 protein-coding gene 1 Mesoderm Immune system 0.44898 0.0 0.0676519 0.0 +Mm Hs AXL Dendritic cells UFO|JTK11|Tyro7 0.054 AXL receptor tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.047619 0.047619 0.0571429 0.0524352 +Mm Hs PPP1R14A Dendritic cells CPI-17|PPP1INL 0.07 protein phosphatase 1 regulatory inhibitor subunit 14A protein-coding gene 1 Mesoderm Immune system 0.0136054 0.0238095 0.0778325 0.0705141 +Hs SIGLEC6 Dendritic cells OB-BP1|SIGLEC-6|CD327|CD33L|CD33L1 0.0 sialic acid binding Ig like lectin 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs CD22 Dendritic cells SIGLEC-2|SIGLEC2 0.003 CD22 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00328407 0.00231616 +Mm Hs DAB2 Dendritic cells DOC-2 0.068 DAB2, clathrin adaptor protein protein-coding gene 1 Mesoderm Immune system 0.0748299 0.0238095 0.0466338 0.0739883 +Mm Hs S100A8 Dendritic cells P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.367347 0.0 0.0660098 0.0 +Mm Hs VCAN Dendritic cells PG-M|CSPG2 0.056 versican protein-coding gene 1 Mesoderm Immune system 0.0952381 0.0 0.0968801 0.0 +Hs LYZ Dendritic cells NA 0.008 lysozyme protein-coding gene 1 Mesoderm Immune system 0.442177 0.0 0.0213465 0.0 +Mm Hs ANXA1 Dendritic cells ANX1|LPC1 0.161 annexin A1 protein-coding gene 1 Mesoderm Immune system 0.748299 0.47619 0.341215 0.11806 +Mm Hs FCER1A Dendritic cells FCE1A 0.004 Fc fragment of IgE receptor Ia protein-coding gene 1 Mesoderm Immune system 0.204082 0.0 0.00952381 0.00167278 +Hs C1ORF54 Dendritic cells FLJ23221 0.008 chromosome 1 open reading frame 54 protein-coding gene 1 Mesoderm Immune system 0.122449 0.0 0.0367816 0.0 +Mm Hs CADM1 Dendritic cells NECL2|ST17|BL2|SYNCAM|IGSF4A|Necl-2|SYNCAM1|RA175|TSLC1|IGSF4 0.161 cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.047619 0.428571 0.0738916 0.182462 +Mm Hs CAMK2D Dendritic cells CAMKD 0.052 calcium/calmodulin dependent protein kinase II delta protein-coding gene 1 Mesoderm Immune system 0.047619 0.0 0.0298851 0.0588046 +Mm Hs LGALS3 Dendritic cells MAC-2|GALIG|LGALS2 0.164 galectin 3 protein-coding gene 1 Mesoderm Immune system 0.585034 0.880952 0.295566 0.126295 +Mm Hs NAPSA Dendritic cells NAPA|Kdap 0.054 napsin A aspartic peptidase protein-coding gene 1 Mesoderm Immune system 0.00680272 0.761905 0.00853859 0.0608634 +Mm Hs PLBD1 Dendritic cells FLJ22662 0.03 phospholipase B domain containing 1 protein-coding gene 1 Mesoderm Immune system 0.0680272 0.571429 0.00952381 0.0317828 +Mm Hs RNASE6 Dendritic cells RNaseK6|RNS6 0.024 ribonuclease A family member k6 protein-coding gene 1 Mesoderm Immune system 0.44898 0.0 0.0187192 0.0 +Mm Hs PLAC8 Dendritic cells onzin|C15 0.14 placenta specific 8 protein-coding gene 1 Mesoderm Immune system 0.360544 0.380952 0.155008 0.129705 +Mm IFITM6 Dendritic cells NA 0.02 interferon induced transmembrane protein 6 protein coding gene 1 Mesoderm Immune system 0.0 0.047619 0.0 0.02477 +Mm EAR2 Dendritic cells NA 0.009 eosinophil-associated, ribonuclease A family, member 2 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0108087 +Mm Hs H2AFY Dendritic cells macroH2A1.2 0.385 H2A histone family member Y protein-coding gene 1 Mesoderm Immune system 0.62585 0.785714 0.28046 0.401853 +Mm Hs SLC11A1 Dendritic cells NRAMP|NRAMP1 0.017 solute carrier family 11 member 1 protein-coding gene 1 Mesoderm Immune system 0.0748299 0.0 0.00328407 0.0 +Mm Hs PDPN Dendritic cells T1A-2|Gp38|aggrus|PA2.26 0.062 podoplanin protein-coding gene 1 Mesoderm Immune system 0.0 0.0238095 0.0246305 0.0716078 +Mm Hs S100B Dendritic cells S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Mesoderm Immune system 0.14966 0.0 0.0275862 0.0 +Mm Hs CD28 Dendritic cells NA 0.011 CD28 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00295567 0.0129319 +Mm Hs PPL Dendritic cells NA 0.004 periplakin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00558292 0.00431062 +Mm Hs SLURP1 Dendritic cells ANUP|MDM|ArsB|LY6LS 0.001 secreted LY6/PLAUR domain containing 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs HLA-A Dendritic cells NA 0.126 major histocompatibility complex, class I, A protein-coding gene 1 Mesoderm Immune system 0.993197 0.0 0.679475 0.0 +Hs HLA-B Dendritic cells NA 0.116 major histocompatibility complex, class I, B protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.637767 0.0 +Hs HLA-C Dendritic cells HLA-JY3|D6S204|PSORS1 0.113 major histocompatibility complex, class I, C protein-coding gene 1 Mesoderm Immune system 0.986395 0.0 0.607553 0.0 +Hs HLA-DRB5 Dendritic cells NA 0.011 major histocompatibility complex, class II, DR beta 5 protein-coding gene 1 Mesoderm Immune system 0.387755 0.0 0.0469622 0.0 +Mm Hs SERPINB9 Dendritic cells CAP3|PI9 0.018 serpin family B member 9 protein-coding gene 1 Mesoderm Immune system 0.22449 0.0 0.0236453 0.0 +Mm Hs CLDN8 Distal tubule cells NA 0.004 claudin 8 protein-coding gene 1 Mesoderm Kidney 0.0 0.148936 0.000626566 0.00405458 +Mm Hs SLC12A3 Distal tubule cells NCCT 0.001 solute carrier family 12 member 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs UMOD Distal tubule cells NA 0.0 uromodulin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs JAG1 Distal tubule cells AHD|AWS|HJ1|CD339|AGS|JAGL1 0.027 jagged 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0238095 0.0285107 +Mm Hs CALB1 Distal tubule cells CALB 0.019 calbindin 1 protein-coding gene NA Mesoderm Kidney 0.0 0.638298 0.00125313 0.0216888 +Mm Hs PVALB Distal tubule cells D22S749 0.005 parvalbumin protein-coding gene NA Mesoderm Kidney 0.0 0.319149 0.00344612 0.00489123 +Mm Hs PGAM2 Distal tubule cells PGAM-M 0.012 phosphoglycerate mutase 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.531915 0.0 0.0135796 +Mm Hs WNK4 Distal tubule cells PRKWNK4 0.003 WNK lysine deficient protein kinase 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626566 0.0 +Mm Hs SGMS2 Distal tubule cells MGC26963|SMS2 0.017 sphingomyelin synthase 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0156642 0.0 +Mm Hs SLC16A7 Distal tubule cells MCT2 0.008 solute carrier family 16 member 7 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00814536 0.0 +Mm Hs LHX1 Distal tubule cells LIM-1 0.011 LIM homeobox 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0212766 0.00657895 0.0125499 +Mm Hs ABCA13 Distal tubule cells FLJ33876|FLJ33951 0.001 ATP binding cassette subfamily A member 13 protein-coding gene NA Mesoderm Kidney 0.0 0.191489 0.00250627 0.000257433 +Mm HOXB5OS Distal tubule cells NA 0.001 homeobox B5 and homeobox B6, opposite strand antisense lncRNA gene NA Mesoderm Kidney 0.0 0.12766 0.0 0.00128717 +Mm Hs EMX1 Distal tubule cells NA 0.023 empty spiracles homeobox 1 protein-coding gene NA Mesoderm Kidney 0.0 0.191489 0.0 0.0286395 +Mm Hs TRPM6 Distal tubule cells CHAK2|FLJ22628|HOMG|HSH 0.001 transient receptor potential cation channel subfamily M member 6 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00093985 0.0 +Mm Hs CWH43 Distal tubule cells FLJ21511|CWH43-C|PGAP2IP 0.001 cell wall biogenesis 43 C-terminal homolog protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.00173768 +Mm Hs TRPM7 Distal tubule cells CHAK1|LTRPC7|TRP-PLIK 0.031 transient receptor potential cation channel subfamily M member 7 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00595238 0.0 +Mm Hs UROC1 Distal tubule cells FLJ31300|HMFN0320 0.001 urocanate hydratase 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs TFRC Distal tubule cells CD71|TFR1|p90 0.042 transferrin receptor protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0614035 0.0 +Mm LHX1OS Distal tubule cells NA 0.013 LIM homeobox 1, opposite strand lincRNA gene NA Mesoderm Kidney 0.0 0.0425532 0.0 0.0164114 +Mm Hs TSC22D2 Distal tubule cells KIAA0669|TILZ4a|TILZ4b|TILZ4c 0.015 TSC22 domain family member 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0156642 0.0 +Mm Hs LARP1B Distal tubule cells FLJ10378|DKFZp434K245|DKFZp686E0316|LARP2 0.026 La ribonucleoprotein domain family member 1B protein-coding gene NA Mesoderm Kidney 0.0 0.12766 0.0435464 0.0225254 +Mm Hs CLCNKB Distal tubule cells hClC-Kb 0.002 chloride voltage-gated channel Kb protein-coding gene NA Mesoderm Kidney 0.0 0.489362 0.0 0.00141588 +None GBAS Distal tubule cells NA 0.042 NA NA NA Mesoderm Kidney 0.0 0.170213 0.0 0.0525808 +Mm Hs KLHL3 Distal tubule cells KIAA1129 0.014 kelch like family member 3 protein-coding gene NA Mesoderm Kidney 0.0 0.468085 0.000626566 0.0164757 +Mm Hs KLK1 Distal tubule cells Klk6 0.013 kallikrein 1 protein-coding gene NA Mesoderm Kidney 0.0 0.851064 0.00814536 0.0116489 +Mm Hs KCNJ1 Distal tubule cells Kir1.1|ROMK1 0.002 potassium voltage-gated channel subfamily J member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.723404 0.000626566 0.000450508 +Mm Hs HOXD8 Distal tubule cells HOX4E 0.007 homeobox D8 protein-coding gene NA Mesoderm Kidney 0.0 0.340426 0.018797 0.00353971 +Mm Hs KL Distal tubule cells NA 0.004 klotho protein-coding gene NA Mesoderm Kidney 0.0 0.468085 0.0 0.00334663 +Mm Hs EGF Distal tubule cells NA 0.002 epidermal growth factor protein-coding gene NA Mesoderm Kidney 0.0 0.702128 0.0 6.43583e-05 +Mm Hs TMEM213 Distal tubule cells NA 0.005 transmembrane protein 213 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.000626566 0.0 +Mm KNG2 Distal tubule cells NA 0.005 kininogen 2 protein coding gene NA Mesoderm Kidney 0.0 0.87234 0.0 0.00399022 +Mm Hs TMEM52B Distal tubule cells FLJ31166|C12orf59 0.002 transmembrane protein 52B protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00281955 0.0 +Mm WFDC15B Distal tubule cells NA 0.006 WAP four-disulfide core domain 15B protein coding gene NA Mesoderm Kidney NA NA NA NA +Mm Hs DEFB1 Distal tubule cells HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene NA Mesoderm Kidney 0.0 0.914894 0.0260025 0.00257433 +Mm Hs FXYD2 Distal tubule cells MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.00438596 0.0276741 +Mm Hs USMG5 Distal tubule cells NA 0.022 upregulated during skeletal muscle growth 5 protein coding gene NA Mesoderm Kidney 0.0 0.0 0.023183 0.0 +Mm Hs TRHDE Distal tubule cells PGPEP2|TRH-DE|PAP-II 0.001 thyrotropin releasing hormone degrading enzyme protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00125313 0.0 +Mm KAP Distal tubule cells NA 0.007 kidney androgen regulated protein protein coding gene NA Mesoderm Kidney 0.0 0.574468 0.0 0.00746557 +Mm ACSM2 Distal tubule cells NA 0.004 acyl-CoA synthetase medium-chain family member 2 protein coding gene NA Mesoderm Kidney 0.0 0.106383 0.0 0.00450508 +Mm Hs KCNJ16 Distal tubule cells Kir5.1|BIR9 0.005 potassium voltage-gated channel subfamily J member 16 protein-coding gene 1 Mesoderm Kidney 0.0 0.361702 0.00156642 0.00547046 +Mm Hs RHCG Distal tubule cells RHGK|PDRC2|SLC42A3|C15orf6 0.002 Rh family C glycoprotein protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00219298 0.0 +Mm Hs SOSTDC1 Distal tubule cells DKFZp564D206|USAG1|DAND7 0.009 sclerostin domain containing 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0018797 0.0 +Mm Hs SCNN1A Distal tubule cells ENaCalpha|SCNN1 0.008 sodium channel epithelial 1 alpha subunit protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0106516 0.0 +Mm Hs VDR Distal tubule cells NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00250627 0.0 +Mm Hs WNK1 Distal tubule cells HSAN2|PPP1R167|PRKWNK1|HSN2 0.368 WNK lysine deficient protein kinase 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0952381 0.0 +Mm Hs SLC8A1 Distal tubule cells NCX1 0.002 solute carrier family 8 member A1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00595238 0.0 +Mm Hs AQP2 Distal tubule cells NA 0.001 aquaporin 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0212766 0.000626566 0.000707942 +Mm Hs AVPR2 Distal tubule cells V2R|DIR3|DIR 0.0 arginine vasopressin receptor 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs TH Dopaminergic neurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs SLC6A3 Dopaminergic neurons DAT 0.0 solute carrier family 6 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs FOXA2 Dopaminergic neurons HNF3B 0.009 forkhead box A2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00595238 0.00994546 +Mm Hs KCNJ6 Dopaminergic neurons Kir3.2|GIRK2|KATP2|BIR1|hiGIRK2|KCNJ7 0.002 potassium voltage-gated channel subfamily J member 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0106516 6.41643e-05 +Mm Hs NR4A2 Dopaminergic neurons TINUR|NOT|RNR1|HZF-3|NURR1 0.033 nuclear receptor subfamily 4 group A member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0780075 0.0255374 +Mm Hs LMX1B Dopaminergic neurons NPS1 0.001 LIM homeobox transcription factor 1 beta protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0008983 +Mm Hs CACNA2D2 Dopaminergic neurons KIAA0558 0.027 calcium voltage-gated channel auxiliary subunit alpha2delta 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125313 0.0343279 +Mm Hs CADPS2 Dopaminergic neurons CAPS2 0.004 calcium dependent secretion activator 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00156642 0.00474816 +Mm Hs CHRNA6 Dopaminergic neurons NA 0.003 cholinergic receptor nicotinic alpha 6 subunit protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00397818 +Mm Hs MAPK8IP2 Dopaminergic neurons IB2|JIP2|PRKM8IPL 0.025 mitogen-activated protein kinase 8 interacting protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0315047 +Mm Hs NTN1 Dopaminergic neurons NTN1L 0.007 netrin 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00866218 +Mm Hs PRKCG Dopaminergic neurons PKCC|MGC57564|PKCG|SCA14 0.005 protein kinase C gamma protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00596728 +Hs SCN2A Dopaminergic neurons Nav1.2|HBSCII|SCN2A1|SCN2A2 0.002 sodium voltage-gated channel alpha subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs TENM1 Dopaminergic neurons TEN-M1|TNM|ODZ1 0.013 teneurin transmembrane protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ZIM3 Dopaminergic neurons ZNF657 0.0 zinc finger imprinted 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DDC Dopaminergic neurons AADC 0.014 dopa decarboxylase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.0166185 +Mm Hs SLC18A2 Dopaminergic neurons SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs SLC18A3 Dopaminergic neurons VACHT 0.002 solute carrier family 18 member A3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs NEUROD6 Dopaminergic neurons Atoh2|NEX1M|Math-2|bHLHa2|Nex1 0.087 neuronal differentiation 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00501253 0.108694 +Mm Hs SMAD3 Dopaminergic neurons JV15-2|HsT17436|MADH3 0.008 SMAD family member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0225564 0.0 +Mm Hs PITX3 Dopaminergic neurons ASMD 0.001 paired like homeodomain 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00102663 +Mm Hs CFTR Ductal cells ABC35|TNR-CFTR|CFTR/MRP|CF|ABCC7 0.003 cystic fibrosis transmembrane conductance regulator protein-coding gene 1 Endoderm Pancreas 0.257143 0.0 0.00380108 0.00288739 +Mm Hs HNF1B Ductal cells LFB3|VHNF1|HNF1beta|MODY5|TCF2 0.005 HNF1 homeobox B protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00950269 0.00461983 +Mm Hs KRT20 Ductal cells CK20|K20|MGC35423 0.012 keratin 20 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0152043 0.0117421 +Mm Hs MUC1 Ductal cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Endoderm Pancreas 0.228571 0.0 0.0307254 0.012512 +Mm Hs ONECUT1 Ductal cells HNF-6|HNF6|HNF6A 0.001 one cut homeobox 1 protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.000316756 0.00109079 +Mm Hs AMBP Ductal cells UTI|EDC1|HI30|IATIL|ITILC|ITI|ITIL 0.013 alpha-1-microglobulin/bikunin precursor protein-coding gene 1 Endoderm Pancreas 0.171429 0.0 0.0120367 0.0121912 +Mm Hs HHEX Ductal cells HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0231232 0.0395893 +Mm Hs ANXA4 Ductal cells ANX4 0.06 annexin A4 protein-coding gene 1 Endoderm Pancreas 0.342857 0.0 0.0706367 0.0565287 +Mm Hs SPP1 Ductal cells BSPI|ETA-1|BNSP|OPN 0.057 secreted phosphoprotein 1 protein-coding gene 1 Endoderm Pancreas 0.285714 0.0 0.050681 0.0 +Mm Hs PDX1 Ductal cells IDX-1|STF-1|PDX-1|MODY4|IPF1 0.005 pancreatic and duodenal homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00601837 0.00474816 +Hs SERPINA3 Ductal cells AACT 0.0 serpin family A member 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000316756 0.0 +Mm Hs CFB Ductal cells H2-Bf|BFD|BF 0.001 complement factor B protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00153994 +Mm Hs GDF15 Ductal cells PLAB|MIC-1|PDF|NAG-1|PTGFB 0.014 growth differentiation factor 15 protein-coding gene 1 Endoderm Pancreas 0.628571 0.0 0.050681 0.00307988 +Hs AKR1C3 Ductal cells KIAA0119|DDX|HAKRB|PGFS|HSD17B5 0.007 aldo-keto reductase family 1 member C3 protein-coding gene 1 Endoderm Pancreas 0.371429 0.0 0.038961 0.0 +Mm Hs MMP7 Ductal cells PUMP-1|MPSL1 0.007 matrix metallopeptidase 7 protein-coding gene 1 Endoderm Pancreas 0.657143 0.0 0.0180551 0.00365736 +Mm Hs DEFB1 Ductal cells HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene 1 Endoderm Pancreas 0.4 0.0 0.0218562 0.00532563 +Mm Hs SERPING1 Ductal cells C1IN|C1-INH|HAE1|HAE2|C1NH 0.066 serpin family G member 1 protein-coding gene 1 Endoderm Pancreas 0.285714 0.0 0.0972442 0.0 +Mm Hs TSPAN8 Ductal cells CO-029|TM4SF3 0.047 tetraspanin 8 protein-coding gene 1 Endoderm Pancreas 0.485714 0.0 0.0430789 0.0 +Mm Hs CLDN10 Ductal cells OSP-L|CPETRL3 0.028 claudin 10 protein-coding gene 1 Endoderm Pancreas 0.342857 0.0 0.0202724 0.0302214 +Mm Hs SLPI Ductal cells HUSI-I|BLPI|HUSI|WAP4|WFDC4 0.048 secretory leukocyte peptidase inhibitor protein-coding gene 1 Endoderm Pancreas 0.885714 0.0 0.0861577 0.0 +Mm Hs SERPINA5 Ductal cells PAI3|PROCI|PLANH3|PCI 0.005 serpin family A member 5 protein-coding gene 1 Endoderm Pancreas 0.257143 0.0 0.0237567 0.0 +Mm Hs PIGR Ductal cells NA 0.031 polymeric immunoglobulin receptor protein-coding gene 1 Endoderm Pancreas 0.2 0.0 0.0424454 0.0291306 +Mm Hs CLDN1 Ductal cells SEMP1|ILVASC 0.01 claudin 1 protein-coding gene 1 Endoderm Pancreas 0.228571 0.0 0.0262908 0.00564646 +Mm Hs LGALS4 Ductal cells GAL4 0.032 galectin 4 protein-coding gene 1 Endoderm Pancreas 0.228571 0.0 0.036427 0.0307347 +Mm Hs PERP Ductal cells PIGPC1|dJ496H19.1|KCP1|THW|KRTCAP1 0.077 PERP, TP53 apoptosis effector protein-coding gene 1 Endoderm Pancreas 0.971429 0.0 0.158695 0.0519731 +Mm Hs PDLIM3 Ductal cells NA 0.013 PDZ and LIM domain 3 protein-coding gene 1 Endoderm Pancreas 0.114286 0.0 0.0183719 0.0120629 +Mm Hs WFDC2 Ductal cells HE4|WAP5|dJ461P17.6|EDDM4 0.056 WAP four-disulfide core domain 2 protein-coding gene 1 Endoderm Pancreas 0.685714 0.0 0.0877415 0.0 +Mm Hs SLC3A1 Ductal cells CSNU1|D2H|RBAT|ATR1|NBAT 0.0 solute carrier family 3 member 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000316756 0.0 +Mm Hs AQP1 Ductal cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0180551 0.0424767 +Mm Hs ALDH1A3 Ductal cells RALDH3|ALDH6 0.008 aldehyde dehydrogenase 1 family member A3 protein-coding gene 1 Endoderm Pancreas 0.485714 0.0 0.0297751 0.00327238 +Mm Hs VTCN1 Ductal cells B7-H4|FLJ22418|B7S1|B7X|B7H4 0.0 V-set domain containing T cell activation inhibitor 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000633513 0.0 +Mm Hs KRT19 Ductal cells K19|CK19|K1CS|MGC15366 0.088 keratin 19 protein-coding gene 1 Endoderm Pancreas 0.942857 0.0 0.162179 0.0654475 +Mm Hs TFF1 Ductal cells D21S21|pS2|pNR-2|HP1.A|BCEI 0.006 trefoil factor 1 protein-coding gene 1 Endoderm Pancreas 0.0571429 0.0 0.0199557 0.0 +Mm Hs TFF2 Ductal cells SML1 0.002 trefoil factor 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000316756 0.0 +Mm Hs KRT7 Ductal cells CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Endoderm Pancreas 0.914286 0.0 0.0921761 0.0474174 +Mm Hs CLDN4 Ductal cells CPE-R|WBSCR8|hCPE-R|CPETR|CPETR1 0.047 claudin 4 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.118784 0.0286814 +Mm Hs LAMB3 Ductal cells nicein-125kDa|kalinin-140kDa|BM600-125kDa|LAMNB1 0.017 laminin subunit beta 3 protein-coding gene 1 Endoderm Pancreas 0.4 0.0 0.0497308 0.00943215 +Mm Hs TACSTD2 Ductal cells TROP2|GA733-1|EGP-1|M1S1 0.033 tumor associated calcium signal transducer 2 protein-coding gene 1 Endoderm Pancreas 0.971429 0.0 0.0886918 0.0 +Mm Hs CCL2 Ductal cells MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Endoderm Pancreas 0.371429 0.0 0.0614507 0.0318896 +Hs DCDC2 Ductal cells KIAA1154|DCDC2A|NPHP19|DFNB66 0.003 doublecortin domain containing 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0186886 0.0 +Mm Hs CXCL2 Ductal cells SCYB2|GROb|MIP-2a|MGSA-b|CINC-2a|GRO2 0.041 C-X-C motif chemokine ligand 2 protein-coding gene 1 Endoderm Pancreas 0.285714 0.0 0.0541653 0.0381136 +Mm Hs CTSH Ductal cells ACC-4|ACC-5|ACC4|ACC5|CPSB 0.147 cathepsin H protein-coding gene 1 Endoderm Pancreas 0.542857 0.0 0.104213 0.154187 +Mm Hs S100A10 Ductal cells 42C|CLP11|ANX2LG|CAL1L 0.374 S100 calcium binding protein A10 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.526449 0.0 +Mm Hs MYC Embryonic stem cells c-Myc|bHLHe39|MYCC 0.047 MYC proto-oncogene, bHLH transcription factor protein-coding gene NA Epiblast Zygote 0.0 0.0 0.109023 0.0331321 +Mm Hs FOXD3 Embryonic stem cells Genesis|HFH2 0.0 forkhead box D3 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0 0.000449467 +Mm Hs POU5F1 Embryonic stem cells Oct4|MGC22487|OTF3 0.003 POU class 5 homeobox 1 protein-coding gene 1 Epiblast Zygote 0.0 0.909091 0.000626566 0.00192629 +Mm Hs FUT4 Embryonic stem cells FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0 0.000706305 +Hs CD24 Embryonic stem cells CD24A 0.039 CD24 molecule protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.192043 0.0 +Mm Hs ITGA4 Embryonic stem cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0112782 0.0412868 +Mm Hs CDH1 Embryonic stem cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0416667 0.0565686 +Mm Hs ABCG2 Embryonic stem cells EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene NA Epiblast Zygote 0.0 0.181818 0.00469925 0.0466162 +Mm Hs PODXL Embryonic stem cells PCLP|Gp200|PC 0.04 podocalyxin like protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0410401 0.0398099 +Hs ALPP Embryonic stem cells PALP 0.0 alkaline phosphatase, placental protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0 0.0 +Mm Hs ZIC1 Embryonic stem cells ZIC|ZNF201 0.046 Zic family member 1 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00845865 0.0 +Mm Hs PRDM5 Embryonic stem cells NA 0.001 PR/SET domain 5 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00814536 0.000192629 +Mm Hs ANO6 Embryonic stem cells DKFZp313M0720|TMEM16F 0.012 anoctamin 6 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00845865 0.0130345 +Mm Hs CDK8 Embryonic stem cells K35 0.009 cyclin dependent kinase 8 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00595238 0.00988828 +Mm Hs SLC46A2 Embryonic stem cells Ly110|TSCOT 0.002 solute carrier family 46 member 2 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0 0.0 +Hs TEX19 Embryonic stem cells FLJ35767 0.001 testis expressed 19 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00469925 0.0 +Mm Hs ZSCAN10 Embryonic stem cells ZNF206 0.0 zinc finger and SCAN domain containing 10 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.000313283 0.0 +Mm Hs KCNIP3 Embryonic stem cells DREAM|KCHIP3|CSEN 0.007 potassium voltage-gated channel interacting protein 3 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0 0.00879671 +Mm Hs PCGF2 Embryonic stem cells MEL-18|ZNF144|RNF110 0.005 polycomb group ring finger 2 protein-coding gene NA Epiblast Zygote 0.0 0.909091 0.0147243 0.00186208 +Mm Hs NANOG Embryonic stem cells FLJ12581|FLJ40451 0.002 Nanog homeobox protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0 0.00147682 +Mm Hs GAL Embryonic stem cells GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene NA Epiblast Zygote 0.0 0.0 0.0184837 0.0112367 +Mm Hs PITX2 Embryonic stem cells IGDS|Brx1|Otlx2|IRID2|IHG2|RIEG|RIEG1|RGS 0.01 paired like homeodomain 2 protein-coding gene NA Epiblast Zygote 0.0 0.0909091 0.0109649 0.00860408 +Mm Hs BCL3 Embryonic stem cells D19S37|BCL4 0.012 B cell CLL/lymphoma 3 protein-coding gene NA Epiblast Zygote 0.0 0.636364 0.00877193 0.0127777 +Mm Hs SALL4 Embryonic stem cells dJ1112F19.1|ZNF797 0.015 spalt like transcription factor 4 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0115915 0.0 +Mm DPPA5A Embryonic stem cells NA 0.013 developmental pluripotency associated 5A protein coding gene NA Epiblast Zygote 0.0 1.0 0.0 0.0128419 +Mm Hs TDGF1 Embryonic stem cells CRIPTO|Cripto-1 0.007 teratocarcinoma-derived growth factor 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00814536 0.0 +Mm Hs HOXB5 Embryonic stem cells HOX2A 0.003 homeobox B5 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00501253 0.00237575 +Mm Hs SUMO2 Embryonic stem cells SMT3B|SMT3H2 0.163 small ubiquitin-like modifier 2 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.717105 0.0 +Mm Hs BNIP3 Embryonic stem cells Nip3 0.042 BCL2 interacting protein 3 protein-coding gene NA Epiblast Zygote 0.0 0.0909091 0.162594 0.00661359 +Mm Hs GJC1 Embryonic stem cells CX45|GJA7 0.026 gap junction protein gamma 1 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0112782 0.0290869 +Mm Hs TRIM6 Embryonic stem cells RNF89 0.006 tripartite motif containing 6 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.000626566 0.0 +Mm Hs PUM2 Embryonic stem cells PUMH2|KIAA0235 0.094 pumilio RNA binding family member 2 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0093985 0.113458 +Mm Hs GJB4 Embryonic stem cells CX30.3 0.003 gap junction protein beta 4 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.000626566 0.00378837 +Mm Hs SOX15 Embryonic stem cells SOX27|SOX26|SOX20 0.003 SRY-box 15 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0037594 0.0 +Mm Hs UTF1 Embryonic stem cells NA 0.0 undifferentiated embryonic cell transcription factor 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0 0.0 +Mm Hs GJB1 Embryonic stem cells CX32|CMTX1|CMTX 0.033 gap junction protein beta 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0103383 0.0384615 +Mm Hs LMNA Embryonic stem cells LMN1|CMD1A|LGMD1B 0.201 lamin A/C protein-coding gene 1 Epiblast Zygote 0.0 0.0909091 0.33302 0.167266 +Mm Hs FBXO15 Embryonic stem cells MGC39671|FBX15 0.005 F-box protein 15 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0109649 0.00231154 +Mm Hs PML Embryonic stem cells MYL|TRIM19|RNF71 0.007 promyelocytic leukemia protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.00783208 0.00590728 +Mm Hs THY1 Embryonic stem cells CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0322682 0.0 +Mm Hs KIT Embryonic stem cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Epiblast Zygote 0.0 0.909091 0.00250627 0.0179145 +Mm Hs EPCAM Embryonic stem cells Ly74|TROP1|GA733-2|EGP34|EGP40|EGP-2|KSA|CD326|Ep-CAM|HEA125|KS1/4|MK-1|MH99|MOC31|323/A3|17-1A|TACST-1|CO-17A|M4S1|MIC18|TACSTD1 0.117 epithelial cell adhesion molecule protein-coding gene 1 Epiblast Zygote 0.0 0.818182 0.16886 0.103698 +Mm Hs CD9 Embryonic stem cells BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.27099 0.365738 +Mm Hs ITGB1 Embryonic stem cells CD29|GPIIA|FNRB|MSK12|MDF2 0.276 integrin subunit beta 1 protein-coding gene 1 Epiblast Zygote 0.0 0.818182 0.168546 0.301657 +Hs CD59 Embryonic stem cells 16.3A5|EJ16|EJ30|EL32|G344|p18-20|MIC11|MIN1|MSK21|MIN2|MIN3 0.07 CD59 molecule (CD59 blood group) protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.371554 0.0 +Mm Hs PROM1 Embryonic stem cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00720551 0.024207 +Mm Hs PECAM1 Embryonic stem cells CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Epiblast Zygote 0.0 0.545455 0.0441729 0.0531655 +Mm Hs ITGA6 Embryonic stem cells CD49f 0.059 integrin subunit alpha 6 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0501253 0.0609349 +Mm Hs FZD1 Embryonic stem cells DKFZp564G072 0.01 frizzled class receptor 1 protein-coding gene NA Epiblast Zygote 0.0 0.0 0.00281955 0.012264 +Hs KITLG Embryonic stem cells SCF|Kitl|KL-1|FPH2|SLF|DFNA69 0.001 KIT ligand protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00626566 0.0 +Mm Hs SOX2 Embryonic stem cells NA 0.082 SRY-box 2 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0288221 0.0 +Mm Hs KLF4 Embryonic stem cells EZF|GKLF 0.126 Kruppel like factor 4 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.138784 0.126878 +Mm Hs ZFP42 Embryonic stem cells REX1|ZNF754 0.006 ZFP42 zinc finger protein protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00313283 0.0 +Mm Hs ZFX Embryonic stem cells ZNF926 0.006 zinc finger protein X-linked protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0140977 0.0 +Mm Hs TAF8 Embryonic stem cells FLJ32821|TAF(II)43|TBN 0.001 TATA-box binding protein associated factor 8 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00532581 0.0 +Mm Hs HMGA2 Embryonic stem cells BABL|LIPO|HMGIC 0.038 high mobility group AT-hook 2 protein-coding gene 1 Epiblast Zygote 0.0 0.454545 0.0604637 0.0274817 +Mm Hs NACC1 Embryonic stem cells NAC-1|BEND8|BTBD30|BTBD14B 0.01 nucleus accumbens associated 1 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.00125313 0.0108514 +Mm Hs NR6A1 Embryonic stem cells GCNF1|RTR|CT150|GCNF 0.017 nuclear receptor subfamily 6 group A member 1 protein-coding gene 1 Epiblast Zygote 0.0 0.272727 0.0704887 0.00410941 +Mm Hs STAT3 Embryonic stem cells APRF 0.099 signal transducer and activator of transcription 3 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.149436 0.0 +Mm Hs LEF1 Embryonic stem cells TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0093985 0.0278027 +Mm Hs L1TD1 Embryonic stem cells FLJ10884|ECAT11 0.011 LINE1 type transposase domain containing 1 protein-coding gene 1 Epiblast Zygote 0.0 0.909091 0.0260025 0.0060357 +Hs KHDC3L Embryonic stem cells ECAT1|C6orf221 0.0 KH domain containing 3 like, subcortical maternal complex member protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0 0.0 +Mm Hs GDF3 Embryonic stem cells NA 0.003 growth differentiation factor 3 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.00501253 0.00224734 +Hs DPPA5 Embryonic stem cells Esg1 0.0 developmental pluripotency associated 5 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0 0.0 +Mm Hs DPPA4 Embryonic stem cells FLJ10713 0.007 developmental pluripotency associated 4 protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.0128446 0.00327469 +Mm Hs DPPA2 Embryonic stem cells PESCRG1|CT100 0.003 developmental pluripotency associated 2 protein-coding gene 1 Epiblast Zygote 0.0 0.909091 0.00313283 0.00192629 +Mm Hs DPPA3 Embryonic stem cells Stella|Pgc7 0.002 developmental pluripotency associated 3 protein-coding gene 1 Epiblast Zygote 0.0 0.363636 0.0 0.00173366 +Mm Hs SMAD1 Embryonic stem cells MADR1|JV4-1|MADH1 0.036 SMAD family member 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0153509 0.0 +Mm Hs SMAD5 Embryonic stem cells Dwfc|JV5-1|MADH5 0.019 SMAD family member 5 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0272556 0.0 +Mm Hs SMAD9 Embryonic stem cells SMAD8|SMAD8/9|MADH9 0.002 SMAD family member 9 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00845865 0.0 +Mm Hs SMAD4 Embryonic stem cells DPC4|MADH4 0.018 SMAD family member 4 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00908521 0.0 +Mm Hs SMAD2 Embryonic stem cells MADR2|JV18-1|MADH2 0.024 SMAD family member 2 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0689223 0.0 +Mm Hs SMAD3 Embryonic stem cells JV15-2|HsT17436|MADH3 0.008 SMAD family member 3 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0225564 0.0 +Mm Hs CTNNB1 Embryonic stem cells beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.212406 0.0114293 +Mm Hs HHEX Embryonic stem cells HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Epiblast Zygote 0.0 0.363636 0.0228697 0.0393605 +Mm Hs HES1 Embryonic stem cells FLJ20408|HES-1|Hes1|bHLHb39|HRY 0.129 hes family bHLH transcription factor 1 protein-coding gene 1 Epiblast Zygote 0.0 0.909091 0.145677 0.127071 +Mm Hs ESRRB Embryonic stem cells ERR2|ERRbeta|NR3B2|ERRb|ESRL2|DFNB35 0.002 estrogen related receptor beta protein-coding gene 1 Epiblast Zygote 0.0 1.0 0.000313283 0.00128419 +Mm Hs DNMT3B Embryonic stem cells NA 0.012 DNA methyltransferase 3 beta protein-coding gene 1 Epiblast Zygote 0.0 0.363636 0.0103383 0.0114293 +Mm Hs TRIM28 Embryonic stem cells TIF1B|KAP1|TF1B|RNF96|PPP1R157 0.18 tripartite motif containing 28 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0971178 0.0 +Mm Hs PIWIL1 Embryonic stem cells PIWI|HIWI|CT80.1 0.003 piwi like RNA-mediated gene silencing 1 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0140977 0.0013484 +Mm Hs PIWIL2 Embryonic stem cells HILI|FLJ10351|Mili|CT80 0.005 piwi like RNA-mediated gene silencing 2 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0197368 0.0026968 +Mm Hs PIWIL4 Embryonic stem cells FLJ36156|HIWI2|Miwi2 0.001 piwi like RNA-mediated gene silencing 4 protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.00344612 0.000256838 +Mm Hs LIFR Embryonic stem cells CD118 0.042 LIF receptor alpha protein-coding gene 1 Epiblast Zygote 0.0 0.363636 0.0222431 0.0461667 +Mm Hs IL6ST Embryonic stem cells CD130 0.055 interleukin 6 signal transducer protein-coding gene 1 Epiblast Zygote 0.0 0.0 0.0911654 0.0477077 +Mm ZSCAN4D Embryonic stem cells NA 0.0 zinc finger and SCAN domain containing 4D protein coding gene 1 Epiblast Zygote NA NA NA NA +Mm Hs PECAM1 Endothelial cells CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.798077 0.910156 0.0187824 0.00911116 +Mm Hs ICAM1 Endothelial cells CD54 0.009 intercellular adhesion molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.0865385 0.0768229 0.00323834 0.00654653 +Mm Hs ITGB3 Endothelial cells CD61|GPIIIa|GP3A 0.001 integrin subunit beta 3 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.000323834 0.00128231 +Mm Hs SELE Endothelial cells ESEL|CD62E|ELAM1|ELAM 0.001 selectin E protein-coding gene 1 Mesoderm Vasculature 0.105769 0.0 0.00194301 0.0 +Mm Hs VCAM1 Endothelial cells CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00744819 0.0 +Mm Hs MCAM Endothelial cells MUC18|CD146 0.031 melanoma cell adhesion molecule protein-coding gene 1 Mesoderm Vasculature 0.278846 0.184896 0.0126295 0.0258487 +Mm Hs PROCR Endothelial cells EPCR|CCD41|CD201 0.016 protein C receptor protein-coding gene 1 Mesoderm Vasculature 0.240385 0.0638021 0.0213731 0.0101235 +Mm Hs TEK Endothelial cells TIE2|TIE-2|VMCM1|CD202b|VMCM 0.02 TEK receptor tyrosine kinase protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.0 0.000323834 0.0 +Mm Hs FLT4 Endothelial cells VEGFR3 0.007 fms related tyrosine kinase 4 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.154948 0.000647668 0.00033745 +Mm Hs APLN Endothelial cells apelin|XNPEP2 0.015 apelin protein-coding gene 1 Mesoderm Vasculature 0.25 0.207031 0.00453368 0.00593912 +Mm Hs VWF Endothelial cells F8VWF 0.016 von Willebrand factor protein-coding gene 1 Mesoderm Vasculature 0.711538 0.0 0.00356218 0.0 +Mm Hs NOS3 Endothelial cells ECNOS|eNOS 0.003 nitric oxide synthase 3 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0377604 0.00744819 0.00060741 +Mm Hs THBD Endothelial cells CD141 0.022 thrombomodulin protein-coding gene 1 Mesoderm Vasculature 0.259615 0.0 0.00485751 0.0 +Mm Hs PLVAP Endothelial cells gp68|PV-1|PV1|FELS 0.026 plasmalemma vesicle associated protein protein-coding gene 1 Mesoderm Vasculature 0.394231 0.338542 0.00485751 0.0121482 +Mm Hs ACKR1 Endothelial cells CCBP1|GPD|Dfy|CD234|FY|DARC 0.008 atypical chemokine receptor 1 (Duffy blood group) protein-coding gene 1 Mesoderm Vasculature 0.201923 0.0729167 0.00582902 0.0040494 +Mm Hs SLCO1C1 Endothelial cells OATP-F|OATP1C1|OATP1|SLC21A14 0.032 solute carrier organic anion transporter family member 1C1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs TMEM100 Endothelial cells FLJ10970|FLJ37856 0.021 transmembrane protein 100 protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0 0.00291451 0.0 +Mm Hs ADGRF5 Endothelial cells DKFZp564O1923|KIAA0758|GPR116 0.047 adhesion G protein-coupled receptor F5 protein-coding gene 1 Mesoderm Vasculature 0.346154 0.873698 0.00680052 0.0121482 +Mm ABCB1A Endothelial cells NA 0.023 ATP-binding cassette, sub-family B (MDR/TAP), member 1A protein coding gene 1 Mesoderm Vasculature 0.0 0.5 0.0 0.00465681 +Mm Hs ABCG2 Endothelial cells EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.598958 0.00356218 0.0180873 +Mm Hs PODXL Endothelial cells PCLP|Gp200|PC 0.04 podocalyxin like protein-coding gene 1 Mesoderm Vasculature 0.346154 0.542969 0.0307642 0.0137005 +Mm Hs NOSTRIN Endothelial cells MGC20702 0.025 nitric oxide synthase trafficking protein-coding gene 1 Mesoderm Vasculature 0.384615 0.43099 0.011658 0.00512924 +Mm Hs MFSD2A Endothelial cells FLJ14490|MFSD2 0.02 major facilitator superfamily domain containing 2A protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.294271 0.00777202 0.0095161 +Mm Hs ACVRL1 Endothelial cells HHT2|HHT|ACVRLK1|ORW2 0.03 activin A receptor like type 1 protein-coding gene 1 Mesoderm Vasculature 0.269231 0.53125 0.00388601 0.00823379 +Mm Hs AQP1 Endothelial cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Mesoderm Vasculature 0.173077 0.304688 0.0126295 0.0288857 +Mm Hs MYLK Endothelial cells smMLCK|MYLK1|MLCK1 0.047 myosin light chain kinase protein-coding gene 1 Mesoderm Vasculature 0.0576923 0.0872396 0.0553756 0.0446784 +Mm Hs RASIP1 Endothelial cells FLJ20401|RAIN 0.026 Ras interacting protein 1 protein-coding gene 1 Mesoderm Vasculature 0.163462 0.0 0.000971503 0.0 +Mm Hs FLI1 Endothelial cells SIC-1 0.036 Fli-1 proto-oncogene, ETS transcription factor protein-coding gene 1 Mesoderm Vasculature 0.144231 0.410156 0.00129534 0.0246339 +Mm Hs TIE1 Endothelial cells JTK14|TIE 0.025 tyrosine kinase with immunoglobulin like and EGF like domains 1 protein-coding gene 1 Mesoderm Vasculature 0.413462 0.0 0.00194301 0.0 +Mm Hs APLNR Endothelial cells FLJ90771|APJ|APJR|AGTRL1 0.015 apelin receptor protein-coding gene 1 Mesoderm Vasculature 0.201923 0.295573 0.0103627 0.00047243 +Mm Hs NRP2 Endothelial cells VEGF165R2 0.04 neuropilin 2 protein-coding gene 1 Mesoderm Vasculature 0.336538 0.173177 0.0252591 0.0345549 +Mm Hs ADAMTS1 Endothelial cells C3-C5|METH1|KIAA1346 0.053 ADAM metallopeptidase with thrombospondin type 1 motif 1 protein-coding gene 1 Mesoderm Vasculature 0.115385 0.35026 0.0540803 0.0390767 +Mm Hs RPRM Endothelial cells FLJ90327|REPRIMO 0.039 reprimo, TP53 dependent G2 arrest mediator homolog protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00291451 0.0 +Mm Hs FABP4 Endothelial cells A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Vasculature 0.0961538 0.273438 0.00744819 0.0207869 +Mm Hs GPIHBP1 Endothelial cells LOC338328|GPI-HBP1 0.017 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 protein-coding gene 1 Mesoderm Vasculature 0.134615 0.334635 0.000323834 0.00330701 +Mm Hs FHL2 Endothelial cells SLIM3|DRAL 0.043 four and a half LIM domains 2 protein-coding gene 1 Mesoderm Vasculature 0.173077 0.00260417 0.101684 0.0299656 +Mm Hs LOX Endothelial cells NA 0.017 lysyl oxidase protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.00260417 0.0152202 0.0176149 +Mm Hs KLK1 Endothelial cells Klk6 0.013 kallikrein 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00841969 0.0149153 +Mm Hs ADORA2A Endothelial cells RDC8|ADORA2 0.01 adenosine A2a receptor protein-coding gene NA Mesoderm Vasculature 0.0 0.197917 0.0 0.00296956 +Mm Hs ARAP3 Endothelial cells FLJ21065|DRAG1|CENTD3 0.009 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.214844 0.0 0.00026996 +Mm Hs ARHGEF15 Endothelial cells KIAA0915|Vsm-RhoGEF|ARGEF15|FLJ13791|MGC44868 0.01 Rho guanine nucleotide exchange factor 15 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.166667 0.0 0.00465681 +Mm Hs CARD10 Endothelial cells CARMA3|BIMP1 0.002 caspase recruitment domain family member 10 protein-coding gene 1 Mesoderm Vasculature 0.0192308 0.00651042 0.000323834 0.00175474 +Mm Hs CLEC14A Endothelial cells C14orf27 0.024 C-type lectin domain containing 14A protein-coding gene 1 Mesoderm Vasculature 0.769231 0.445312 0.00420984 0.00188972 +Mm Hs DLL4 Endothelial cells NA 0.007 delta like canonical Notch ligand 4 protein-coding gene 1 Mesoderm Vasculature 0.0769231 0.144531 0.000323834 0.0006749 +Mm Hs ESM1 Endothelial cells NA 0.006 endothelial cell specific molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.269231 0.0299479 0.00356218 0.00357697 +Mm EXOC3L Endothelial cells NA 0.0 exocyst complex component 3-like protein coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs GIMAP5 Endothelial cells HIMAP3|IAN5|IAN4L1 0.016 GTPase, IMAP family member 5 protein-coding gene 1 Mesoderm Vasculature 0.0 0.164062 0.0 0.0122832 +Mm Hs GJA4 Endothelial cells CX37 0.02 gap junction protein alpha 4 protein-coding gene NA Mesoderm Vasculature 0.115385 0.09375 0.0100389 0.0180873 +Mm Hs MMRN2 Endothelial cells EndoGlyx-1|FLJ13465|EMILIN3 0.022 multimerin 2 protein-coding gene 1 Mesoderm Vasculature 0.259615 0.497396 0.0 0.00182223 +Mm Hs NOTCH4 Endothelial cells NA 0.003 notch 4 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0664062 0.00226684 0.00040494 +Mm Hs NPR1 Endothelial cells GUCY2A|ANPa|ANPRA|NPRA 0.009 natriuretic peptide receptor 1 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.110677 0.00161917 0.0060741 +Mm Hs PRKCH Endothelial cells PKC-L|PKCL|PRKCL 0.012 protein kinase C eta protein-coding gene 1 Mesoderm Vasculature 0.105769 0.117188 0.0200777 0.00519673 +Mm Hs RASGRP3 Endothelial cells KIAA0846|GRP3|CalDAG-GEFIII 0.025 RAS guanyl releasing protein 3 protein-coding gene 1 Mesoderm Vasculature 0.0769231 0.0 0.00712435 0.0 +Mm Hs ROBO4 Endothelial cells FLJ20798|MRB|ECSM4 0.013 roundabout guidance receptor 4 protein-coding gene 1 Mesoderm Vasculature 0.125 0.0 0.000323834 0.0 +Mm Hs SCARF1 Endothelial cells SREC|KIAA0149|SREC1 0.004 scavenger receptor class F member 1 protein-coding gene 1 Mesoderm Vasculature 0.0673077 0.0 0.000323834 0.0 +Mm Hs SOX18 Endothelial cells NA 0.012 SRY-box 18 protein-coding gene 1 Mesoderm Vasculature 0.365385 0.0 0.00809585 0.0 +Mm Hs SOX7 Endothelial cells NA 0.011 SRY-box 7 protein-coding gene 1 Mesoderm Vasculature 0.0961538 0.0 0.00323834 0.0 +Mm Hs SPNS2 Endothelial cells NA 0.002 sphingolipid transporter 2 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs THSD1 Endothelial cells TMTSP 0.008 thrombospondin type 1 domain containing 1 protein-coding gene 1 Mesoderm Vasculature 0.0576923 0.0 0.00323834 0.0 +Mm Hs APOLD1 Endothelial cells FLJ25138|DKFZP434F0318 0.03 apolipoprotein L domain containing 1 protein-coding gene 1 Mesoderm Vasculature 0.0769231 0.509115 0.00323834 0.0117433 +Mm Hs EMP1 Endothelial cells TMP|CL-20 0.076 epithelial membrane protein 1 protein-coding gene 1 Mesoderm Vasculature 0.75 0.259115 0.0913212 0.0591213 +Mm Hs CD36 Endothelial cells SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Vasculature 0.115385 0.28776 0.0317358 0.0315179 +Mm Hs RNASE1 Endothelial cells RAC1|RNS1 0.022 ribonuclease A family member 1, pancreatic protein-coding gene 1 Mesoderm Vasculature 0.807692 0.0 0.0660622 0.0 +Mm Hs CTGF Endothelial cells IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Mesoderm Vasculature 0.644231 0.00130208 0.0812824 0.0130256 +Mm Hs HYAL2 Endothelial cells LuCa-2|LUCA2 0.031 hyaluronoglucosaminidase 2 protein-coding gene 1 Mesoderm Vasculature 0.567308 0.153646 0.0540803 0.0143754 +Mm Hs CLEC4G Endothelial cells UNQ431|LSECtin 0.001 C-type lectin domain family 4 member G protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0130208 0.0 0.00026996 +Mm Hs GPR182 Endothelial cells hrhAMR|G10D|AM-R|ADMR 0.005 G protein-coupled receptor 182 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0950521 0.00356218 0.00040494 +Mm Hs F8 Endothelial cells FVIII|DXS1253E|HEMA|F8C 0.003 coagulation factor VIII protein-coding gene 1 Mesoderm Vasculature 0.182692 0.046875 0.0 0.00020247 +Mm Hs RBP7 Endothelial cells CRBPIV 0.009 retinol binding protein 7 protein-coding gene 1 Mesoderm Vasculature 0.326923 0.0 0.0119819 0.0 +Mm Hs CALCRL Endothelial cells CGRPR|CRLR 0.017 calcitonin receptor like receptor protein-coding gene 1 Mesoderm Vasculature 0.605769 0.24349 0.00518135 0.00425187 +Mm Hs FOXF1 Endothelial cells FREAC1|FKHL5 0.008 forkhead box F1 protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.09375 0.00777202 0.00371195 +Mm Hs CASZ1 Endothelial cells FLJ20321|ZNF693|castor|cst|SRG 0.016 castor zinc finger 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0403646 0.0 0.0193022 +Mm Hs AQP7 Endothelial cells AQP9|AQPap|AQP7L 0.005 aquaporin 7 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0325521 0.00939119 0.00330701 +Mm Hs TCF15 Endothelial cells EC2|PARAXIS|bHLHa40 0.006 transcription factor 15 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0 0.000323834 0.0 +Mm Hs CD300LG Endothelial cells Trem4|CLM9 0.008 CD300 molecule like family member g protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.174479 0.0 0.000944861 +Mm Hs BTNL9 Endothelial cells FLJ32535|BTN8 0.004 butyrophilin like 9 protein-coding gene 1 Mesoderm Vasculature 0.115385 0.0729167 0.0 0.00026996 +Mm Hs MEOX2 Endothelial cells GAX 0.004 mesenchyme homeobox 2 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0325521 0.00420984 0.00256462 +Mm Hs ERG Endothelial cells erg-3 0.01 ERG, ETS transcription factor protein-coding gene 1 Mesoderm Vasculature 0.240385 0.1875 0.000323834 0.00215968 +Mm Hs HEXIM1 Endothelial cells CLP-1|MAQ1 0.019 hexamethylene bisacetamide inducible 1 protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.0455729 0.0297927 0.0162651 +Mm Hs GLYCAM1 Endothelial cells NA 0.004 glycosylation dependent cell adhesion molecule 1 (pseudogene) pseudogene 1 Mesoderm Vasculature 0.0 0.0286458 0.0 0.00391442 +Mm Hs CD55 Endothelial cells TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Vasculature 0.326923 0.0351562 0.119171 0.0188972 +Mm Hs MMRN1 Endothelial cells ECM|EMILIN4|GPIa*|MMRN 0.005 multimerin 1 protein-coding gene 1 Mesoderm Vasculature 0.134615 0.0703125 0.00485751 0.00047243 +Mm Hs C7 Endothelial cells NA 0.003 complement C7 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0 0.0145725 0.0013498 +Mm Hs RAMP3 Endothelial cells NA 0.014 receptor activity modifying protein 3 protein-coding gene 1 Mesoderm Vasculature 0.423077 0.0 0.000971503 0.0 +Mm Hs VEGFC Endothelial cells NA 0.005 vascular endothelial growth factor C protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0142487 0.0 +Mm Hs GJA5 Endothelial cells CX40 0.002 gap junction protein alpha 5 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.00390625 0.00129534 0.00155227 +Mm Hs HEY1 Endothelial cells HESR-1|CHF2|HESR1|HRT-1|CHF-2|HERP2|bHLHb31 0.01 hes related family bHLH transcription factor with YRPW motif 1 protein-coding gene 1 Mesoderm Vasculature 0.201923 0.0390625 0.0113342 0.00620908 +Mm Hs RND1 Endothelial cells Rho6|ARHS|RHOS 0.007 Rho family GTPase 1 protein-coding gene 1 Mesoderm Vasculature 0.105769 0.0 0.00161917 0.0 +Mm Hs BDP1 Endothelial cells TFIIIB150|TFC5|KIAA1689|HSA238520|KIAA1241|TFNR|TAF3B1 0.037 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0208333 0.102332 0.0172775 +Mm Hs CD46 Endothelial cells TRA2.10|MGC26544|MIC10 0.014 CD46 molecule protein-coding gene 1 Mesoderm Vasculature 0.134615 0.0 0.0767487 0.000944861 +Mm Hs MEOX1 Endothelial cells NA 0.005 mesenchyme homeobox 1 protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.0924479 0.000647668 0.0020247 +Mm Hs CCL19 Endothelial cells ELC|MIP-3b|exodus-3|CKb11|SCYA19 0.002 C-C motif chemokine ligand 19 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0104167 0.00161917 0.0020247 +Mm CLCA3A1 Endothelial cells NA 0.003 chloride channel accessory 3A1 protein coding gene 1 Mesoderm Vasculature 0.0 0.0559896 0.0 0.00060741 +Mm Hs MADCAM1 Endothelial cells MACAM1 0.001 mucosal vascular addressin cell adhesion molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.0673077 0.0247396 0.0 0.00026996 +Mm Hs CYP1B1 Endothelial cells CP1B|GLC3A 0.016 cytochrome P450 family 1 subfamily B member 1 protein-coding gene 1 Mesoderm Vasculature 0.0673077 0.00911458 0.0485751 0.00897618 +Mm Hs IRX3 Endothelial cells IRX-1 0.015 iroquois homeobox 3 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0195312 0.0110104 0.0155227 +Mm Hs BIRC2 Endothelial cells cIAP1|hiap-2|MIHB|RNF48|c-IAP1|API1 0.015 baculoviral IAP repeat containing 2 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0078125 0.0359456 0.0111359 +Mm Hs LYVE1 Endothelial cells LYVE-1|XLKD1 0.012 lymphatic vessel endothelial hyaluronan receptor 1 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.128906 0.00420984 0.00762638 +Mm Hs SEMA3D Endothelial cells coll-2|Sema-Z2 0.005 semaphorin 3D protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0 0.000971503 0.0 +Mm SLCO1A4 Endothelial cells NA 0.014 solute carrier organic anion transporter family, member 1a4 protein coding gene 1 Mesoderm Vasculature NA NA NA NA +Mm Hs EMCN Endothelial cells MUC14 0.043 endomucin protein-coding gene 1 Mesoderm Vasculature 0.653846 0.742188 0.0100389 0.0116083 +Mm Hs WFDC1 Endothelial cells PS20 0.024 WAP four-disulfide core domain 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0152202 0.0 +Mm Hs ADGRL4 Endothelial cells ETL|ELTD1 0.042 adhesion G protein-coupled receptor L4 protein-coding gene 1 Mesoderm Vasculature 0.778846 0.75 0.0126295 0.00796383 +Mm Hs VWA1 Endothelial cells FLJ22215|VWA-1|WARP 0.034 von Willebrand factor A domain containing 1 protein-coding gene 1 Mesoderm Vasculature 0.269231 0.0 0.0145725 0.0 +Mm Hs ECE1 Endothelial cells ECE 0.062 endothelin converting enzyme 1 protein-coding gene 1 Mesoderm Vasculature 0.259615 0.740885 0.0197539 0.0372545 +Mm Hs PTPRB Endothelial cells PTPB 0.041 protein tyrosine phosphatase, receptor type B protein-coding gene 1 Mesoderm Vasculature 0.336538 0.872396 0.000647668 0.00526422 +Mm Hs CLDN5 Endothelial cells CPETRL1|AWAL|TMVCF 0.054 claudin 5 protein-coding gene 1 Mesoderm Vasculature 0.971154 0.880208 0.0210492 0.0128231 +None SDPR Endothelial cells NA 0.044 NA NA 1 Mesoderm Vasculature NA NA NA NA +Mm CAR4 Endothelial cells NA 0.032 carbonic anhydrase 4 protein coding gene 1 Mesoderm Vasculature 0.0 0.389323 0.0 0.0217993 +Mm Hs TBX1 Endothelial cells VCF 0.003 T-box 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.000971503 0.0 +Mm Hs SEMA7A Endothelial cells H-Sema-L|CD108|SEMAL 0.006 semaphorin 7A (John Milton Hagen blood group) protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.000323834 0.0 +Mm Hs FOXF2 Endothelial cells FREAC2|FKHL6 0.016 forkhead box F2 protein-coding gene 1 Mesoderm Vasculature 0.0192308 0.230469 0.000647668 0.00863873 +Mm Hs PDGFB Endothelial cells SSV|SIS 0.01 platelet derived growth factor subunit B protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.207031 0.0 0.00249713 +Mm Hs ECSCR Endothelial cells ECSM2|ARIA 0.047 endothelial cell surface expressed chemotaxis and apoptosis regulator protein-coding gene 1 Mesoderm Vasculature 0.855769 0.654948 0.00906736 0.0195046 +Mm Hs ELK3 Endothelial cells ERP|SAP2 0.034 ELK3, ETS transcription factor protein-coding gene 1 Mesoderm Vasculature 0.269231 0.515625 0.0148964 0.0122157 +Mm Hs CDH5 Endothelial cells 7B4|CD144 0.043 cadherin 5 protein-coding gene 1 Mesoderm Vasculature 0.644231 0.825521 0.00453368 0.00742391 +Mm Hs PLEC Endothelial cells PLTN|EBS1|PLEC1 0.056 plectin protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.174479 0.0310881 0.0569616 +Mm Hs STAB1 Endothelial cells KIAA0246|STAB-1|FEEL-1|CLEVER-1|FELE-1|FEX1|SCARH2 0.018 stabilin 1 protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0 0.00161917 0.0 +Mm Hs TGFBR2 Endothelial cells TBRII|TBR-ii|MFS2 0.044 transforming growth factor beta receptor 2 protein-coding gene 1 Mesoderm Vasculature 0.528846 0.0 0.0229922 0.0 +Mm Hs CD93 Endothelial cells C1qRP|C1qR(P)|dJ737E23.1|CDw93|ECSM3|MXRA4|C1QR1 0.044 CD93 molecule protein-coding gene 1 Mesoderm Vasculature 0.471154 0.705729 0.00388601 0.0149153 +Mm Hs CXCL1 Endothelial cells SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0989583 0.0463083 0.026996 +Mm LY6C1 Endothelial cells NA 0.054 lymphocyte antigen 6 complex, locus C1 protein coding gene 1 Mesoderm Vasculature 0.0 0.809896 0.0 0.0280759 +Mm Hs RGS5 Endothelial cells NA 0.043 regulator of G protein signaling 5 protein-coding gene 1 Mesoderm Vasculature NA NA NA NA +Mm Hs SLC7A5 Endothelial cells E16|D16S469E|MPE16 0.043 solute carrier family 7 member 5 protein-coding gene 1 Mesoderm Vasculature 0.0673077 0.0 0.0297927 0.0 +Mm Hs ENG Endothelial cells END|HHT1|CD105|ORW1|ORW 0.058 endoglin protein-coding gene 1 Mesoderm Vasculature 0.846154 0.865885 0.0395078 0.0174799 +Mm Hs KDR Endothelial cells FLK1|VEGFR|VEGFR2|CD309 0.041 kinase insert domain receptor protein-coding gene 1 Mesoderm Vasculature 0.25 0.799479 0.0110104 0.00755889 +Mm Hs SLC2A1 Endothelial cells DYT18|DYT9|GLUT1|GLUT|HTLVR|CSE 0.062 solute carrier family 2 member 1 protein-coding gene 1 Mesoderm Vasculature 0.0576923 0.0 0.0563472 0.0 +Mm Hs EGFL7 Endothelial cells ZNEU1 0.092 EGF like domain multiple 7 protein-coding gene 1 Mesoderm Vasculature 0.913462 0.996094 0.0880829 0.0387393 +Mm Hs FLT1 Endothelial cells VEGFR1|FLT 0.051 fms related tyrosine kinase 1 protein-coding gene 1 Mesoderm Vasculature 0.615385 0.894531 0.0262306 0.0112033 +Mm Hs EPAS1 Endothelial cells MOP2|PASD2|HIF2A|HLF|bHLHe73 0.076 endothelial PAS domain protein 1 protein-coding gene 1 Mesoderm Vasculature 0.576923 0.858073 0.0391839 0.0429237 +Mm Hs EDNRB Endothelial cells ETB|HSCR2|HSCR 0.057 endothelin receptor type B protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.0989583 0.0204016 0.0658028 +Mm Hs KCNJ8 Endothelial cells Kir6.1 0.017 potassium voltage-gated channel subfamily J member 8 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0794271 0.00194301 0.0172775 +Mm Hs CD82 Endothelial cells R2|IA4|TSPAN27|ST6|KAI1 0.097 CD82 molecule protein-coding gene 1 Mesoderm Vasculature 0.0480769 0.247396 0.0637953 0.0975231 +Mm Hs CHST1 Endothelial cells KSGal6ST 0.032 carbohydrate sulfotransferase 1 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0963542 0.0132772 0.0346224 +Mm Hs PLAC8 Endothelial cells onzin|C15 0.14 placenta specific 8 protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0455729 0.169041 0.134778 +Mm Hs TSPAN8 Endothelial cells CO-029|TM4SF3 0.047 tetraspanin 8 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0495466 0.0 +Mm Hs ETS1 Endothelial cells FLJ10768|ETS-1 0.095 ETS proto-oncogene 1, transcription factor protein-coding gene 1 Mesoderm Vasculature 0.259615 0.709635 0.0314119 0.0780185 +Mm Hs CD34 Endothelial cells NA 0.071 CD34 molecule protein-coding gene 1 Mesoderm Vasculature 0.538462 0.752604 0.0236399 0.044341 +Mm Hs PDPN Endothelial cells T1A-2|Gp38|aggrus|PA2.26 0.062 podoplanin protein-coding gene 1 Mesoderm Vasculature 0.0288462 0.0403646 0.0233161 0.0730917 +Mm Hs PROX1 Endothelial cells NA 0.028 prospero homeobox 1 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0494792 0.0100389 0.0315853 +Mm Hs EHD3 Endothelial cells PAST3 0.017 EH domain containing 3 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0598958 0.0 0.0193022 +Mm Hs SRGN Endothelial cells PPG 0.236 serglycin protein-coding gene 1 Mesoderm Vasculature 0.798077 0.0 0.314767 0.0 +Mm Hs S100A10 Endothelial cells 42C|CLP11|ANX2LG|CAL1L 0.374 S100 calcium binding protein A10 protein-coding gene 1 Mesoderm Vasculature 0.971154 0.0 0.516839 0.0 +Mm Hs CLIC4 Endothelial cells DKFZP566G223|CLIC4L|P64H1|huH1|p64H1 0.152 chloride intracellular channel 4 protein-coding gene 1 Mesoderm Vasculature 0.451923 0.746094 0.0634715 0.141257 +Mm LY6A Endothelial cells NA 0.098 lymphocyte antigen 6 complex, locus A protein coding gene 1 Mesoderm Vasculature 0.0 0.65625 0.0 0.0907066 +Mm Hs USHBP1 Endothelial cells MCC2|AIEBP|FLJ38709 0.001 USH1 protein network component harmonin binding protein 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs MYF6 Endothelial cells MRF4|bHLHc4 0.0 myogenic factor 6 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.000323834 0.00013498 +Mm Hs OIT3 Endothelial cells LZP|FLJ39116 0.0 oncoprotein induced transcript 3 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0117188 0.0 0.0 +Mm Hs IL1A Endothelial cells IL1F1|IL-1A|IL1-ALPHA|IL1 0.006 interleukin 1 alpha protein-coding gene 1 Mesoderm Vasculature 0.0 0.00130208 0.00582902 0.006749 +Mm Hs BMP2 Endothelial cells BMP2A 0.008 bone morphogenetic protein 2 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0169271 0.00874352 0.00728892 +Mm Hs C1QTNF1 Endothelial cells CTRP1|ZSIG37|FLJ90694 0.002 C1q and TNF related 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.00260417 0.00388601 0.0020247 +Mm Hs PCDH12 Endothelial cells VE-cadherin-2 0.003 protocadherin 12 protein-coding gene 1 Mesoderm Vasculature 0.0576923 0.0729167 0.0 0.00013498 +Mm Hs DPP4 Endothelial cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Mesoderm Vasculature 0.0 0.015625 0.013601 0.0215968 +Mm Hs IGFBP7 Endothelial cells MAC25|IGFBP-7|FSTL2 0.172 insulin like growth factor binding protein 7 protein-coding gene 1 Mesoderm Vasculature 0.913462 0.889323 0.216321 0.125599 +Mm Hs PALMD Endothelial cells FLJ20271|PALML|C1orf11 0.026 palmdelphin protein-coding gene 1 Mesoderm Vasculature 0.461538 0.403646 0.0123057 0.00749139 +Mm Hs POSTN Endothelial cells OSF-2|PN|periostin 0.033 periostin protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0299479 0.0226684 0.0349598 +Mm Hs BMX Endothelial cells PSCTK3 0.003 BMX non-receptor tyrosine kinase protein-coding gene 1 Mesoderm Vasculature 0.125 0.0143229 0.00194301 0.00182223 +Mm Hs SLC38A5 Endothelial cells SN2|JM24 0.02 solute carrier family 38 member 5 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0 0.0223446 0.0 +Mm Hs XDH Endothelial cells XOR|XO 0.011 xanthine dehydrogenase protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00518135 0.0 +Mm Hs SPARC Endothelial cells ON 0.307 secreted protein acidic and cysteine rich protein-coding gene 1 Mesoderm Vasculature 0.884615 0.0 0.208873 0.0 +Mm Hs MGLL Endothelial cells HU-K5|MGL 0.064 monoglyceride lipase protein-coding gene 1 Mesoderm Vasculature 0.307692 0.22526 0.0563472 0.0567591 +Mm Hs SLC9A3R2 Endothelial cells TKA-1|NHERF-2|E3KARP 0.078 SLC9A3 regulator 2 protein-coding gene 1 Mesoderm Vasculature 0.740385 0.0 0.0569948 0.0 +Mm Hs RGCC Endothelial cells bA157L14.2|RGC-32|RGC32|C13orf15 0.14 regulator of cell cycle protein-coding gene 1 Mesoderm Vasculature 0.423077 0.0 0.118523 0.0 +Mm Hs ICAM2 Endothelial cells CD102 0.035 intercellular adhesion molecule 2 protein-coding gene 1 Mesoderm Vasculature 0.0 0.611979 0.0 0.0128906 +Mm Hs MGP Endothelial cells NA 0.082 matrix Gla protein protein-coding gene 1 Mesoderm Vasculature 0.596154 0.166667 0.100389 0.0683674 +Mm Hs SPARCL1 Endothelial cells MAST9 0.156 SPARC like 1 protein-coding gene 1 Mesoderm Vasculature 0.557692 0.0 0.0867876 0.0 +Mm Hs TM4SF1 Endothelial cells M3S1 0.118 transmembrane 4 L six family member 1 protein-coding gene 1 Mesoderm Vasculature 0.961538 0.0 0.150259 0.0 +Mm Hs ID1 Endothelial cells dJ857M17.1.2|bHLHb24 0.149 inhibitor of DNA binding 1, HLH protein protein-coding gene 1 Mesoderm Vasculature 0.769231 0.824219 0.190738 0.0923939 +Hs ADIRF Endothelial cells APM2|AFRO|C10orf116 0.0 adipogenesis regulatory factor protein-coding gene 1 Mesoderm Vasculature NA NA NA NA +Mm Hs CD9 Endothelial cells BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Mesoderm Vasculature 0.634615 0.43099 0.258744 0.362826 +Mm Hs SRPX Endothelial cells ETX1 0.014 sushi repeat containing protein X-linked protein-coding gene 1 Mesoderm Vasculature 0.221154 0.0 0.0139249 0.0 +Mm Hs ID3 Endothelial cells HEIR-1|bHLHb25 0.245 inhibitor of DNA binding 3, HLH protein protein-coding gene 1 Mesoderm Vasculature 0.923077 0.971354 0.206282 0.203887 +Mm Hs CAV1 Endothelial cells NA 0.077 caveolin 1 protein-coding gene 1 Mesoderm Vasculature 0.807692 0.690104 0.0981218 0.0355673 +Mm Hs GNG11 Endothelial cells GNGT11 0.138 G protein subunit gamma 11 protein-coding gene 1 Mesoderm Vasculature 1.0 0.964844 0.0867876 0.102855 +Mm Hs HSPG2 Endothelial cells perlecan|PRCAN|SJS1 0.042 heparan sulfate proteoglycan 2 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.398438 0.0 0.03388 +Hs CCL14 Endothelial cells HCC-1|HCC-3|NCC-2|SCYL2|CKb1|MCIF|SCYA14 0.0 C-C motif chemokine ligand 14 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs CLEC1B Endothelial cells CLEC2 0.003 C-type lectin domain family 1 member B protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0117188 0.000647668 0.00283458 +Hs FCN2 Endothelial cells P35|FCNL|EBP-37|ficolin-2 0.0 ficolin 2 protein-coding gene 1 Mesoderm Vasculature 0.0192308 0.0 0.000323834 0.0 +Mm Hs S100A13 Endothelial cells NA 0.229 S100 calcium binding protein A13 protein-coding gene 1 Mesoderm Vasculature 0.730769 0.0 0.146049 0.0 +Hs FCN3 Endothelial cells FCNH|HAKA1 0.001 ficolin 3 protein-coding gene 1 Mesoderm Vasculature 0.0961538 0.0 0.00129534 0.0 +Mm Hs CRHBP Endothelial cells CRF-BP|CRFBP 0.003 corticotropin releasing hormone binding protein protein-coding gene 1 Mesoderm Vasculature 0.0865385 0.0 0.00388601 0.00256462 +Mm Hs IFI27 Endothelial cells P27|FAM14D|ISG12 0.15 interferon alpha inducible protein 27 protein-coding gene 1 Mesoderm Vasculature 0.740385 0.30599 0.0835492 0.153472 +Hs CCL23 Endothelial cells Ckb-8|MPIF-1|MIP-3|CKb8|SCYA23 0.0 C-C motif chemokine ligand 23 protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0 0.000647668 0.0 +Mm Hs SGK1 Endothelial cells SGK 0.096 serum/glucocorticoid regulated kinase 1 protein-coding gene 1 Mesoderm Vasculature 0.211538 0.0 0.0440415 0.0 +Mm Hs DNASE1L3 Endothelial cells DNAS1L3|LSD 0.015 deoxyribonuclease 1 like 3 protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0703125 0.00906736 0.0134305 +Mm Hs LIFR Endothelial cells CD118 0.042 LIF receptor alpha protein-coding gene 1 Mesoderm Vasculature 0.346154 0.179688 0.0113342 0.0394817 +Hs PCAT19 Endothelial cells LINC01190|LOC100505495 0.005 prostate cancer associated transcript 19 non-coding RNA 1 Mesoderm Vasculature 0.75 0.0 0.00809585 0.0 +Mm Hs CDKN1C Endothelial cells P57|BWCR|BWS 0.097 cyclin dependent kinase inhibitor 1C protein-coding gene 1 Mesoderm Vasculature 0.0 0.354167 0.0485751 0.0958359 +Mm Hs INMT Endothelial cells NA 0.016 indolethylamine N-methyltransferase protein-coding gene 1 Mesoderm Vasculature 0.0384615 0.0325521 0.00874352 0.0158602 +Mm Hs PTGDS Endothelial cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Mesoderm Vasculature 0.0769231 0.00911458 0.0576425 0.0575015 +Mm Hs TIMP3 Endothelial cells NA 0.147 TIMP metallopeptidase inhibitor 3 protein-coding gene 1 Mesoderm Vasculature 0.759615 0.0 0.140868 0.0 +Mm Hs GPM6A Endothelial cells GPM6 0.241 glycoprotein M6A protein-coding gene 1 Mesoderm Vasculature 0.00961538 0.0950521 0.0239637 0.306337 +Mm Hs FAM167B Endothelial cells MGC10820|C1orf90 0.008 family with sequence similarity 167 member B protein-coding gene 1 Mesoderm Vasculature 0.240385 0.135417 0.000971503 0.00060741 +Mm Hs LTC4S Endothelial cells MGC33147 0.037 leukotriene C4 synthase protein-coding gene 1 Mesoderm Vasculature 0.0961538 0.0481771 0.00485751 0.0446784 +Mm Hs STAB2 Endothelial cells DKFZP434E0321|FELL|STAB-2|HARE|FEEL-2|SCARH1 0.003 stabilin 2 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0 +Mm Hs ITGA5 Endothelial cells (aorta) CD49e|FNRA 0.016 integrin subunit alpha 5 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.0184837 0.0161176 +Mm Hs TMTC2 Endothelial cells (aorta) DKFZp762A217 0.002 transmembrane and tetratricopeptide repeat containing 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00250627 0.0 +Mm Hs NR1D1 Endothelial cells (aorta) ear-1|hRev|Rev-ErbAalpha|REVERBA|REVERBalpha|THRAL 0.005 nuclear receptor subfamily 1 group D member 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.333333 0.000626566 0.00642137 +Mm Hs HFE Endothelial cells (aorta) HLA-H 0.017 homeostatic iron regulator protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.000313283 0.0209979 +Mm Hs PKN3 Endothelial cells (aorta) PKNbeta|UTDP4-1 0.001 protein kinase N3 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.000313283 0.000321069 +Mm Hs SULT1A1 Endothelial cells (aorta) P-PST|STP1 0.012 sulfotransferase family 1A member 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0203634 0.0 +Mm Hs TMTC1 Endothelial cells (aorta) ARG99|OLF|FLJ31400|FLJ41625 0.005 transmembrane and tetratricopeptide repeat containing 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00689223 0.0 +Mm Hs SHE Endothelial cells (aorta) NA 0.006 Src homology 2 domain containing E protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00438596 0.0 +Mm Hs ITGBL1 Endothelial cells (aorta) TIED 0.004 integrin subunit beta like 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.333333 0.0 0.00430232 +Mm Hs GRASP Endothelial cells (aorta) Tamalin 0.011 general receptor for phosphoinositides 1 associated scaffold protein protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.000626566 0.0128427 +Mm Hs ENPP4 Endothelial cells (aorta) NPP4|KIAA0879 0.01 ectonucleotide pyrophosphatase/phosphodiesterase 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.00156642 0.01143 +Mm Hs ARHGEF15 Endothelial cells (aorta) KIAA0915|Vsm-RhoGEF|ARGEF15|FLJ13791|MGC44868 0.01 Rho guanine nucleotide exchange factor 15 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00125313 0.0120722 +Mm Hs TMEM184B Endothelial cells (aorta) HS5O6A|DKFZP586A1024|FM08|C22orf5 0.015 transmembrane protein 184B protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0159774 0.0 +Mm Hs FOXC2 Endothelial cells (aorta) MFH-1|FKHL14 0.003 forkhead box C2 protein-coding gene NA Mesoderm Vasculature 0.0 0.333333 0.00814536 0.00218327 +Mm Hs DHH Endothelial cells (aorta) HHG-3|MGC35145 0.002 desert hedgehog protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.0 0.0028254 +Mm Hs DENND5B Endothelial cells (aorta) MGC24039 0.013 DENN domain containing 5B protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.00595238 0.0147049 +Mm Hs KAZALD1 Endothelial cells (aorta) FKSG40|FKSG28 0.009 Kazal type serine peptidase inhibitor domain 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.000313283 0.0104668 +Mm Hs FGD5 Endothelial cells (aorta) ZFYVE23|FLJ39957|FLJ00274 0.007 FYVE, RhoGEF and PH domain containing 5 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.00093985 0.00815514 +Mm Hs FAS Endothelial cells (aorta) CD95|APO-1|FAS1|APT1|TNFRSF6 0.011 Fas cell surface death receptor protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0147243 0.0104026 +Mm Hs ITGB4 Endothelial cells (aorta) CD104 0.013 integrin subunit beta 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.0140977 0.0133565 +Mm Hs EMILIN1 Endothelial cells (aorta) DKFZp586M121|gp115 0.028 elastin microfibril interfacer 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.0297619 0.0271624 +Mm Hs MICAL2 Endothelial cells (aorta) KIAA0750 0.008 microtubule associated monooxygenase, calponin and LIM domain containing 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0100251 0.00764143 +Mm Hs NKX2-3 Endothelial cells (aorta) NKX2.3|CSX3|NKX4-3|NKX2C 0.003 NK2 homeobox 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.333333 0.00438596 0.00263276 +Mm Hs STXBP6 Endothelial cells (aorta) amisyn|HSPC156 0.014 syntaxin binding protein 6 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0140977 0.0 +Mm Hs SYNPO Endothelial cells (aorta) KIAA1029 0.009 synaptopodin protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0093985 0.0 +Mm Hs ATP2A3 Endothelial cells (aorta) SERCA3 0.01 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.0109649 0.00950363 +Mm Hs GIMAP4 Endothelial cells (aorta) HIMAP4|FLJ11110|IMAP4|IAN1 0.043 GTPase, IMAP family member 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.0573308 0.0398767 +None SQRDL Endothelial cells (aorta) NA 0.015 NA NA NA Mesoderm Vasculature NA NA NA NA +Mm Hs CMKLR1 Endothelial cells (aorta) RVER1 0.003 chemerin chemokine-like receptor 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.000313283 0.0028254 +Mm Hs ITGA9 Endothelial cells (aorta) RLC|ITGA4L|ALPHA-RLC 0.004 integrin subunit alpha 9 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0 0.00436653 +Mm Hs SMAD6 Endothelial cells (aorta) HsT17432 0.005 SMAD family member 6 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00093985 0.0 +Mm Hs EFNB2 Endothelial cells (aorta) LERK5|Htk-L|HTKL|MGC126226|MGC126227|MGC126228|EPLG5 0.016 ephrin B2 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0291353 0.0136775 +Mm Hs LOX Endothelial cells (aorta) NA 0.017 lysyl oxidase protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0150376 0.0165029 +Mm Hs FZD4 Endothelial cells (aorta) CD344 0.007 frizzled class receptor 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.000626566 0.00802671 +Mm Hs NTN1 Endothelial cells (aorta) NTN1L 0.007 netrin 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.0 0.00802671 +Mm Hs NPR1 Endothelial cells (aorta) GUCY2A|ANPa|ANPRA|NPRA 0.009 natriuretic peptide receptor 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.0018797 0.0106595 +Mm Hs ARL4D Endothelial cells (aorta) ARF4L 0.014 ADP ribosylation factor like GTPase 4D protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.0363409 0.007513 +Mm Hs HEY2 Endothelial cells (aorta) bHLHb32|HERP1|HESR2 0.004 hes related family bHLH transcription factor with YRPW motif 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0150376 0.00102742 +Mm Hs HYAL2 Endothelial cells (aorta) LuCa-2|LUCA2 0.031 hyaluronoglucosaminidase 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.070802 0.020741 +Mm Hs FKBP7 Endothelial cells (aorta) FKBP23 0.031 FK506 binding protein 7 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0184837 0.0315931 +Mm Hs NXN Endothelial cells (aorta) FLJ12614|NRX 0.022 nucleoredoxin protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0191103 0.0224748 +Mm Hs PDIA5 Endothelial cells (aorta) FLJ30401 0.011 protein disulfide isomerase family A member 5 protein-coding gene NA Mesoderm Vasculature 0.0 0.333333 0.00469925 0.0125859 +Mm Hs APH1B Endothelial cells (aorta) PSFL|APH-1B|DKFZp564D0372 0.007 aph-1 homolog B, gamma-secretase subunit protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0357143 0.00102742 +Mm GSTT1 Endothelial cells (aorta) NA 0.022 glutathione S-transferase theta 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0 0.0274835 +Mm Hs SOX18 Endothelial cells (aorta) NA 0.012 SRY-box 18 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0197368 0.0 +Mm Hs WBP1L Endothelial cells (aorta) FLJ20154|OPAL1|C10orf26 0.014 WW domain binding protein 1 like protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0037594 0.0 +Mm Hs LAMB2 Endothelial cells (aorta) NPHS5|LAMS 0.019 laminin subunit beta 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.916667 0.0131579 0.0203557 +Mm Hs CHST12 Endothelial cells (aorta) C4S-2|C4ST2 0.023 carbohydrate sulfotransferase 12 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0266291 0.0179798 +Mm Hs P3H3 Endothelial cells (aorta) GRCB|HSU47926|LEPREL2 0.014 prolyl 3-hydroxylase 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.00438596 0.0166313 +Mm Hs KLK10 Endothelial cells (aorta) NES1 0.004 kallikrein related peptidase 10 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.00219298 0.00366018 +Mm Hs MALL Endothelial cells (aorta) BENE 0.008 mal, T cell differentiation protein like protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00281955 0.00886149 +Mm Hs CLEC1A Endothelial cells (aorta) CLEC1|MGC34328 0.007 C-type lectin domain family 1 member A protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00156642 0.007513 +Mm Hs MARVELD1 Endothelial cells (aorta) MGC4415|GB14|FLJ23440|FLJ22343|bA548K23.8|MRVLDC1 0.007 MARVEL domain containing 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.0100251 0.00642137 +Mm Hs FAM198B Endothelial cells (aorta) FLJ38155|DKFZp434L142|ENED|C4orf18 0.011 family with sequence similarity 198 member B protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.00501253 0.0118795 +Mm Hs THBD Endothelial cells (aorta) CD141 0.022 thrombomodulin protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0131579 0.0 +Mm Hs NOS3 Endothelial cells (aorta) ECNOS|eNOS 0.003 nitric oxide synthase 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00720551 0.0018622 +Mm Hs TNS2 Endothelial cells (aorta) KIAA1075|C1-TEN|TENC1 0.007 tensin 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00313283 0.0 +Mm Hs ATL2 Endothelial cells (aorta) ARL6IP2 0.013 atlastin GTPase 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00438596 0.0148976 +Mm Hs ACKR3 Endothelial cells (aorta) GPR159|CMKOR1|CXCR7 0.01 atypical chemokine receptor 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.00657895 0.0110448 +Mm Hs COL4A4 Endothelial cells (aorta) CA44 0.007 collagen type IV alpha 4 chain protein-coding gene NA Mesoderm Vasculature 0.0 0.583333 0.00250627 0.00764143 +Mm Hs CALCRL Endothelial cells (aorta) CGRPR|CRLR 0.017 calcitonin receptor like receptor protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0247494 0.0156681 +Mm CAR8 Endothelial cells (aorta) NA 0.013 carbonic anhydrase 8 protein coding gene NA Mesoderm Vasculature 0.0 0.583333 0.0 0.0156039 +Mm Hs COL4A3 Endothelial cells (aorta) NA 0.006 collagen type IV alpha 3 chain protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.000626566 0.00661401 +Mm Hs PER3 Endothelial cells (aorta) NA 0.025 period circadian regulator 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.000313283 0.0308226 +Mm Hs STAB1 Endothelial cells (aorta) KIAA0246|STAB-1|FEEL-1|CLEVER-1|FELE-1|FEX1|SCARH2 0.018 stabilin 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00250627 0.0 +Mm Hs CYP1B1 Endothelial cells (aorta) CP1B|GLC3A 0.016 cytochrome P450 family 1 subfamily B member 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.5 0.0491855 0.00860464 +Mm Hs EPHX2 Endothelial cells (aorta) NA 0.009 epoxide hydrolase 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0056391 0.00963206 +Mm Hs KLK8 Endothelial cells (aorta) HNP|TADG14|ovasin|PRSS19 0.016 kallikrein related peptidase 8 protein-coding gene NA Mesoderm Vasculature 0.0 0.416667 0.0 0.0197136 +None SSFA2 Endothelial cells (aorta) NA 0.011 NA NA NA Mesoderm Vasculature 0.0 0.0 0.0234962 0.0 +Mm Hs BACE2 Endothelial cells (aorta) CEAP1|DRAP|ALP56|AEPLC 0.018 beta-secretase 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0494987 0.011109 +Mm Hs BMP6 Endothelial cells (aorta) VGR1|VGR 0.004 bone morphogenetic protein 6 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.0 0.00391704 +Mm ADH1 Endothelial cells (aorta) NA 0.017 alcohol dehydrogenase 1 (class I) protein coding gene NA Mesoderm Vasculature 0.0 0.75 0.0 0.0211905 +Mm H2-Q6 Endothelial cells (aorta) NA 0.023 histocompatibility 2, Q region locus 6 protein coding gene NA Mesoderm Vasculature 0.0 0.75 0.0 0.0272908 +Mm Hs SULF1 Endothelial cells (aorta) KIAA1077|SULF-1|hSulf-1 0.013 sulfatase 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0175439 0.0 +Mm Hs CPQ Endothelial cells (aorta) LDP|PGCP 0.03 carboxypeptidase Q protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.0131579 0.0342259 +Mm Hs PI16 Endothelial cells (aorta) MGC45378|dJ90K10.5|MSMBBP|CD364 0.011 peptidase inhibitor 16 protein-coding gene NA Mesoderm Vasculature 0.0 1.0 0.00219298 0.0123932 +Mm Hs AMIGO2 Endothelial cells (aorta) ALI1|DEGA 0.004 adhesion molecule with Ig like domain 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.666667 0.00250627 0.00333911 +Mm Hs PTPRJ Endothelial cells (aorta) DEP1|HPTPeta|CD148 0.011 protein tyrosine phosphatase, receptor type J protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.000313283 0.0133565 +Mm Hs TRIM47 Endothelial cells (aorta) GOA|RNF100 0.02 tripartite motif containing 47 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0137845 0.0 +Mm Hs LMCD1 Endothelial cells (aorta) NA 0.01 LIM and cysteine rich domains 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.916667 0.0253759 0.00597187 +Mm Hs PDE3A Endothelial cells (aorta) CGI-PDE 0.01 phosphodiesterase 3A protein-coding gene NA Mesoderm Vasculature 0.0 0.916667 0.000626566 0.0113658 +Mm Hs BMX Endothelial cells (aorta) PSCTK3 0.003 BMX non-receptor tyrosine kinase protein-coding gene 1 Mesoderm Vasculature 0.0 0.833333 0.00595238 0.00179798 +Mm Hs PROCR Endothelial cells (aorta) EPCR|CCD41|CD201 0.016 protein C receptor protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.0285088 0.0121364 +Mm Hs SMOC1 Endothelial cells (aorta) NA 0.006 SPARC related modular calcium binding 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00595238 0.0 +Mm Hs CRACR2B Endothelial cells (aorta) MGC45840|EFCAB4A 0.016 calcium release activated channel regulator 2B protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.00657895 0.0179798 +Mm Hs GJA5 Endothelial cells (aorta) CX40 0.002 gap junction protein alpha 5 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.00156642 0.00102742 +Mm Hs BMP4 Endothelial cells (aorta) BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.833333 0.0241228 0.0159892 +Mm Hs SOD3 Endothelial cells (aorta) EC-SOD 0.027 superoxide dismutase 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0614035 0.0 +Mm Hs ADH7 Endothelial cells (aorta) ADH-4 0.006 alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide protein-coding gene NA Mesoderm Vasculature 0.0 0.916667 0.00438596 0.00558659 +Mm Hs PCOLCE2 Endothelial cells (aorta) PCPE2 0.017 procollagen C-endopeptidase enhancer 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.75 0.0103383 0.0187504 +Mm Hs PTGIS Endothelial cells (aorta) PGIS|CYP8A1 0.019 prostaglandin I2 synthase protein-coding gene NA Mesoderm Vasculature 0.0 1.0 0.00250627 0.0213832 +Mm Hs ACE Endothelial cells (aorta) ACE1|CD143|DCP1 0.022 angiotensin I converting enzyme protein-coding gene NA Mesoderm Vasculature 0.0 1.0 0.0256892 0.0208695 +Mm Hs GXYLT2 Endothelial cells (aorta) GLT8D4 0.01 glucoside xylosyltransferase 2 protein-coding gene NA Mesoderm Vasculature 0.0 1.0 0.00344612 0.0102742 +Mm GKN3 Endothelial cells (aorta) NA 0.004 gastrokine 3 protein coding gene NA Mesoderm Vasculature 0.0 0.916667 0.0 0.00398125 +Mm Hs CYTL1 Endothelial cells (aorta) C17|C4orf4 0.012 cytokine like 1 protein-coding gene NA Mesoderm Vasculature 0.0 1.0 0.0278822 0.00725615 +Mm Hs EHD3 Endothelial cells (aorta) PAST3 0.017 EH domain containing 3 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.0 0.0213189 +Mm Hs ABCG2 Endothelial cells (blood brain barrier) EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00469925 0.0467116 +Mm Hs GFAP Endothelial cells (blood brain barrier) FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0056391 0.0149503 +Mm Hs GPR37L1 Endothelial cells (blood brain barrier) ETBR-LP-2 0.041 G protein-coupled receptor 37 like 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00438596 0.0506898 +Mm Hs SLC13A4 Endothelial cells (blood brain barrier) SUT-1|SUT1 0.004 solute carrier family 13 member 4 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0018797 0.0 +Mm Hs SLC19A1 Endothelial cells (blood brain barrier) FOLT|RFC1 0.015 solute carrier family 19 member 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00125313 0.0 +Mm Hs SLC23A2 Endothelial cells (blood brain barrier) SVCT2|KIAA0238|YSPL2|SLC23A1 0.007 solute carrier family 23 member 2 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.000313283 0.0 +Mm Hs SLC38A3 Endothelial cells (blood brain barrier) SN1 0.018 solute carrier family 38 member 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00125313 0.0 +Mm Hs TNFRSF19 Endothelial cells (blood brain barrier) TAJ-alpha|TROY|TAJ|TRADE 0.017 TNF receptor superfamily member 19 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00156642 0.0 +Mm Hs TNFRSF21 Endothelial cells (blood brain barrier) DR6|CD358 0.047 TNF receptor superfamily member 21 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.037594 0.0 +Mm Hs FOXF2 Endothelial cells (blood brain barrier) FREAC2|FKHL6 0.016 forkhead box F2 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00125313 0.0195701 +Mm Hs FOXL2 Endothelial cells (blood brain barrier) BPES1|BPES 0.0 forkhead box L2 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0 0.00044915 +Mm Hs FOXQ1 Endothelial cells (blood brain barrier) HFH1 0.026 forkhead box Q1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00093985 0.0325313 +Mm Hs LEF1 Endothelial cells (blood brain barrier) TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0093985 0.0277831 +Mm Hs PPARD Endothelial cells (blood brain barrier) NUC1|NUCII|FAAR|NR1C2 0.009 peroxisome proliferator activated receptor delta protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0018797 0.0104588 +Mm ZFP551 Endothelial cells (blood brain barrier) NA 0.0 zinc fingr protein 551 protein coding gene NA Mesoderm Vasculature NA NA NA NA +Mm Hs ZIC3 Endothelial cells (blood brain barrier) HTX|ZNF203|HTX1 0.01 Zic family member 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.000626566 0.0 +Mm Hs ALCAM Endothelial cells (blood brain barrier) CD166|MEMD 0.0 activated leukocyte cell adhesion molecule protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0545113 0.0852101 +Mm Hs GFRA3 Enteric glia cells GFRa-3 0.005 GDNF family receptor alpha 3 protein-coding gene 1 Endoderm GI tract 0.833333 0.0 0.00094162 0.00558229 +Mm Hs MPZ Enteric glia cells HMSNIB|CMT2I|CMT2J|CMT1|CMT1B 0.002 myelin protein zero protein-coding gene NA Endoderm GI tract 1.0 0.0 0.000313873 0.0017966 +Mm Hs LGI4 Enteric glia cells NA 0.002 leucine rich repeat LGI family member 4 protein-coding gene NA Endoderm GI tract 0.833333 0.0 0.00282486 0.00128329 +Mm Hs RGS16 Enteric glia cells A28-RGS14|RGS-r 0.01 regulator of G protein signaling 16 protein-coding gene NA Endoderm GI tract 0.833333 0.0 0.0188324 0.0 +Mm Hs ALDH1A1 Enteric glia cells RALDH1|PUMB1|ALDH1 0.039 aldehyde dehydrogenase 1 family member A1 protein-coding gene NA Endoderm GI tract 1.0 0.0 0.0863151 0.0287456 +Mm Hs L1CAM Enteric glia cells CD171|HSAS1|SPG1|HSAS|MIC5 0.018 L1 cell adhesion molecule protein-coding gene NA Endoderm GI tract 0.666667 0.0 0.000313873 0.0213667 +Mm Hs CXCL14 Enteric glia cells BRAK|NJAC|bolekine|Kec|MIP-2g|BMAC|SCYB14 0.049 C-X-C motif chemokine ligand 14 protein-coding gene NA Endoderm GI tract 0.166667 0.0 0.0423729 0.0483157 +Mm Hs DKK3 Enteric glia cells REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene NA Endoderm GI tract 1.0 0.0 0.0357815 0.0354187 +Mm Hs INTS6 Enteric glia cells DICE1|HDB|Notchl2|DBI-1|DDX26A|DDX26 0.034 integrator complex subunit 6 protein-coding gene NA Endoderm GI tract 0.833333 0.0 0.116133 0.0166827 +Mm Hs DHRS3 Enteric glia cells retSDR1|Rsdr1|RDH17|SDR16C1 0.082 dehydrogenase/reductase 3 protein-coding gene NA Endoderm GI tract 1.0 0.0 0.142498 0.0693616 +Mm Hs SOX10 Enteric glia cells DOM|WS4|WS2E 0.04 SRY-box 10 protein-coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs GFAP Enteric glia cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00564972 0.0149503 +Mm Hs S100B Enteric glia cells S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Endoderm GI tract 1.0 0.0 0.0313873 0.0 +Mm Hs NOS2 Enteric glia cells iNOS|HEP-NOS|NOS2A 0.001 nitric oxide synthase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00156937 0.000384986 +Mm Hs FOXD3 Enteric glia cells Genesis|HFH2 0.0 forkhead box D3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.00044915 +Mm Hs ALDH1A3 Enteric glia cells RALDH3|ALDH6 0.008 aldehyde dehydrogenase 1 family member A3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0348399 0.00327238 +Mm Hs SLC18A2 Enteric glia cells SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00125549 0.0 +Mm Hs HIVEP3 Enteric neurons KRC|KBP1|KBP-1|SHN3|FLJ16752|KIAA1555|ZAS3|Schnurri-3|ZNF40C 0.007 human immunodeficiency virus type I enhancer binding protein 3 protein-coding gene NA Endoderm GI tract 0.0 0.388889 0.00438596 0.00693775 +Mm Hs PLEKHA5 Enteric neurons KIAA1686|FLJ10667 0.026 pleckstrin homology domain containing A5 protein-coding gene NA Endoderm GI tract 0.0 0.555556 0.052005 0.018051 +Mm Hs IGF2BP3 Enteric neurons IMP-3|CT98 0.03 insulin like growth factor 2 mRNA binding protein 3 protein-coding gene NA Endoderm GI tract 0.0 0.277778 0.0018797 0.0366802 +Mm Hs ARHGAP26 Enteric neurons GRAF|KIAA0621|OPHN1L|OPHN1L1 0.016 Rho GTPase activating protein 26 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0112782 0.016702 +Mm Hs TTBK2 Enteric neurons KIAA0847|SCA11 0.011 tau tubulin kinase 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00657895 0.0 +Mm Hs ASTN1 Enteric neurons ASTN 0.013 astrotactin 1 protein-coding gene NA Endoderm GI tract 0.0 0.277778 0.0 0.0162523 +Mm Hs CACNA1E Enteric neurons Cav2.3|BII|CACH6|CACNL1A6 0.023 calcium voltage-gated channel subunit alpha1 E protein-coding gene NA Endoderm GI tract 0.0 0.277778 0.0018797 0.0276868 +Mm Hs TUB Enteric neurons rd5 0.004 tubby bipartite transcription factor protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00125313 0.0 +Mm Hs FILIP1 Enteric neurons FILIP|KIAA1275 0.006 filamin A interacting protein 1 protein-coding gene NA Endoderm GI tract 0.0 0.5 0.0109649 0.00436821 +Mm Hs GCNT2 Enteric neurons IGNT|NAGCT1|bA421M1.1|bA360O19.2|ULG3|NACGT1|II|GCNT5|CCAT 0.015 glucosaminyl (N-acetyl) transferase 2 (I blood group) protein-coding gene NA Endoderm GI tract 0.0 0.444444 0.0109649 0.0155457 +Mm Hs VEZT Enteric neurons DKFZP761C241 0.017 vezatin, adherens junctions transmembrane protein protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0206767 0.0 +Mm Hs RET Enteric neurons CDHF12|RET51|CDHR16|HSCR1|MEN2A|MTC1|MEN2B 0.007 ret proto-oncogene protein-coding gene NA Endoderm GI tract 0.0 0.0 0.000626566 0.0 +Mm Hs AHDC1 Enteric neurons DJ159A19.3|RP1-159A19.1 0.009 AT-hook DNA binding motif containing 1 protein-coding gene NA Endoderm GI tract 0.0 0.388889 0.00156642 0.00982848 +Mm Hs MAP6 Enteric neurons KIAA1878|STOP|FLJ41346|MAP6-N 0.012 microtubule associated protein 6 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.012218 0.0120126 +Mm Hs RGMB Enteric neurons FLJ90406|DRAGON 0.009 repulsive guidance molecule BMP co-receptor b protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00626566 0.0 +Mm Hs FBXO7 Enteric neurons FBX7|Fbx|PARK15 0.046 F-box protein 7 protein-coding gene NA Endoderm GI tract 0.0 0.5 0.176378 0.0159311 +Mm Hs PPP2R5B Enteric neurons FLJ35411|B56B|PR61B|B56beta 0.015 protein phosphatase 2 regulatory subunit B'beta protein-coding gene NA Endoderm GI tract 0.0 0.611111 0.000313283 0.0177941 +Mm Hs SNX21 Enteric neurons dJ337O18.4|SNX-L|C20orf161 0.014 sorting nexin family member 21 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0018797 0.0 +Mm Hs FSTL5 Enteric neurons DKFZp566D234|KIAA1263 0.008 follistatin like 5 protein-coding gene NA Endoderm GI tract 0.0 0.5 0.00125313 0.00944305 +Mm Hs LIX1 Enteric neurons Lft|C5orf11 0.01 limb and CNS expressed 1 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.00689223 0.0091861 +Mm Hs RGS3 Enteric neurons C2PA|FLJ20370|PDZ-RGS3 0.009 regulator of G protein signaling 3 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0225564 0.0 +Mm Hs CYTH3 Enteric neurons GRP1|ARNO3|cytohesin-3|PSCD3 0.01 cytohesin 3 protein-coding gene NA Endoderm GI tract 0.0 0.777778 0.00626566 0.0103424 +Mm Hs TSHZ1 Enteric neurons NY-CO-33|SDCCAG33 0.015 teashirt zinc finger homeobox 1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00469925 0.0 +Mm Hs STXBP5 Enteric neurons tomosyn|LLGL3 0.004 syntaxin binding protein 5 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00281955 0.0 +Mm Hs ATF5 Enteric neurons NA 0.032 activating transcription factor 5 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0260025 0.0325689 +Mm Hs DMKN Enteric neurons ZD52F10 0.032 dermokine protein-coding gene NA Endoderm GI tract 0.0 0.444444 0.0645363 0.0190146 +Mm Hs CACNA1B Enteric neurons Cav2.2|CACNN|CACNL1A5 0.016 calcium voltage-gated channel subunit alpha1 B protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0 0.0197854 +Mm Hs PIK3CA Enteric neurons PI3K 0.017 phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha protein-coding gene NA Endoderm GI tract 0.0 0.777778 0.000626566 0.0206205 +Mm Hs ZDHHC2 Enteric neurons ZNF372|DHHC2 0.015 zinc finger DHHC-type containing 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0056391 0.0 +Mm Hs MYL1 Enteric neurons NA 0.003 myosin light chain 1 protein-coding gene NA Endoderm GI tract 0.0 0.388889 0.000626566 0.00244106 +Mm Hs EML5 Enteric neurons HuEMAP-2 0.01 echinoderm microtubule associated protein like 5 protein-coding gene NA Endoderm GI tract 0.0 0.833333 0.0 0.0111133 +Mm Hs MFSD6 Enteric neurons FLJ20160 0.017 major facilitator superfamily domain containing 6 protein-coding gene NA Endoderm GI tract 0.0 0.888889 0.00344612 0.0199782 +Mm Hs SCN7A Enteric neurons Nav2.1|Nav2.2|NaG|SCN6A 0.017 sodium voltage-gated channel alpha subunit 7 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00814536 0.0 +Mm Hs ARHGEF28 Enteric neurons RGNEF|p190RhoGEF 0.008 Rho guanine nucleotide exchange factor 28 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0018797 0.00860795 +Mm Hs HAND2 Enteric neurons dHand|Thing2|Hed|bHLHa26 0.004 heart and neural crest derivatives expressed 2 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0093985 0.00115629 +Mm Hs VSTM2L Enteric neurons dJ1118M15.2|C20orf102 0.011 V-set and transmembrane domain containing 2 like protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00501253 0.0 +Mm Hs FAM19A5 Enteric neurons TAFA-5 0.014 family with sequence similarity 19 member A5, C-C motif chemokine like protein-coding gene NA Endoderm GI tract 0.0 0.277778 0.000313283 0.0174086 +Mm Hs EFNA5 Enteric neurons AF1|LERK7|EPLG7 0.029 ephrin A5 protein-coding gene NA Endoderm GI tract 0.0 0.722222 0.0247494 0.0291643 +Mm Hs HOXB4 Enteric neurons HOX2F 0.006 homeobox B4 protein-coding gene NA Endoderm GI tract 0.0 0.444444 0.00501253 0.00346888 +Mm Hs TLX2 Enteric neurons Enx|Tlx2|NCX|HOX11L1 0.004 T cell leukemia homeobox 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs GOLGA7B Enteric neurons bA459F3.4|bA451M19.3|C10orf133|C10orf132 0.018 golgin A7 family member B protein-coding gene NA Endoderm GI tract 0.0 0.5 0.0 0.0215841 +Mm Hs SLC18A3 Enteric neurons VACHT 0.002 solute carrier family 18 member A3 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00125313 0.0 +Mm Hs TOX Enteric neurons KIAA0808|TOX1 0.016 thymocyte selection associated high mobility group box protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00344612 0.0 +Mm Hs CELF6 Enteric neurons BRUNOL6 0.014 CUGBP Elav-like family member 6 protein-coding gene NA Endoderm GI tract 0.0 0.888889 0.0 0.016702 +Mm Hs GPR22 Enteric neurons NA 0.007 G protein-coupled receptor 22 protein-coding gene NA Endoderm GI tract 0.0 0.555556 0.000626566 0.00764438 +Mm Hs PLCE1 Enteric neurons KIAA1516|NPHS3 0.005 phospholipase C epsilon 1 protein-coding gene NA Endoderm GI tract 0.0 0.611111 0.00845865 0.00385431 +Mm Hs CYB561 Enteric neurons FRRS2|CYB561A1 0.027 cytochrome b561 protein-coding gene NA Endoderm GI tract 0.0 0.555556 0.0147243 0.0274941 +Mm Hs GFRA2 Enteric neurons RETL2|GDNFRB|NTNRA|TRNR2 0.008 GDNF family receptor alpha 2 protein-coding gene NA Endoderm GI tract 0.0 0.666667 0.00438596 0.00899338 +Mm Hs FLOT2 Enteric neurons ECS-1|ECS1|M17S1 0.022 flotillin 2 protein-coding gene NA Endoderm GI tract 0.0 0.888889 0.0150376 0.0238325 +Mm Hs SLC7A14 Enteric neurons KIAA1613|PPP1R142 0.011 solute carrier family 7 member 14 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs JPH3 Enteric neurons JP-3|CAGL237|HDL2|JP3|TNRC22 0.024 junctophilin 3 protein-coding gene NA Endoderm GI tract 0.0 0.833333 0.000313283 0.0292927 +Mm Hs CASZ1 Enteric neurons FLJ20321|ZNF693|castor|cst|SRG 0.016 castor zinc finger 1 protein-coding gene NA Endoderm GI tract 0.0 0.666667 0.0 0.0195927 +Mm Hs TAC1 Enteric neurons NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00532581 0.0 +Mm Hs SCN3A Enteric neurons Nav1.3 0.022 sodium voltage-gated channel alpha subunit 3 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0056391 0.0 +Mm Hs CHRNA3 Enteric neurons NA 0.004 cholinergic receptor nicotinic alpha 3 subunit protein-coding gene NA Endoderm GI tract 0.0 1.0 0.000313283 0.00327616 +Mm Hs PARVA Enteric neurons FLJ12254|FLJ10793|MXRA2 0.03 parvin alpha protein-coding gene NA Endoderm GI tract 0.0 0.666667 0.0222431 0.0312841 +Mm Hs SLC10A4 Enteric neurons MGC29802 0.005 solute carrier family 10 member 4 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00093985 0.0 +Mm Hs TM4SF4 Enteric neurons il-TMP 0.017 transmembrane 4 L six family member 4 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.02099 0.0 +Mm Hs FAM19A1 Enteric neurons TAFA-1|TAFA1 0.009 family with sequence similarity 19 member A1, C-C motif chemokine like protein-coding gene NA Endoderm GI tract 0.0 0.611111 0.00125313 0.0105993 +Mm Hs SLC5A7 Enteric neurons hCHT|CHT1 0.002 solute carrier family 5 member 7 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs PHOX2B Enteric neurons Phox2b|NBPhox|PMX2B 0.002 paired like homeobox 2b protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0 0.000963577 +Mm Hs PIRT Enteric neurons NA 0.005 phosphoinositide interacting regulator of transient receptor potential channels protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0 0.00578146 +Mm Hs HOXB5 Enteric neurons HOX2A 0.003 homeobox B5 protein-coding gene NA Endoderm GI tract 0.0 0.833333 0.00501253 0.00141325 +Mm Hs HOXA5 Enteric neurons HOX1C 0.005 homeobox A5 protein-coding gene NA Endoderm GI tract 0.0 0.833333 0.0018797 0.0050106 +Mm Hs GAL Enteric neurons GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene 1 Endoderm GI tract 0.0 0.388889 0.0184837 0.0107921 +Mm Hs CARTPT Enteric neurons CART 0.008 CART prepropeptide protein-coding gene 1 Endoderm GI tract 0.0 0.388889 0.00720551 0.00770861 +Mm Hs NMU Enteric neurons NA 0.002 neuromedin U protein-coding gene 1 Endoderm GI tract 0.0 0.111111 0.00845865 0.000192715 +Mm Hs VIP Enteric neurons NA 0.003 vasoactive intestinal peptide protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs CCK Enteric neurons NA 0.033 cholecystokinin protein-coding gene 1 Endoderm GI tract 0.0 0.0555556 0.00344612 0.0384788 +Mm Hs REG4 Enterochromaffin cells REG-IV|RELP|GISP 0.005 regenerating family member 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00501253 0.0 +Mm Hs AFP Enterochromaffin cells FETA|HPAFP 0.007 alpha fetoprotein protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0106516 0.0053898 +Mm Hs SLC18A1 Enterochromaffin cells CGAT|VMAT1|VAT1 0.001 solute carrier family 18 member A1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313283 0.0 +Mm Hs LMX1A Enterochromaffin cells LMX1.1|LMX1 0.003 LIM homeobox transcription factor 1 alpha protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00340071 +Mm Hs TRPA1 Enterochromaffin cells ANKTM1 0.001 transient receptor potential cation channel subfamily A member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00250627 0.0 +Mm Hs FGF1 Enterochromaffin cells AFGF|ECGF|ECGFA|ECGFB|HBGF1|ECGF-beta|FGF-alpha|GLIO703|FGFA 0.011 fibroblast growth factor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00313283 0.0125762 +Mm Hs PIEZO2 Enterochromaffin cells FLJ23403|FLJ23144|HsT748|HsT771|FLJ34907|FAM38B2|C18orf30|C18orf58|FAM38B 0.006 piezo type mechanosensitive ion channel component 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00776388 +Mm Hs ADGRG4 Enterochromaffin cells RP1-299I16|PGR17|GPR112 0.0 adhesion G protein-coupled receptor G4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000128329 +Mm Hs ADM Enterochromaffin cells AM 0.026 adrenomedullin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0635965 0.0177093 +Mm Hs TPH1 Enterochromaffin cells TPRH|TPH 0.002 tryptophan hydroxylase 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00125313 0.0 +Mm Hs CRH Enterochromaffin cells CRH1 0.001 corticotropin releasing hormone protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00128329 +Mm Hs GJB1 Enterochromaffin cells CX32|CMTX1|CMTX 0.033 gap junction protein beta 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0103383 0.0384344 +Mm Hs GATA4 Enterocytes NA 0.008 GATA binding protein 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0231788 0.0047081 0.00765557 +Mm Hs LYPD8 Enterocytes NA 0.024 LY6/PLAUR domain containing 8 protein-coding gene 1 Endoderm GI tract 0.333333 0.903974 0.00408035 0.0102074 +Mm Hs NLRP6 Enterocytes PYPAF5|PAN3|CLR11.4|NALP6 0.008 NLR family pyrin domain containing 6 protein-coding gene 1 Endoderm GI tract 0.0 0.387417 0.0 0.00235556 +Mm Hs KRT20 Enterocytes CK20|K20|MGC35423 0.012 keratin 20 protein-coding gene 1 Endoderm GI tract 0.833333 0.466887 0.0134965 0.00274815 +Mm Hs MYO1A Enterocytes MYHL|DFNA48 0.013 myosin IA protein-coding gene 1 Endoderm GI tract 0.0 0.592715 0.000313873 0.00464568 +Mm Hs PPARG Enterocytes PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Endoderm GI tract 0.666667 0.0298013 0.00973007 0.00412223 +Mm Hs SLC15A1 Enterocytes PEPT1|HPECT1|HPEPT1 0.002 solute carrier family 15 member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00156937 0.0 +Mm Hs FLOT2 Enterocytes ECS-1|ECS1|M17S1 0.022 flotillin 2 protein-coding gene 1 Endoderm GI tract 0.0 0.00993378 0.0150659 0.025126 +Mm Hs APOBEC1 Enterocytes CDAR1|APOBEC-1|HEPR 0.012 apolipoprotein B mRNA editing enzyme catalytic subunit 1 protein-coding gene 1 Endoderm GI tract 0.0 0.00993378 0.0 0.014984 +Mm Hs PLIN3 Enterocytes TIP47|M6PRBP1 0.054 perilipin 3 protein-coding gene NA Endoderm GI tract 0.0 0.476821 0.00313873 0.0579729 +Mm Hs SLC10A2 Enterocytes ASBT|ISBT 0.002 solute carrier family 10 member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs SLC40A1 Enterocytes MTP1|IREG1|FPN1|HFE4|SLC11A3 0.033 solute carrier family 40 member 1 protein-coding gene 1 Endoderm GI tract 0.166667 0.0 0.0351538 0.0 +Mm Hs SLC5A1 Enterocytes D22S675|NAGT|SGLT1 0.011 solute carrier family 5 member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219711 0.0 +Hs TTC7A Enterocytes KIAA1140|TTC7 0.0 tetratricopeptide repeat domain 7A protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00282486 0.0 +Mm Hs NPC1L1 Enterocytes SLC65A2 0.005 NPC1 like intracellular cholesterol transporter 1 protein-coding gene 1 Endoderm GI tract 0.0 0.294702 0.000313873 0.000458025 +Mm Hs FABP1 Enterocytes L-FABP 0.03 fatty acid binding protein 1 protein-coding gene 1 Endoderm GI tract 1.0 0.708609 0.039548 0.0144605 +Mm Hs ANPEP Enterocytes gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Endoderm GI tract 0.666667 0.403974 0.0116133 0.00922594 +Hs CA1 Enterocytes Car1 0.01 carbonic anhydrase 1 protein-coding gene 1 Endoderm GI tract 0.833333 0.0 0.0621469 0.0 +Mm Hs CPS1 Enterocytes NA 0.013 carbamoyl-phosphate synthase 1 protein-coding gene 1 Endoderm GI tract 0.0 0.57947 0.0047081 0.00379507 +Mm Hs DPP4 Enterocytes CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Endoderm GI tract 0.0 0.264901 0.0131827 0.0164889 +Mm Hs SLC2A5 Enterocytes GLUT5 0.012 solute carrier family 2 member 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0131827 0.0 +Mm Hs ALPI Enterocytes NA 0.006 alkaline phosphatase, intestinal protein-coding gene 1 Endoderm GI tract 0.0 0.400662 0.0 0.000130864 +Mm Hs FABP2 Enterocytes I-FABP 0.022 fatty acid binding protein 2 protein-coding gene 1 Endoderm GI tract 0.833333 0.870861 0.00533584 0.00889878 +Mm Hs LCT Enterocytes NA 0.002 lactase protein-coding gene 1 Endoderm GI tract 0.0 0.13245 0.0 0.0 +Hs SI Enterocytes NA 0.0 sucrase-isomaltase protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs VIL1 Enterocytes D2S1471|VIL 0.022 villin 1 protein-coding gene 1 Endoderm GI tract 0.833333 0.0 0.00690521 0.0 +Mm CLCA4B Enterocytes NA 0.005 chloride channel accessory 4B protein coding gene 1 Endoderm GI tract 0.0 0.301325 0.0 0.000785186 +Mm Hs FUOM Enterocytes FLJ26016|FucU|FucM|C10orf125 0.035 fucose mutarotase protein-coding gene 1 Endoderm GI tract 0.333333 0.57947 0.022285 0.0262383 +Mm Hs FAHD1 Enterocytes DKFZP566J2046|C16orf36 0.019 fumarylacetoacetate hydrolase domain containing 1 protein-coding gene 1 Endoderm GI tract 0.166667 0.400662 0.0313873 0.00719754 +Mm Hs OTC Enterocytes NA 0.008 ornithine carbamoyltransferase protein-coding gene 1 Endoderm GI tract 0.0 0.403974 0.000313873 0.00209383 +Mm Hs CDH17 Enterocytes HPT-1|cadherin 0.021 cadherin 17 protein-coding gene 1 Endoderm GI tract 0.833333 0.910596 0.0134965 0.00516914 +Mm Hs KHK Enterocytes NA 0.037 ketohexokinase protein-coding gene 1 Endoderm GI tract 0.0 0.774834 0.000313873 0.0306223 +Mm Hs ABHD11 Enterocytes PP1226|WBSCR21 0.037 abhydrolase domain containing 11 protein-coding gene NA Endoderm GI tract 0.166667 0.440397 0.0128688 0.0323235 +Mm OLFR77 Enterocytes NA 0.026 olfactory receptor 77 protein coding gene NA Endoderm GI tract 0.0 0.188742 0.0 0.0291173 +Mm Hs VDR Enterocytes NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Endoderm GI tract 0.166667 0.0 0.00219711 0.0 +Mm Hs EHF Enterocytes ESE3|ESEJ 0.024 ETS homologous factor protein-coding gene NA Endoderm GI tract 0.166667 0.288079 0.0511613 0.0140025 +Mm Hs CDC42EP5 Enterocytes CEP5|Borg3 0.036 CDC42 effector protein 5 protein-coding gene NA Endoderm GI tract 0.833333 0.629139 0.0398619 0.0240136 +Mm DEFA24 Enterocytes NA 0.017 defensin, alpha, 24 protein coding gene NA Endoderm GI tract 0.0 0.701987 0.0 0.00844075 +Mm Hs CASP6 Enterocytes NA 0.033 caspase 6 protein-coding gene NA Endoderm GI tract 0.0 0.470199 0.0081607 0.0302297 +Mm Hs HNF4A Enterocytes NR2A1|HNF4|TCF14|MODY|MODY1 0.019 hepatocyte nuclear factor 4 alpha protein-coding gene NA Endoderm GI tract 0.833333 0.695364 0.00627746 0.00844075 +Mm Hs AQP1 Enterocytes CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene NA Endoderm GI tract 0.0 0.192053 0.0178908 0.039521 +Mm Hs TMEM45B Enterocytes BC016153|FLJ40787 0.02 transmembrane protein 45B protein-coding gene NA Endoderm GI tract 0.833333 0.0 0.014752 0.0 +Mm Hs RGMB Enterocytes FLJ90406|DRAGON 0.009 repulsive guidance molecule BMP co-receptor b protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00627746 0.0 +Mm Hs PDHA1 Enterocytes PDHA 0.048 pyruvate dehydrogenase E1 alpha 1 subunit protein-coding gene NA Endoderm GI tract 0.166667 0.423841 0.0586943 0.0335667 +Mm Hs CDO1 Enterocytes NA 0.036 cysteine dioxygenase type 1 protein-coding gene NA Endoderm GI tract 0.0 0.152318 0.0119272 0.0396519 +Mm Hs ELF3 Enterocytes ESE-1|ERT|ESX 0.048 E74 like ETS transcription factor 3 protein-coding gene NA Endoderm GI tract 0.833333 0.741722 0.115191 0.0194988 +Mm Hs KRTCAP3 Enterocytes KCP3 0.026 keratinocyte associated protein 3 protein-coding gene NA Endoderm GI tract 0.166667 0.496689 0.0304457 0.0152457 +Mm Hs DEGS2 Enterocytes DES2|FADS8|C14orf66 0.018 delta 4-desaturase, sphingolipid 2 protein-coding gene NA Endoderm GI tract 0.0 0.665563 0.0047081 0.00804816 +Mm Hs TMC4 Enterocytes NA 0.022 transmembrane channel like 4 protein-coding gene NA Endoderm GI tract 0.666667 0.0 0.00721908 0.0 +Mm PRSS32 Enterocytes NA 0.013 protease, serine 32 protein coding gene NA Endoderm GI tract 0.0 0.622517 0.0 0.0038605 +Mm Hs PPP1R14D Enterocytes FLJ20251|GBPI-1|MGC119014|MGC119016 0.018 protein phosphatase 1 regulatory inhibitor subunit 14D protein-coding gene NA Endoderm GI tract 0.833333 0.827815 0.00659134 0.00431852 +Mm Hs TM4SF5 Enterocytes NA 0.022 transmembrane 4 L six family member 5 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00251099 0.0 +Mm Hs RNF186 Enterocytes FLJ20225 0.013 ring finger protein 186 protein-coding gene 1 Endoderm GI tract 0.166667 0.0 0.00219711 0.0 +Mm Hs CEACAM1 Enterocytes BGP1|CD66a|BGP 0.024 carcinoembryonic antigen related cell adhesion molecule 1 protein-coding gene NA Endoderm GI tract 0.666667 0.506622 0.0178908 0.0164235 +Mm Hs KLF5 Enterocytes IKLF|CKLF|BTEB2 0.062 Kruppel like factor 5 protein-coding gene 1 Endoderm GI tract 0.833333 0.745033 0.0897677 0.043447 +Mm Hs CDX1 Enterocytes NA 0.015 caudal type homeobox 1 protein-coding gene NA Endoderm GI tract 0.833333 0.516556 0.00973007 0.00543087 +Mm Hs CDX2 Enterocytes CDX3 0.015 caudal type homeobox 2 protein-coding gene NA Endoderm GI tract 0.666667 0.57947 0.00690521 0.0058889 +Mm Hs CLDN15 Enterocytes NA 0.023 claudin 15 protein-coding gene 1 Endoderm GI tract 0.0 0.768212 0.00156937 0.0115161 +Mm Hs ASCL2 Enterocytes HASH2|bHLHa45 0.005 achaete-scute family bHLH transcription factor 2 protein-coding gene NA Endoderm GI tract 0.0 0.162252 0.00753296 0.00170124 +Mm Hs SMOC2 Enterocytes SMAP2 0.026 SPARC related modular calcium binding 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0178908 0.0 +Mm Hs PRR15L Enterocytes MGC11242|ATAD4 0.024 proline rich 15 like protein-coding gene NA Endoderm GI tract 0.5 0.652318 0.00784683 0.0148531 +Mm Hs FBP2 Enterocytes NA 0.02 fructose-bisphosphatase 2 protein-coding gene NA Endoderm GI tract 0.0 0.857616 0.0 0.00791729 +Mm Hs SDSL Enterocytes SDS-RS1|cSDH 0.015 serine dehydratase like protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0119272 0.0 +Mm GKN3 Enterocytes NA 0.004 gastrokine 3 protein coding gene NA Endoderm GI tract 0.0 0.139073 0.0 0.0020284 +Mm Hs FERMT1 Enterocytes FLJ20116|URP1|KIND1|UNC112A|C20orf42 0.019 fermitin family member 1 protein-coding gene NA Endoderm GI tract 0.166667 0.403974 0.0150659 0.0122358 +Mm Hs ALDOB Enterocytes NA 0.031 aldolase, fructose-bisphosphate B protein-coding gene 1 Endoderm GI tract 0.0 0.943709 0.00627746 0.0191716 +Mm Hs MUC13 Enterocytes DRCC1 0.03 mucin 13, cell surface associated protein-coding gene NA Endoderm GI tract 0.833333 0.966887 0.0163214 0.0153111 +Mm Hs PHGR1 Enterocytes NA 0.031 proline, histidine and glycine rich 1 protein-coding gene NA Endoderm GI tract 1.0 0.986755 0.0404896 0.00974939 +Mm Hs PRAP1 Enterocytes NA 0.018 proline rich acidic protein 1 protein-coding gene 1 Endoderm GI tract 0.166667 0.910596 0.000313873 0.00497285 +Mm Hs CCL25 Enterocytes TECK|Ckb15|SCYA25 0.018 C-C motif chemokine ligand 25 protein-coding gene 1 Endoderm GI tract 0.0 0.834437 0.0 0.00608519 +Mm Hs LGALS2 Enterocytes HL14 0.032 galectin 2 protein-coding gene 1 Endoderm GI tract 0.5 0.897351 0.037037 0.0136753 +Mm Hs SPON2 Enterocytes DIL1 0.017 spondin 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0489642 0.0 +Mm Hs ASPN Enterocytes FLJ20129|SLRR1C|PLAP-1 0.019 asporin protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00721908 0.0222469 +Mm Hs CTRB1 Enterocytes CTRB 0.017 chymotrypsinogen B1 protein-coding gene NA Endoderm GI tract 0.0 0.00331126 0.00439422 0.0204803 +Mm Hs CD55 Enterocytes TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene NA Endoderm GI tract 0.5 0.0629139 0.125235 0.0188445 +Mm Hs CDH19 Enterocytes CDH7 0.003 cadherin 19 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00313873 0.00314074 +Mm Hs SLC35F1 Enterocytes dJ230I3.1|C6orf169 0.015 solute carrier family 35 member F1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0106717 0.0 +Mm Hs G0S2 Enterocytes NA 0.04 G0/G1 switch 2 protein-coding gene NA Endoderm GI tract 0.0 0.00331126 0.0455116 0.0384741 +Mm Hs GULP1 Enterocytes CED6|CED-6|GULP 0.01 GULP, engulfment adaptor PTB domain containing 1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.029818 0.00471112 +Mm Hs NKD2 Enterocytes Naked2 0.004 naked cuticle homolog 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00188324 0.00516914 +Mm Hs COL18A1 Enterocytes KNO1|KNO 0.032 collagen type XVIII alpha 1 chain protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0153798 0.0370346 +Mm Hs SOX10 Enterocytes DOM|WS4|WS2E 0.04 SRY-box 10 protein-coding gene NA Endoderm GI tract NA NA NA NA +Mm Hs COL20A1 Enterocytes KIAA1510 0.003 collagen type XX alpha 1 chain protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00219711 0.00314074 +Mm Hs PMEPA1 Enterocytes STAG1|TMEPAI 0.048 prostate transmembrane protein, androgen induced 1 protein-coding gene NA Endoderm GI tract 0.0 0.0231788 0.0251099 0.0545704 +Mm Hs GFRA2 Enterocytes RETL2|GDNFRB|NTNRA|TRNR2 0.008 GDNF family receptor alpha 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00439422 0.00994569 +Mm Hs ART3 Enterocytes NA 0.021 ADP-ribosyltransferase 3 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0166353 0.0235556 +Mm Hs SLC26A2 Enterocytes DTDST 0.013 solute carrier family 26 member 2 protein-coding gene NA Endoderm GI tract 0.833333 0.0 0.0166353 0.0 +Mm CAR1 Enterocytes NA 0.006 carbonic anhydrase 1 protein coding gene NA Endoderm GI tract 0.0 0.0231788 0.0 0.00706668 +Mm TRY4 Enterocytes NA 0.007 trypsin 4 protein coding gene NA Endoderm GI tract NA NA NA NA +Mm TRY5 Enterocytes NA 0.006 trypsin 5 protein coding gene NA Endoderm GI tract NA NA NA NA +Mm Hs PRSS2 Enterocytes TRY2 0.01 serine protease 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0141243 0.0102729 +Mm Hs L1CAM Enterocytes CD171|HSAS1|SPG1|HSAS|MIC5 0.018 L1 cell adhesion molecule protein-coding gene 1 Endoderm GI tract 0.0 0.0198676 0.00156937 0.0213963 +Mm Hs SLC11A2 Enterocytes DCT1|NRAMP2 0.007 solute carrier family 11 member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00659134 0.0 +Mm Hs SLC26A3 Enterocytes DRA|CLD 0.003 solute carrier family 26 member 3 protein-coding gene 1 Endoderm GI tract 1.0 0.0 0.0103578 0.0 +Mm Hs APOA1 Enterocytes NA 0.032 apolipoprotein A1 protein-coding gene 1 Endoderm GI tract 0.0 0.592715 0.0684244 0.0144605 +Mm Hs APOA4 Enterocytes NA 0.011 apolipoprotein A4 protein-coding gene 1 Endoderm GI tract 0.0 0.427152 0.000313873 0.00601976 +Mm Hs CBR1 Enterocytes SDR21C1|CBR 0.112 carbonyl reductase 1 protein-coding gene 1 Endoderm GI tract 0.166667 0.642384 0.0831764 0.107047 +Mm Hs EPHX2 Enterocytes NA 0.009 epoxide hydrolase 2 protein-coding gene 1 Endoderm GI tract 0.166667 0.238411 0.00533584 0.00562717 +Mm Hs GSTM3 Enterocytes GST5 0.024 glutathione S-transferase mu 3 protein-coding gene 1 Endoderm GI tract 0.0 0.34106 0.0925926 0.00150494 +Mm ADH6A Enterocytes NA 0.004 alcohol dehydrogenase 6A (class V) protein coding gene 1 Endoderm GI tract 0.0 0.274834 0.0 0.000261729 +Mm Hs CREB3L3 Enterocytes CREB-H 0.008 cAMP responsive element binding protein 3 like 3 protein-coding gene 1 Endoderm GI tract 0.0 0.34106 0.000627746 0.00379507 +Mm Hs MEP1A Enterocytes PPHA 0.004 meprin A subunit alpha protein-coding gene 1 Endoderm GI tract 0.333333 0.182119 0.000313873 0.0020284 +Mm FGF15 Enterocytes NA 0.0 fibroblast growth factor 15 protein coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000654322 +Mm MUC3 Enterocytes NA 0.01 mucin 3, intestinal protein coding gene 1 Endoderm GI tract 0.0 0.5 0.0 0.00287902 +Mm CLEC2H Enterocytes NA 0.009 C-type lectin domain family 2, member h protein coding gene 1 Endoderm GI tract 0.0 0.47351 0.0 0.00274815 +Mm Hs FABP6 Enterocytes I-15P|ILLBP|I-BAP|ILBP3|I-BABP|ILBP|I-BALB 0.007 fatty acid binding protein 6 protein-coding gene 1 Endoderm GI tract 0.0 0.264901 0.000627746 0.0038605 +Mm Hs RBP2 Enterocytes CRBP2|RBPC2|CRBPII 0.015 retinol binding protein 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313873 0.0 +Hs CYP3A4 Enterocytes CYP3A3 0.0 cytochrome P450 family 3 subfamily A member 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00188324 0.0 +Mm Hs APOB Enterocytes NA 0.015 apolipoprotein B protein-coding gene 1 Endoderm GI tract 0.0 0.427152 0.0125549 0.00765557 +Mm Hs MTTP Enterocytes MTP 0.014 microsomal triglyceride transfer protein protein-coding gene 1 Endoderm GI tract 0.0 0.493377 0.00910232 0.00562717 +Mm Hs SLC2A2 Enterocytes GLUT2 0.007 solute carrier family 2 member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00188324 0.0 +Mm Hs APOC3 Enterocytes NA 0.018 apolipoprotein C3 protein-coding gene 1 Endoderm GI tract 0.0 0.466887 0.0244821 0.00863705 +Hs UGT2B17 Enterocytes NA 0.0 UDP glucuronosyltransferase family 2 member B17 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs CD36 Enterocytes SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Endoderm GI tract 0.0 0.0198676 0.0345261 0.0446247 +Mm Hs REG3A Enterocytes REG-III|REG3|PBCGF 0.005 regenerating family member 3 alpha protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0141243 0.0 +Mm Hs ISX Enterocytes RAXLX 0.002 intestine specific homeobox protein-coding gene 1 Endoderm GI tract 0.0 0.089404 0.000313873 0.00058889 +Hs AQP10 Enterocytes NA 0.0 aquaporin 10 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs S100G Enterocytes CABP9K|CABP1|CALB3 0.024 S100 calcium binding protein G protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Hs BEST4 Enterocytes VMD2L2 0.0 bestrophin 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219711 0.0 +Mm Hs SLC28A1 Enterocytes CNT1 0.001 solute carrier family 28 member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs SLC28A2 Enterocytes CNT2|SPNT1|HCNT2|HsT17153 0.001 solute carrier family 28 member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00125549 0.0 +Mm Hs SLC30A10 Enterocytes DKFZp547M236|ZnT-10 0.002 solute carrier family 30 member 10 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00282486 0.0 +Mm Hs SLC51B Enterocytes OSTbeta 0.007 solute carrier family 51 beta subunit protein-coding gene 1 Endoderm GI tract 0.833333 0.0 0.00973007 0.0 +Mm Hs VNN1 Enterocytes Tiff66 0.004 vanin 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219711 0.0 +Mm Hs SLC23A1 Enterocytes YSPL3|SVCT1|SLC23A2 0.001 solute carrier family 23 member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs TREH Enterocytes TREA|MGC129621 0.003 trehalase protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00282486 0.0 +Mm Hs ABCC2 Enterocytes DJS|cMRP|CMOAT 0.004 ATP binding cassette subfamily C member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0860927 0.00094162 0.00268272 +Mm Hs ABCG5 Enterocytes STSL 0.002 ATP binding cassette subfamily G member 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0927152 0.0 0.000392593 +Hs SLC52A1 Enterocytes FLJ10060|GPCR42|hRFT1|RFVT1|GPR172B 0.0 solute carrier family 52 member 1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00094162 0.0 +Hs CYP3A7 Enterocytes CP37|P450-HFLA 0.0 cytochrome P450 family 3 subfamily A member 7 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000627746 0.0 +Mm Hs DMBT1 Enterocytes GP340|muclin|SALSA|Gp-340|hensin|vomeroglandin 0.01 deleted in malignant brain tumors 1 protein-coding gene 1 Endoderm GI tract 0.0 0.390728 0.00282486 0.00353334 +Mm Hs ABCG8 Enterocytes GBD4 0.002 ATP binding cassette subfamily G member 8 protein-coding gene 1 Endoderm GI tract 0.0 0.102649 0.0 0.00058889 +Mm Hs PLIN2 Enterocytes ADRP|ADFP 0.101 perilipin 2 protein-coding gene 1 Endoderm GI tract 0.166667 0.155629 0.106403 0.0932409 +Mm Hs GSTA1 Enterocytes NA 0.012 glutathione S-transferase alpha 1 protein-coding gene 1 Endoderm GI tract 0.0 0.298013 0.0301318 0.00261729 +Mm Hs CYBRD1 Enterocytes DCYTB|FLJ23462|FRRS3|CYB561A2 0.005 cytochrome b reductase 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0430464 0.0200879 0.00104691 +Mm Hs ABCG2 Enterocytes EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene 1 Endoderm GI tract 0.5 0.10596 0.00376648 0.0455408 +Mm Hs NR1H4 Enterocytes FXR|RIP14|HRR1|HRR-1 0.002 nuclear receptor subfamily 1 group H member 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0397351 0.000627746 0.00130864 +Mm Hs DAB1 Enterocytes NA 0.045 DAB1, reelin adaptor protein protein-coding gene 1 Endoderm GI tract 0.0 0.0298013 0.00188324 0.0573186 +Mm Hs TM6SF2 Enterocytes Lpr4 0.006 transmembrane 6 superfamily member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs NR5A2 Enterocytes FTZ-F1beta|hB1F|FTZ-F1|hB1F-2|B1F2|LRH1|FTF 0.003 nuclear receptor subfamily 5 group A member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0231788 0.000313873 0.00333704 +Mm Hs PDZK1 Enterocytes PDZD1|NHERF3 0.002 PDZ domain containing 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00376648 0.00130864 +Mm Hs ACSL5 Enterocytes ACS5|FACL5 0.055 acyl-CoA synthetase long chain family member 5 protein-coding gene 1 Endoderm GI tract 0.666667 0.728477 0.0153798 0.0501211 +Mm Hs AQP11 Enterocytes NA 0.018 aquaporin 11 protein-coding gene 1 Endoderm GI tract 0.0 0.135762 0.0112994 0.0176013 +Mm Hs AQP7 Enterocytes AQP9|AQPap|AQP7L 0.005 aquaporin 7 protein-coding gene 1 Endoderm GI tract 0.0 0.013245 0.00910232 0.00458025 +Mm Hs AQP8 Enterocytes NA 0.007 aquaporin 8 protein-coding gene 1 Endoderm GI tract 0.833333 0.0165563 0.00282486 0.00739384 +Mm Hs HMOX1 Enterocytes bK286B10|HO-1 0.046 heme oxygenase 1 protein-coding gene 1 Endoderm GI tract 0.166667 0.0 0.0360954 0.0494013 +Mm Hs SLC39A5 Enterocytes NA 0.01 solute carrier family 39 member 5 protein-coding gene 1 Endoderm GI tract 0.833333 0.0 0.00564972 0.0 +Mm Hs SLC51A Enterocytes OSTalpha 0.006 solute carrier family 51 alpha subunit protein-coding gene 1 Endoderm GI tract 0.166667 0.0 0.00094162 0.0 +Mm Hs TRPM6 Enterocytes CHAK2|FLJ22628|HOMG|HSH 0.001 transient receptor potential cation channel subfamily M member 6 protein-coding gene 1 Endoderm GI tract 0.333333 0.0 0.000313873 0.0 +Mm Hs MOGAT2 Enterocytes MGAT2|DGAT2L5|FLJ22644 0.011 monoacylglycerol O-acyltransferase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.387417 0.0 0.00543087 +Mm Hs GLS Enterocytes KIAA0838|GLS1 0.061 glutaminase protein-coding gene 1 Endoderm GI tract 0.166667 0.284768 0.0194601 0.0681149 +Mm Hs MAOA Enterocytes NA 0.034 monoamine oxidase A protein-coding gene 1 Endoderm GI tract 0.833333 0.576159 0.027307 0.0253877 +Mm Hs DGAT1 Enterocytes ARGP1|DGAT 0.029 diacylglycerol O-acyltransferase 1 protein-coding gene 1 Endoderm GI tract 0.666667 0.698676 0.0128688 0.0199568 +Mm Hs DGAT2 Enterocytes NA 0.023 diacylglycerol O-acyltransferase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.15894 0.0238544 0.0215272 +Mm Hs NPSR1 Enteroendocrine cells PGR14|GPRA|GPR154 0.0 neuropeptide S receptor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 6.43004e-05 +Mm Hs FFAR3 Enteroendocrine cells FFA3R|GPR41 0.0 free fatty acid receptor 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000643004 +Mm Hs SCN3A Enteroendocrine cells Nav1.3 0.022 sodium voltage-gated channel alpha subunit 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00567286 0.0 +Mm Hs NEUROG3 Enteroendocrine cells Atoh5|Math4B|ngn3|bHLHa7 0.001 neurogenin 3 protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.000945477 0.000900206 +Mm Hs FFAR1 Enteroendocrine cells FFA1R|GPR40 0.002 free fatty acid receptor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.00724866 0.00147891 +Mm Hs ARX Enteroendocrine cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Endoderm GI tract 0.0 0.121212 0.00220611 0.0234053 +Mm Hs NKX2-2 Enteroendocrine cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.0104003 0.000578704 +Mm Hs SCT Enteroendocrine cells NA 0.011 secretin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0122912 0.0 +Mm Hs CCK Enteroendocrine cells NA 0.033 cholecystokinin protein-coding gene 1 Endoderm GI tract 0.0 0.151515 0.00346675 0.0382587 +Mm Hs GFRA3 Enteroendocrine cells GFRa-3 0.005 GDNF family receptor alpha 3 protein-coding gene 1 Endoderm GI tract 0.0 0.181818 0.00252127 0.00520833 +Mm Hs VWA5B2 Enteroendocrine cells DKFZp761K032|LOC90113 0.001 von Willebrand factor A domain containing 5B2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00189095 0.0 +Mm Hs NEUROD1 Enteroendocrine cells BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Endoderm GI tract 0.210526 0.363636 0.0220611 0.0423097 +Mm Hs SCGN Enteroendocrine cells SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Endoderm GI tract 0.631579 0.0 0.0261582 0.0 +Mm Hs PCSK1 Enteroendocrine cells PC1|NEC1 0.008 proprotein convertase subtilisin/kexin type 1 protein-coding gene 1 Endoderm GI tract 0.0 0.242424 0.00945477 0.00797325 +Mm Hs ISL1 Enteroendocrine cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Endoderm GI tract 0.105263 0.424242 0.0129215 0.0305427 +Mm Hs FABP5 Enteroendocrine cells E-FABP|PA-FABP|KFABP 0.354 fatty acid binding protein 5 protein-coding gene 1 Endoderm GI tract 0.0 0.151515 0.219666 0.389532 +Mm Hs TAC1 Enteroendocrine cells NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00535771 0.0 +Mm Hs RIMBP2 Enteroendocrine cells KIAA0318|RBP2|MGC15831|RIM-BP2|PPP1R133 0.005 RIMS binding protein 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs PAX6 Enteroendocrine cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Endoderm GI tract 0.0 0.424242 0.0144973 0.0581919 +Mm Hs GIP Enteroendocrine cells NA 0.007 gastric inhibitory polypeptide protein-coding gene 1 Endoderm GI tract 0.0 0.0606061 0.0 0.00855195 +Mm Hs GLP1R Enteroendocrine cells GLP-1R 0.0 glucagon like peptide 1 receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000385802 +Mm Hs PYY Enteroendocrine cells PYY1 0.016 peptide YY protein-coding gene 1 Endoderm GI tract 0.0 0.939394 0.00126064 0.0183256 +Mm Hs GLP2R Enteroendocrine cells NA 0.0 glucagon like peptide 2 receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs GAST Enteroendocrine cells NA 0.001 gastrin protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.00126064 0.00115741 +Mm Hs NTS Enteroendocrine cells NA 0.005 neurotensin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00630318 0.00482253 +Mm Hs SST Enteroendocrine cells SMST 0.027 somatostatin protein-coding gene 1 Endoderm GI tract 1.0 0.0 0.0419162 0.0 +Hs MLN Enteroendocrine cells NA 0.0 motilin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs GPR119 Enteroendocrine cells hGPCR2|GPCR2 0.0 G protein-coupled receptor 119 protein-coding gene 1 Endoderm GI tract 0.0 0.0606061 0.0 0.000257202 +Mm Hs GCG Enteroendocrine cells GLP2|GRPP 0.024 glucagon protein-coding gene 1 Endoderm GI tract 1.0 0.848485 0.0460132 0.018197 +Mm Hs CHGB Enteroendocrine cells SgI|SCG1 0.076 chromogranin B protein-coding gene 1 Endoderm GI tract 0.631579 0.484848 0.0409707 0.0851337 +Mm Hs CPE Enteroendocrine cells NA 0.317 carboxypeptidase E protein-coding gene 1 Endoderm GI tract 0.631579 0.757576 0.130161 0.364648 +Mm Hs GAL Enteroendocrine cells GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0185944 0.0112526 +Mm Hs NUCB2 Enteroendocrine cells NEFA 0.066 nucleobindin 2 protein-coding gene 1 Endoderm GI tract 0.0526316 0.121212 0.244879 0.0236626 +Mm Hs IAPP Enteroendocrine cells AMYLIN 0.023 islet amyloid polypeptide protein-coding gene 1 Endoderm GI tract 0.947368 0.848485 0.0365585 0.01884 +Mm Hs GHRL Enteroendocrine cells MTLRP|ghrelin|obestatin 0.003 ghrelin and obestatin prepropeptide protein-coding gene 1 Endoderm GI tract 0.0 0.181818 0.000630318 0.00340792 +Mm Hs CHGA Enteroendocrine cells NA 0.057 chromogranin A protein-coding gene 1 Endoderm GI tract 0.631579 0.787879 0.0343523 0.0606996 +Mm Hs TRPA1 Enteroendocrine cells ANKTM1 0.001 transient receptor potential cation channel subfamily A member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00252127 0.0 +Mm Hs ENPP2 Enteroendocrine cells PD-IALPHA|PDNP2 0.08 ectonucleotide pyrophosphatase/phosphodiesterase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.0330917 0.091178 +Mm Hs AFP Enteroendocrine cells FETA|HPAFP 0.007 alpha fetoprotein protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0107154 0.00540123 +Mm Hs VEGFA Enteroendocrine cells VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0248976 0.0 +Mm Hs FFAR4 Enteroendocrine cells PGR4|GPR129|GPR120|O3FAR1 0.005 free fatty acid receptor 4 protein-coding gene 1 Endoderm GI tract 0.0526316 0.181818 0.00441223 0.00450103 +Mm Hs MC4R Enteroendocrine cells NA 0.0 melanocortin 4 receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs INSL5 Enteroendocrine cells NA 0.0 insulin like 5 protein-coding gene 1 Endoderm GI tract 0.0 0.030303 0.0 0.000257202 +Mm Hs SSTR2 Enteroendocrine cells NA 0.028 somatostatin receptor 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0116609 0.0 +Mm Hs ALCAM Enteroendocrine cells CD166|MEMD 0.0 activated leukocyte cell adhesion molecule protein-coding gene 1 Endoderm GI tract 0.0 0.363636 0.0548377 0.0846193 +Mm Hs TAS1R2 Enteroendocrine cells T1R2|GPR71 0.0 taste 1 receptor member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs TAS1R3 Enteroendocrine cells T1R3 0.0 taste 1 receptor member 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs GNAT3 Enteroendocrine cells gustducin|GDCA 0.0 G protein subunit alpha transducin 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000192901 +Mm Hs C3AR1 Eosinophils C3AR|AZ3B 0.022 complement C3a receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00626566 0.0265015 +Mm Hs FUT4 Eosinophils FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000705852 +Hs FCER2 Eosinophils CLEC4J|CD23|CD23A|FCE2 0.002 Fc fragment of IgE receptor II protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00219298 0.0 +Mm Hs C5AR1 Eosinophils C5A|C5AR|CD88|C5R1 0.027 complement C5a receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0140977 0.0302233 +Mm Hs CXCR3 Eosinophils CKR-L2|CMKAR3|IP10-R|MigR|CD183|GPR9 0.005 C-X-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00532581 0.00474846 +Mm Hs CCR1 Eosinophils MIP1aR|CD191|SCYAR1|CMKBR1 0.014 C-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00532581 0.0140529 +Mm Hs CCR3 Eosinophils CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00147587 +Mm Hs CD244 Eosinophils 2B4|NAIL|NKR2B4|Nmrk|SLAMF4 0.002 CD244 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00250257 +Mm Hs PTGDR2 Eosinophils CRTH2|CD294|GPR44 0.0 prostaglandin D2 receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs S100A9 Eosinophils MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.103383 0.0 +Hs SIGLEC8 Eosinophils SIGLEC-8|SAF2|SIGLEC8L|MGC59785 0.0 sialic acid binding Ig like lectin 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs SIGLEC10 Eosinophils SIGLEC-10|SLG2|PRO940|MGC126774 0.001 sialic acid binding Ig like lectin 10 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00407268 0.0 +Mm Hs PGLYRP1 Eosinophils TAG7|PGRP|PGRP-S|PGRPS|TNFSF3L|PGLYRP 0.062 peptidoglycan recognition protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0753978 +Mm Hs LTC4S Eosinophils MGC33147 0.037 leukotriene C4 synthase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00783208 0.0448537 +Mm EAR1 Eosinophils NA 0.003 eosinophil-associated, ribonuclease A family, member 1 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.00372177 +Mm EAR2 Eosinophils NA 0.009 eosinophil-associated, ribonuclease A family, member 2 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0107161 +Mm Hs EPX Eosinophils EPP|EPX-PEN 0.0 eosinophil peroxidase protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 6.41684e-05 +Mm Hs CD69 Eosinophils CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.111216 0.00737936 +Hs RNASE3 Eosinophils ECP|RAF1|RNS3 0.0 ribonuclease A family member 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.0 +Hs RNASE2 Eosinophils EDN|RAF3|RNS2 0.001 ribonuclease A family member 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00720551 0.0 +Mm Hs IL5 Eosinophils IL-5|EDF 0.002 interleukin 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00626566 0.000834189 +Mm Hs PRG2 Eosinophils MBP|BMPG|proMBP 0.003 proteoglycan 2, pro eosinophil major basic protein protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00313283 0.00275924 +Mm Hs PRG3 Eosinophils MBPH|MBP2 0.0 proteoglycan 3, pro eosinophil major basic protein 2 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.000128337 +Mm Hs CPA3 Eosinophils NA 0.009 carboxypeptidase A3 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00845865 0.00840606 +Mm Hs IKZF2 Eosinophils Helios|ZNFN1A2 0.011 IKAROS family zinc finger 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000626566 0.0126412 +Mm Hs CCL11 Eosinophils eotaxin|MGC22554|SCYA11 0.008 C-C motif chemokine ligand 11 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00313283 0.00968943 +Mm Hs CCL5 Eosinophils RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0858396 0.0327259 +Mm Hs CSF2 Eosinophils GM-CSF|GMCSF 0.002 colony stimulating factor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0093985 0.000770021 +Mm Hs IL5RA Eosinophils CDw125|CD125|IL5R 0.0 interleukin 5 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm SIGLECF Eosinophils NA 0.002 sialic acid binding Ig-like lectin F protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs FOXJ1 Ependymal cells HFH-4|HFH4|FKHL13 0.01 forkhead box J1 protein-coding gene 1 Ectoderm Brain 0.666667 0.96 0.00753296 0.002138 +Mm Hs TRIM71 Ependymal cells LIN41|LIN-41 0.011 tripartite motif containing 71 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.017263 0.0 +Mm Hs SIX3 Ependymal cells HPE2 0.014 SIX homeobox 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313873 0.0 +Mm Hs USP18 Ependymal cells NA 0.001 ubiquitin specific peptidase 18 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm CETN4 Ependymal cells NA 0.01 centrin 4 protein coding gene NA Ectoderm Brain 0.0 0.42 0.0 0.00842242 +Mm Hs AQP4 Ependymal cells MIWC 0.024 aquaporin 4 protein-coding gene 1 Ectoderm Brain 0.0 0.56 0.00596359 0.0242306 +Mm Hs CELSR2 Ependymal cells KIAA0279|MEGF3|Flamingo1|CDHF10|ADGRC2|EGFL2 0.019 cadherin EGF LAG seven-pass G-type receptor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.02 0.0 0.023194 +Mm Hs AQP1 Ependymal cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0178908 0.0428895 +Mm Hs GFAP Ependymal cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 0.0733333 0.00564972 0.0143829 +Mm Hs ENKUR Ependymal cells MGC26778|enkurin|CFAP106|C10orf63 0.014 enkurin, TRPC channel interacting protein protein-coding gene 1 Ectoderm Brain 1.0 0.84 0.0106717 0.0069323 +Mm Hs FAM216B Ependymal cells FLJ40919|C13orf30 0.005 family with sequence similarity 216 member B protein-coding gene NA Ectoderm Brain 0.833333 0.586667 0.0 0.0 +Mm Hs KRT15 Ependymal cells K15|CK15|K1CO 0.022 keratin 15 protein-coding gene 1 Ectoderm Brain 0.166667 0.193333 0.0477087 0.0156139 +Mm Hs CATIP Ependymal cells MGC50811|C2orf62 0.003 ciliogenesis associated TTC17 interacting protein protein-coding gene NA Ectoderm Brain 0.0 0.366667 0.000313873 0.000777454 +Mm Hs DNAH12 Ependymal cells DLP12|Dnahc3|HL-19|hdhc3|DHC3|FLJ40427|FLJ44290|DNHD2|DNAH12L|DNAH7L 0.008 dynein axonemal heavy chain 12 protein-coding gene NA Ectoderm Brain 0.833333 0.626667 0.00878845 0.0016197 +Mm Hs FAM166B Ependymal cells NA 0.003 family with sequence similarity 166 member B protein-coding gene NA Ectoderm Brain 0.5 0.42 0.0 0.0 +Mm Hs IQCG Ependymal cells DKFZp434B227|DRC9|CFAP122 0.011 IQ motif containing G protein-coding gene NA Ectoderm Brain 1.0 0.68 0.0241682 0.00226757 +Mm Hs SPEF2 Ependymal cells KPL2|FLJ23577|CT122 0.009 sperm flagellar 2 protein-coding gene NA Ectoderm Brain 0.666667 0.0 0.0116133 0.0 +Mm RABL2 Ependymal cells NA 0.009 RAB, member RAS oncogene family-like 2 protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs MYO16 Ependymal cells MYR8|KIAA0865|Myo16b|NYAP3|PPP1R107 0.001 myosin XVI protein-coding gene NA Ectoderm Brain 0.0 0.126667 0.0 0.000712666 +Mm Hs ODF3B Ependymal cells NA 0.009 outer dense fiber of sperm tails 3B protein-coding gene 1 Ectoderm Brain 0.833333 0.673333 0.0204018 0.000907029 +Mm Hs PLXNB2 Ependymal cells MM1|KIAA0315|PLEXB2 0.046 plexin B2 protein-coding gene NA Ectoderm Brain 0.166667 0.546667 0.0329567 0.045481 +Mm Hs TEKT1 Ependymal cells NA 0.015 tektin 1 protein-coding gene NA Ectoderm Brain 1.0 0.0 0.014752 0.0 +Mm Hs CHEK2 Ependymal cells CDS1|CHK2|HuCds1|PP1425|bA444G7|RAD53 0.005 checkpoint kinase 2 protein-coding gene NA Ectoderm Brain 0.0 0.353333 0.0081607 0.00136054 +Mm Hs CROCC Ependymal cells rootletin|ROLT 0.003 ciliary rootlet coiled-coil, rootletin protein-coding gene 1 Ectoderm Brain 0.0 0.38 0.0 0.000194363 +Mm Hs NME9 Ependymal cells TXL-2|NM23-H9|TXNDC6 0.003 NME/NM23 family member 9 protein-coding gene NA Ectoderm Brain 0.0 0.386667 0.000313873 0.000194363 +Mm Hs CFAP126 Ependymal cells Flattop|Fltp|C1orf192 0.013 cilia and flagella associated protein 126 protein-coding gene NA Ectoderm Brain 0.0 0.8 0.0 0.00816326 +Mm Hs MEIG1 Ependymal cells bA2K17.3|SPATA39 0.018 meiosis/spermiogenesis associated 1 protein-coding gene NA Ectoderm Brain 0.0 0.866667 0.0141243 0.0113379 +Mm Hs HSPA2 Ependymal cells NA 0.03 heat shock protein family A (Hsp70) member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.866667 0.0430006 0.0207969 +Mm Hs CFAP65 Ependymal cells DKFZp434O0527|MGC35338|CCDC108 0.006 cilia and flagella associated protein 65 protein-coding gene NA Ectoderm Brain 0.0 0.433333 0.0106717 0.000971817 +Mm Hs LRRC23 Ependymal cells B7|LRPB7 0.008 leucine rich repeat containing 23 protein-coding gene NA Ectoderm Brain 1.0 0.7 0.0081607 0.0016197 +Mm Hs TEKT4 Ependymal cells MGC27019 0.008 tektin 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0106717 0.0 +Mm Hs CALML4 Ependymal cells MGC4809|NY-BR-20 0.038 calmodulin like 4 protein-coding gene 1 Ectoderm Brain 0.0 0.766667 0.0 0.0395854 +Mm Hs PIFO Ependymal cells FLJ23853|pitchfork|C1orf88 0.014 primary cilia formation protein-coding gene NA Ectoderm Brain 1.0 0.84 0.0235405 0.00466472 +Mm Hs CRYGN Ependymal cells NA 0.004 crystallin gamma N protein-coding gene NA Ectoderm Brain 0.0 0.426667 0.000627746 0.000518303 +Mm Hs HDC Ependymal cells NA 0.019 histidine decarboxylase protein-coding gene 1 Ectoderm Brain 0.0 0.68 0.00156937 0.0164561 +Mm FAM183B Ependymal cells NA 0.021 family with sequence similarity 183, member B protein coding gene NA Ectoderm Brain 0.0 0.913333 0.0 0.0172983 +Mm Hs PCP4L1 Ependymal cells IQM1 0.044 Purkinje cell protein 4 like 1 protein-coding gene 1 Ectoderm Brain 0.0 0.78 0.0 0.0482669 +Mm Hs DYNLRB2 Ependymal cells DNLC2B|ROBLD2|DNCL2B 0.019 dynein light chain roadblock-type 2 protein-coding gene NA Ectoderm Brain 1.0 0.946667 0.0357815 0.00667315 +Mm Hs TMEM107 Ependymal cells MGC10744 0.032 transmembrane protein 107 protein-coding gene NA Ectoderm Brain 0.5 0.0 0.0266792 0.0 +Mm Hs RIIAD1 Ependymal cells FLJ36032|NCRNA00166|C1orf230 0.019 regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1 protein-coding gene 1 Ectoderm Brain 0.166667 0.0 0.0116133 0.0 +Mm Hs TMEM212 Ependymal cells FLJ23172 0.006 transmembrane protein 212 protein-coding gene 1 Ectoderm Brain 0.166667 0.0 0.0 0.0 +Mm Hs RSPH1 Ependymal cells FLJ32753|RSP44|RSPH10A|CILD24|TSGA2 0.021 radial spoke head component 1 protein-coding gene 0 Ectoderm Brain 1.0 0.0 0.0144382 0.0 +Mm Hs CCDC153 Ependymal cells LOC283152 0.006 coiled-coil domain containing 153 protein-coding gene 1 Ectoderm Brain 0.666667 0.76 0.000313873 0.000518303 +Mm Hs S100B Ependymal cells S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0332706 0.0 +Mm Hs AK7 Ependymal cells FLJ32864 0.006 adenylate kinase 7 protein-coding gene 1 Ectoderm Brain 0.5 0.6 0.00094162 0.00174927 +Mm Hs RARRES2 Ependymal cells TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0787822 0.0 +Mm Hs PVALB Ependymal cells D22S749 0.005 parvalbumin protein-coding gene 1 Ectoderm Brain 0.0 0.18 0.00345261 0.00414642 +Mm Hs ANGPTL2 Ependymal cells NA 0.013 angiopoietin like 2 protein-coding gene 1 Ectoderm Brain 0.0 0.00666667 0.00596359 0.014966 +Mm Hs CFAP54 Ependymal cells FLJ31514|FLJ44112|C12orf63|C12orf55 0.005 cilia and flagella associated protein 54 protein-coding gene 0 Ectoderm Brain 0.333333 0.486667 0.00156937 0.000712666 +Mm Hs STOML3 Ependymal cells SRO|Epb7.2l 0.004 stomatin like 3 protein-coding gene 1 Ectoderm Brain 0.166667 0.0 0.0 0.0 +Mm Hs PLTP Ependymal cells BPIFE 0.009 phospholipid transfer protein protein-coding gene 1 Ectoderm Brain 0.166667 0.04 0.0257376 0.00485909 +Mm Hs SSPO Ependymal cells SCO-spondin|KIAA0543|FLJ36112 0.0 SCO-spondin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs EFNB3 Ependymal cells LERK-8|EPLG8 0.046 ephrin B3 protein-coding gene 1 Ectoderm Brain 0.0 0.0333333 0.00251099 0.0567541 +Mm Hs MYB Ependymal cells c-myb 0.027 MYB proto-oncogene, transcription factor protein-coding gene 1 Ectoderm Brain 0.166667 0.246667 0.0131827 0.0261743 +Mm Hs RFX2 Ependymal cells FLJ14226 0.004 regulatory factor X2 protein-coding gene 1 Ectoderm Brain 0.166667 0.0 0.017263 0.0 +Mm Hs ZMYND10 Ependymal cells BLU|CILD22|DNAAF7 0.009 zinc finger MYND-type containing 10 protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0235405 0.0 +Mm Hs AK8 Ependymal cells FLJ32704|C9orf98 0.004 adenylate kinase 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0466667 0.00847458 0.00330418 +Mm Hs CFAP44 Ependymal cells FLJ11142|WDR52 0.007 cilia and flagella associated protein 44 protein-coding gene 1 Ectoderm Brain 0.666667 0.593333 0.00878845 0.00149012 +Mm Hs TM4SF1 Ependymal cells M3S1 0.118 transmembrane 4 L six family member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.177024 0.0 +Mm Hs NANOG Epiblast cells FLJ12581|FLJ40451 0.002 Nanog homeobox protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0 0.00218158 +Mm Hs POU5F1 Epiblast cells Oct4|MGC22487|OTF3 0.003 POU class 5 homeobox 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.000626566 0.00256657 +Mm Hs ERAS Epiblast cells HRAS2|HRASP 0.0 ES cell expressed Ras protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0 0.000192493 +Mm Hs CDH1 Epiblast cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0416667 0.0572345 +Mm Hs EPCAM Epiblast cells Ly74|TROP1|GA733-2|EGP34|EGP40|EGP-2|KSA|CD326|Ep-CAM|HEA125|KS1/4|MK-1|MH99|MOC31|323/A3|17-1A|TACST-1|CO-17A|M4S1|MIC18|TACSTD1 0.117 epithelial cell adhesion molecule protein-coding gene 1 Zygote Embryo 0.0 0.0 0.16886 0.104203 +Mm Hs CLDN6 Epiblast cells NA 0.018 claudin 6 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00626566 0.0192493 +Mm Hs CLDN7 Epiblast cells Hs.84359|CEPTRL2|CPETRL2 0.079 claudin 7 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.113722 0.0700032 +Mm FGF15 Epiblast cells NA 0.0 fibroblast growth factor 15 protein coding gene 1 Zygote Embryo 0.0 0.0 0.0 0.000641643 +Mm Hs SLC35D3 Epiblast cells FRCL1 0.001 solute carrier family 35 member D3 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0 0.0 +Mm Hs TDGF1 Epiblast cells CRIPTO|Cripto-1 0.007 teratocarcinoma-derived growth factor 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00814536 0.0 +Mm Hs CXCL12 Epiblast cells SCYB12|SDF-1a|SDF-1b|PBSF|TLSF-a|TLSF-b|TPAR1|SDF1A|SDF1B|SDF1 0.07 C-X-C motif chemokine ligand 12 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0269424 0.0814244 +Mm Hs SOX11 Epiblast cells NA 0.241 SRY-box 11 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0604637 0.0 +Mm Hs LEF1 Epiblast cells TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0093985 0.0277831 +Mm Hs CRMP1 Epiblast cells DPYSL1 0.149 collapsin response mediator protein 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0219298 0.181264 +Mm Hs DPYSL5 Epiblast cells CRMP5|Ulip6|CRMP-5|CRAM 0.055 dihydropyrimidinase like 5 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00438596 0.0682066 +Mm Hs BCL11A Epiblast cells BCL11A-XL|BCL11A-L|BCL11A-S|CTIP1|HBFQTL5|ZNF856|EVI9 0.134 B cell CLL/lymphoma 11A protein-coding gene 1 Zygote Embryo 0.0 0.0 0.113409 0.142637 +Mm Hs INA Epiblast cells NF-66|NEF5 0.098 internexin neuronal intermediate filament protein alpha protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0194236 0.118768 +Mm Hs MFAP2 Epiblast cells MAGP|MAGP-1 0.126 microfibril associated protein 2 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.0056391 0.157267 +Hs CD24 Epithelial cells CD24A 0.039 CD24 molecule protein-coding gene 1 Mesoderm Epithelium 0.735294 0.0 0.186194 0.0 +Mm Hs CEACAM1 Epithelial cells BGP1|CD66a|BGP 0.024 carcinoembryonic antigen related cell adhesion molecule 1 protein-coding gene NA Mesoderm Epithelium 0.647059 0.290323 0.0123496 0.0253954 +Mm Hs ST6GAL1 Epithelial cells SIAT1 0.006 ST6 beta-galactoside alpha-2,6-sialyltransferase 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00759975 0.0 +Mm Hs ITGB4 Epithelial cells CD104 0.013 integrin subunit beta 4 protein-coding gene NA Mesoderm Epithelium 0.0882353 0.0645161 0.0132996 0.0135656 +Mm Hs IL1R1 Epithelial cells D2S1473|CD121A|IL1R 0.008 interleukin 1 receptor type 1 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.0 0.0189994 0.00636492 +Mm Hs PROM1 Epithelial cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0645161 0.00728309 0.0241096 +Mm Hs CDH1 Epithelial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Epithelium 0.294118 0.290323 0.0389487 0.05677 +Mm Hs KRT1 Epithelial cells KRT1A 0.006 keratin 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00474984 0.00681497 +Mm Hs KRT7 Epithelial cells CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Mesoderm Epithelium 0.0 0.225806 0.10228 0.0470618 +Mm Hs MUC1 Epithelial cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Mesoderm Epithelium 0.382353 0.0 0.0291324 0.012537 +Mm Hs ICAM1 Epithelial cells CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00601647 0.0100296 +Mm Hs KRT14 Epithelial cells EBS3|EBS4 0.019 keratin 14 protein-coding gene 1 Mesoderm Epithelium 0.0 0.0 0.0199493 0.0192234 +Mm Hs KRT5 Epithelial cells KRT5A|EBS2 0.019 keratin 5 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.129032 0.0446485 0.0148515 +Mm Hs ITGAL Epithelial cells CD11A 0.013 integrin subunit alpha L protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00411653 0.0148515 +Mm Hs CD2 Epithelial cells NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0949968 0.029703 +Hs KLK3 Epithelial cells NA 0.002 kallikrein related peptidase 3 protein-coding gene NA Mesoderm Epithelium 0.0588235 0.0 0.010133 0.0 +Mm Hs ITGA5 Epithelial cells CD49e|FNRA 0.016 integrin subunit alpha 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0186827 0.016716 +Mm Hs ITGA4 Epithelial cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0113996 0.0413398 +Mm Hs ITGA2 Epithelial cells CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene NA Mesoderm Epithelium 0.0882353 0.0322581 0.0446485 0.00302173 +Hs KRT3 Epithelial cells CK3|K3 0.0 keratin 3 protein-coding gene 1 Mesoderm Epithelium 0.0 0.0 0.0 0.0 +Mm Hs KRT16 Epithelial cells NEPPK 0.005 keratin 16 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00854972 0.00456474 +Mm Hs SCNN1A Epithelial cells ENaCalpha|SCNN1 0.008 sodium channel epithelial 1 alpha subunit protein-coding gene NA Mesoderm Epithelium 0.0882353 0.0 0.00981634 0.0 +Mm Hs KRT15 Epithelial cells K15|CK15|K1CO 0.022 keratin 15 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.129032 0.0481317 0.0171017 +Mm Hs ITGA1 Epithelial cells VLA1|CD49a 0.043 integrin subunit alpha 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0231159 0.0489906 +Mm Hs KRT2 Epithelial cells KRTE|KRT2A 0.0 keratin 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +None KRT6 Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +Mm Hs SCNN1B Epithelial cells ENaCbeta 0.003 sodium channel epithelial 1 beta subunit protein-coding gene NA Mesoderm Epithelium 0.0882353 0.0 0.00221659 0.0 +Hs SCNN1D Epithelial cells ENaCdelta|dNaCh 0.0 sodium channel epithelial 1 delta subunit protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.000316656 0.0 +Mm Hs SCNN1G Epithelial cells ENaCgamma|SCNEG 0.002 sodium channel epithelial 1 gamma subunit protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +Hs IFI16 Epithelial cells IFNGIP1|PYHIN2 0.029 interferon gamma inducible protein 16 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.0 0.159911 0.0 +Mm Hs BOK Epithelial cells BCL2L9|BOKL|MGC4631 0.045 BOK, BCL2 family apoptosis regulator protein-coding gene NA Mesoderm Epithelium 0.0 0.0322581 0.00569981 0.0542626 +Mm Hs NKD1 Epithelial cells NA 0.043 naked cuticle homolog 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0117163 0.0516909 +Mm Hs FZD6 Epithelial cells Hfz6 0.012 frizzled class receptor 6 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00569981 0.0144014 +Mm Hs DKK3 Epithelial cells REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.0322581 0.0379987 0.035425 +Mm Hs NRP2 Epithelial cells VEGF165R2 0.04 neuropilin 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0357821 0.0414684 +Mm KAP Epithelial cells NA 0.007 kidney androgen regulated protein protein coding gene NA Mesoderm Epithelium 0.0 0.0322581 0.0 0.00912948 +Mm Hs SFRP5 Epithelial cells SARP3 0.004 secreted frizzled related protein 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00126662 0.0 +Mm Hs RAI14 Epithelial cells NORPEG|KIAA1334|RAI13|DKFZp564G013 0.024 retinoic acid induced 14 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0642812 0.0 +Mm Hs DEFB1 Epithelial cells HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene NA Mesoderm Epithelium 0.0588235 0.0322581 0.0256491 0.00527196 +Mm Hs KLK1 Epithelial cells Klk6 0.013 kallikrein 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.225806 0.00823306 0.0137585 +Mm Hs AGR2 Epithelial cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene NA Mesoderm Epithelium 0.852941 0.0967742 0.0649145 0.0123441 +Mm Hs APOA1 Epithelial cells NA 0.032 apolipoprotein A1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.069031 0.0257169 +Mm Hs GPA33 Epithelial cells A33 0.018 glycoprotein A33 protein-coding gene NA Mesoderm Epithelium 0.647059 0.225806 0.00538315 0.0190948 +Mm Hs ANPEP Epithelial cells gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Mesoderm Epithelium 0.176471 0.0967742 0.011083 0.016716 +None APN Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +Mm Hs CRYBA1 Epithelial cells CRYB1 0.0 crystallin beta A1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +Mm Hs BMI1 Epithelial cells RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00538315 0.00932236 +Mm Hs BRCA1 Epithelial cells RNF53|PPP1R53|FANCS 0.007 BRCA1, DNA repair associated protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0300823 0.00122155 +Mm Hs MUC16 Epithelial cells FLJ14303 0.001 mucin 16, cell surface associated protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00221659 0.000964382 +Mm Hs CEACAM5 Epithelial cells CD66e 0.004 carcinoembryonic antigen related cell adhesion molecule 5 protein-coding gene NA Mesoderm Epithelium 0.882353 0.0 0.0123496 0.000128584 +Mm Hs CTSE Epithelial cells NA 0.009 cathepsin E protein-coding gene NA Mesoderm Epithelium 0.0588235 0.16129 0.00823306 0.00867944 +Mm Hs SCGB1A1 Epithelial cells CC10|CCSP|CC16|UGB 0.028 secretoglobin family 1A member 1 protein-coding gene 1 Mesoderm Epithelium 0.0294118 0.0 0.0107663 0.0 +None DESMIN Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +Mm Hs EXO1 Epithelial cells HEX1|hExoI 0.005 exonuclease 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00126662 0.00591488 +Mm Hs FOXA1 Epithelial cells HNF3A 0.008 forkhead box A1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0322581 0.0107663 0.00617205 +Mm Hs GABRP Epithelial cells NA 0.002 gamma-aminobutyric acid type A receptor pi subunit protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00538315 0.00173589 +Mm Hs GGT1 Epithelial cells D22S672|D22S732|CD224 0.01 gamma-glutamyltransferase 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00189994 0.0122155 +Mm Hs SFN Epithelial cells YWHAS 0.051 stratifin protein-coding gene NA Mesoderm Epithelium 0.823529 0.0 0.070931 0.0 +Mm Hs KRT13 Epithelial cells CK13|MGC3781|MGC161462 0.004 keratin 13 protein-coding gene 1 Mesoderm Epithelium 0.0 0.0322581 0.00411653 0.00392182 +Mm Hs LTF Epithelial cells HLF2 0.016 lactotransferrin protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00633312 0.0183876 +Mm Hs SLC46A2 Epithelial cells Ly110|TSCOT 0.002 solute carrier family 46 member 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +None MEP1 Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +None MEP7 Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +None NES1 Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +Mm Hs KLK10 Epithelial cells NES1 0.004 kallikrein related peptidase 10 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00221659 0.00405041 +Mm Hs P2RX7 Epithelial cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00886637 0.00347178 +Mm Hs CDKN2A Epithelial cells p16|INK4a|CMM2|ARF|INK4|p16INK4a|p19Arf|p14ARF|CDKN2|MLM 0.025 cyclin dependent kinase inhibitor 2A protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.030399 0.0173589 +Hs TP63 Epithelial cells SHFM4|EEC3|p63|p73L|OFC8|KET|p73H|p53CP|TP73L|TP53L|TP53CP 0.001 tumor protein p63 protein-coding gene 1 Mesoderm Epithelium 0.0 0.0 0.00569981 0.0 +Mm Hs CDH3 Epithelial cells CDHP|PCAD 0.006 cadherin 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0113996 0.00385753 +None PPN1 Epithelial cells NA 0.0 NA NA NA Mesoderm Epithelium NA NA NA NA +Mm Hs PSCA Epithelial cells NA 0.004 prostate stem cell antigen protein-coding gene NA Mesoderm Epithelium 0.0588235 0.0645161 0.0132996 0.00154301 +Mm Hs AGER Epithelial cells SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00126662 0.0135656 +Mm Hs ZFP42 Epithelial cells REX1|ZNF754 0.006 ZFP42 zinc finger protein protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00316656 0.0 +Mm Hs SPRR1B Epithelial cells GADD33|SPRR1 0.002 small proline rich protein 1B protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00538315 0.0 +Hs SI Epithelial cells NA 0.0 sucrase-isomaltase protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +Mm Hs TTR Epithelial cells HsT2651|CTS|PALB|CTS1 0.055 transthyretin protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0740975 0.0 +Mm Hs TM4SF20 Epithelial cells FLJ22800|TCCE518 0.019 transmembrane 4 L six family member 20 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00316656 0.0 +Mm Hs TSTD1 Epithelial cells KAT 0.058 thiosulfate sulfurtransferase like domain containing 1 protein-coding gene NA Mesoderm Epithelium 0.5 0.0 0.214693 0.0 +Mm Hs SYCN Epithelial cells SYL|FLJ27441|INSSA1 0.008 syncollin protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00474984 0.0 +Mm Hs HBEGF Epithelial cells HEGFL|DTS|DTR 0.051 heparin binding EGF like growth factor protein-coding gene NA Mesoderm Epithelium 0.117647 0.258065 0.0329322 0.0557413 +Mm Hs PIGR Epithelial cells NA 0.031 polymeric immunoglobulin receptor protein-coding gene NA Mesoderm Epithelium 0.911765 0.290323 0.0348322 0.02861 +Mm PRSS32 Epithelial cells NA 0.013 protease, serine 32 protein coding gene NA Mesoderm Epithelium 0.0 0.225806 0.0 0.0154301 +Mm Hs MUC13 Epithelial cells DRCC1 0.03 mucin 13, cell surface associated protein-coding gene NA Mesoderm Epithelium 0.794118 0.258065 0.00949968 0.0333033 +Mm Hs SELENBP1 Epithelial cells hSP56|hSBP|LPSB 0.046 selenium binding protein 1 protein-coding gene NA Mesoderm Epithelium 0.647059 0.0 0.0576314 0.0 +Mm Hs ELF3 Epithelial cells ESE-1|ERT|ESX 0.048 E74 like ETS transcription factor 3 protein-coding gene NA Mesoderm Epithelium 0.941176 0.354839 0.107663 0.0328533 +Mm MUC3 Epithelial cells NA 0.01 mucin 3, intestinal protein coding gene NA Mesoderm Epithelium 0.0 0.193548 0.0 0.0121512 +Mm OIT1 Epithelial cells NA 0.013 oncoprotein induced transcript 1 protein coding gene NA Mesoderm Epithelium 0.0 0.354839 0.0 0.0153015 +Mm Hs TSPAN1 Epithelial cells TSPAN-1|NET-1 0.028 tetraspanin 1 protein-coding gene NA Mesoderm Epithelium 0.970588 0.0 0.0557315 0.0 +Mm Hs GUCA2A Epithelial cells STARA|GUCA2 0.015 guanylate cyclase activator 2A protein-coding gene NA Mesoderm Epithelium 0.823529 0.225806 0.00759975 0.0149801 +Mm Hs PHGR1 Epithelial cells NA 0.031 proline, histidine and glycine rich 1 protein-coding gene NA Mesoderm Epithelium 0.911765 0.290323 0.0329322 0.02816 +Mm Hs LYPD8 Epithelial cells NA 0.024 LY6/PLAUR domain containing 8 protein-coding gene NA Mesoderm Epithelium 0.294118 0.290323 0.00158328 0.0270027 +Mm Hs LGALS4 Epithelial cells GAL4 0.032 galectin 4 protein-coding gene NA Mesoderm Epithelium 0.882353 0.290323 0.029449 0.0302173 +Mm Hs GATA2 Epithelial cells NFE1B 0.02 GATA binding protein 2 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.225806 0.0132996 0.0214093 +Mm Hs SEC23B Epithelial cells CDA-II|CDAII|HEMPAS|CDAN2 0.02 Sec23 homolog B, coat complex II component protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0240659 0.0 +Mm Hs TSPAN8 Epithelial cells CO-029|TM4SF3 0.047 tetraspanin 8 protein-coding gene NA Mesoderm Epithelium 0.941176 0.0 0.0383154 0.0 +Mm Hs DLX5 Epithelial cells NA 0.019 distal-less homeobox 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.0967742 0.00569981 0.0223094 +Mm Hs DGAT2 Epithelial cells NA 0.023 diacylglycerol O-acyltransferase 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0967742 0.0240659 0.0240453 +Mm Hs ITPR2 Epithelial cells IP3R2|CFAP48 0.016 inositol 1,4,5-trisphosphate receptor type 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.258065 0.00569981 0.0174232 +Mm Hs THRSP Epithelial cells SPOT14|Lpgp|THRP|LPGP1 0.019 thyroid hormone responsive protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.000316656 0.0 +Mm Hs PLA2G4A Epithelial cells cPLA2-alpha|PLA2G4 0.007 phospholipase A2 group IVA protein-coding gene NA Mesoderm Epithelium 0.0 0.16129 0.000316656 0.0081651 +Mm Hs SLC25A48 Epithelial cells FLJ44862|HDMCP 0.001 solute carrier family 25 member 48 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0 0.0 +Mm Hs PGR Epithelial cells NR3C3 0.003 progesterone receptor protein-coding gene NA Mesoderm Epithelium 0.0 0.193548 0.00664978 0.00154301 +Mm ZFP322A Epithelial cells NA 0.009 zinc finger protein 322A protein coding gene NA Mesoderm Epithelium NA NA NA NA +Mm Hs FERMT1 Epithelial cells FLJ20116|URP1|KIND1|UNC112A|C20orf42 0.019 fermitin family member 1 protein-coding gene NA Mesoderm Epithelium 0.0588235 0.322581 0.0148828 0.0192234 +Mm ZFP704 Epithelial cells NA 0.021 zinc finger protein 704 protein coding gene NA Mesoderm Epithelium NA NA NA NA +Mm Hs EHF Epithelial cells ESE3|ESEJ 0.024 ETS homologous factor protein-coding gene NA Mesoderm Epithelium 0.176471 0.354839 0.0500317 0.0186447 +Mm Hs PLEKHS1 Epithelial cells FLJ23537|bA211N11.2|C10orf81 0.001 pleckstrin homology domain containing S1 protein-coding gene NA Mesoderm Epithelium 0.0 0.193548 0.00221659 0.000385753 +Mm Hs CDKL1 Epithelial cells KKIALRE 0.002 cyclin dependent kinase like 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.16129 0.0 0.00199306 +Mm Hs MECOM Epithelial cells MDS1-EVI1|PRDM3|KMT8E|MDS1|EVI1 0.011 MDS1 and EVI1 complex locus protein-coding gene NA Mesoderm Epithelium 0.0 0.290323 0.0196327 0.00887232 +Mm Hs MSX1 Epithelial cells HYD1|OFC5|HOX7 0.015 msh homeobox 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.258065 0.0250158 0.0127298 +Mm Hs RNF128 Epithelial cells FLJ23516|GRAIL 0.024 ring finger protein 128, E3 ubiquitin protein ligase protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00158328 0.0 +Mm Hs ANLN Epithelial cells ANILLIN|Scraps|scra 0.023 anillin actin binding protein protein-coding gene NA Mesoderm Epithelium 0.0 0.16129 0.0205826 0.0228237 +None CASC5 Epithelial cells NA 0.034 NA NA NA Mesoderm Epithelium 0.0 0.225806 0.0 0.0423685 +Mm Hs CKAP2 Epithelial cells LB1|FLJ10749|se20-10|TMAP 0.033 cytoskeleton associated protein 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.225806 0.0794807 0.0216022 +Mm Hs HMMR Epithelial cells RHAMM|CD168 0.046 hyaluronan mediated motility receptor protein-coding gene NA Mesoderm Epithelium 0.0 0.290323 0.0414819 0.0459046 +Mm Hs KIF15 Epithelial cells HKLP2|NY-BR-62|KNSL7 0.022 kinesin family member 15 protein-coding gene NA Mesoderm Epithelium 0.0 0.322581 0.019316 0.022888 +Mm Hs CKAP2L Epithelial cells FLJ40629|radmis 0.019 cytoskeleton associated protein 2 like protein-coding gene NA Mesoderm Epithelium 0.0 0.354839 0.0126662 0.0201234 +Mm Hs KIF20B Epithelial cells MPP1|KRMP1|MPHOSPH1 0.043 kinesin family member 20B protein-coding gene NA Mesoderm Epithelium 0.0 0.354839 0.0782141 0.0331105 +Mm Hs HIRIP3 Epithelial cells NA 0.035 HIRA interacting protein 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.322581 0.0319823 0.0352964 +Mm Hs INCENP Epithelial cells FLJ31633 0.047 inner centromere protein protein-coding gene NA Mesoderm Epithelium 0.0 0.387097 0.0 0.0576701 +Mm Hs KIF23 Epithelial cells MKLP1|MKLP-1|KNSL5 0.032 kinesin family member 23 protein-coding gene NA Mesoderm Epithelium 0.0 0.419355 0.0183661 0.0344606 +Mm Hs PRC1 Epithelial cells ASE1 0.043 protein regulator of cytokinesis 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.387097 0.0554148 0.0376109 +Mm Hs ECT2 Epithelial cells ARHGEF31 0.015 epithelial cell transforming 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0645161 0.0104497 0.0147872 +Mm Hs CXCL10 Epithelial cells IFI10|IP-10|crg-2|mob-1|C7|gIP-10|INP10|SCYB10 0.009 C-X-C motif chemokine ligand 10 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.010133 0.00893661 +Hs CXCL8 Epithelial cells SCYB8|LUCT|LECT|MDNCF|TSG-1|IL-8|NAP-1|3-10C|MONAP|AMCF-I|LYNAP|NAF|b-ENAP|GCP-1|K60|GCP1|IL8 0.02 C-X-C motif chemokine ligand 8 protein-coding gene NA Mesoderm Epithelium 0.0588235 0.0 0.119379 0.0 +Mm Hs CCL20 Epithelial cells LARC|MIP-3a|exodus-1|ST38|CKb4|SCYA20 0.005 C-C motif chemokine ligand 20 protein-coding gene NA Mesoderm Epithelium 0.147059 0.0 0.0246992 0.00090009 +Mm Hs CXCL17 Epithelial cells Dcip1|UNQ473|VCC1 0.007 C-X-C motif chemokine ligand 17 protein-coding gene NA Mesoderm Epithelium 0.0294118 0.0 0.0275491 0.00366465 +Mm Hs PRG4 Epithelial cells JCAP|SZP|HAPO|bG174L6.2|FLJ32635|CACP 0.004 proteoglycan 4 protein-coding gene NA Mesoderm Epithelium 0.0 0.0322581 0.00158328 0.00437187 +Mm Hs ALOX15 Epithelial cells 15-LOX-1 0.002 arachidonate 15-lipoxygenase protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00474984 0.00180018 +Mm Hs F5 Epithelial cells NA 0.003 coagulation factor V protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00253325 0.00282885 +Mm Hs EMILIN2 Epithelial cells FLJ33200|FOAP-10 0.017 elastin microfibril interfacer 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0177327 0.0163302 +Mm SAA3 Epithelial cells NA 0.006 serum amyloid A 3 protein coding gene NA Mesoderm Epithelium NA NA NA NA +Mm SPRR2A1 Epithelial cells NA 0.007 small proline-rich protein 2A1 protein coding gene NA Mesoderm Epithelium NA NA NA NA +Mm Hs SPTSSB Epithelial cells ADMP|ssSPTb|C3orf57 0.005 serine palmitoyltransferase small subunit B protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00221659 0.0 +Mm Hs FMO5 Epithelial cells NA 0.005 flavin containing monooxygenase 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.16129 0.00284991 0.00597917 +Mm Hs IVL Epithelial cells NA 0.001 involucrin protein-coding gene NA Mesoderm Epithelium 0.0 0.16129 0.000316656 0.00135013 +Mm Hs VSIG2 Epithelial cells CTXL|CTH 0.008 V-set and immunoglobulin domain containing 2 protein-coding gene NA Mesoderm Epithelium 0.617647 0.0 0.0167828 0.0 +Mm Hs AQP3 Epithelial cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene NA Mesoderm Epithelium 0.0588235 0.129032 0.0712476 0.0156873 +Mm Hs PAQR5 Epithelial cells FLJ20190|MPRG 0.013 progestin and adipoQ receptor family member 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.129032 0.000633312 0.0157516 +Mm Hs EPCAM Epithelial cells Ly74|TROP1|GA733-2|EGP34|EGP40|EGP-2|KSA|CD326|Ep-CAM|HEA125|KS1/4|MK-1|MH99|MOC31|323/A3|17-1A|TACST-1|CO-17A|M4S1|MIC18|TACSTD1 0.117 epithelial cell adhesion molecule protein-coding gene 1 Mesoderm Epithelium 0.911765 0.645161 0.160861 0.103125 +Mm Hs CLDN1 Epithelial cells SEMP1|ILVASC 0.01 claudin 1 protein-coding gene 1 Mesoderm Epithelium 0.0294118 0.0 0.0284991 0.00565771 +Mm Hs OCLN Epithelial cells PPP1R115 0.013 occludin protein-coding gene 1 Mesoderm Epithelium 0.0 0.0322581 0.000316656 0.0160087 +Mm Hs MUC5AC Epithelial cells NA 0.0 mucin 5AC, oligomeric mucus/gel-forming protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.000316656 0.000578629 +Mm Hs GHRL Epsilon cells MTLRP|ghrelin|obestatin 0.003 ghrelin and obestatin prepropeptide protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000626566 0.00378569 +Mm Hs ANXA13 Epsilon cells ANX13 0.013 annexin A13 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00156642 0.0153353 +Mm Hs PHGR1 Epsilon cells NA 0.031 proline, histidine and glycine rich 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0422932 0.0286814 +Mm Hs BMP4 Epsilon cells BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0241228 0.0166185 +Mm Hs HMGCS2 Epsilon cells NA 0.021 3-hydroxy-3-methylglutaryl-CoA synthase 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0134712 0.0232275 +Mm Hs TM4SF5 Epsilon cells NA 0.022 transmembrane 4 L six family member 5 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00250627 0.0 +Mm Hs OLFML3 Epsilon cells HNOEL-iso|OLF44 0.053 olfactomedin like 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.031015 0.0580687 +Mm Hs ASGR1 Epsilon cells CLEC4H1 0.004 asialoglycoprotein receptor 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0147243 0.00198909 +Mm Hs COX6A2 Epsilon cells NA 0.011 cytochrome c oxidase subunit 6A2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313283 0.0130895 +Mm Hs NPY1R Epsilon cells NA 0.002 neuropeptide Y receptor Y1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313283 0.00288739 +Hs FAXDC2 Epsilon cells FLJ13758|C5orf4 0.0 fatty acid hydroxylase domain containing 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0018797 0.0 +Mm Hs SLC7A9 Epsilon cells CSNU3 0.006 solute carrier family 7 member 9 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm GRAMD2 Epsilon cells NA 0.002 GRAM domain containing 2 protein coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00211742 +Hs C2ORF54 Epsilon cells FLJ22671 0.0 chromosome 2 open reading frame 54 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Hs GHRLOS Epsilon cells NCRNA00068|GHRL-AS1 0.0 ghrelin opposite strand/antisense RNA non-coding RNA 1 Endoderm Pancreas NA NA NA NA +Mm Hs BHMT Epsilon cells BHMT1 0.003 betaine--homocysteine S-methyltransferase protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00219298 0.00346487 +Mm Hs OPRK1 Epsilon cells KOR|OPRK 0.001 opioid receptor kappa 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.000705807 +Mm Hs PTGER4 Epsilon cells EP4 0.005 prostaglandin E receptor 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0134712 0.00391402 +Mm Hs ITGA4 Epsilon cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0112782 0.0412576 +Mm Hs EYA4 Epsilon cells DFNA10|CMD1J 0.002 EYA transcriptional coactivator and phosphatase 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00156642 0.00237408 +Mm Hs XYLB Epsilon cells FLJ10343|FLJ12539 0.001 xylulokinase protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs ELOVL2 Epsilon cells Ssc2 0.003 ELOVL fatty acid elongase 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00093985 0.00295156 +Mm Hs AFF3 Epsilon cells MLLT2-like|LAF4 0.006 AF4/FMR2 family member 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00595238 0.00680141 +Mm Hs CORIN Epsilon cells PRSC|ATC2|Lrp4|TMPRSS10 0.001 corin, serine peptidase protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00102663 +Mm Hs MYO1A Epsilon cells MYHL|DFNA48 0.013 myosin IA protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313283 0.0160411 +Mm Hs HRH2 Epsilon cells NA 0.001 histamine receptor H2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0037594 6.41643e-05 +Mm Hs CALCR Epsilon cells CTR 0.0 calcitonin receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313283 0.000384986 +Mm Hs SLC6A16 Epsilon cells NTT5 0.004 solute carrier family 6 member 16 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0178571 0.0 +Mm Hs PCSK6 Epsilon cells SPC4|PACE4 0.007 proprotein convertase subtilisin/kexin type 6 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00853385 +Mm Hs ADAMTS6 Epsilon cells ADAM-TS6 0.001 ADAM metallopeptidase with thrombospondin type 1 motif 6 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00657895 0.0 +Mm Hs COL22A1 Epsilon cells NA 0.003 collagen type XXII alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0018797 0.00384986 +Mm Hs FAM124A Epsilon cells FLJ30707 0.002 family with sequence similarity 124 member A protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00256657 +Mm Hs COL12A1 Epsilon cells COL12A1L 0.013 collagen type XII alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0056391 0.0127045 +Mm Hs CD109 Epsilon cells FLJ38569|DKFZp762L1111|CPAMD7 0.006 CD109 molecule protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00219298 0.00635226 +Mm Hs THSD4 Epsilon cells FVSY9334|PRO34005|FLJ13710|ADAMTSL6 0.004 thrombospondin type 1 domain containing 4 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00689223 0.0 +Mm Hs ARX Epsilon cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00219298 0.0236124 +Mm Hs NKX2-2 Epsilon cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0103383 0.000641643 +Mm Hs ACSL1 Epsilon cells LACS|ACS1|LACS1|FACL1|FACL2 0.022 acyl-CoA synthetase long chain family member 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0191103 0.0233558 +Mm Hs FRZB Epsilon cells FRZB-PEN|FRZB1|SRFP3|FRP-3|SFRP3|FRE|FRITZ|FRZB-1|FZRB|hFIZ 0.012 frizzled related protein protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0303885 0.00795637 +Mm MS4A8A Epsilon cells NA 0.006 membrane-spanning 4-domains, subfamily A, member 8A protein coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.00725056 +Mm Hs VTN Epsilon cells VN 0.029 vitronectin protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00971178 0.0 +Mm Hs APOH Epsilon cells BG|B2G1 0.004 apolipoprotein H protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00783208 0.00340071 +Mm Hs SPINK1 Epsilon cells Spink3|PCTT|PSTI|TATI 0.029 serine peptidase inhibitor, Kazal type 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0388471 0.0 +Mm Hs VSTM2L Epsilon cells dJ1118M15.2|C20orf102 0.011 V-set and transmembrane domain containing 2 like protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00501253 0.0 +Mm Hs SPTSSB Epsilon cells ADMP|ssSPTb|C3orf57 0.005 serine palmitoyltransferase small subunit B protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00219298 0.0 +Mm Hs S100A6 Epsilon cells 2A9|PRA|CABP|CACY 0.317 S100 calcium binding protein A6 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.659774 0.0 +Mm Hs KRT8 Epsilon cells K8|CK8|CYK8|K2C8|KO 0.12 keratin 8 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.211153 0.0931023 +Mm Hs CGA Erythroblasts GPHa|GPHA1|FSHA|LHA|TSHA 0.003 glycoprotein hormones, alpha polypeptide protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00845865 0.00147578 +Mm Hs TFRC Erythroblasts CD71|TFR1|p90 0.042 transferrin receptor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0614035 0.0 +Mm Hs CDH1 Erythroblasts uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0416667 0.0572345 +Mm Hs WRN Erythroblasts RECQL2|RECQ3 0.004 Werner syndrome RecQ like helicase protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00595238 0.0 +Mm Hs CD44 Erythroblasts IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.300439 0.0877767 +Mm Hs KLF1 Erythroblasts EKLF 0.009 Kruppel like factor 1 protein-coding gene NA Mesoderm Blood 0.0 0.0 0.0253759 0.00641643 +Mm Hs BCL11A Erythroblasts BCL11A-XL|BCL11A-L|BCL11A-S|CTIP1|HBFQTL5|ZNF856|EVI9 0.134 B cell CLL/lymphoma 11A protein-coding gene NA Mesoderm Blood 0.0 0.0 0.113409 0.142637 +Mm Hs BPGM Erythroblasts NA 0.063 bisphosphoglycerate mutase protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0460526 0.0692332 +Mm Hs ETS1 Erythroblasts FLJ10768|ETS-1 0.095 ETS proto-oncogene 1, transcription factor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0388471 0.109143 +Mm Hs EPOR Erythroblasts NA 0.004 erythropoietin receptor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0147243 0.00250241 +Mm Hs IGBP1 Erythroblasts NA 0.089 immunoglobulin binding protein 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.128759 0.0712223 +Mm Hs TFR2 Erythroblasts HFE3|TFRC2 0.003 transferrin receptor 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00783208 0.0 +Mm Hs GYPA Erythroblasts GPA|CD235a 0.011 glycophorin A (MNS blood group) protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0272556 0.00821303 +Mm Hs LMNB1 Erythroblasts NA 0.138 lamin B1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.037594 0.161052 +Mm Hs LRP8 Erythroblasts APOER2|MCI1|LRP-8|HSZ75190 0.029 LDL receptor related protein 8 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00125313 0.0367661 +Mm Hs GRSF1 Erythroblasts NA 0.056 G-rich RNA sequence binding factor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.106516 0.0408726 +Mm Hs USE1 Erythroblasts SLT1|MDS032|D12 0.015 unconventional SNARE in the ER 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs ITGB1 Erythroblasts CD29|GPIIA|FNRB|MSK12|MDF2 0.276 integrin subunit beta 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.168546 0.302021 +Mm Hs CFP Erythroblasts PFC 0.035 complement factor properdin protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.035401 0.034777 +Mm Hs ENG Erythroblasts END|HHT1|CD105|ORW1|ORW 0.058 endoglin protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0657895 0.0592878 +Mm Hs KIT Erythroblasts CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00250627 0.0185435 +Mm Hs LMO2 Erythroblasts TTG2|RHOM2|RBTN2|RBTNL1 0.072 LIM domain only 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.018797 0.0841835 +Mm Hs GATA1 Erythroblasts ERYF1|NFE1|GATA-1 0.008 GATA binding protein 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0178571 0.00590311 +Mm Hs TAL1 Erythroblasts bHLHa17|TCL5 0.004 TAL bHLH transcription factor 1, erythroid differentiation factor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00657895 0.0 +Hs KMT5A Erythroblasts SET8|SET07|PR-Set7|SETD8 0.002 lysine methyltransferase 5A protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0103383 0.0 +Mm Hs PIEZO1 Erythroblasts KIAA0233|FAM38A 0.01 piezo type mechanosensitive ion channel component 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0162907 0.00827719 +Mm HBB-BS Erythroid-like and erythroid precursor cells NA 0.124 hemoglobin, beta adult s chain protein coding gene 1 Mesoderm Blood 0.0 0.953587 0.0 0.141973 +Mm Hs ALAS2 Erythroid-like and erythroid precursor cells ASB 0.019 5'-aminolevulinate synthase 2 protein-coding gene 1 Mesoderm Blood 0.842105 0.675106 0.000662032 0.00462601 +Mm Hs HEXA Erythroid-like and erythroid precursor cells NA 0.141 hexosaminidase subunit alpha protein-coding gene NA Mesoderm Blood 0.0 0.0337553 0.0456802 0.164451 +Mm Hs AQP1 Erythroid-like and erythroid precursor cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene NA Mesoderm Blood 0.0701754 0.181435 0.0148957 0.040331 +Mm Hs CCNA2 Erythroid-like and erythroid precursor cells CCNA 0.069 cyclin A2 protein-coding gene NA Mesoderm Blood 0.152047 0.181435 0.0344257 0.0721918 +Mm Hs PKLR Erythroid-like and erythroid precursor cells NA 0.0 pyruvate kinase L/R protein-coding gene NA Mesoderm Blood 0.0116959 0.0 0.0 0.000521241 +Mm Hs LOX Erythroid-like and erythroid precursor cells NA 0.017 lysyl oxidase protein-coding gene NA Mesoderm Blood 0.0 0.00421941 0.0158888 0.0170706 +Mm Hs ARG1 Erythroid-like and erythroid precursor cells NA 0.007 arginase 1 protein-coding gene NA Mesoderm Blood 0.0 0.0 0.00364118 0.00729737 +Hs HBB Erythroid-like and erythroid precursor cells CD113t-C|beta-globin 0.03 hemoglobin subunit beta protein-coding gene 1 Mesoderm Blood 0.959064 0.0 0.129096 0.0 +Hs HBA1 Erythroid-like and erythroid precursor cells HBA-T3 0.025 hemoglobin subunit alpha 1 protein-coding gene NA Mesoderm Blood 0.994152 0.0 0.10427 0.0 +Hs HBA2 Erythroid-like and erythroid precursor cells HBA-T2 0.03 hemoglobin subunit alpha 2 protein-coding gene NA Mesoderm Blood 1.0 0.0 0.132406 0.0 +Hs HBG1 Erythroid-like and erythroid precursor cells HBG-T2 0.003 hemoglobin subunit gamma 1 protein-coding gene NA Mesoderm Blood 0.157895 0.0 0.00959947 0.0 +Hs HBG2 Erythroid-like and erythroid precursor cells HBG-T1 0.004 hemoglobin subunit gamma 2 protein-coding gene NA Mesoderm Blood 0.134503 0.0 0.020192 0.0 +Mm Hs CEACAM1 Erythroid-like and erythroid precursor cells BGP1|CD66a|BGP 0.024 carcinoembryonic antigen related cell adhesion molecule 1 protein-coding gene NA Mesoderm Blood 0.0 0.0 0.020192 0.0263226 +Mm Hs CD36 Erythroid-like and erythroid precursor cells SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Blood 0.274854 0.0295359 0.020854 0.0443706 +Mm Hs GYPA Erythroid-like and erythroid precursor cells GPA|CD235a 0.011 glycophorin A (MNS blood group) protein-coding gene 1 Mesoderm Blood 0.497076 0.49789 0.000662032 0.000651551 +Mm Hs THBS1 Erythroid-like and erythroid precursor cells TSP1|THBS|TSP|THBS-1|TSP-1 0.04 thrombospondin 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0549487 0.0 +Mm Hs ITGA4 Erythroid-like and erythroid precursor cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene 1 Mesoderm Blood 0.0760234 0.135021 0.00761337 0.0398097 +Hs GYPB Erythroid-like and erythroid precursor cells GPB|CD235b 0.005 glycophorin B (MNS blood group) protein-coding gene 1 Mesoderm Blood 0.561404 0.0 0.000331016 0.0 +Hs AHSP Erythroid-like and erythroid precursor cells EDRF|ERAF 0.01 alpha hemoglobin stabilizing protein protein-coding gene NA Mesoderm Blood 0.900585 0.0 0.0158888 0.0 +Hs HBM Erythroid-like and erythroid precursor cells HBK|HBAP2 0.01 hemoglobin subunit mu protein-coding gene NA Mesoderm Blood 0.900585 0.0 0.0122476 0.0 +Mm Hs FECH Erythroid-like and erythroid precursor cells NA 0.04 ferrochelatase protein-coding gene NA Mesoderm Blood 0.660819 0.881857 0.00331016 0.0286682 +Mm Hs EPOR Erythroid-like and erythroid precursor cells NA 0.004 erythropoietin receptor protein-coding gene NA Mesoderm Blood 0.245614 0.151899 0.00165508 0.000195465 +Mm Hs KIT Erythroid-like and erythroid precursor cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Blood 0.0 0.0421941 0.00264813 0.0181783 +Mm Hs BPGM Erythroid-like and erythroid precursor cells NA 0.063 bisphosphoglycerate mutase protein-coding gene NA Mesoderm Blood 0.538012 0.662447 0.0182059 0.060073 +Mm Hs DCAF12 Erythroid-like and erythroid precursor cells DKFZP434O125|MGC1058|CT102|TCC52|KIAA1892|WDR40A 0.039 DDB1 and CUL4 associated factor 12 protein-coding gene NA Mesoderm Blood 0.415205 0.177215 0.040053 0.0343367 +Hs HBD Erythroid-like and erythroid precursor cells NA 0.016 hemoglobin subunit delta protein-coding gene NA Mesoderm Blood 0.894737 0.0 0.0546177 0.0 +Mm Hs HEMGN Erythroid-like and erythroid precursor cells EDAG|CT155 0.011 hemogen protein-coding gene NA Mesoderm Blood 0.608187 0.206751 0.0139027 0.00143341 +Mm Hs HMBS Erythroid-like and erythroid precursor cells PBGD|UPS 0.046 hydroxymethylbilane synthase protein-coding gene NA Mesoderm Blood 0.51462 0.308017 0.0294604 0.0364868 +Mm Hs NCOA4 Erythroid-like and erythroid precursor cells ARA70|RFG|ELE1|PTC3|DKFZp762E1112 0.02 nuclear receptor coactivator 4 protein-coding gene NA Mesoderm Blood 0.643275 0.0 0.0635551 0.00351837 +Mm Hs RBM38 Erythroid-like and erythroid precursor cells HSRNASEB|SEB4D|seb4B|dJ800J21.2|RNPC1 0.01 RNA binding motif protein 38 protein-coding gene NA Mesoderm Blood 0.105263 0.0 0.020523 0.0 +Mm Hs UCP2 Erythroid-like and erythroid precursor cells SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene NA Mesoderm Blood 0.0 0.0 0.00529626 0.0 +Mm Hs UBB Erythroid-like and erythroid precursor cells MGC8385|FLJ25987 0.022 ubiquitin B protein-coding gene NA Mesoderm Blood 0.0 0.0 0.00529626 0.0 +Mm Hs TMCC2 Erythroid-like and erythroid precursor cells HUCEP11|FLJ38497 0.014 transmembrane and coiled-coil domain family 2 protein-coding gene NA Mesoderm Blood 0.134503 0.0 0.0 0.0 +Mm Hs SLC4A1 Erythroid-like and erythroid precursor cells RTA1A|CD233|FR|SW|WR|EPB3|AE1|DI|WD 0.009 solute carrier family 4 member 1 (Diego blood group) protein-coding gene NA Mesoderm Blood 0.619883 0.0 0.000662032 0.0 +Mm Hs SLC25A39 Erythroid-like and erythroid precursor cells FLJ22407|CGI-69 0.108 solute carrier family 25 member 39 protein-coding gene NA Mesoderm Blood 0.871345 0.0 0.19232 0.0 +Mm Hs SLC25A37 Erythroid-like and erythroid precursor cells MSCP|MFRN|MFRN1|HT015 0.032 solute carrier family 25 member 37 protein-coding gene 1 Mesoderm Blood 0.877193 0.0 0.0791129 0.0 +Mm Hs FOSB Erythroid-like and erythroid precursor cells G0S3|GOSB|GOS3|MGC42291|DKFZp686C0818 0.125 FosB proto-oncogene, AP-1 transcription factor subunit protein-coding gene NA Mesoderm Blood 0.116959 0.0 0.206554 0.115455 +Mm GH Erythroid-like and erythroid precursor cells NA 0.005 growth hormone protein coding gene NA Mesoderm Blood 0.0 0.0548523 0.0 0.00540787 +Mm Hs HTATSF1 Erythroid-like and erythroid precursor cells TAT-SF1 0.07 HIV-1 Tat specific factor 1 protein-coding gene NA Mesoderm Blood 0.0935673 0.092827 0.082423 0.0666536 +Mm Hs EPB41 Erythroid-like and erythroid precursor cells 4.1R|EL1 0.027 erythrocyte membrane protein band 4.1 protein-coding gene 1 Mesoderm Blood 0.0292398 0.43038 0.00463423 0.026062 +Mm Hs RSAD2 Erythroid-like and erythroid precursor cells cig5|viperin|vig1 0.011 radical S-adenosyl methionine domain containing 2 protein-coding gene NA Mesoderm Blood 0.00584795 0.0 0.0115856 0.0 +Mm CAR1 Erythroid-like and erythroid precursor cells NA 0.006 carbonic anhydrase 1 protein coding gene NA Mesoderm Blood 0.0 0.135021 0.0 0.00540787 +Mm Hs COX6B2 Erythroid-like and erythroid precursor cells COXVIB2|FLJ32865|CT59 0.038 cytochrome c oxidase subunit 6B2 protein-coding gene NA Mesoderm Blood 0.0 0.177215 0.00628931 0.0416992 +Mm Hs APOA1 Erythroid-like and erythroid precursor cells NA 0.032 apolipoprotein A1 protein-coding gene NA Mesoderm Blood 0.0116959 0.00843882 0.0714995 0.0259317 +Mm Hs ASNS Erythroid-like and erythroid precursor cells NA 0.033 asparagine synthetase (glutamine-hydrolyzing) protein-coding gene NA Mesoderm Blood 0.0 0.160338 0.000993049 0.0381809 +Mm HIST1H2AO Erythroid-like and erythroid precursor cells NA 0.014 histone cluster 1, H2ao protein coding gene NA Mesoderm Blood 0.0 0.113924 0.0 0.0154418 +Mm STFA1 Erythroid-like and erythroid precursor cells NA 0.006 stefin A1 protein coding gene NA Mesoderm Blood NA NA NA NA +Mm Hs ALAD Erythroid-like and erythroid precursor cells ALADH|PBGS 0.06 aminolevulinate dehydratase protein-coding gene NA Mesoderm Blood 0.245614 0.265823 0.00331016 0.0676961 +Mm Hs S100A9 Erythroid-like and erythroid precursor cells MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene NA Mesoderm Blood 0.269006 0.0 0.0940086 0.0 +Mm Hs AHSG Erythroid-like and erythroid precursor cells FETUA|A2HS|HSGA 0.004 alpha 2-HS glycoprotein protein-coding gene NA Mesoderm Blood 0.0 0.00843882 0.00364118 0.00371384 +Mm Hs S100A8 Erythroid-like and erythroid precursor cells P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene NA Mesoderm Blood 0.263158 0.0 0.0695134 0.0 +Mm HBA-A2 Erythroid-like and erythroid precursor cells NA 0.047 hemoglobin alpha, adult chain 2 protein coding gene 1 Mesoderm Blood 0.0 0.940928 0.0 0.0451525 +Mm HBB-BT Erythroid-like and erythroid precursor cells NA 0.058 hemoglobin, beta adult t chain protein coding gene 1 Mesoderm Blood 0.0 0.945148 0.0 0.058835 +Mm HBA-A1 Erythroid-like and erythroid precursor cells NA 0.074 hemoglobin alpha, adult chain 1 protein coding gene 1 Mesoderm Blood 0.0 0.962025 0.0 0.0780558 +Mm Hs ERMAP Erythroid-like and erythroid precursor cells BTN5|SC 0.003 erythroblast membrane associated protein (Scianna blood group) protein-coding gene NA Mesoderm Blood 0.0409357 0.219409 0.0 0.000586396 +Mm Hs KCNN4 Erythroid-like and erythroid precursor cells KCa3.1|hSK4|hKCa4|hIKCa1|IK 0.027 potassium calcium-activated channel subfamily N member 4 protein-coding gene NA Mesoderm Blood 0.0409357 0.189873 0.00827541 0.026909 +Mm Hs PAN3 Erythroid-like and erythroid precursor cells NA 0.093 poly(A) specific ribonuclease subunit PAN3 protein-coding gene NA Mesoderm Blood 0.0760234 0.109705 0.0443562 0.102815 +Mm Hs PFAS Erythroid-like and erythroid precursor cells PURL|FGARAT|KIAA0361|GATD8 0.02 phosphoribosylformylglycinamidine synthase protein-coding gene NA Mesoderm Blood 0.0 0.105485 0.000993049 0.0229346 +Mm Hs VAMP5 Erythroid-like and erythroid precursor cells NA 0.067 vesicle associated membrane protein 5 protein-coding gene NA Mesoderm Blood 0.0175439 0.0 0.126448 0.0 +Mm HBB-BH1 Erythroid-like and erythroid precursor cells NA 0.001 hemoglobin Z, beta-like embryonic chain protein coding gene NA Mesoderm Blood 0.0 0.0506329 0.0 0.00110764 +Mm HBA-X Erythroid-like and erythroid precursor cells NA 0.005 hemoglobin X, alpha-like embryonic chain in Hba complex protein coding gene NA Mesoderm Blood 0.0 0.0548523 0.0 0.00560334 +Mm Hs PNPO Erythroid-like and erythroid precursor cells PDXPO 0.009 pyridoxamine 5'-phosphate oxidase protein-coding gene NA Mesoderm Blood 0.00584795 0.219409 0.00132406 0.00762314 +Mm Hs TSPO2 Erythroid-like and erythroid precursor cells dJ34B21.2|BZRPL1 0.006 translocator protein 2 protein-coding gene NA Mesoderm Blood 0.22807 0.0 0.0 0.0 +Mm Hs RHD Erythroid-like and erythroid precursor cells Rh30a|Rh4|RhPI|RhII|DIIIc|CD240D 0.006 Rh blood group D antigen protein-coding gene 1 Mesoderm Blood 0.251462 0.0 0.0 0.0 +Mm Hs KLF1 Erythroid-like and erythroid precursor cells EKLF 0.009 Kruppel like factor 1 protein-coding gene 1 Mesoderm Blood 0.438596 0.240506 0.0019861 0.00280167 +Mm CLDN13 Erythroid-like and erythroid precursor cells NA 0.003 claudin 13 protein coding gene 1 Mesoderm Blood 0.0 0.227848 0.0 0.00013031 +Mm Hs TSPAN33 Erythroid-like and erythroid precursor cells MGC50844|Penumbra 0.009 tetraspanin 33 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00529626 0.0 +Mm Hs EPB42 Erythroid-like and erythroid precursor cells MGC116735|MGC116737 0.006 erythrocyte membrane protein band 4.2 protein-coding gene 1 Mesoderm Blood 0.526316 0.0843882 0.000331016 6.51551e-05 +Mm Hs CD44 Erythroid-like and erythroid precursor cells IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Blood 0.210526 0.0759494 0.305528 0.0879593 +Mm Hs CD47 Erythroid-like and erythroid precursor cells OA3|MER6 0.401 CD47 molecule protein-coding gene 1 Mesoderm Blood 0.25731 0.265823 0.217809 0.445596 +Mm Hs CD55 Erythroid-like and erythroid precursor cells TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Blood 0.0292398 0.0126582 0.131413 0.0198071 +Mm CD59A Erythroid-like and erythroid precursor cells NA 0.033 CD59a antigen protein coding gene 1 Mesoderm Blood 0.0 0.0337553 0.0 0.0415038 +Mm Hs EDRF1 Erythroid-like and erythroid precursor cells DKFZp586F1019|FLJ21617|C10orf137 0.001 erythroid differentiation regulatory factor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00662032 0.000586396 +Mm Hs EPB41L2 Erythroid-like and erythroid precursor cells 4.1-G 0.076 erythrocyte membrane protein band 4.1 like 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0678583 0.080271 +Mm Hs GYPC Erythroid-like and erythroid precursor cells GPC|GYPD|Ge|CD236|CD236R 0.049 glycophorin C (Gerbich blood group) protein-coding gene 1 Mesoderm Blood 0.935673 0.147679 0.190996 0.00436539 +Mm Hs KEL Erythroid-like and erythroid precursor cells ECE3|CD238 0.002 Kell metallo-endopeptidase (Kell blood group) protein-coding gene 1 Mesoderm Blood 0.0643275 0.122363 0.0 0.0 +Mm Hs RHAG Erythroid-like and erythroid precursor cells RH50A|CD241|SLC42A1 0.005 Rh associated glycoprotein protein-coding gene 1 Mesoderm Blood 0.362573 0.0 0.000331016 0.0 +Mm Hs THRB Erythroid-like and erythroid precursor cells THRB1|THRB2|NR1A2|THR1|ERBA-BETA|ERBA2|PRTH 0.004 thyroid hormone receptor beta protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000331016 0.0 +Mm Hs UROD Erythroid-like and erythroid precursor cells NA 0.004 uroporphyrinogen decarboxylase protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00496524 0.0 +Mm Hs UROS Erythroid-like and erythroid precursor cells NA 0.002 uroporphyrinogen III synthase protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00529626 0.0 +Mm Hs SNCA Erythroid-like and erythroid precursor cells NACP|PARK1|PARK4 0.096 synuclein alpha protein-coding gene 1 Mesoderm Blood 0.812865 0.0 0.041046 0.0 +Mm Hs IL1R1 Fibroblasts D2S1473|CD121A|IL1R 0.008 interleukin 1 receptor type 1 protein-coding gene NA Mesoderm Connective tissue 0.234234 0.0837104 0.0113599 0.0040943 +Mm Hs FAP Fibroblasts NA 0.006 fibroblast activation protein alpha protein-coding gene NA Mesoderm Connective tissue 0.0720721 0.147059 0.0 0.00244337 +Mm Hs FLI1 Fibroblasts SIC-1 0.036 Fli-1 proto-oncogene, ETS transcription factor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.00226244 0.00616683 0.0448392 +Mm Hs CELA1 Fibroblasts ELA1 0.017 chymotrypsin like elastase family member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0226244 0.0 0.0209998 +Mm Hs LOX Fibroblasts NA 0.017 lysyl oxidase protein-coding gene 1 Mesoderm Connective tissue 0.234234 0.348416 0.00714054 0.00719805 +Mm Hs PDGFRB Fibroblasts JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene 1 Mesoderm Connective tissue 0.198198 0.226244 0.0305096 0.0278016 +Mm Hs P4HA1 Fibroblasts C-P4Halpha(I)|P4HA 0.04 prolyl 4-hydroxylase subunit alpha 1 protein-coding gene 1 Mesoderm Connective tissue 0.0990991 0.294118 0.0275884 0.0305752 +Mm Hs UCP2 Fibroblasts SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00519312 0.0 +Mm Hs CCR2 Fibroblasts CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0270752 +Mm MS4A4C Fibroblasts NA 0.011 membrane-spanning 4-domains, subfamily A, member 4C protein coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.012481 +Mm Hs ITGAL Fibroblasts CD11A 0.013 integrin subunit alpha L protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00421941 0.0152546 +Mm EAR2 Fibroblasts NA 0.009 eosinophil-associated, ribonuclease A family, member 2 protein coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0110942 +Mm Hs FGR Fibroblasts c-fgr|p55c-fgr|SRC2 0.013 FGR proto-oncogene, Src family tyrosine kinase protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0227199 0.0121508 +Mm Hs HCK Fibroblasts JTK9 0.031 HCK proto-oncogene, Src family tyrosine kinase protein-coding gene NA Mesoderm Connective tissue 0.0 0.00452489 0.0236936 0.0346034 +Mm ADGRE4 Fibroblasts NA 0.004 adhesion G protein-coupled receptor E4 protein coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.00515089 +Mm Hs TNFRSF1B Fibroblasts TNFBR|TNFR80|TNF-R75|TNF-R-II|CD120b|TNFR2 0.02 TNF receptor superfamily member 1B protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0295359 0.0 +Mm Hs PRKCD Fibroblasts NA 0.042 protein kinase C delta protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0135747 0.00811425 0.0494618 +Mm Hs ENO3 Fibroblasts NA 0.01 enolase 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.00452489 0.00032457 0.0108961 +Mm CD209A Fibroblasts NA 0.003 CD209a antigen protein coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0040943 +Mm Hs ABI3 Fibroblasts NESH|SSH3BP3 0.006 ABI family member 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.027913 0.00138678 +Mm Hs TREML4 Fibroblasts TLT4 0.003 triggering receptor expressed on myeloid cells like 4 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm LY6I Fibroblasts NA 0.004 lymphocyte antigen 6 complex, locus I protein coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.00416034 +Mm Hs PIP4K2A Fibroblasts PIP5KIIA|PIP5KIIalpha|PIP5K2A 0.038 phosphatidylinositol-5-phosphate 4-kinase type 2 alpha protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0834145 0.028528 +Mm Hs CD300E Fibroblasts IREM2|CLM2|CD300LE 0.001 CD300e molecule protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00227199 0.00132074 +Mm Hs SERPINB10 Fibroblasts bomapin|PI10 0.004 serpin family B member 10 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00032457 0.0 +Mm Hs CTHRC1 Fibroblasts NA 0.031 collagen triple helix repeat containing 1 protein-coding gene 1 Mesoderm Connective tissue 0.0900901 0.235294 0.0298604 0.0259526 +Mm Hs TBX18 Fibroblasts NA 0.004 T-box 18 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00032457 0.0 +Mm Hs COL15A1 Fibroblasts NA 0.016 collagen type XV alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.144144 0.266968 0.0240182 0.00680182 +Mm Hs GJB2 Fibroblasts CX26|NSRD1|DFNB1 0.009 gap junction protein beta 2 protein-coding gene 1 Mesoderm Connective tissue 0.0720721 0.0452489 0.0097371 0.00812257 +Mm Hs IL34 Fibroblasts MGC34647|IL-34|C16orf77 0.012 interleukin 34 protein-coding gene NA Mesoderm Connective tissue 0.018018 0.106335 0.00097371 0.012481 +Mm Hs EDN3 Fibroblasts ET3 0.003 endothelin 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0542986 0.00259656 0.0023113 +Mm Hs SLC6A13 Fibroblasts GAT2 0.005 solute carrier family 6 member 13 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00032457 0.0 +Mm Hs VTN Fibroblasts VN 0.029 vitronectin protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.0 0.00876339 0.0 +Mm Hs ITIH5 Fibroblasts MGC10848 0.036 inter-alpha-trypsin inhibitor heavy chain family member 5 protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.479638 0.00681597 0.030311 +Mm Hs LUM Fibroblasts SLRR2D|LDC 0.051 lumican protein-coding gene 1 Mesoderm Connective tissue 0.873874 0.746606 0.0587472 0.0221885 +Mm Hs DPT Fibroblasts NA 0.021 dermatopontin protein-coding gene 1 Mesoderm Connective tissue 0.0630631 0.658371 0.00389484 0.00581127 +Mm Hs POSTN Fibroblasts OSF-2|PN|periostin 0.033 periostin protein-coding gene 1 Mesoderm Connective tissue 0.171171 0.438914 0.0178513 0.0229149 +Mm Hs PENK Fibroblasts NA 0.02 proenkephalin protein-coding gene NA Mesoderm Connective tissue 0.00900901 0.239819 0.0282376 0.0132074 +Mm Hs MMP14 Fibroblasts MT1-MMP 0.054 matrix metallopeptidase 14 protein-coding gene 1 Mesoderm Connective tissue 0.306306 0.606335 0.025641 0.0408109 +Mm Hs COL6A2 Fibroblasts NA 0.056 collagen type VI alpha 2 chain protein-coding gene 1 Mesoderm Connective tissue 0.792793 0.852941 0.0785459 0.0206036 +Mm Hs FABP4 Fibroblasts A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Connective tissue 0.018018 0.104072 0.0100617 0.0311695 +Mm Hs ASPN Fibroblasts FLJ20129|SLRR1C|PLAP-1 0.019 asporin protein-coding gene 1 Mesoderm Connective tissue 0.162162 0.332579 0.00162285 0.0127452 +Mm Hs ANGPTL2 Fibroblasts NA 0.013 angiopoietin like 2 protein-coding gene 1 Mesoderm Connective tissue 0.0900901 0.323529 0.00292113 0.0058773 +Mm Hs EFEMP1 Fibroblasts S1-5|FBLN3|MTLV|DHRD|FBNL 0.021 EGF containing fibulin extracellular matrix protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.342342 0.364253 0.0311587 0.00647164 +Mm Hs SCARA5 Fibroblasts FLJ23907|MGC45780|NET33 0.007 scavenger receptor class A member 5 protein-coding gene 1 Mesoderm Connective tissue 0.297297 0.0 0.00129828 0.0 +Mm Hs IGFBP3 Fibroblasts IBP3|BP-53 0.031 insulin like growth factor binding protein 3 protein-coding gene 1 Mesoderm Connective tissue 0.396396 0.18552 0.0470626 0.0209338 +Mm Hs COPZ2 Fibroblasts MGC23008 0.038 coatomer protein complex subunit zeta 2 protein-coding gene NA Mesoderm Connective tissue 0.234234 0.567873 0.0129828 0.0278677 +Mm Hs DPEP1 Fibroblasts NA 0.023 dipeptidase 1 protein-coding gene 1 Mesoderm Connective tissue 0.018018 0.493213 0.0116845 0.0120188 +Mm Hs ADAMTS5 Fibroblasts ADMP-2|ADAMTS11 0.016 ADAM metallopeptidase with thrombospondin type 1 motif 5 protein-coding gene 1 Mesoderm Connective tissue 0.279279 0.339367 0.00486855 0.00739616 +Mm Hs COL5A1 Fibroblasts NA 0.028 collagen type V alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.369369 0.5181 0.0236936 0.0105659 +Mm Hs CD248 Fibroblasts TEM1|CD164L1 0.022 CD248 molecule protein-coding gene 1 Mesoderm Connective tissue 0.288288 0.341629 0.00454398 0.0147923 +Mm Hs PI16 Fibroblasts MGC45378|dJ90K10.5|MSMBBP|CD364 0.011 peptidase inhibitor 16 protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.294118 0.00064914 0.00495278 +Mm Hs PAMR1 Fibroblasts DKFZP586H2123 0.006 peptidase domain containing associated with muscle regeneration 1 protein-coding gene NA Mesoderm Connective tissue 0.153153 0.113122 0.00194742 0.00303771 +Mm Hs TNXB Fibroblasts TNXBS|XBS|XB|TNXB1|TNXB2 0.008 tenascin XB protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00259656 0.0 +Mm Hs MMP2 Fibroblasts TBE-1|CLG4|CLG4A 0.045 matrix metallopeptidase 2 protein-coding gene 1 Mesoderm Connective tissue 0.666667 0.79638 0.0460889 0.0164432 +Mm Hs COL14A1 Fibroblasts UND 0.017 collagen type XIV alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.333333 0.402715 0.00811425 0.00554712 +Mm Hs CLEC3B Fibroblasts TNA 0.021 C-type lectin domain family 3 member B protein-coding gene NA Mesoderm Connective tissue 0.0 0.626697 0.0 0.0092452 +Mm Hs IGFBP6 Fibroblasts NA 0.039 insulin like growth factor binding protein 6 protein-coding gene 1 Mesoderm Connective tissue 0.684685 0.576923 0.0623174 0.0134716 +Mm AKR1C18 Fibroblasts NA 0.001 aldo-keto reductase family 1, member C18 protein coding gene NA Mesoderm Connective tissue 0.0 0.0158371 0.0 0.000264148 +Mm Hs COL5A2 Fibroblasts NA 0.044 collagen type V alpha 2 chain protein-coding gene 1 Mesoderm Connective tissue 0.333333 0.726244 0.0243427 0.0228488 +Mm Hs FBN1 Fibroblasts MASS|OCTD|SGS|FBN|MFS1|WMS 0.028 fibrillin 1 protein-coding gene 1 Mesoderm Connective tissue 0.459459 0.656109 0.0126582 0.00931123 +Mm Hs MFAP5 Fibroblasts MAGP2|MP25 0.021 microfibril associated protein 5 protein-coding gene NA Mesoderm Connective tissue 0.162162 0.572398 0.00519312 0.00805653 +Mm Hs FKBP10 Fibroblasts hFKBP65|FLJ22041|FKBP6|FLJ20683|FLJ23833 0.041 FK506 binding protein 10 protein-coding gene 1 Mesoderm Connective tissue 0.378378 0.361991 0.0545278 0.0207357 +Mm Hs PALLD Fibroblasts KIAA0992|SIH002|CGI-151 0.053 palladin, cytoskeletal associated protein protein-coding gene NA Mesoderm Connective tissue 0.423423 0.255656 0.090555 0.0362544 +Mm Hs WIF1 Fibroblasts NA 0.007 WNT inhibitory factor 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0032457 0.0 +Mm Hs SNHG18 Fibroblasts NA 0.046 small nucleolar RNA host gene 18 non-coding RNA 1 Mesoderm Connective tissue 0.126126 0.0 0.0103862 0.0 +Mm Hs CDH11 Fibroblasts CAD11 0.039 cadherin 11 protein-coding gene 1 Mesoderm Connective tissue 0.540541 0.377828 0.0340798 0.0263488 +Mm Hs PTCH1 Fibroblasts BCNS|NBCCS|PTCH 0.012 patched 1 protein-coding gene 1 Mesoderm Connective tissue 0.0540541 0.0746606 0.0178513 0.00917916 +Mm Hs ARAP1 Fibroblasts CENTD2 0.007 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.133484 0.00032457 0.00528297 +Mm Hs FBLN2 Fibroblasts NA 0.025 fibulin 2 protein-coding gene 1 Mesoderm Connective tissue 0.288288 0.447964 0.0100617 0.0146602 +Mm Hs IGF1 Fibroblasts IGF1A|IGFI|IGF-I|IGF 0.044 insulin like growth factor 1 protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.504525 0.00162285 0.0412072 +Mm Hs PRRX1 Fibroblasts PHOX1|PMX1 0.033 paired related homeobox 1 protein-coding gene 1 Mesoderm Connective tissue 0.27027 0.459276 0.0266147 0.0183583 +Mm Hs FKBP7 Fibroblasts FKBP23 0.031 FK506 binding protein 7 protein-coding gene NA Mesoderm Connective tissue 0.117117 0.61991 0.0149302 0.0147923 +Mm Hs OAF Fibroblasts MGC52117 0.036 out at first homolog protein-coding gene NA Mesoderm Connective tissue 0.0810811 0.5181 0.0266147 0.0237073 +Mm Hs COL6A3 Fibroblasts NA 0.032 collagen type VI alpha 3 chain protein-coding gene 1 Mesoderm Connective tissue 0.567568 0.615385 0.0259656 0.010698 +Mm Hs CTSK Fibroblasts PKND|CTSO2|CTSO|PYCD 0.027 cathepsin K protein-coding gene 1 Mesoderm Connective tissue 0.288288 0.4819 0.00778968 0.0154527 +Mm Hs DKK1 Fibroblasts SK|DKK-1 0.006 dickkopf WNT signaling pathway inhibitor 1 protein-coding gene NA Mesoderm Connective tissue 0.306306 0.0 0.0146056 0.00145282 +Hs C1S Fibroblasts NA 0.013 complement C1s protein-coding gene 1 Mesoderm Connective tissue 0.792793 0.0 0.0516066 0.0 +Mm Hs RARRES2 Fibroblasts TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene NA Mesoderm Connective tissue 0.54955 0.0 0.0616683 0.0 +Mm Hs GREM1 Fibroblasts DRM|gremlin|DAND2|HMPS|CKTSF1B1|CRAC1 0.01 gremlin 1, DAN family BMP antagonist protein-coding gene 1 Mesoderm Connective tissue 0.0540541 0.0656109 0.0366764 0.00237734 +Mm Hs SPON2 Fibroblasts DIL1 0.017 spondin 2 protein-coding gene 1 Mesoderm Connective tissue 0.558559 0.0 0.0305096 0.0 +Mm Hs TCF21 Fibroblasts POD1|bHLHa23 0.014 transcription factor 21 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00616683 0.0 +Mm Hs PCSK6 Fibroblasts SPC4|PACE4 0.007 proprotein convertase subtilisin/kexin type 6 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.108597 0.0 0.00561315 +Mm Hs COL8A1 Fibroblasts MGC9568|C3orf7 0.011 collagen type VIII alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.180995 0.00486855 0.00779238 +Mm Hs ENTPD2 Fibroblasts NTPDase-2|CD39L1 0.012 ectonucleoside triphosphate diphosphohydrolase 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.328054 0.00097371 0.00541504 +Mm MMP23 Fibroblasts NA 0.012 matrix metallopeptidase 23 protein coding gene 1 Mesoderm Connective tissue 0.0 0.38914 0.0 0.00442449 +Hs CXCL8 Fibroblasts SCYB8|LUCT|LECT|MDNCF|TSG-1|IL-8|NAP-1|3-10C|MONAP|AMCF-I|LYNAP|NAF|b-ENAP|GCP-1|K60|GCP1|IL8 0.02 C-X-C motif chemokine ligand 8 protein-coding gene 1 Mesoderm Connective tissue 0.153153 0.0 0.117494 0.0 +Mm Hs CXCL3 Fibroblasts SCYB3|GROg|MIP-2b|CINC-2b|GRO3 0.006 C-X-C motif chemokine ligand 3 protein-coding gene NA Mesoderm Connective tissue 0.045045 0.00226244 0.030185 0.00092452 +Mm Hs IL6 Fibroblasts IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene NA Mesoderm Connective tissue 0.135135 0.124434 0.00908796 0.00303771 +Mm Hs CYP1B1 Fibroblasts CP1B|GLC3A 0.016 cytochrome P450 family 1 subfamily B member 1 protein-coding gene 1 Mesoderm Connective tissue 0.216216 0.167421 0.0431678 0.00435845 +Mm Hs COL13A1 Fibroblasts NA 0.004 collagen type XIII alpha 1 chain protein-coding gene NA Mesoderm Connective tissue 0.0 0.0701357 0.00292113 0.0028396 +Mm Hs ADAMTS10 Fibroblasts ADAM-TS10 0.002 ADAM metallopeptidase with thrombospondin type 1 motif 10 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0452489 0.0 0.00125471 +Mm Hs CCL11 Fibroblasts eotaxin|MGC22554|SCYA11 0.008 C-C motif chemokine ligand 11 protein-coding gene 1 Mesoderm Connective tissue 0.0720721 0.264706 0.00064914 0.00224526 +Mm Hs ADAM33 Fibroblasts DKFZp434K0521|dJ964F7.1|C20orf153 0.003 ADAM metallopeptidase domain 33 protein-coding gene NA Mesoderm Connective tissue 0.0 0.061086 0.0 0.00211319 +Mm Hs COL4A3 Fibroblasts NA 0.006 collagen type IV alpha 3 chain protein-coding gene NA Mesoderm Connective tissue 0.00900901 0.020362 0.00032457 0.00653767 +Mm Hs COL4A4 Fibroblasts CA44 0.007 collagen type IV alpha 4 chain protein-coding gene NA Mesoderm Connective tissue 0.036036 0.0361991 0.00129828 0.00726408 +Mm Hs LAMA2 Fibroblasts LAMM 0.007 laminin subunit alpha 2 protein-coding gene NA Mesoderm Connective tissue 0.279279 0.192308 0.00259656 0.00112263 +Mm Hs ACKR3 Fibroblasts GPR159|CMKOR1|CXCR7 0.01 atypical chemokine receptor 3 protein-coding gene NA Mesoderm Connective tissue 0.0720721 0.169683 0.00421941 0.00680182 +Mm Hs CD55 Fibroblasts TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Connective tissue 0.279279 0.151584 0.120415 0.0158489 +Mm Hs FBLN7 Fibroblasts FLJ37440|TM14 0.002 fibulin 7 protein-coding gene NA Mesoderm Connective tissue 0.00900901 0.0271493 0.00194742 0.00198111 +Mm Hs FIBIN Fibroblasts MGC24932 0.009 fin bud initiation factor homolog (zebrafish) protein-coding gene NA Mesoderm Connective tissue 0.0810811 0.18552 0.00551769 0.00488675 +Mm Hs THBS2 Fibroblasts TSP2 0.01 thrombospondin 2 protein-coding gene NA Mesoderm Connective tissue 0.027027 0.0 0.00227199 0.0 +Mm Hs NOV Fibroblasts IGFBP9|CCN3 0.004 nephroblastoma overexpressed protein-coding gene NA Mesoderm Connective tissue 0.117117 0.0361991 0.00064914 0.00376412 +Mm Hs PTX3 Fibroblasts TSG-14|TNFAIP5 0.013 pentraxin 3 protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.190045 0.0123337 0.0087169 +Mm Hs MMP3 Fibroblasts STMY1|STMY 0.003 matrix metallopeptidase 3 protein-coding gene 1 Mesoderm Connective tissue 0.00900901 0.0859729 0.00194742 0.000594334 +Mm Hs LRRK1 Fibroblasts FLJ23119|KIAA1790|Roco1|RIPK6 0.008 leucine rich repeat kinase 1 protein-coding gene NA Mesoderm Connective tissue 0.00900901 0.0520362 0.00129828 0.00832068 +Mm Hs HGF Fibroblasts F-TCF|HGFB|HPTA|DFNB39 0.002 hepatocyte growth factor protein-coding gene NA Mesoderm Connective tissue 0.0900901 0.0 0.00454398 0.000594334 +Mm Hs FRZB Fibroblasts FRZB-PEN|FRZB1|SRFP3|FRP-3|SFRP3|FRE|FRITZ|FRZB-1|FZRB|hFIZ 0.012 frizzled related protein protein-coding gene 1 Mesoderm Connective tissue 0.198198 0.040724 0.0243427 0.00699993 +Mm Hs COL12A1 Fibroblasts COL12A1L 0.013 collagen type XII alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.230769 0.00454398 0.00633956 +Mm Hs COL7A1 Fibroblasts EBDCT|EBD1|EBR1 0.003 collagen type VII alpha 1 chain protein-coding gene NA Mesoderm Connective tissue 0.00900901 0.0588235 0.00129828 0.00244337 +Mm Hs MEOX1 Fibroblasts NA 0.005 mesenchyme homeobox 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0475113 0.00227199 0.00528297 +Mm Hs PRG4 Fibroblasts JCAP|SZP|HAPO|bG174L6.2|FLJ32635|CACP 0.004 proteoglycan 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.061086 0.00162285 0.00277356 +Mm Hs PKD2 Fibroblasts PKD4|Pc-2|TRPP2 0.01 polycystin 2, transient receptor potential cation channel protein-coding gene 1 Mesoderm Connective tissue 0.126126 0.176471 0.0064914 0.00508486 +Mm Hs CCL19 Fibroblasts ELC|MIP-3b|exodus-3|CKb11|SCYA19 0.002 C-C motif chemokine ligand 19 protein-coding gene 1 Mesoderm Connective tissue 0.027027 0.0475113 0.00064914 0.00112263 +Mm Hs NNMT Fibroblasts NA 0.017 nicotinamide N-methyltransferase protein-coding gene 1 Mesoderm Connective tissue 0.495495 0.167421 0.0447907 0.00323582 +Mm Hs FOXF1 Fibroblasts FREAC1|FKHL5 0.008 forkhead box F1 protein-coding gene 1 Mesoderm Connective tissue 0.162162 0.0497738 0.00292113 0.0069339 +Mm Hs HAS1 Fibroblasts HAS 0.003 hyaluronan synthase 1 protein-coding gene 1 Mesoderm Connective tissue 0.018018 0.115385 0.00097371 0.000198111 +Mm Hs CTGF Fibroblasts IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Mesoderm Connective tissue 0.576577 0.106335 0.0824408 0.00970746 +Mm Hs ERCC1 Fibroblasts RAD10 0.033 ERCC excision repair 1, endonuclease non-catalytic subunit protein-coding gene 1 Mesoderm Connective tissue 0.153153 0.0158371 0.092827 0.0114905 +Mm Hs WISP1 Fibroblasts CCN4|WISP-1|WISP1-OT1|WISP1-UT1 0.008 WNT1 inducible signaling pathway protein 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs TWIST2 Fibroblasts DERMO1|Dermo-1|bHLHa39 0.012 twist family bHLH transcription factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.162162 0.0 0.00129828 0.0 +Mm Hs RIPK3 Fibroblasts RIP3 0.01 receptor interacting serine/threonine kinase 3 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs DDR2 Fibroblasts TKT|TYRO10|NTRKR3 0.018 discoidin domain receptor tyrosine kinase 2 protein-coding gene 1 Mesoderm Connective tissue 0.144144 0.366516 0.00811425 0.00964142 +Mm Hs ELN Fibroblasts SVAS 0.026 elastin protein-coding gene 1 Mesoderm Connective tissue 0.18018 0.438914 0.00421941 0.0180942 +Mm Hs FN1 Fibroblasts CIG|LETS|GFND2|FINC 0.091 fibronectin 1 protein-coding gene 1 Mesoderm Connective tissue 0.468468 0.638009 0.086011 0.0708578 +Mm Hs HHIP Fibroblasts FLJ20992 0.008 hedgehog interacting protein protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0248869 0.0129828 0.00686786 +Mm Hs FMO2 Fibroblasts NA 0.014 flavin containing monooxygenase 2 protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.199095 0.00227199 0.010698 +Mm Hs COL1A2 Fibroblasts NA 0.097 collagen type I alpha 2 chain protein-coding gene 1 Mesoderm Connective tissue 0.711712 1.0 0.103213 0.0615466 +Mm Hs COL3A1 Fibroblasts EDS4A 0.086 collagen type III alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.666667 0.963801 0.0788705 0.0554712 +Mm Hs VIM Fibroblasts NA 0.427 vimentin protein-coding gene 1 Mesoderm Connective tissue 0.918919 0.0 0.578708 0.0 +Mm Hs FSTL1 Fibroblasts FSL1|tsc36 0.123 follistatin like 1 protein-coding gene 1 Mesoderm Connective tissue 0.594595 0.963801 0.0918533 0.102622 +Mm Hs GSN Fibroblasts DKFZp313L0718 0.206 gelsolin protein-coding gene 1 Mesoderm Connective tissue 0.63964 0.884615 0.186628 0.191376 +Mm Hs SPARC Fibroblasts ON 0.307 secreted protein acidic and cysteine rich protein-coding gene 1 Mesoderm Connective tissue 0.837838 0.0 0.209023 0.0 +Mm Hs S100A4 Fibroblasts P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Connective tissue 0.747748 0.0 0.357676 0.0 +Mm Hs NT5E Fibroblasts CD73|eN|eNT|CALJA|NT5 0.005 5'-nucleotidase ecto protein-coding gene 1 Mesoderm Connective tissue 0.027027 0.0339367 0.0064914 0.0028396 +Mm Hs COL1A1 Fibroblasts NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.657658 0.970588 0.0798442 0.0470845 +Mm Hs MGP Fibroblasts NA 0.082 matrix Gla protein protein-coding gene 1 Mesoderm Connective tissue 0.621622 0.61086 0.0983447 0.0575183 +Mm Hs NOX4 Fibroblasts KOX-1|KOX 0.003 NADPH oxidase 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0339367 0.0 0.00237734 +Mm Hs THY1 Fibroblasts CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Mesoderm Connective tissue 0.306306 0.0 0.0223953 0.0 +Mm Hs CD40 Fibroblasts Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Connective tissue 0.00900901 0.00226244 0.0133074 0.0110942 +Mm Hs SERPINH1 Fibroblasts HSP47|colligen|CBP1|CBP2|SERPINH2 0.219 serpin family H member 1 protein-coding gene 1 Mesoderm Connective tissue 0.522523 0.0 0.142486 0.0 +Mm Hs CD44 Fibroblasts IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Connective tissue 0.396396 0.230769 0.296982 0.083603 +Mm Hs PDGFRA Fibroblasts CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene 1 Mesoderm Connective tissue 0.396396 0.604072 0.0350536 0.0276696 +Mm Hs EN1 Fibroblasts NA 0.003 engrailed homeobox 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0361991 0.0 0.00277356 +Mm Hs DCN Fibroblasts DSPG2|SLRR1B 0.084 decorin protein-coding gene 1 Mesoderm Connective tissue 0.936937 0.923077 0.0772476 0.0573202 +Mm Hs CEBPB Fibroblasts NFIL6|IL6DBP|C/EBP-beta|TCF5 0.138 CCAAT enhancer binding protein beta protein-coding gene 1 Mesoderm Connective tissue 0.477477 0.515837 0.14703 0.119263 +Mm Hs EGR1 Fibroblasts TIS8|G0S30|NGFI-A|KROX-24|ZIF-268|AT225|ZNF225 0.202 early growth response 1 protein-coding gene 1 Mesoderm Connective tissue 0.63964 0.823529 0.171373 0.190517 +Mm Hs FOSB Fibroblasts G0S3|GOSB|GOS3|MGC42291|DKFZp686C0818 0.125 FosB proto-oncogene, AP-1 transcription factor subunit protein-coding gene 1 Mesoderm Connective tissue 0.54955 0.533937 0.189224 0.101433 +Mm Hs FOSL2 Fibroblasts FRA2|FLJ23306 0.045 FOS like 2, AP-1 transcription factor subunit protein-coding gene 1 Mesoderm Connective tissue 0.135135 0.221719 0.0311587 0.0425279 +Mm Hs HIF1A Fibroblasts MOP1|HIF-1alpha|PASD8|HIF1|bHLHe78 0.089 hypoxia inducible factor 1 subunit alpha protein-coding gene 1 Mesoderm Connective tissue 0.189189 0.167421 0.0986693 0.0832728 +Mm Hs KLF2 Fibroblasts LKLF 0.162 Kruppel like factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.117117 0.531674 0.0944499 0.170574 +Mm Hs KLF4 Fibroblasts EZF|GKLF 0.126 Kruppel like factor 4 protein-coding gene 1 Mesoderm Connective tissue 0.396396 0.565611 0.129503 0.114706 +Mm Hs KLF6 Fibroblasts CPBP|GBF|Zf9|ST12|COPEB 0.3 Kruppel like factor 6 protein-coding gene 1 Mesoderm Connective tissue 0.648649 0.69457 0.423239 0.26395 +Mm Hs KLF9 Fibroblasts BTEB1 0.13 Kruppel like factor 9 protein-coding gene 1 Mesoderm Connective tissue 0.198198 0.59276 0.0217462 0.143036 +Mm Hs NFAT5 Fibroblasts TONEBP|KIAA0827|NFATL1|OREBP|NFATZ|NF-AT5 0.017 nuclear factor of activated T cells 5 protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.0701357 0.0201233 0.0157829 +Mm Hs NFATC1 Fibroblasts NF-ATC|NFATc|NFAT2 0.006 nuclear factor of activated T cells 1 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0294118 0.00519312 0.00627353 +Mm Hs NFKB1 Fibroblasts KBF1|NFKB-p50|NF-kappaB|NFkappaB|NF-kB1 0.028 nuclear factor kappa B subunit 1 protein-coding gene 1 Mesoderm Connective tissue 0.027027 0.113122 0.025641 0.0255564 +Mm Hs NR4A1 Fibroblasts N10|NAK-1|NGFIB|NUR77|HMR|GFRP1 0.083 nuclear receptor subfamily 4 group A member 1 protein-coding gene 1 Mesoderm Connective tissue 0.0540541 0.40724 0.00292113 0.0929142 +Mm Hs NR4A2 Fibroblasts TINUR|NOT|RNR1|HZF-3|NURR1 0.033 nuclear receptor subfamily 4 group A member 2 protein-coding gene 1 Mesoderm Connective tissue 0.0810811 0.10181 0.0778968 0.0233111 +Mm Hs PBX1 Fibroblasts NA 0.175 PBX homeobox 1 protein-coding gene 1 Mesoderm Connective tissue 0.198198 0.321267 0.0730282 0.196328 +Mm Hs RUNX1 Fibroblasts PEBP2A2|AMLCR1|AML1|CBFA2 0.054 runt related transcription factor 1 protein-coding gene 1 Mesoderm Connective tissue 0.117117 0.0 0.0282376 0.0 +Mm Hs STAT3 Fibroblasts APRF 0.099 signal transducer and activator of transcription 3 protein-coding gene 1 Mesoderm Connective tissue 0.504505 0.0 0.136644 0.0 +Mm Hs TCF4 Fibroblasts SEF2-1B|ITF2|bHLHb19|E2-2 0.394 transcription factor 4 protein-coding gene 1 Mesoderm Connective tissue 0.441441 0.0 0.159688 0.0 +Mm Hs ZEB2 Fibroblasts KIAA0569|ZFHX1B 0.144 zinc finger E-box binding homeobox 2 protein-coding gene 1 Mesoderm Connective tissue 0.126126 0.0 0.083739 0.0 +Mm Hs LAMC1 Fibroblasts LAMB2 0.058 laminin subunit gamma 1 protein-coding gene 1 Mesoderm Connective tissue 0.405405 0.452489 0.0379747 0.0485373 +Mm Hs MEDAG Fibroblasts FLJ14834|AWMS3|MEDA-4|C13orf33 0.007 mesenteric estrogen dependent adipogenesis protein-coding gene 1 Mesoderm Connective tissue 0.189189 0.20362 0.00292113 0.00092452 +Mm MS4A4D Fibroblasts NA 0.009 membrane-spanning 4-domains, subfamily A, member 4D protein coding gene 1 Mesoderm Connective tissue 0.0 0.355204 0.0 0.00112263 +Mm Hs LAMB1 Fibroblasts NA 0.051 laminin subunit beta 1 protein-coding gene 1 Mesoderm Connective tissue 0.378378 0.377828 0.0344044 0.0429241 +Mm Hs DKK3 Fibroblasts REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene 1 Mesoderm Connective tissue 0.234234 0.201357 0.0305096 0.0305752 +Mm Hs TBX20 Fibroblasts NA 0.004 T-box 20 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs MDK Fibroblasts FLJ27379|NEGF2 0.222 midkine protein-coding gene 1 Mesoderm Connective tissue 0.333333 0.445701 0.24148 0.202074 +Mm Hs GSTM5 Fibroblasts NA 0.201 glutathione S-transferase mu 5 protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.373303 0.00389484 0.246318 +Mm Hs NGF Fibroblasts NGFB 0.003 nerve growth factor protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0294118 0.00064914 0.00270752 +Mm Hs VEGFA Fibroblasts VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Mesoderm Connective tissue 0.045045 0.0 0.0240182 0.0 +Mm Hs FGF2 Fibroblasts FGFB 0.004 fibroblast growth factor 2 protein-coding gene 1 Mesoderm Connective tissue 0.171171 0.00904977 0.0123337 0.000726408 +Mm Hs P4HTM Fibroblasts P4H-TM|PHD4|PH4|HIFPH4|FLJ20262|EGLN4|PH-4 0.013 prolyl 4-hydroxylase, transmembrane protein-coding gene 1 Mesoderm Connective tissue 0.018018 0.0 0.0431678 0.00746219 +Mm Hs CKAP4 Fibroblasts P63|CLIMP-63|ERGIC-63 0.078 cytoskeleton associated protein 4 protein-coding gene 1 Mesoderm Connective tissue 0.207207 0.459276 0.0610191 0.0660371 +Mm Hs INMT Fibroblasts NA 0.016 indolethylamine N-methyltransferase protein-coding gene 1 Mesoderm Connective tissue 0.036036 0.235294 0.00876339 0.0103018 +Mm Hs CXCL14 Fibroblasts BRAK|NJAC|bolekine|Kec|MIP-2g|BMAC|SCYB14 0.049 C-X-C motif chemokine ligand 14 protein-coding gene 1 Mesoderm Connective tissue 0.540541 0.266968 0.0246673 0.0419336 +Mm Hs TTF1 Follicular cells NA 0.009 transcription termination factor 1 protein-coding gene NA Endoderm Thyroid 0.0 0.0 0.0350877 0.0 +Mm Hs SLC6A4 Follicular cells 5-HTT|SERT1|HTT|OCD1 0.002 solute carrier family 6 member 4 protein-coding gene NA Endoderm Thyroid 0.0 0.0 0.00125313 0.0 +Mm Hs KCNIP3 Follicular cells DREAM|KCHIP3|CSEN 0.007 potassium voltage-gated channel interacting protein 3 protein-coding gene NA Endoderm Thyroid 0.0 0.0 0.0 0.00879163 +Mm Hs TSHR Follicular cells LGR3 0.0 thyroid stimulating hormone receptor protein-coding gene NA Endoderm Thyroid 0.0 0.0 0.0 0.0 +Mm Hs TG Follicular cells TGN|AITD3 0.001 thyroglobulin protein-coding gene 1 Endoderm Thyroid 0.0 0.0 0.0 0.0 +Mm Hs IYD Follicular cells dJ422F24.1|DEHAL1|C6orf71 0.001 iodotyrosine deiodinase protein-coding gene 1 Endoderm Thyroid 0.0 1.0 0.0 0.000834242 +Mm Hs ASGR1 Follicular cells CLEC4H1 0.004 asialoglycoprotein receptor 1 protein-coding gene NA Endoderm Thyroid 0.0 1.0 0.0147243 0.001861 +Mm Hs PRLR Follicular cells NA 0.013 prolactin receptor protein-coding gene 1 Endoderm Thyroid 0.0 1.0 0.0106516 0.0137329 +Mm Hs TPO Follicular cells TPX 0.0 thyroid peroxidase protein-coding gene 1 Endoderm Thyroid 0.0 0.0 0.0 0.0 +Mm Hs DIO1 Follicular cells TXDI1 0.002 iodothyronine deiodinase 1 protein-coding gene 1 Endoderm Thyroid 0.0 1.0 0.0 0.00211769 +Mm Hs SLC26A7 Follicular cells SUT2 0.002 solute carrier family 26 member 7 protein-coding gene 1 Endoderm Thyroid 0.0 0.0 0.000313283 0.0 +Mm Hs CDH16 Follicular cells NA 0.004 cadherin 16 protein-coding gene NA Endoderm Thyroid 0.0 1.0 0.00093985 0.00481294 +Mm Hs SLC16A11 Follicular cells FLJ90193|MCT11 0.008 solute carrier family 16 member 11 protein-coding gene 1 Endoderm Thyroid 0.0 0.0 0.0 0.0 +Mm Hs FOXE1 Follicular cells TTF-2|HFKH4|FKHL15|TITF2|FOXE2 0.0 forkhead box E1 protein-coding gene 1 Endoderm Thyroid 0.0 1.0 0.0 0.0 +Mm Hs MUC1 Foveolar cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene NA Endoderm GI tract 0.0 0.583333 0.0328947 0.0120722 +Mm Hs ANXA10 Foveolar cells ANX14 0.001 annexin A10 protein-coding gene NA Endoderm GI tract 0.0 1.0 0.000626566 6.42137e-05 +Mm Hs MUC5AC Foveolar cells NA 0.0 mucin 5AC, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm GI tract 0.0 0.75 0.000313283 0.0 +Mm Hs TFF1 Foveolar cells D21S21|pS2|pNR-2|HP1.A|BCEI 0.006 trefoil factor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0203634 0.0 +Mm Hs FOXQ1 Foveolar cells HFH1 0.026 forkhead box Q1 protein-coding gene NA Endoderm GI tract 0.0 0.0833333 0.00093985 0.0324921 +Mm Hs SULT1C2 Foveolar cells ST1C1|SULT1C1 0.002 sulfotransferase family 1C member 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs PTGR1 Foveolar cells ZADH3|LTB4DH 0.042 prostaglandin reductase 1 protein-coding gene NA Endoderm GI tract 0.0 0.916667 0.0623434 0.0346112 +Mm GSDMA2 Foveolar cells NA 0.0 gasdermin A2 protein coding gene NA Endoderm GI tract 0.0 0.75 0.0 0.0 +Mm Hs PLA2G1B Foveolar cells PLA2|PPLA2|PLA2A 0.007 phospholipase A2 group IB protein-coding gene NA Endoderm GI tract 0.0 1.0 0.00469925 0.00661401 +Mm Hs CLPS Foveolar cells NA 0.021 colipase protein-coding gene NA Endoderm GI tract 0.0 1.0 0.00250627 0.0249791 +Mm Hs GSTA1 Foveolar cells NA 0.012 glutathione S-transferase alpha 1 protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0300752 0.00757722 +Mm Hs PGC Foveolar cells NA 0.005 progastricsin protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0056391 0.00398125 +Mm SPRR2A1 Foveolar cells NA 0.007 small proline-rich protein 2A1 protein coding gene NA Endoderm GI tract NA NA NA NA +Mm Hs TFF2 Foveolar cells SML1 0.002 trefoil factor 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.000313283 0.0 +Mm Hs LGALS2 Foveolar cells HL14 0.032 galectin 2 protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0379073 0.030052 +Mm Hs PSCA Foveolar cells NA 0.004 prostate stem cell antigen protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0137845 0.000898992 +Mm SPRR2A3 Foveolar cells NA 0.011 small proline-rich protein 2A3 protein coding gene NA Endoderm GI tract NA NA NA NA +Mm Hs GKN2 Foveolar cells TFIZ1|PRO813|VLTI465|blottin|GDDR|BRICD1B 0.001 gastrokine 2 protein-coding gene NA Endoderm GI tract 0.0 1.0 0.00156642 0.000192641 +Mm Hs GKN1 Foveolar cells AMP18|CA11|BRICD1 0.001 gastrokine 1 protein-coding gene NA Endoderm GI tract 0.0 1.0 0.0 0.000449496 +Mm Hs CLDN18 Foveolar cells SFTPJ 0.01 claudin 18 protein-coding gene 1 Endoderm GI tract 0.0 0.916667 0.00407268 0.0111732 +Mm Hs KRT20 Foveolar cells CK20|K20|MGC35423 0.012 keratin 20 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0150376 0.0117511 +Mm Hs LGALS4 Foveolar cells GAL4 0.032 galectin 4 protein-coding gene 1 Endoderm GI tract 0.0 0.333333 0.0385338 0.0305015 +Mm Hs AKR1B10 Foveolar cells AKR1B12|ARL-1|ARL1|HSI|ALDRLn|AKR1B11 0.005 aldo-keto reductase family 1 member B10 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0137845 0.00250433 +Mm Hs IL33 Foveolar cells DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Endoderm GI tract 0.0 0.0833333 0.0106516 0.0205484 +Mm Hs SLC6A1 GABAergic neurons GAT1|GABATR|GABATHG 0.043 solute carrier family 6 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313283 0.0 +Mm Hs GABBR2 GABAergic neurons HG20|GABABR2|GPRC3B|GPR51 0.023 gamma-aminobutyric acid type B receptor subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00657895 0.0262567 +Mm Hs GAD1 GABAergic neurons GAD 0.03 glutamate decarboxylase 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00344612 0.036785 +Mm Hs GADD45B GABAergic neurons GADD45BETA|DKFZP566B133|MYD118 0.108 growth arrest and DNA damage inducible beta protein-coding gene NA Ectoderm Brain 0.0 0.0 0.194236 0.0912884 +Mm Hs PAX2 GABAergic neurons NA 0.002 paired box 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.00166913 +Mm Hs SLC32A1 GABAergic neurons VGAT|bA122O1.1|VIAAT 0.026 solute carrier family 32 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs GAD2 GABAergic neurons GAD65 0.073 glutamate decarboxylase 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0244361 0.0862169 +Mm Hs VIP GABAergic neurons NA 0.003 vasoactive intestinal peptide protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SST GABAergic neurons SMST 0.027 somatostatin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.047619 0.0 +Mm Hs PVALB GABAergic neurons D22S749 0.005 parvalbumin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.00584195 +Mm Hs TNFAIP8L3 GABAergic neurons FLJ41287 0.001 TNF alpha induced protein 8 like 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SEMA3C GABAergic neurons SemE|SEMAE 0.04 semaphorin 3C protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0128446 0.0 +Mm Hs MYBPC1 GABAergic neurons NA 0.001 myosin binding protein C, slow type protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00281955 0.000770367 +Mm Hs PARM1 GABAergic neurons DKFZP564O0823|Cipar1|WSC4 0.02 prostate androgen-regulated mucin-like protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.125 0.018797 0.0207357 +Mm Hs DLX1 GABAergic neurons NA 0.036 distal-less homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.375 0.0 0.0446813 +Mm Hs PPY Gamma (PP) cells PNP 0.019 pancreatic polypeptide protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0386185 0.0153994 +Mm Hs SCGN Gamma (PP) cells SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0276295 0.0 +Mm Hs FXYD2 Gamma (PP) cells MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene 1 Endoderm Pancreas 0.285714 0.0 0.00376766 0.0306064 +Hs SCGB2A1 Gamma (PP) cells UGB3|LPHC|MGC71973|MGB2 0.003 secretoglobin family 2A member 1 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0153846 0.0 +Hs GPC5-AS1 Gamma (PP) cells NA 0.001 GPC5 antisense RNA 1 non-coding RNA 1 Endoderm Pancreas 0.857143 0.0 0.0021978 0.0 +Mm Hs CMTM8 Gamma (PP) cells CKLFSF8 0.035 CKLF like MARVEL transmembrane domain containing 8 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0241758 0.0371511 +Mm Hs ARX Gamma (PP) cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Endoderm Pancreas 0.142857 0.0 0.00188383 0.0236124 +Mm Hs ETV1 Gamma (PP) cells ER81 0.037 ETS variant 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00816326 0.0450433 +Hs PPY2P Gamma (PP) cells PPY2 0.0 pancreatic polypeptide 2, pseudogene pseudogene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs PXK Gamma (PP) cells FLJ20335|Slob 0.012 PX domain containing serine/threonine kinase like protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.011303 0.0123195 +Mm Hs SERTM1 Gamma (PP) cells C13orf36 0.001 serine rich and transmembrane domain containing 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000627943 0.0 +Mm Hs SLITRK6 Gamma (PP) cells FLJ22774 0.003 SLIT and NTRK like family member 6 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00156986 0.0 +Mm Hs SEMA3E Gamma (PP) cells M-SemaK|KIAA0331|coll-5|SEMAH 0.005 semaphorin 3E protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0 0.0 +Mm Hs APOBEC2 Gamma (PP) cells ARCD1 0.002 apolipoprotein B mRNA editing enzyme catalytic subunit 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00282575 0.00224575 +Mm Hs ABCC9 Gamma (PP) cells SUR2|CMD1O 0.016 ATP binding cassette subfamily C member 9 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00125589 0.0199551 +Mm Hs NEUROD1 Gamma (PP) cells BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.0210361 0.0429901 +Mm Hs PAX6 Gamma (PP) cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Endoderm Pancreas 0.285714 0.0 0.0138148 0.058967 +Mm Hs ISL1 Gamma (PP) cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.428571 0.0 0.0125589 0.0313763 +Mm Hs CARTPT Gamma (PP) cells CART 0.008 CART prepropeptide protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00722135 0.00814886 +Mm Hs THSD7A Gamma (PP) cells KIAA0960 0.016 thrombospondin type 1 domain containing 7A protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0197802 0.0 +Mm Hs AQP3 Gamma (PP) cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Endoderm Pancreas 0.714286 0.0 0.0697017 0.0159127 +Mm Hs ENTPD2 Gamma (PP) cells NTPDase-2|CD39L1 0.012 ectonucleoside triphosphate diphosphohydrolase 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000941915 0.0145653 +Mm Hs PTGFR Gamma (PP) cells NA 0.001 prostaglandin F receptor protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313972 0.00160411 +Mm Hs CHN2 Gamma (PP) cells ARHGAP3|RhoGAP3 0.021 chimerin 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00659341 0.0248316 +Mm Hs EGR3 Gamma (PP) cells PILOT 0.004 early growth response 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00345369 0.0044915 +Mm Hs LMO3 Gamma (PP) cells Rhom-3|RBTNL2 0.01 LIM domain only 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00722135 0.0107154 +Mm Hs MEIS1 Gamma (PP) cells NA 0.024 Meis homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0379906 0.0196343 +Hs ZNF503 Gamma (PP) cells FLJ45745|MGC2555|Nlz2 0.006 zinc finger protein 503 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0298273 0.0 +Mm Hs FGB Gamma (PP) cells NA 0.009 fibrinogen beta chain protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0175824 0.00686558 +Hs GNLY Gamma delta T cells NKG5|LAG-2|D2S69E|TLA519|LAG2 0.013 granulysin protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0596728 0.0 +Mm Hs PTGDS Gamma delta T cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0596728 0.0551489 +Mm Hs GZMB Gamma delta T cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 0.933333 0.666667 0.039461 0.00796097 +Mm Hs S100B Gamma delta T cells S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Mesoderm Immune system 0.0133333 0.0 0.0336862 0.0 +Hs FGFBP2 Gamma delta T cells NA 0.005 fibroblast growth factor binding protein 2 protein-coding gene 1 Mesoderm Immune system 0.773333 0.0 0.0109079 0.0 +Mm Hs NKG7 Gamma delta T cells GMP-17 0.056 natural killer cell granule protein 7 protein-coding gene 1 Mesoderm Immune system 1.0 1.0 0.0863009 0.0453903 +Mm Hs PRF1 Gamma delta T cells PFP|HPLH2 0.009 perforin 1 protein-coding gene 1 Mesoderm Immune system 0.786667 0.333333 0.012512 0.0045583 +Hs KLRF1 Gamma delta T cells CLEC5C|NKp80 0.003 killer cell lectin like receptor F1 protein-coding gene 1 Mesoderm Immune system 0.626667 0.0 0.0060956 0.0 +Mm Hs HOPX Gamma delta T cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Mesoderm Immune system 0.853333 0.0 0.0734681 0.0222779 +Mm Hs CST7 Gamma delta T cells NA 0.028 cystatin F protein-coding gene 1 Mesoderm Immune system 0.973333 0.222222 0.0474816 0.0186184 +Mm Hs KLRD1 Gamma delta T cells CD94 0.02 killer cell lectin like receptor D1 protein-coding gene 1 Mesoderm Immune system 0.853333 1.0 0.0192493 0.0160503 +Mm Hs CTSW Gamma delta T cells NA 0.026 cathepsin W protein-coding gene 1 Mesoderm Immune system 0.96 0.555556 0.0401027 0.019132 +Mm Hs SPON2 Gamma delta T cells DIL1 0.017 spondin 2 protein-coding gene 1 Mesoderm Immune system 0.533333 0.0 0.0372153 0.0 +Mm Hs IFITM1 Gamma delta T cells 9-27|CD225|DSPA2a|IFI17 0.059 interferon induced transmembrane protein 1 protein-coding gene 1 Mesoderm Immune system 0.133333 0.0 0.0298364 0.0649076 +Mm Hs GZMA Gamma delta T cells HFSP|CTLA3 0.026 granzyme A protein-coding gene 1 Mesoderm Immune system 0.92 1.0 0.0452358 0.0177838 +Mm Hs CD247 Gamma delta T cells CD3H|CD3Q|CD3Z 0.019 CD247 molecule protein-coding gene 1 Mesoderm Immune system 0.8 0.0 0.0375361 0.0125193 +Mm Hs CLIC3 Gamma delta T cells NA 0.015 chloride intracellular channel 3 protein-coding gene 1 Mesoderm Immune system 0.453333 0.0 0.0141161 0.0120056 +Mm Hs CD7 Gamma delta T cells LEU-9|TP41|Tp40 0.03 CD7 molecule protein-coding gene 1 Mesoderm Immune system 0.906667 0.555556 0.084376 0.0157935 +Mm Hs ADGRG1 Gamma delta T cells TM7LN4|TM7XN1|GPR56 0.045 adhesion G protein-coupled receptor G1 protein-coding gene 1 Mesoderm Immune system 0.0933333 0.0 0.0195701 0.050398 +Mm Hs CCL5 Gamma delta T cells RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Immune system 0.986667 1.0 0.0641643 0.0321649 +Mm Hs TRDC Gamma delta T cells NA 0.011 T cell receptor delta constant other 1 Mesoderm Immune system 0.653333 0.0 0.0105871 0.0 +Mm Hs STMN1 Gamma delta T cells OP18|PR22|PP19|Lag|FLJ32206|LAP18|C1orf215 0.43 stathmin 1 protein-coding gene 1 Mesoderm Immune system 0.08 0.0 0.427655 0.0 +Mm Hs HMGB2 Gamma delta T cells HMG2 0.279 high mobility group box 2 protein-coding gene 1 Mesoderm Immune system 0.386667 0.222222 0.32403 0.262134 +Mm Hs TYMS Gamma delta T cells Tsase|TMS|HsT422 0.087 thymidylate synthetase protein-coding gene 1 Mesoderm Immune system 0.04 0.0 0.106833 0.0 +Mm Hs MKI67 Gamma delta T cells MIB-|PPP1R105 0.083 marker of proliferation Ki-67 protein-coding gene 1 Mesoderm Immune system 0.0533333 0.0 0.0773179 0.0812147 +Mm Hs UBE2C Gamma delta T cells UBCH10 0.004 ubiquitin conjugating enzyme E2 C protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0157202 0.0 +Mm Hs TUBA1B Gamma delta T cells K-ALPHA-1 0.517 tubulin alpha 1b protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00866218 0.0 +Mm Hs ASPM Gamma delta T cells Calmbp1|FLJ10517|FLJ10549|MCPH5 0.021 abnormal spindle microtubule assembly protein-coding gene 1 Mesoderm Immune system 0.0266667 0.0 0.0352903 0.0162429 +Mm Hs CENPA Gamma delta T cells CENP-A|CenH3 0.083 centromere protein A protein-coding gene 1 Mesoderm Immune system 0.0266667 0.0 0.0160411 0.0957884 +Mm Hs TOP2A Gamma delta T cells TOP2 0.107 DNA topoisomerase II alpha protein-coding gene 1 Mesoderm Immune system 0.0266667 0.0 0.0927174 0.0 +Mm Hs PCNA Gamma delta T cells NA 0.121 proliferating cell nuclear antigen protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.150144 0.112994 +Mm Hs AURKB Gamma delta T cells Aik2|IPL1|AurB|ARK2|STK5|PPP1R48|STK12 0.04 aurora kinase B protein-coding gene 1 Mesoderm Immune system 0.0266667 0.0 0.0384986 0.0370442 +Mm Hs BIRC5 Gamma delta T cells survivin|API4 0.121 baculoviral IAP repeat containing 5 protein-coding gene 1 Mesoderm Immune system 0.0266667 0.111111 0.11325 0.118002 +Mm Hs NUSAP1 Gamma delta T cells FLJ13421|ANKT|NuSAP1|BM037|PRO0310p1|Q0310 0.064 nucleolar and spindle associated protein 1 protein-coding gene 1 Mesoderm Immune system 0.0533333 0.0 0.0837344 0.0575244 +Mm Hs TROAP Gamma delta T cells TASTIN 0.005 trophinin associated protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0157202 0.0 +Hs TUBB Gamma delta T cells OK/SW-cl.56|MGC16435|M40|Tubb5 0.104 tubulin beta class I protein-coding gene 1 Mesoderm Immune system 0.0666667 0.0 0.512993 0.0 +Mm Hs H2AFX Gamma delta T cells H2AX 0.128 H2A histone family member X protein-coding gene 1 Mesoderm Immune system 0.0266667 0.0 0.0641643 0.138803 +Mm Hs CENPF Gamma delta T cells hcp-1 0.086 centromere protein F protein-coding gene 1 Mesoderm Immune system 0.04 0.0 0.112287 0.07717 +Mm Hs CCNB1 Gamma delta T cells CCNB 0.069 cyclin B1 protein-coding gene 1 Mesoderm Immune system 0.0133333 0.0 0.084376 0.0618259 +Mm Hs H2AFZ Gamma delta T cells H2A.Z|H2AZ 0.486 H2A histone family member Z protein-coding gene 1 Mesoderm Immune system 0.16 0.333333 0.655117 0.440357 +Mm Hs TRGV2 Gamma delta T cells VIS2|TCRGV2 0.0 T cell receptor gamma variable 2 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV10 Gamma delta T cells V3P|TCRGV10 0.0 T cell receptor gamma variable 10 (non-functional) other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV11 Gamma delta T cells V4P|TCRGV11 0.0 T cell receptor gamma variable 11 (non-functional) other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV1 Gamma delta T cells V1S1P|TCRGV1 0.0 T cell receptor gamma variable 1 (non-functional) other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV3 Gamma delta T cells V1S3|TCRGV3 0.0 T cell receptor gamma variable 3 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV4 Gamma delta T cells V1S4|TCRGV4 0.0 T cell receptor gamma variable 4 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV5 Gamma delta T cells V1S5|TCRGV5 0.0 T cell receptor gamma variable 5 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV8 Gamma delta T cells V1S8|TCRGV8 0.0 T cell receptor gamma variable 8 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGV9 Gamma delta T cells V2|TCRGV9 0.0 T cell receptor gamma variable 9 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRGJ1 Gamma delta T cells TCRGJ1 0.0 T cell receptor gamma joining 1 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRGJ2 Gamma delta T cells TCRGJ2 0.0 T cell receptor gamma joining 2 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGJP1 Gamma delta T cells JP1|TCRGJP1 0.0 T cell receptor gamma joining P1 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGJP2 Gamma delta T cells JP2|TCRGJP2 0.0 T cell receptor gamma joining P2 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGJP Gamma delta T cells JP|TCRGJP 0.0 T cell receptor gamma joining P other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRGC1 Gamma delta T cells TCRGC1 0.0 T cell receptor gamma constant 1 other NA Mesoderm Immune system 0.0133333 0.0 0.00160411 0.0 +Hs TRGC2 Gamma delta T cells TRGC2(2X)|TRGC2(3X)|TCRGC2 0.001 T cell receptor gamma constant 2 other NA Mesoderm Immune system 0.0266667 0.0 0.00384986 0.0 +Mm Hs TRDD1 Gamma delta T cells NA 0.0 T cell receptor delta diversity 1 other NA Mesoderm Immune system NA NA NA NA +Mm Hs TRDD2 Gamma delta T cells NA 0.0 T cell receptor delta diversity 2 other NA Mesoderm Immune system NA NA NA NA +Hs TRDD3 Gamma delta T cells NA 0.0 T cell receptor delta diversity 3 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRDJ1 Gamma delta T cells NA 0.0 T cell receptor delta joining 1 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRDJ2 Gamma delta T cells NA 0.0 T cell receptor delta joining 2 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRDJ3 Gamma delta T cells NA 0.0 T cell receptor delta joining 3 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRDJ4 Gamma delta T cells NA 0.0 T cell receptor delta joining 4 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRDV1 Gamma delta T cells hDV101S1 0.0 T cell receptor delta variable 1 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs TRDV2 Gamma delta T cells hDV102S1|MGC117421 0.0 T cell receptor delta variable 2 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRDV3 Gamma delta T cells hDV103S1 0.0 T cell receptor delta variable 3 other NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs ANPEP Gastric chief cells gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0128446 0.0168752 +Mm Hs BHLHA15 Gastric chief cells MIST1|bHLHa15|BHLHB8 0.0 basic helix-loop-helix family member a15 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.000513314 +Mm Hs RAB3D Gastric chief cells RAB16|D2-2|RAD3D|GOV 0.015 RAB3D, member RAS oncogene family protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs LEP Gastric chief cells OBS 0.0 leptin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs LGR5 Gastric chief cells HG38|FEX|GPR67|GPR49 0.002 leucine rich repeat containing G protein-coupled receptor 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313283 0.00198909 +Mm Hs KCNQ1 Gastric chief cells Kv7.1|KCNA8|KVLQT1|JLNS1|LQT1|LQT|KCNA9 0.004 potassium voltage-gated channel subfamily Q member 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00093985 0.00532563 +Mm Hs EGFR Gastric chief cells ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0222431 0.0127687 +Mm Hs PRKCZ Gastric chief cells PKC2 0.022 protein kinase C zeta protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0281039 +Hs CHIA Gastric chief cells AMCase|TSA1902|CHIT2 0.0 chitinase, acidic protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs CHRM3 Gastric chief cells NA 0.002 cholinergic receptor muscarinic 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313283 0.00205326 +Mm Hs EGFR Germ cells ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0238175 0.0129045 +Mm Hs POU5F1 Germ cells Oct4|MGC22487|OTF3 0.003 POU class 5 homeobox 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000670916 0.00259387 +Mm Hs TFAP2C Germ cells AP2-GAMMA|TFAP2G|hAP-2g 0.012 transcription factor AP-2 gamma protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00704462 0.0 +Mm Hs DAZL Germ cells DAZH|SPGYLA|MGC26406|DAZL1|DAZLA 0.01 deleted in azoospermia like protein-coding gene 1 Mesoderm Reproductive 0.49763 0.182927 0.000335458 0.00343687 +Mm Hs MAGEA4 Germ cells MAGE4A|MAGE4B|MAGE-41|MAGE-X2|MGC21336|CT1.4|MAGE4 0.006 MAGE family member A4 protein-coding gene NA Mesoderm Reproductive 0.336493 0.0 0.00100637 0.0 +Mm Hs DDX4 Germ cells VASA 0.013 DEAD-box helicase 4 protein-coding gene 1 Mesoderm Reproductive 0.739336 0.426829 0.00100637 0.00188055 +Mm Hs ZAR1 Germ cells Z3CXXC6 0.0 zygote arrest 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Hs TESMIN Germ cells CXCDC2|MTL5 0.004 testis expressed metallothionein like protein protein-coding gene NA Mesoderm Reproductive 0.312796 0.0 0.000335458 0.0 +Mm Hs TEX101 Germ cells MGC4766|SGRG|CT131|SPATA44 0.005 testis expressed 101 protein-coding gene NA Mesoderm Reproductive 0.151659 0.0 0.000335458 0.0 +Hs GCNA Germ cells NAAR1|ACRC 0.0 germ cell nuclear acidic peptidase protein-coding gene NA Mesoderm Reproductive 0.028436 0.0 0.0 0.0 +Mm Hs PRM1 Germ cells CT94.1 0.022 protamine 1 protein-coding gene 1 Mesoderm Reproductive 0.853081 0.841463 0.0399195 0.00019454 +Mm Hs TNP2 Germ cells NA 0.008 transition protein 2 protein-coding gene 1 Mesoderm Reproductive 0.113744 0.0 0.0 0.0 +Mm Hs FABP9 Germ cells PERF|T-FABP|PERF15 0.008 fatty acid binding protein 9 protein-coding gene NA Mesoderm Reproductive 0.0 0.932927 0.0 0.000129693 +Mm Hs ODF2 Germ cells ODF84|CT134 0.028 outer dense fiber of sperm tails 2 protein-coding gene 1 Mesoderm Reproductive 0.753555 0.926829 0.00234821 0.0151093 +Mm Hs CRISP2 Germ cells CRISP-2|CT36|GAPDL5|TPX1 0.016 cysteine rich secretory protein 2 protein-coding gene NA Mesoderm Reproductive 0.654028 0.932927 0.00704462 0.0 +Mm Hs TCP11 Germ cells FPPR 0.015 t-complex 11 protein-coding gene NA Mesoderm Reproductive 0.611374 0.0 0.00100637 0.0 +Mm Hs GGNBP1 Germ cells NA 0.008 gametogenetin binding protein 1 (pseudogene) pseudogene NA Mesoderm Reproductive 0.0331754 0.871951 0.0 0.00077816 +Mm Hs PHF7 Germ cells NYD-SP6|HSPC226 0.018 PHD finger protein 7 protein-coding gene NA Mesoderm Reproductive 0.810427 0.817073 0.00872191 0.00077816 +Mm Hs CREB5 Germ cells H_GS165L15.1|CRE-BPA 0.026 cAMP responsive element binding protein 5 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0150956 0.0292458 +Mm CETN4 Germ cells NA 0.01 centrin 4 protein coding gene NA Mesoderm Reproductive 0.0 0.743902 0.0 0.00460411 +Mm Hs SLFNL1 Germ cells FLJ23878 0.003 schlafen like 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs COX7B2 Germ cells NA 0.013 cytochrome c oxidase subunit 7B2 protein-coding gene NA Mesoderm Reproductive 0.445498 0.786585 0.0 0.00188055 +Mm Hs KIF2B Germ cells NA 0.006 kinesin family member 2B protein-coding gene NA Mesoderm Reproductive 0.241706 0.365854 0.0 0.0 +Mm Hs CCDC30 Germ cells FLJ20972|PFD6L|LOC728621 0.01 coiled-coil domain containing 30 protein-coding gene NA Mesoderm Reproductive 0.137441 0.689024 0.00100637 0.00311264 +Mm Hs LRRC57 Germ cells FLJ36812 0.005 leucine rich repeat containing 57 protein-coding gene NA Mesoderm Reproductive 0.0 0.286585 0.00167729 0.00278841 +Mm FAM209 Germ cells NA 0.004 family with sequence similarity 209 protein coding gene NA Mesoderm Reproductive 0.0 0.432927 0.0 0.0 +Mm Hs BCL2L14 Germ cells BCLG|BCL-G 0.009 BCL2 like 14 protein-coding gene NA Mesoderm Reproductive 0.279621 0.402439 0.00134183 0.00311264 +Mm Hs AQP11 Germ cells NA 0.018 aquaporin 11 protein-coding gene NA Mesoderm Reproductive 0.170616 0.768293 0.0 0.0119318 +Mm ADAM3 Germ cells NA 0.006 a disintegrin and metallopeptidase domain 3 (cyritestin) protein coding gene NA Mesoderm Reproductive 0.0 0.664634 0.0 0.0 +Mm Hs TEX35 Germ cells DKFZP564J047|TSC24|C1orf49 0.006 testis expressed 35 protein-coding gene NA Mesoderm Reproductive 0.2891 0.0 0.0 0.0 +Mm Hs SPINK2 Germ cells HUSI-II 0.024 serine peptidase inhibitor, Kazal type 2 protein-coding gene NA Mesoderm Reproductive 0.92891 0.0 0.0382422 0.0 +Mm Hs TSSK3 Germ cells SPOGA3|STK22C 0.005 testis specific serine kinase 3 protein-coding gene NA Mesoderm Reproductive 0.151659 0.0 0.0 0.0 +None GSG2 Germ cells NA 0.006 NA NA NA Mesoderm Reproductive 0.0 0.640244 0.0 0.00058362 +Mm Hs CREB3L4 Germ cells AIbZIP|CREB4|CREB3|hJAL|ATCE1 0.004 cAMP responsive element binding protein 3 like 4 protein-coding gene NA Mesoderm Reproductive 0.0 0.396341 0.00167729 0.00116724 +Mm Hs TSACC Germ cells SSTK-IP|C1orf182 0.018 TSSK6 activating cochaperone protein-coding gene NA Mesoderm Reproductive 0.85782 0.0 0.0120765 0.0 +Mm Hs SPATA46 Germ cells C1orf111 0.006 spermatogenesis associated 46 protein-coding gene NA Mesoderm Reproductive 0.218009 0.0 0.0 0.0 +Mm TSGA8 Germ cells NA 0.004 testis specific gene A8 protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs TEKT1 Germ cells NA 0.015 tektin 1 protein-coding gene NA Mesoderm Reproductive 0.222749 0.0 0.00201275 0.0 +Mm Hs MORN5 Germ cells FLJ46909|C9orf113|C9orf18 0.014 MORN repeat containing 5 protein-coding gene NA Mesoderm Reproductive 0.407583 0.792683 0.00201275 0.00395565 +Mm TMCO5 Germ cells NA 0.004 transmembrane and coiled-coil domains 5 protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs OTUB2 Germ cells FLJ21916|MGC3102|C14orf137 0.006 OTU deubiquitinase, ubiquitin aldehyde binding 2 protein-coding gene NA Mesoderm Reproductive 0.21327 0.420732 0.0 0.000713313 +Mm TSSK1 Germ cells NA 0.004 testis-specific serine kinase 1 protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs TSKS Germ cells TSSKS|PPP1R161 0.007 testis specific serine kinase substrate protein-coding gene NA Mesoderm Reproductive 0.312796 0.0 0.0 0.0 +Mm PRDX6B Germ cells NA 0.007 peroxiredoxin 6B protein coding gene NA Mesoderm Reproductive 0.0 0.780488 0.0 6.48466e-05 +Mm Hs H2AFB1 Germ cells NA 0.003 H2A histone family member B1 protein-coding gene NA Mesoderm Reproductive 0.00473934 0.408537 0.0 0.0 +Mm Hs ATL3 Germ cells DKFZP564J0863 0.016 atlastin GTPase 3 protein-coding gene NA Mesoderm Reproductive 0.364929 0.414634 0.0181147 0.00629012 +Mm Hs DMRTB1 Germ cells NA 0.013 DMRT like family B with proline rich C-terminal 1 protein-coding gene NA Mesoderm Reproductive 0.407583 0.847561 0.0 0.00142663 +Mm WBSCR25 Germ cells NA 0.003 Williams Beuren syndrome chromosome region 25 (human) antisense lncRNA gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs TMCO2 Germ cells dJ39G22.2 0.008 transmembrane and coiled-coil domains 2 protein-coding gene NA Mesoderm Reproductive 0.364929 0.0 0.0 0.0 +Mm TUBA3A Germ cells NA 0.009 tubulin, alpha 3A protein coding gene 1 Mesoderm Reproductive NA NA NA NA +Mm Hs FHL5 Germ cells FLJ33049|dJ393D12.2 0.006 four and a half LIM domains 5 protein-coding gene NA Mesoderm Reproductive 0.322275 0.347561 0.000335458 0.0 +Mm Hs MS4A5 Germ cells CD20L2 0.008 membrane spanning 4-domains A5 protein-coding gene NA Mesoderm Reproductive 0.303318 0.597561 0.0 0.0 +Mm Hs CST8 Germ cells CRES|CTES5 0.006 cystatin 8 protein-coding gene NA Mesoderm Reproductive 0.0758294 0.439024 0.0 0.00259387 +Mm Hs TMEM247 Germ cells NA 0.007 transmembrane protein 247 protein-coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs GALNTL5 Germ cells NA 0.006 polypeptide N-acetylgalactosaminyltransferase like 5 protein-coding gene NA Mesoderm Reproductive 0.255924 0.451219 0.0 0.0 +Mm Hs OSBP2 Germ cells KIAA1664|ORP-4|ORP4|OSBPL1 0.01 oxysterol binding protein 2 protein-coding gene NA Mesoderm Reproductive 0.236967 0.426829 0.00536733 0.00356656 +Mm Hs MARCH11 Germ cells MARCH-XI|RNF226 0.012 membrane associated ring-CH-type finger 11 protein-coding gene NA Mesoderm Reproductive 0.199052 0.731707 0.0 0.00447442 +Mm Hs TEX33 Germ cells MGC35206|EAN57|C22orf33 0.008 testis expressed 33 protein-coding gene NA Mesoderm Reproductive 0.265403 0.0 0.0 0.0 +Mm Hs SPATA20 Germ cells FLJ21347|SSP411|Tisp78 0.01 spermatogenesis associated 20 protein-coding gene NA Mesoderm Reproductive 0.331754 0.0 0.0107347 0.0 +Mm TUBA3B Germ cells NA 0.009 tubulin, alpha 3B protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs CDRT4 Germ cells FLJ36674 0.004 CMT1A duplicated region transcript 4 protein-coding gene NA Mesoderm Reproductive 0.014218 0.414634 0.0 0.0 +Mm Hs SPATA18 Germ cells FLJ32906 0.008 spermatogenesis associated 18 protein-coding gene 1 Mesoderm Reproductive 0.331754 0.0 0.00100637 0.0 +Mm Hs LRRC18 Germ cells UNQ933|MGC34773|UNQ9338|VKGE9338 0.007 leucine rich repeat containing 18 protein-coding gene NA Mesoderm Reproductive 0.14218 0.615854 0.0 0.000129693 +Mm Hs SCP2D1 Germ cells dJ1068E13.2|HSD22|C20orf79 0.006 SCP2 sterol binding domain containing 1 protein-coding gene NA Mesoderm Reproductive 0.180095 0.0 0.0 0.0 +Mm Hs IQCF1 Germ cells MGC39725 0.008 IQ motif containing F1 protein-coding gene NA Mesoderm Reproductive 0.312796 0.487805 0.0 0.000259387 +Mm Hs PGK2 Germ cells PGKPS|PGK-2 0.012 phosphoglycerate kinase 2 protein-coding gene 1 Mesoderm Reproductive 0.50237 0.786585 0.0 0.0 +Mm Hs TULP2 Germ cells TUBL2|CT65 0.008 tubby like protein 2 protein-coding gene NA Mesoderm Reproductive 0.194313 0.0 0.0 0.0 +Mm CMTM2A Germ cells NA 0.007 CKLF-like MARVEL transmembrane domain containing 2A protein coding gene NA Mesoderm Reproductive 0.0 0.871951 0.0 0.0 +Mm Hs CCDC54 Germ cells NYD-SP17|FLJ25362 0.008 coiled-coil domain containing 54 protein-coding gene NA Mesoderm Reproductive 0.369668 0.530488 0.0 0.0 +Mm Hs AKAP4 Germ cells p82|hAKAP82|AKAP82|Fsc1|CT99 0.008 A-kinase anchoring protein 4 protein-coding gene NA Mesoderm Reproductive 0.317536 0.560976 0.0 0.0 +Mm Hs GTSF1 Germ cells FLJ32942|FAM112B 0.022 gametocyte specific factor 1 protein-coding gene NA Mesoderm Reproductive 0.938389 0.945122 0.00436095 0.00168601 +Mm Hs PPP3R2 Germ cells PPP3RL 0.011 protein phosphatase 3 regulatory subunit B, beta protein-coding gene NA Mesoderm Reproductive 0.364929 0.884146 0.000335458 0.0 +Mm Hs TPPP2 Germ cells p25beta|CT152|C14orf8 0.009 tubulin polymerization promoting protein family member 2 protein-coding gene NA Mesoderm Reproductive 0.450237 0.0 0.000670916 0.0 +Mm GSTT4 Germ cells HS322B1A|GSTTP1 0.005 glutathione S-transferase theta 4 protein-coding gene NA Mesoderm Reproductive 0.0 0.628049 0.0 0.0 +Mm Hs LELP1 Germ cells NA 0.011 late cornified envelope like proline rich 1 protein-coding gene NA Mesoderm Reproductive 0.554502 0.5 0.00335458 0.0 +Mm NUPR1L Germ cells NA 0.006 nuclear protein transcriptional regulator 1 like protein coding gene NA Mesoderm Reproductive 0.0 0.762195 0.0 0.000129693 +Mm Hs SPERT Germ cells NURIT|CBY2 0.008 spermatid associated protein-coding gene NA Mesoderm Reproductive 0.2891 0.0 0.0 0.0 +Mm CMTM2B Germ cells NA 0.007 CKLF-like MARVEL transmembrane domain containing 2B protein coding gene NA Mesoderm Reproductive 0.0 0.890244 0.0 0.0 +Mm Hs CATSPERZ Germ cells DKFZP566E164|C11orf20|TEX40 0.008 catsper channel auxiliary subunit zeta protein-coding gene NA Mesoderm Reproductive 0.0 0.884146 0.0 0.00038908 +Mm Hs MAEL Germ cells FLJ14904|CT128|SPATA35 0.019 maelstrom spermatogenic transposon silencer protein-coding gene NA Mesoderm Reproductive 0.824645 0.957317 0.00234821 0.00188055 +Mm Hs PGAM2 Germ cells PGAM-M 0.012 phosphoglycerate mutase 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.902439 0.0 0.0057065 +Mm Hs TMEM53 Germ cells FLJ22353|NET4 0.012 transmembrane protein 53 protein-coding gene NA Mesoderm Reproductive 0.322275 0.0 0.00167729 0.0 +Mm Hs ACTRT2 Germ cells Arp-T2|ARPM2|FLJ25424 0.009 actin related protein T2 protein-coding gene NA Mesoderm Reproductive 0.407583 0.518293 0.0 0.0 +Mm Hs ROPN1 Germ cells ODF6|ropporin|ROPN1A|CT91 0.011 rhophilin associated tail protein 1 protein-coding gene NA Mesoderm Reproductive 0.436019 0.0 0.000670916 0.0 +Mm Hs RNF151 Germ cells NA 0.01 ring finger protein 151 protein-coding gene NA Mesoderm Reproductive 0.345972 0.0 0.0 0.0 +Mm Hs IQCF3 Germ cells NA 0.009 IQ motif containing F3 protein-coding gene NA Mesoderm Reproductive 0.303318 0.670732 0.0 0.0 +Mm Hs CABS1 Germ cells NYD-SP26|FLJ32897|CLPH|C4orf35 0.008 calcium binding protein, spermatid associated 1 protein-coding gene 1 Mesoderm Reproductive 0.341232 0.573171 0.0 0.0 +Mm Hs CCDC91 Germ cells FLJ11088|DKFZp779L1558 0.02 coiled-coil domain containing 91 protein-coding gene NA Mesoderm Reproductive 0.582938 0.579268 0.0150956 0.00616043 +Mm Hs SPATA3 Germ cells TSARG1 0.009 spermatogenesis associated 3 protein-coding gene NA Mesoderm Reproductive 0.2891 0.0 0.0 0.0 +Mm Hs LRRC46 Germ cells MGC16309 0.011 leucine rich repeat containing 46 protein-coding gene NA Mesoderm Reproductive 0.251185 0.817073 0.00201275 0.00213994 +Mm Hs PDCL2 Germ cells GCPHLP 0.011 phosducin like 2 protein-coding gene NA Mesoderm Reproductive 0.345972 0.902439 0.0 0.0 +Mm Hs H1FNT Germ cells HANP1|H1T2 0.009 H1 histone family member N, testis specific protein-coding gene 1 Mesoderm Reproductive 0.407583 0.597561 0.000335458 0.0 +Mm Hs TSSK6 Germ cells SSTK|FLJ24002|CT72 0.008 testis specific serine kinase 6 protein-coding gene NA Mesoderm Reproductive 0.303318 0.0 0.0 0.0 +Mm Hs COX8C Germ cells COX8-3 0.016 cytochrome c oxidase subunit 8C protein-coding gene NA Mesoderm Reproductive 0.78673 0.926829 0.000670916 0.000129693 +Mm Hs CETN1 Germ cells CEN1|CETN 0.012 centrin 1 protein-coding gene NA Mesoderm Reproductive 0.436019 0.902439 0.000335458 0.0 +Mm Hs SPATA19 Germ cells FLJ25851|spergen1|SPAS1|CT132 0.01 spermatogenesis associated 19 protein-coding gene NA Mesoderm Reproductive 0.317536 0.0 0.0 0.0 +Mm Hs TSSK2 Germ cells SPOGA2|FLJ38613|STK22B 0.006 testis specific serine kinase 2 protein-coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs ZNRF4 Germ cells spzn|Ssrzf1|RNF204 0.01 zinc and ring finger 4 protein-coding gene NA Mesoderm Reproductive 0.28436 0.0 0.0 0.0 +Mm CYPT4 Germ cells NA 0.006 cysteine-rich perinuclear theca 4 protein coding gene NA Mesoderm Reproductive 0.0 0.780488 0.0 0.0 +Mm Hs SPATA24 Germ cells T6441|CCDC161 0.018 spermatogenesis associated 24 protein-coding gene NA Mesoderm Reproductive 0.440758 0.0 0.0 0.0 +Mm Hs SPATA4 Germ cells TSARG2|SPEF1B 0.012 spermatogenesis associated 4 protein-coding gene NA Mesoderm Reproductive 0.454976 0.0 0.000335458 0.0 +Mm Hs FAM71E1 Germ cells NA 0.012 family with sequence similarity 71 member E1 protein-coding gene NA Mesoderm Reproductive 0.50237 0.792683 0.00134183 0.00019454 +Mm Hs FAM229A Germ cells NA 0.012 family with sequence similarity 229 member A protein-coding gene NA Mesoderm Reproductive 0.450237 0.817073 0.000670916 0.000129693 +Mm CYPT12 Germ cells NA 0.007 cysteine-rich perinuclear theca 12 protein coding gene NA Mesoderm Reproductive 0.0 0.798781 0.0 0.0 +Mm Hs HILS1 Germ cells NA 0.008 histone linker H1 domain, spermatid-specific 1 (pseudogene) pseudogene NA Mesoderm Reproductive 0.146919 0.786585 0.0 0.0 +Mm Hs HRASLS5 Germ cells HRLP5 0.011 HRAS like suppressor family member 5 protein-coding gene NA Mesoderm Reproductive 0.345972 0.920732 0.0 0.0 +Mm Hs GAPDHS Germ cells GAPDH-2|GAPD2|GAPDS 0.006 glyceraldehyde-3-phosphate dehydrogenase, spermatogenic protein-coding gene 1 Mesoderm Reproductive 0.0 0.72561 0.0 0.0 +Mm FHL4 Germ cells NA 0.008 four and a half LIM domains 4 protein coding gene NA Mesoderm Reproductive 0.0 0.914634 0.0 0.0 +Mm Hs HSPB9 Germ cells CT51 0.011 heat shock protein family B (small) member 9 protein-coding gene NA Mesoderm Reproductive 0.28436 0.920732 0.0 0.0 +Mm Hs SPATA33 Germ cells FLJ31606|C16orf55 0.023 spermatogenesis associated 33 protein-coding gene NA Mesoderm Reproductive 0.876777 0.0 0.0130829 0.0 +Mm Hs SPZ1 Germ cells NYD-TSP1|FLJ25709|PPP1R148 0.009 spermatogenic leucine zipper 1 protein-coding gene NA Mesoderm Reproductive 0.203791 0.0 0.0 0.0 +Mm IRGC1 Germ cells NA 0.006 immunity-related GTPase family, cinema 1 protein coding gene NA Mesoderm Reproductive 0.0 0.762195 0.0 6.48466e-05 +Mm Hs PRM3 Germ cells NA 0.01 protamine 3 protein-coding gene 1 Mesoderm Reproductive 0.308057 0.798781 0.0 0.0 +Mm Hs RBAKDN Germ cells NA 0.008 RBAK downstream neighbor non-coding RNA NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs DNAJB3 Germ cells HCG3 0.011 DnaJ heat shock protein family (Hsp40) member B3 other NA Mesoderm Reproductive 0.21327 0.926829 0.0 0.000648466 +Mm Hs HMGB4 Germ cells FLJ40388 0.015 high mobility group box 4 protein-coding gene NA Mesoderm Reproductive 0.63981 0.786585 0.00905736 0.0 +Mm Hs ROPN1L Germ cells FLJ25776|RSPH11 0.018 rhophilin associated tail protein 1 like protein-coding gene NA Mesoderm Reproductive 0.720379 0.0 0.00771553 0.0 +Mm Hs GSG1 Germ cells MGC3146 0.014 germ cell associated 1 protein-coding gene NA Mesoderm Reproductive 0.459716 0.859756 0.0 0.00201025 +Mm DBIL5 Germ cells NA 0.008 diazepam binding inhibitor-like 5 protein coding gene NA Mesoderm Reproductive 0.0 0.920732 0.0 6.48466e-05 +Mm Hs TNP1 Germ cells NA 0.018 transition protein 1 protein-coding gene 1 Mesoderm Reproductive 0.729858 0.0 0.0231466 0.0 +Mm Hs SMCP Germ cells NA 0.013 sperm mitochondria associated cysteine rich protein protein-coding gene 1 Mesoderm Reproductive 0.535545 0.0 0.00369004 0.0 +Mm Hs LDHC Germ cells CT32 0.014 lactate dehydrogenase C protein-coding gene NA Mesoderm Reproductive 0.554502 0.939024 0.00167729 0.000259387 +Mm Hs PRM2 Germ cells CT94.2 0.022 protamine 2 protein-coding gene 1 Mesoderm Reproductive 0.834123 0.865854 0.0362295 0.00019454 +Mm Hs DNAAF1 Germ cells FLJ25330|ODA7|CILD13|swt|LRRC50 0.009 dynein axonemal assembly factor 1 protein-coding gene NA Mesoderm Reproductive 0.189573 0.762195 0.00167729 0.000324233 +Mm Hs ACYP1 Germ cells NA 0.051 acylphosphatase 1 protein-coding gene NA Mesoderm Reproductive 0.165877 0.743902 0.0355585 0.0427339 +Mm Hs SORD Germ cells NA 0.033 sorbitol dehydrogenase protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0110701 0.0 +Mm Hs DKKL1 Germ cells SGY-1|CT34 0.019 dickkopf like acrosomal protein 1 protein-coding gene NA Mesoderm Reproductive 0.530806 0.908537 0.000335458 0.00687374 +Mm Hs RSPH1 Germ cells FLJ32753|RSP44|RSPH10A|CILD24|TSGA2 0.021 radial spoke head component 1 protein-coding gene NA Mesoderm Reproductive 0.194313 0.0 0.00369004 0.0 +Mm Hs COX6B2 Germ cells COXVIB2|FLJ32865|CT59 0.038 cytochrome c oxidase subunit 6B2 protein-coding gene NA Mesoderm Reproductive 0.0900474 0.853659 0.0 0.0351469 +Mm Hs MLF1 Germ cells NA 0.042 myeloid leukemia factor 1 protein-coding gene NA Mesoderm Reproductive 0.995261 0.945122 0.0301912 0.0201673 +Mm Hs SMIM24 Germ cells HSPC323|C19orf77 0.037 small integral membrane protein 24 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0375713 0.0 +Mm Hs SPA17 Germ cells CT22 0.02 sperm autoantigenic protein 17 protein-coding gene NA Mesoderm Reproductive 0.483412 0.0 0.000670916 0.0 +Mm Hs MEIG1 Germ cells bA2K17.3|SPATA39 0.018 meiosis/spermiogenesis associated 1 protein-coding gene NA Mesoderm Reproductive 0.21327 0.939024 0.0 0.00979184 +Mm Hs FKBP6 Germ cells FKBP36 0.008 FK506 binding protein 6 protein-coding gene 1 Mesoderm Reproductive 0.255924 0.195122 0.0 0.00499319 +Mm Hs TAF7L Germ cells CT40|TAF2Q 0.003 TATA-box binding protein associated factor 7 like protein-coding gene 1 Mesoderm Reproductive 0.042654 0.0 0.00167729 0.0 +Mm TEX19.1 Germ cells NA 0.007 testis expressed gene 19.1 protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs SYCP1 Germ cells HOM-TES-14|CT8 0.008 synaptonemal complex protein 1 protein-coding gene 1 Mesoderm Reproductive 0.379147 0.0 0.0 0.0 +Mm Hs SOHLH1 Germ cells NOHLH|TEB2|bA100C15.3|bHLHe80|SPATA27|C9orf157 0.005 spermatogenesis and oogenesis specific basic helix-loop-helix 1 protein-coding gene 1 Mesoderm Reproductive 0.274882 0.0 0.00134183 0.0 +Mm Hs SLC25A31 Germ cells DKFZP434N1235|ANT4 0.006 solute carrier family 25 member 31 protein-coding gene 1 Mesoderm Reproductive 0.2891 0.0 0.0 0.0 +Mm Hs PHF13 Germ cells MGC43399 0.008 PHD finger protein 13 protein-coding gene 1 Mesoderm Reproductive 0.132701 0.170732 0.0 0.00629012 +Mm Hs EGR4 Germ cells NGFI-C|PAT133 0.004 early growth response 4 protein-coding gene 1 Mesoderm Reproductive 0.0805687 0.0609756 0.00100637 0.00330718 +Mm Hs SMC1B Germ cells bK268H5|SMC1L2 0.011 structural maintenance of chromosomes 1B protein-coding gene 1 Mesoderm Reproductive 0.478673 0.0 0.00100637 0.0 +Mm Hs TEX15 Germ cells CT42 0.007 testis expressed 15, meiosis and synapsis associated protein-coding gene NA Mesoderm Reproductive 0.28436 0.0 0.000670916 0.0 +Mm Hs MOV10L1 Germ cells DJ402G11.8|DKFZp434B0717 0.006 Mov10 like RISC complex RNA helicase 1 protein-coding gene NA Mesoderm Reproductive 0.279621 0.140244 0.0 0.0019454 +Mm TRAP1A Germ cells NA 0.011 tumor rejection antigen P1A protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm Hs WDR5 Germ cells SWD3|CFAP89 0.024 WD repeat domain 5 protein-coding gene NA Mesoderm Reproductive 0.450237 0.0 0.016102 0.0 +Mm Hs DMRT1 Germ cells CT154 0.005 doublesex and mab-3 related transcription factor 1 protein-coding gene NA Mesoderm Reproductive 0.227488 0.0670732 0.00201275 0.00265871 +Mm Hs STRA8 Germ cells NA 0.002 stimulated by retinoic acid 8 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs ZMYND19 Germ cells MIZIP 0.012 zinc finger MYND-type containing 19 protein-coding gene NA Mesoderm Reproductive 0.227488 0.0 0.00570278 0.0 +Mm Hs MDN1 Germ cells KIAA0301|Rea1 0.018 midasin AAA ATPase 1 protein-coding gene NA Mesoderm Reproductive 0.0663507 0.0914634 0.0127474 0.0180922 +Mm Hs PIWIL2 Germ cells HILI|FLJ10351|Mili|CT80 0.005 piwi like RNA-mediated gene silencing 2 protein-coding gene NA Mesoderm Reproductive 0.28436 0.115854 0.00100637 0.00149147 +Mm CYCT Germ cells NA 0.006 cytochrome c, testis protein coding gene NA Mesoderm Reproductive 0.0 0.353659 0.0 0.00330718 +Mm Hs NR6A1 Germ cells GCNF1|RTR|CT150|GCNF 0.017 nuclear receptor subfamily 6 group A member 1 protein-coding gene 1 Mesoderm Reproductive 0.601896 0.115854 0.0328749 0.00311264 +Mm Hs RSBN1L Germ cells FLJ42526|FLJ45813|MGC71764 0.026 round spermatid basic protein 1 like protein-coding gene 1 Mesoderm Reproductive 0.601896 0.0 0.0805099 0.0 +Mm Hs DYNLT1 Germ cells TCTEL1 0.083 dynein light chain Tctex-type 1 protein-coding gene 1 Mesoderm Reproductive 0.691943 0.134146 0.328078 0.0149147 +Mm Hs PARN Germ cells NA 0.009 poly(A)-specific ribonuclease protein-coding gene 1 Mesoderm Reproductive 0.28436 0.0243902 0.0120765 0.00350172 +Mm Hs MKI67 Germ cells MIB-|PPP1R105 0.083 marker of proliferation Ki-67 protein-coding gene 1 Mesoderm Reproductive 0.0236967 0.0182927 0.0805099 0.0818365 +Mm Hs CHEK1 Germ cells CHK1 0.01 checkpoint kinase 1 protein-coding gene 1 Mesoderm Reproductive 0.123223 0.00609756 0.0268366 0.00363141 +Mm Hs BRCA1 Germ cells RNF53|PPP1R53|FANCS 0.007 BRCA1, DNA repair associated protein-coding gene 1 Mesoderm Reproductive 0.180095 0.0 0.0191211 0.00123209 +Mm Hs DMC1 Germ cells LIM15 0.001 DNA meiotic recombinase 1 protein-coding gene 1 Mesoderm Reproductive 0.0853081 0.0121951 0.0 0.000453926 +Mm Hs MRPL14 Germ cells RPML32 0.259 mitochondrial ribosomal protein L14 protein-coding gene 1 Mesoderm Reproductive 0.63981 0.097561 0.249245 0.24966 +Mm Hs MLH3 Germ cells NA 0.001 mutL homolog 3 protein-coding gene 1 Mesoderm Reproductive 0.0379147 0.0426829 0.0 0.000129693 +Mm Hs SPAG6 Germ cells Repro-SA-1|pf16|CT141 0.011 sperm associated antigen 6 protein-coding gene 1 Mesoderm Reproductive 0.308057 0.0 0.00201275 0.0 +Mm Hs ZPBP2 Germ cells ZPBPL|MGC41930 0.008 zona pellucida binding protein 2 protein-coding gene 1 Mesoderm Reproductive 0.436019 0.0 0.0 0.0 +Mm Hs DNAH6 Germ cells Dnahc6|FLJ37357|DNHL1 0.005 dynein axonemal heavy chain 6 protein-coding gene 1 Mesoderm Reproductive 0.14218 0.054878 0.00134183 0.00343687 +Mm Hs CAMK4 Germ cells CaMK-GR 0.027 calcium/calmodulin dependent protein kinase IV protein-coding gene 1 Mesoderm Reproductive 0.246445 0.109756 0.0174438 0.025355 +Mm Hs CREM Germ cells hCREM-2 0.065 cAMP responsive element modulator protein-coding gene 1 Mesoderm Reproductive 0.872038 0.487805 0.107682 0.0384541 +Mm Hs MYO1D Germ cells KIAA0727|myr4|PPP1R108 0.01 myosin ID protein-coding gene 1 Mesoderm Reproductive 0.184834 0.0 0.0063737 0.00855976 +Mm Hs HOOK1 Germ cells NA 0.035 hook microtubule tethering protein 1 protein-coding gene 1 Mesoderm Reproductive 0.312796 0.457317 0.00738007 0.0326827 +Hs SPATA12 Germ cells NA 0.003 spermatogenesis associated 12 protein-coding gene 1 Mesoderm Reproductive 0.241706 0.0 0.0 0.0 +Mm Hs DRD2 Glomus cells NA 0.0 dopamine receptor D2 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.000577478 +Mm Hs NOS1 Glomus cells nNOS 0.004 nitric oxide synthase 1 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00404235 +Mm Hs PHOX2B Glomus cells Phox2b|NBPhox|PMX2B 0.002 paired like homeobox 2b protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00211742 +Mm Hs TH Glomus cells DYT5b 0.002 tyrosine hydroxylase protein-coding gene 1 NA NA 0.0 0.0 0.0018797 0.0 +Mm Hs HMOX2 Glomus cells HO-2 0.027 heme oxygenase 2 protein-coding gene 1 NA NA 0.0 0.0 0.109962 0.00648059 +Mm Hs NDUFA4L2 Glomus cells NUOMS|FLJ26118 0.031 NDUFA4, mitochondrial complex associated like 2 protein-coding gene 1 NA NA 0.0 0.0 0.0234962 0.0318896 +Mm Hs COX4I2 Glomus cells COXIV-2|COX4B|dJ857M17.2|COX4-2|COX4L2 0.018 cytochrome c oxidase subunit 4I2 protein-coding gene 1 NA NA 0.0 0.0 0.00720551 0.0213025 +Mm Hs IL1R1 Glomus cells D2S1473|CD121A|IL1R 0.008 interleukin 1 receptor type 1 protein-coding gene 1 NA NA 0.0 0.0 0.0191103 0.00635226 +Mm Hs TNFRSF1A Glomus cells TNF-R|TNFAR|TNFR60|TNF-R-I|CD120a|TNF-R55|TNFR1 0.097 TNF receptor superfamily member 1A protein-coding gene 1 NA NA 0.0 0.0 0.104637 0.0 +Mm Hs CTH Glomus cells NA 0.008 cystathionine gamma-lyase protein-coding gene 1 NA NA 0.0 0.0 0.0018797 0.010138 +Mm Hs CBS Glomus cells HIP4 0.007 cystathionine-beta-synthase protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00866218 +Mm Hs GJA1 Glomus cells CX43|ODOD|SDTY3|ODDD|GJAL 0.1 gap junction protein alpha 1 protein-coding gene 1 NA NA 0.0 0.0 0.0632832 0.107154 +Mm Hs KCNK3 Glomus cells K2p3.1|TASK|TASK-1 0.005 potassium two pore domain channel subfamily K member 3 protein-coding gene 1 NA NA 0.0 0.0 0.00156642 0.00641643 +Mm Hs ASIC1 Glomus cells BNaC2|hBNaC2|ACCN2 0.002 acid sensing ion channel subunit 1 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00301572 +Mm Hs ASIC3 Glomus cells TNaC1|DRASIC|ACCN3 0.001 acid sensing ion channel subunit 3 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.000769971 +Mm Hs CALD1 Glomus cells H-CAD|L-CAD 0.186 caldesmon 1 protein-coding gene 1 NA NA 0.0 0.0 0.268797 0.165544 +Mm Hs COL4A1 Glomus cells NA 0.105 collagen type IV alpha 1 chain protein-coding gene 1 NA NA 0.0 0.0 0.0808271 0.113186 +Mm Hs VIM Glomus cells NA 0.427 vimentin protein-coding gene 1 NA NA 0.0 0.0 0.590539 0.0 +Mm Hs EPAS1 Glomus cells MOP2|PASD2|HIF2A|HLF|bHLHe73 0.076 endothelial PAS domain protein 1 protein-coding gene 1 NA NA 0.0 0.0 0.0567043 0.0830927 +Mm Hs GFRA1 Glomus cells RETL1|GDNFR|GFR-ALPHA-1|RET1L|TRNR1|GDNFRA 0.005 GDNF family receptor alpha 1 protein-coding gene 1 NA NA 0.0 0.0 0.00281955 0.00410651 +Mm Hs GFRA2 Glomus cells RETL2|GDNFRB|NTNRA|TRNR2 0.008 GDNF family receptor alpha 2 protein-coding gene 1 NA NA 0.0 0.0 0.00438596 0.00975297 +Mm Hs GAP43 Glomus cells B-50|PP46 0.149 growth associated protein 43 protein-coding gene 1 NA NA 0.0 0.0 0.0250627 0.180943 +Mm Hs MMP9 Glomus cells CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene 1 NA NA 0.0 0.0 0.00971178 0.0170035 +Mm Hs IL6ST Glomus cells CD130 0.055 interleukin 6 signal transducer protein-coding gene 1 NA NA 0.0 0.0 0.0911654 0.047674 +Mm Hs KCNJ11 Glomus cells Kir6.2|BIR 0.001 potassium voltage-gated channel subfamily J member 11 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00109079 +Mm Hs KCNJ8 Glomus cells Kir6.1 0.017 potassium voltage-gated channel subfamily J member 8 protein-coding gene 1 NA NA 0.0 0.0 0.0018797 0.0203401 +Mm Hs ABCC8 Glomus cells PHHI|SUR1|ABC36|HHF1|TNDM2|SUR|HRINS 0.008 ATP binding cassette subfamily C member 8 protein-coding gene 1 NA NA 0.0 0.0 0.0150376 0.0071864 +Mm Hs KCNK9 Glomus cells K2p9.1|TASK3|TASK-3 0.004 potassium two pore domain channel subfamily K member 9 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00500481 +Mm Hs SLC17A7 Glutaminergic neurons BNPI|VGLUT1 0.012 solute carrier family 17 member 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC17A6 Glutaminergic neurons DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs GRIN1 Glutaminergic neurons GluN1|NMDAR1 0.016 glutamate ionotropic receptor NMDA type subunit 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125313 0.0203401 +Mm Hs GRIN2B Glutaminergic neurons GluN2B|NMDAR2B 0.076 glutamate ionotropic receptor NMDA type subunit 2B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00501253 0.0946423 +Mm Hs GLS Glutaminergic neurons KIAA0838|GLS1 0.061 glutaminase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0197368 0.0723131 +Mm Hs MEIS2 Glutaminergic neurons HsT18361 0.17 Meis homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0548246 0.200706 +Mm Hs SLC17A8 Glutaminergic neurons VGLUT3|DFNA25 0.001 solute carrier family 17 member 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC1A1 Glutaminergic neurons EAAC1|EAAT3 0.013 solute carrier family 1 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs SLC1A2 Glutaminergic neurons GLT-1|EAAT2 0.071 solute carrier family 1 member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0 +Mm Hs SLC1A6 Glutaminergic neurons EAAT4 0.003 solute carrier family 1 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313283 0.0 +Mm Hs SLC6A9 Glycinergic neurons NA 0.001 solute carrier family 6 member 9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC32A1 Glycinergic neurons VGAT|bA122O1.1|VIAAT 0.026 solute carrier family 32 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs CREB3L1 Goblet cells OASIS 0.015 cAMP responsive element binding protein 3 like 1 protein-coding gene NA Endoderm GI tract 0.235294 0.548387 0.00850394 0.0156873 +Mm Hs NLRP6 Goblet cells PYPAF5|PAN3|CLR11.4|NALP6 0.008 NLR family pyrin domain containing 6 protein-coding gene NA Endoderm GI tract 0.0 0.0645161 0.0 0.00970811 +Mm Hs MUC5AC Goblet cells NA 0.0 mucin 5AC, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000314961 0.000578629 +Mm Hs MUC2 Goblet cells NA 0.007 mucin 2, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm GI tract 0.823529 0.806452 0.0015748 0.00578629 +Mm Hs SLC9A8 Goblet cells KIAA0939|NHE8 0.001 solute carrier family 9 member A8 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs OTOGL Goblet cells FLJ90579|C12orf64 0.0 otogelin like protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.000128584 +Mm Hs ITLN1 Goblet cells ITLN|FLJ20022|LFR|HL-1|hIntL 0.009 intelectin 1 protein-coding gene 1 Endoderm GI tract 0.764706 0.516129 0.00188976 0.00925807 +Mm Hs AQP3 Goblet cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene NA Endoderm GI tract 0.176471 0.0 0.0705512 0.0159445 +Mm Hs CDON Goblet cells ORCAM|CDO|CDON1 0.005 cell adhesion associated, oncogene regulated protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.00630063 +Mm Hs MUC4 Goblet cells NA 0.005 mucin 4, cell surface associated protein-coding gene 1 Endoderm GI tract 0.294118 0.290323 0.0151181 0.00205735 +Mm Hs MUC5B Goblet cells MG1 0.002 mucin 5B, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm GI tract 0.352941 0.0 0.00755905 0.000514337 +Mm Hs TMEM207 Goblet cells NA 0.0 transmembrane protein 207 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs TFF3 Goblet cells HITF|ITF 0.022 trefoil factor 3 protein-coding gene 1 Endoderm GI tract 1.0 0.0 0.04 0.0 +Mm Hs AGR2 Goblet cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene 1 Endoderm GI tract 0.823529 1.0 0.0692913 0.0105439 +Mm Hs CDX2 Goblet cells CDX3 0.015 caudal type homeobox 2 protein-coding gene NA Endoderm GI tract 0.235294 0.516129 0.00692913 0.0160087 +Mm Hs KRT7 Goblet cells CK7|K2C7 0.056 keratin 7 protein-coding gene NA Endoderm GI tract 0.0 0.903226 0.101732 0.0457117 +Mm Hs KRT20 Goblet cells CK20|K20|MGC35423 0.012 keratin 20 protein-coding gene NA Endoderm GI tract 0.411765 0.387097 0.0129134 0.010994 +Mm MUC3 Goblet cells NA 0.01 mucin 3, intestinal protein coding gene 1 Endoderm GI tract 0.0 0.193548 0.0 0.0121512 +Mm Hs GUCA2A Goblet cells STARA|GUCA2 0.015 guanylate cyclase activator 2A protein-coding gene 1 Endoderm GI tract 0.352941 0.935484 0.0144882 0.0135656 +Mm Hs PHGR1 Goblet cells NA 0.031 proline, histidine and glycine rich 1 protein-coding gene 1 Endoderm GI tract 1.0 0.967742 0.0371654 0.0268098 +Mm Hs MUC13 Goblet cells DRCC1 0.03 mucin 13, cell surface associated protein-coding gene 1 Endoderm GI tract 0.647059 0.967742 0.0144882 0.0318889 +Mm Hs FCGBP Goblet cells FC(GAMMA)BP 0.011 Fc fragment of IgG binding protein protein-coding gene NA Endoderm GI tract 0.823529 0.967742 0.0103937 0.00829369 +Mm Hs CLCA1 Goblet cells CaCC|CLCRG1 0.003 chloride channel accessory 1 protein-coding gene NA Endoderm GI tract 0.411765 0.548387 0.0 0.00225023 +Mm Hs ZG16 Goblet cells hZG16|JCLN1|ZG16A|JCLN 0.013 zymogen granule protein 16 protein-coding gene NA Endoderm GI tract 0.882353 0.0 0.00976378 0.0 +Mm Hs TPSG1 Goblet cells TMT|PRSS31 0.003 tryptase gamma 1 protein-coding gene NA Endoderm GI tract 0.176471 0.0 0.0 0.0 +Mm Hs GALNT12 Goblet cells GalNAc-T12 0.004 polypeptide N-acetylgalactosaminyltransferase 12 protein-coding gene NA Endoderm GI tract 0.0588235 0.645161 0.00188976 0.00276456 +Mm Hs ATOH1 Goblet cells HATH1|MATH-1|Math1|bHLHa14 0.003 atonal bHLH transcription factor 1 protein-coding gene 1 Endoderm GI tract 0.176471 0.645161 0.0 0.00154301 +Mm Hs REP15 Goblet cells RAB15EP 0.001 RAB15 effector protein protein-coding gene NA Endoderm GI tract 0.235294 0.0 0.0 0.0 +Mm Hs PDIA5 Goblet cells FLJ30401 0.011 protein disulfide isomerase family A member 5 protein-coding gene NA Endoderm GI tract 0.117647 0.451613 0.00409449 0.0119583 +Mm Hs PLA2G10 Goblet cells GXPLA2 0.004 phospholipase A2 group X protein-coding gene NA Endoderm GI tract 0.235294 0.483871 0.00472441 0.0032789 +Mm Hs KLK1 Goblet cells Klk6 0.013 kallikrein 1 protein-coding gene NA Endoderm GI tract 0.588235 0.903226 0.00503937 0.0124084 +Mm Hs SPDEF Goblet cells PDEF|bA375E1.3 0.004 SAM pointed domain containing ETS transcription factor protein-coding gene 1 Endoderm GI tract 0.411765 0.0 0.00755905 0.0 +Mm Hs LRRC26 Goblet cells bA350O14.10|OTTHUMG00000020980 0.003 leucine rich repeat containing 26 protein-coding gene NA Endoderm GI tract 0.0 0.709677 0.0 0.00237881 +Mm Hs BACE2 Goblet cells CEAP1|DRAP|ALP56|AEPLC 0.018 beta-secretase 2 protein-coding gene NA Endoderm GI tract 0.176471 0.516129 0.0488189 0.0106082 +Mm Hs MANF Goblet cells ARMET 0.431 mesencephalic astrocyte derived neurotrophic factor protein-coding gene 1 Endoderm GI tract 0.411765 0.935484 0.211339 0.476662 +Mm CCL9 Goblet cells NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Endoderm GI tract 0.0 0.290323 0.0 0.0436544 +Mm Hs SPINK4 Goblet cells PEC-60|MGC133107 0.014 serine peptidase inhibitor, Kazal type 4 protein-coding gene 1 Endoderm GI tract 0.705882 0.0 0.00251969 0.0 +Mm Hs AMH Granulosa cells MIS 0.004 anti-Mullerian hormone protein-coding gene 1 Mesoderm Reproductive 1.0 0.5 0.0147289 0.00237438 +Mm Hs MCAM Granulosa cells MUC18|CD146 0.031 melanoma cell adhesion molecule protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0213099 0.0336906 +Mm KITL Granulosa cells NA 0.041 kit ligand protein coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.050953 +Mm Hs BOK Granulosa cells BCL2L9|BOKL|MGC4631 0.045 BOK, BCL2 family apoptosis regulator protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00564086 0.0542258 +Mm Hs ADAMTS1 Granulosa cells C3-C5|METH1|KIAA1346 0.053 ADAM metallopeptidase with thrombospondin type 1 motif 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0560953 0.0544183 +Mm Hs LOX Granulosa cells NA 0.017 lysyl oxidase protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0150423 0.0168774 +Mm Hs FHL1 Granulosa cells SLIM1|KYO-T|bA535K18.1|FHL1B|XMPMA|FLH1A|MGC111107 0.063 four and a half LIM domains 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0886869 0.0574986 +Mm Hs INHA Granulosa cells NA 0.006 inhibin subunit alpha protein-coding gene 1 Mesoderm Reproductive 1.0 1.0 0.013162 0.00487711 +Mm Hs HSD3B1 Granulosa cells SDR11E1|HSDB3|HSD3B 0.001 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.000626763 0.00121928 +Mm AKR1CL Granulosa cells NA 0.005 aldo-keto reductase family 1, member C-like protein coding gene NA Mesoderm Reproductive 0.0 1.0 0.0 0.00603221 +Mm Hs HTRA1 Granulosa cells HtrA|IGFBP5-protease|ARMD7|PRSS11 0.065 HtrA serine peptidase 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.0338452 0.0726433 +Mm Hs GAPDH Granulosa cells GAPD 0.052 glyceraldehyde-3-phosphate dehydrogenase protein-coding gene NA Mesoderm Reproductive 0.0 0.5 0.105923 0.0321504 +Mm Hs TNNI3 Granulosa cells TNNC1|CMH7|CMD2A 0.01 troponin I3, cardiac type protein-coding gene NA Mesoderm Reproductive 1.0 0.0 0.0103416 0.0 +Mm Hs HSD17B1 Granulosa cells MGC138140|SDR28C1|EDH17B2 0.002 hydroxysteroid 17-beta dehydrogenase 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.5 0.00470072 0.00166848 +Mm Hs HJURP Granulosa cells DKFZp762E1312|URLC9|hFLEG1|FAKTS 0.048 Holliday junction recognition protein protein-coding gene NA Mesoderm Reproductive 0.0 0.5 0.010655 0.0576911 +Mm Hs FSHR Granulosa cells FSHRO|LGR1|ODG1 0.0 follicle stimulating hormone receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs FOXL2 Granulosa cells BPES1|BPES 0.0 forkhead box L2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.000449207 +Mm Hs CYP19A1 Granulosa cells ARO|P-450AROM|CPV1|ARO1|CYAR|aromatase|CYP19 0.0 cytochrome P450 family 19 subfamily A member 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00219367 0.0 +Mm Hs ETV2 Hemangioblasts ER71 0.002 ETS variant 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0137845 0.0 +Mm Hs T Hemangioblasts NA 0.0 brachyury, T-box transcription factor T protein coding gene NA Zygote Embryo 0.0 0.0 0.0 0.0 +Mm Hs TAL1 Hemangioblasts bHLHa17|TCL5 0.004 TAL bHLH transcription factor 1, erythroid differentiation factor protein-coding gene NA Zygote Embryo 0.0 0.0 0.00657895 0.0 +Mm Hs THY1 Hematopoietic stem cells CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0322682 0.0 +Mm Hs MPL Hematopoietic stem cells CD110|TPOR 0.001 MPL proto-oncogene, thrombopoietin receptor protein-coding gene 1 Mesoderm Bone 0.0 0.3125 0.0 0.000578667 +Mm Hs KIT Hematopoietic stem cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Bone 0.0 0.71875 0.00250627 0.0171028 +Mm Hs PROM1 Hematopoietic stem cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00720551 0.0242397 +Mm Hs FLT3 Hematopoietic stem cells FLK2|CD135 0.009 fms related tyrosine kinase 3 protein-coding gene 1 Mesoderm Bone 0.0 0.4375 0.00093985 0.00835852 +Mm Hs SLAMF1 Hematopoietic stem cells CD150|SLAM 0.001 signaling lymphocytic activation molecule family member 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00156642 0.0 +Mm Hs CXCR4 Hematopoietic stem cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.198308 0.00880859 +Mm Hs TEK Hematopoietic stem cells TIE2|TIE-2|VMCM1|CD202b|VMCM 0.02 TEK receptor tyrosine kinase protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0018797 0.0 +Hs ABCB1 Hematopoietic stem cells P-gp|CD243|GP170|ABC20|PGY1|CLCS 0.001 ATP binding cassette subfamily B member 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0056391 0.0 +Mm Hs ABCG2 Hematopoietic stem cells EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.00469925 0.0466791 +Mm Hs BAALC Hematopoietic stem cells NA 0.018 BAALC, MAP3K1 and KLF4 binding protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0153509 0.0186459 +Mm Hs SPN Hematopoietic stem cells LSN|CD43|GPL115 0.029 sialophorin protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0507519 0.0 +Mm Hs CDCP1 Hematopoietic stem cells CD318|SIMA135 0.01 CUB domain containing protein 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0250627 0.00752266 +Mm Hs MYADM Hematopoietic stem cells NA 0.063 myeloid associated differentiation marker protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.119361 0.0518871 +Hs KITLG Hematopoietic stem cells SCF|Kitl|KL-1|FPH2|SLF|DFNA69 0.001 KIT ligand protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00626566 0.0 +Mm Hs TGFB2 Hematopoietic stem cells NA 0.041 transforming growth factor beta 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00156642 0.0 +Mm Hs PTPRE Hematopoietic stem cells PTPE 0.054 protein tyrosine phosphatase, receptor type E protein-coding gene 1 Mesoderm Bone 0.0 0.9375 0.0404135 0.0547161 +Mm Hs TAF7 Hematopoietic stem cells TAFII55|TAF2F 0.092 TATA-box binding protein associated factor 7 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.309211 0.0 +Mm Hs GATA2 Hematopoietic stem cells NFE1B 0.02 GATA binding protein 2 protein-coding gene 1 Mesoderm Bone 0.0 0.46875 0.0134712 0.0208963 +Mm Hs GPR171 Hematopoietic stem cells H963 0.016 G protein-coupled receptor 171 protein-coding gene 1 Mesoderm Bone 0.0 0.59375 0.0206767 0.0143381 +Mm Hs ANGPT1 Hematopoietic stem cells KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0018797 0.0103517 +Mm Hs PROCR Hematopoietic stem cells EPCR|CCD41|CD201 0.016 protein C receptor protein-coding gene 1 Mesoderm Bone 0.0 0.125 0.0285088 0.0125378 +Mm Hs NFE2 Hematopoietic stem cells NF-E2 0.015 nuclear factor, erythroid 2 protein-coding gene 1 Mesoderm Bone 0.0 0.9375 0.0175439 0.0119591 +Mm Hs NKX2-3 Hematopoietic stem cells NKX2.3|CSX3|NKX4-3|NKX2C 0.003 NK2 homeobox 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.00438596 0.00276474 +Mm Hs HHEX Hematopoietic stem cells HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Mesoderm Bone 0.0 0.96875 0.0228697 0.0376776 +Mm Hs MEIS1 Hematopoietic stem cells NA 0.024 Meis homeobox 1 protein-coding gene 1 Mesoderm Bone 0.0 0.9375 0.0379073 0.0177458 +Mm Hs LYL1 Hematopoietic stem cells bHLHa18 0.039 LYL1, basic helix-loop-helix family member protein-coding gene 1 Mesoderm Bone 0.0 0.9375 0.0635965 0.0322767 +Mm Hs ELF1 Hematopoietic stem cells NA 0.094 E74 like ETS transcription factor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.9375 0.123747 0.0851283 +Mm Hs HLF Hematopoietic stem cells MGC33822 0.02 HLF, PAR bZIP transcription factor protein-coding gene 1 Mesoderm Bone 0.0 0.84375 0.0 0.0229538 +Mm Hs RGS18 Hematopoietic stem cells RGS13 0.019 regulator of G protein signaling 18 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00344612 0.0 +Mm Hs MYCT1 Hematopoietic stem cells MTLC|FLJ21269 0.022 MYC target 1 protein-coding gene 1 Mesoderm Bone 0.0 0.71875 0.0216165 0.0215393 +Mm Hs ADGRG1 Hematopoietic stem cells TM7LN4|TM7XN1|GPR56 0.045 adhesion G protein-coupled receptor G1 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0213033 0.0484151 +Mm Hs DNMT3B Hematopoietic stem cells NA 0.012 DNA methyltransferase 3 beta protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.0103383 0.0115733 +Mm Hs MYCN Hematopoietic stem cells bHLHe37|N-myc|MYCNOT|NMYC 0.012 MYCN proto-oncogene, bHLH transcription factor protein-coding gene 1 Mesoderm Bone 0.0 0.09375 0.00344612 0.0138237 +Mm Hs ARID3A Hematopoietic stem cells BRIGHT|DRIL1 0.018 AT-rich interaction domain 3A protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0479323 0.00868 +Mm Hs ITGA2B Hematopoietic stem cells CD41B|CD41|PPP1R93|GP2B 0.003 integrin subunit alpha 2b protein-coding gene 1 Mesoderm Bone 0.0 0.125 0.00407268 0.00289333 +Mm Hs GATA3 Hematopoietic stem cells HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0200501 0.0298335 +Mm Hs ROBO4 Hematopoietic stem cells FLJ20798|MRB|ECSM4 0.013 roundabout guidance receptor 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00438596 0.0 +Mm Hs PITX2 Hematopoietic stem cells IGDS|Brx1|Otlx2|IRID2|IHG2|RIEG|RIEG1|RGS 0.01 paired like homeodomain 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0109649 0.00868 +Mm Hs TXNIP Hematopoietic stem cells VDUP1|EST01027|HHCPA78|THIF|ARRDC6 0.194 thioredoxin interacting protein protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.354637 0.0 +Mm Hs RUNX1 Hematopoietic stem cells PEBP2A2|AMLCR1|AML1|CBFA2 0.054 runt related transcription factor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0313283 0.0 +Mm Hs PTPRS Hematopoietic stem cells NA 0.209 protein tyrosine phosphatase, receptor type S protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.0 0.261429 +Mm Hs PTPRC Hematopoietic stem cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Bone 0.0 0.21875 0.216165 0.10596 +Mm Hs CD44 Hematopoietic stem cells IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Bone 0.0 0.125 0.300439 0.0877001 +Mm Hs GFI1 Hematopoietic stem cells GFI1A|GFI-1|ZNF163 0.001 growth factor independent 1 transcriptional repressor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.00128593 +Mm Hs CD48 Hematopoietic stem cells BLAST|mCD48|hCD48|SLAMF2|BCM1 0.076 CD48 molecule protein-coding gene 1 Mesoderm Bone 0.0 0.34375 0.116228 0.0648106 +Mm Hs HMGB3 Hematopoietic stem cells HMG2A|MGC90319|HMG4 0.271 high mobility group box 3 protein-coding gene 1 Mesoderm Bone 0.0 0.8125 0.161028 0.292805 +Mm Hs TLR2 Hematopoietic stem cells TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00093985 0.0 +Mm Hs APC Hematopoietic stem cells DP2.5|PPP1R46 0.1 APC, WNT signaling pathway regulator protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.0131579 0.122806 +Mm Hs GNL3 Hematopoietic stem cells C77032|E2IG3|MGC800 0.094 G protein nucleolar 3 protein-coding gene 1 Mesoderm Bone 0.0 0.5625 0.120301 0.0807561 +Mm Hs MGST1 Hematopoietic stem cells MGST-I|GST12 0.157 microsomal glutathione S-transferase 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.182018 0.145631 +Mm Hs G0S2 Hematopoietic stem cells NA 0.04 G0/G1 switch 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0454261 0.0378705 +Mm Hs PRNP Hematopoietic stem cells CD230|AltPrP|GSS|CJD 0.242 prion protein protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0802005 0.283611 +Mm Hs CD34 Hematopoietic stem cells NA 0.071 CD34 molecule protein-coding gene 1 Mesoderm Bone 0.0 0.78125 0.0404135 0.0777985 +Mm Hs BMI1 Hematopoietic stem cells RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00532581 0.00932296 +Hs CD59 Hematopoietic stem cells 16.3A5|EJ16|EJ30|EL32|G344|p18-20|MIC11|MIN1|MSK21|MIN2|MIN3 0.07 CD59 molecule (CD59 blood group) protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.371554 0.0 +Mm Hs ITGA4 Hematopoietic stem cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene 1 Mesoderm Bone 0.0 0.5625 0.0112782 0.0401852 +Mm Hs ANPEP Hematopoietic stem cells gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0128446 0.0169099 +Mm Hs CD33 Hematopoietic stem cells SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0125313 0.0172957 +Mm Hs IL3RA Hematopoietic stem cells CD123 0.008 interleukin 3 receptor subunit alpha protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.00790844 +Mm Hs HLX Hematopoietic stem cells HB24|HLX1 0.022 H2.0 like homeobox protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00281955 0.0261043 +Mm Hs NKX3-1 Hematopoietic stem cells NKX3.1|BAPX2|NKX3A 0.002 NK3 homeobox 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0134712 0.0 +Mm Hs THSD1 Hematopoietic stem cells TMTSP 0.008 thrombospondin type 1 domain containing 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00501253 0.0 +Mm Hs NCOR2 Hematopoietic stem cells SMRT|SMRTE|TRAC-1|CTG26|TNRC14 0.021 nuclear receptor corepressor 2 protein-coding gene 1 Mesoderm Bone 0.0 0.03125 0.00657895 0.0238539 +Mm Hs EGR1 Hematopoietic stem cells TIS8|G0S30|NGFI-A|KROX-24|ZIF-268|AT225|ZNF225 0.202 early growth response 1 protein-coding gene 1 Mesoderm Bone 0.0 0.125 0.187657 0.208641 +Mm Hs FGD5 Hematopoietic stem cells ZFYVE23|FLJ39957|FLJ00274 0.007 FYVE, RhoGEF and PH domain containing 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00093985 0.00868 +Mm Hs MECOM Hematopoietic stem cells MDS1-EVI1|PRDM3|KMT8E|MDS1|EVI1 0.011 MDS1 and EVI1 complex locus protein-coding gene 1 Mesoderm Bone 0.0 0.03125 0.0194236 0.00938726 +Mm Hs CTNNAL1 Hematopoietic stem cells CLLP|alpha-CATU 0.028 catenin alpha like 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0924185 0.00913007 +Mm Hs VWF Hematopoietic stem cells F8VWF 0.016 von Willebrand factor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0266291 0.0 +Mm Hs PBX2 Hematopoietic stem cells HOX12|PBX2MHC 0.009 PBX homeobox 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00250627 0.00996592 +Mm Hs TAL1 Hematopoietic stem cells bHLHa17|TCL5 0.004 TAL bHLH transcription factor 1, erythroid differentiation factor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00657895 0.0 +Mm Hs ERG Hematopoietic stem cells erg-3 0.01 ERG, ETS transcription factor protein-coding gene 1 Mesoderm Bone 0.0 0.125 0.00814536 0.011059 +Mm Hs NEO1 Hematopoietic stem cells NGN|HsT17534|IGDCC2|NTN1R2 0.02 neogenin 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00501253 0.0233395 +Mm Hs EGR3 Hematopoietic stem cells PILOT 0.004 early growth response 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00344612 0.00450074 +Mm Hs MAFF Hematopoietic stem cells hMafF 0.054 MAF bZIP transcription factor F protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0961779 0.0477078 +Mm Hs ITGA6 Hematopoietic stem cells CD49f 0.059 integrin subunit alpha 6 protein-coding gene 1 Mesoderm Bone 0.0 0.03125 0.0501253 0.0616601 +Mm Hs GJB1 Hematopoietic stem cells CX32|CMTX1|CMTX 0.033 gap junction protein beta 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0103383 0.0385135 +Mm Hs CDH2 Hematopoietic stem cells CDHN|CD325|NCAD 0.059 cadherin 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0491855 0.0621745 +Mm Hs ALDH1A1 Hematopoietic stem cells RALDH1|PUMB1|ALDH1 0.039 aldehyde dehydrogenase 1 family member A1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0880326 0.0288047 +Mm Hs GFI1B Hematopoietic stem cells ZNF163B 0.005 growth factor independent 1B transcriptional repressor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0191103 0.00192889 +Mm Hs NOTCH1 Hematopoietic stem cells TAN1 0.007 notch 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0625 0.00469925 0.00752266 +Mm Hs NOTCH2 Hematopoietic stem cells NA 0.096 notch 2 protein-coding gene 1 Mesoderm Bone 0.0 0.28125 0.0200501 0.114254 +Mm Hs PLXDC2 Hematopoietic stem cells TEM7R|FLJ14623 0.046 plexin domain containing 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.018797 0.0541375 +Mm Hs ESAM Hematopoietic stem cells W117m 0.064 endothelial cell adhesion molecule protein-coding gene 1 Mesoderm Bone 0.0 0.03125 0.0429198 0.0707902 +Mm Hs ACE Hematopoietic stem cells ACE1|CD143|DCP1 0.022 angiotensin I converting enzyme protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0256892 0.0216678 +Mm Hs TRPC6 Hematopoietic stem cells TRP6|FSGS2 0.001 transient receptor potential cation channel subfamily C member 6 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000626566 0.0 +Mm Hs HOXB5 Hematopoietic stem cells HOX2A 0.003 homeobox B5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00501253 0.00237896 +Mm Hs TET2 Hematopoietic stem cells FLJ20032|KIAA1546 0.008 tet methylcytosine dioxygenase 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00438596 0.0 +Mm Hs ADAMTS13 Hepatic stellate cells VWFCP|vWF-CP|FLJ42993|MGC118899|MGC118900|DKFZp434C2322|C9orf8 0.0 ADAM metallopeptidase with thrombospondin type 1 motif 13 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0 6.41725e-05 +Mm Hs CYGB Hepatic stellate cells HGB|STAP 0.038 cytoglobin protein-coding gene NA Endoderm Liver 0.0 0.5 0.0219436 0.0432523 +Mm Hs PPARG Hepatic stellate cells PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene NA Endoderm Liver 0.5 0.0 0.0106583 0.00462042 +Mm Hs PDGFRA Hepatic stellate cells CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene NA Endoderm Liver 0.0 0.5 0.0476489 0.0439582 +Mm Hs RGS5 Hepatic stellate cells NA 0.043 regulator of G protein signaling 5 protein-coding gene NA Endoderm Liver NA NA NA NA +Mm Hs PPARA Hepatic stellate cells hPPAR|NR1C1|PPAR 0.001 peroxisome proliferator activated receptor alpha protein-coding gene NA Endoderm Liver 0.0 0.0 0.00250784 0.000705897 +Mm Hs FOXF1 Hepatic stellate cells FREAC1|FKHL5 0.008 forkhead box F1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.00846395 0.00814991 +Mm Hs ALB Hepatic stellate cells NA 0.008 albumin protein-coding gene NA Endoderm Liver 0.5 0.0 0.0275862 0.00378618 +Mm Hs NR1H4 Hepatic stellate cells FXR|RIP14|HRR1|HRR-1 0.002 nuclear receptor subfamily 1 group H member 4 protein-coding gene NA Endoderm Liver 0.0 0.0 0.000626959 0.00205352 +Mm Hs CTGF Hepatic stellate cells IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Endoderm Liver 1.0 0.5 0.0990596 0.0123853 +Mm Hs SEMA7A Hepatic stellate cells H-Sema-L|CD108|SEMAL 0.006 semaphorin 7A (John Milton Hagen blood group) protein-coding gene NA Endoderm Liver 0.0 0.0 0.00031348 0.0 +Hs AGTR1 Hepatic stellate cells AT2R1|AGTR1A|AT2R1A|HAT1R|AG2S|AT2R1B|AT1B|AGTR1B 0.0 angiotensin II receptor type 1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.00188088 0.0 +Mm Hs PNPLA3 Hepatic stellate cells dJ796I17.1|FLJ22012|adiponutrin|iPLA2epsilon|C22orf20|ADPN 0.0 patatin like phospholipase domain containing 3 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0 6.41725e-05 +Mm Hs WT1 Hepatic stellate cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0225705 0.0 +Mm Hs FGF10 Hepatic stellate cells NA 0.001 fibroblast growth factor 10 protein-coding gene NA Endoderm Liver 0.0 0.0 0.000626959 0.00173266 +Mm Hs GFAP Hepatic stellate cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene NA Endoderm Liver 0.0 0.5 0.00564263 0.014888 +Mm Hs NGFR Hepatic stellate cells TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene NA Endoderm Liver 0.0 0.0 0.00219436 0.00744401 +Mm Hs VEGFA Hepatic stellate cells VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene NA Endoderm Liver 0.0 0.0 0.0247649 0.0 +Mm Hs ACTA2 Hepatic stellate cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene 1 Endoderm Liver 0.5 0.0 0.0191223 0.0388885 +Mm Hs MYB Hepatic stellate cells c-myb 0.027 MYB proto-oncogene, transcription factor protein-coding gene NA Endoderm Liver 0.0 0.0 0.0134796 0.0283001 +Mm Hs DES Hepatic stellate cells CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene NA Endoderm Liver 0.0 0.5 0.00940439 0.0232304 +Mm Hs FAP Hepatic stellate cells NA 0.006 fibroblast activation protein alpha protein-coding gene NA Endoderm Liver 0.0 0.0 0.00250784 0.00654559 +Mm Hs SLC8A1 Hepatic stellate cells NCX1 0.002 solute carrier family 8 member A1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.00595611 0.0 +Mm Hs RELN Hepatic stellate cells RL|PRO1598 0.018 reelin protein-coding gene NA Endoderm Liver 0.0 0.0 0.00344828 0.0 +Mm Hs SYP Hepatic stellate cells MRX96 0.049 synaptophysin protein-coding gene NA Endoderm Liver 0.0 0.0 0.00721003 0.0 +Mm Hs VCL Hepatic stellate cells NA 0.018 vinculin protein-coding gene NA Endoderm Liver 0.5 0.0 0.0667712 0.0 +Mm Hs TIMP1 Hepatic stellate cells TIMP|CLGI 0.097 TIMP metallopeptidase inhibitor 1 protein-coding gene NA Endoderm Liver 1.0 0.0 0.409404 0.0 +Mm Hs COL1A1 Hepatic stellate cells NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Endoderm Liver 1.0 0.5 0.099373 0.0732208 +Mm Hs TAGLN Hepatic stellate cells SM22|WS3-10|TAGLN1|DKFZp686P11128 0.01 transgelin protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000626959 0.0 +Mm Hs COL1A2 Hepatic stellate cells NA 0.097 collagen type I alpha 2 chain protein-coding gene 1 Endoderm Liver 1.0 0.5 0.123824 0.0881088 +Mm Hs COL3A1 Hepatic stellate cells EDS4A 0.086 collagen type III alpha 1 chain protein-coding gene 1 Endoderm Liver 1.0 0.5 0.0987461 0.0811782 +Mm Hs SPARC Hepatic stellate cells ON 0.307 secreted protein acidic and cysteine rich protein-coding gene 1 Endoderm Liver 1.0 0.0 0.230408 0.0 +Mm Hs RBP1 Hepatic stellate cells CRBP1|CRBP|RBPC|CRBPI 0.114 retinol binding protein 1 protein-coding gene 1 Endoderm Liver 0.5 0.0 0.164263 0.0 +Mm Hs DCN Hepatic stellate cells DSPG2|SLRR1B 0.084 decorin protein-coding gene 1 Endoderm Liver 1.0 0.5 0.106583 0.0818199 +Mm Hs MYL9 Hepatic stellate cells MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Endoderm Liver 1.0 0.0 0.159875 0.0634024 +Mm Hs TPM2 Hepatic stellate cells NEM4|AMCD1 0.075 tropomyosin 2 protein-coding gene 1 Endoderm Liver 1.0 0.0 0.146395 0.0 +Mm Hs MEG3 Hepatic stellate cells GTL2|NCRNA00023|LINC00023|onco-lncRNA-83 0.288 maternally expressed 3 non-coding RNA 1 Endoderm Liver 0.5 0.0 0.115047 0.33498 +Mm Hs BGN Hepatic stellate cells DSPG1|SLRR1A 0.097 biglycan protein-coding gene 1 Endoderm Liver 1.0 0.5 0.0648903 0.106911 +Mm Hs IGFBP7 Hepatic stellate cells MAC25|IGFBP-7|FSTL2 0.172 insulin like growth factor binding protein 7 protein-coding gene 1 Endoderm Liver 1.0 0.5 0.238558 0.163191 +Mm Hs IGFBP3 Hepatic stellate cells IBP3|BP-53 0.031 insulin like growth factor binding protein 3 protein-coding gene 1 Endoderm Liver 0.5 0.5 0.0589342 0.0255407 +Mm Hs CYR61 Hepatic stellate cells IGFBP10 0.125 cysteine rich angiogenic inducer 61 protein-coding gene 1 Endoderm Liver 1.0 0.5 0.13511 0.123789 +Mm Hs OLFML3 Hepatic stellate cells HNOEL-iso|OLF44 0.053 olfactomedin like 3 protein-coding gene 1 Endoderm Liver 0.5 0.0 0.030721 0.0580761 +Mm Hs IGFBP6 Hepatic stellate cells NA 0.039 insulin like growth factor binding protein 6 protein-coding gene 1 Endoderm Liver 1.0 0.0 0.0833856 0.0294552 +Mm Hs CCL2 Hepatic stellate cells MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Endoderm Liver 1.0 0.5 0.0642633 0.0318296 +Mm Hs COLEC11 Hepatic stellate cells MGC3279|CL-K1 0.002 collectin subfamily member 11 protein-coding gene 1 Endoderm Liver 0.5 0.0 0.00658307 0.000962587 +Mm Hs HGF Hepatic stellate cells F-TCF|HGFB|HPTA|DFNB39 0.002 hepatocyte growth factor protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00752351 0.000577552 +Mm Hs AFP Hepatoblasts FETA|HPAFP 0.007 alpha fetoprotein protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0106516 0.0053898 +Mm Hs ALB Hepatoblasts NA 0.008 albumin protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0278822 0.00378569 +Mm Hs CEBPA Hepatoblasts C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene NA Endoderm Liver 0.0 0.0 0.0 0.0299647 +Mm Hs KRT14 Hepatoblasts EBS3|EBS4 0.019 keratin 14 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0197368 0.0191851 +Mm Hs DLK1 Hepatoblasts FA1|pG2|Pref-1|ZOG|Delta1 0.055 delta like non-canonical Notch ligand 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0460526 0.0580045 +Mm Hs CDH1 Hepatoblasts uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0416667 0.0572345 +Mm Hs FOXM1 Hepatoblasts HFH-11|trident|HNF-3|INS-1|MPP2|MPHOSPH2|TGT3|FKHL16 0.001 forkhead box M1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0 0.00166827 +Mm Hs GGT1 Hepatoblasts D22S672|D22S732|CD224 0.01 gamma-glutamyltransferase 1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0018797 0.0121912 +Mm Hs HNF4A Hepatoblasts NR2A1|HNF4|TCF14|MODY|MODY1 0.019 hepatocyte nuclear factor 4 alpha protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00783208 0.0217517 +Mm Hs PROX1 Hepatoblasts NA 0.028 prospero homeobox 1 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0109649 0.0324671 +Mm Hs MAP2K4 Hepatoblasts MEK4|JNKK1|PRKMK4|MKK4|SERK1 0.023 mitogen-activated protein kinase kinase 4 protein-coding gene NA Endoderm Liver 0.0 0.0 0.00344612 0.0284889 +Mm Hs SMAD5 Hepatoblasts Dwfc|JV5-1|MADH5 0.019 SMAD family member 5 protein-coding gene NA Endoderm Liver 0.0 0.0 0.0272556 0.0 +Mm Hs KRT18 Hepatoblasts NA 0.126 keratin 18 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.237782 0.0927815 +Mm Hs KRT8 Hepatoblasts K8|CK8|CYK8|K2C8|KO 0.12 keratin 8 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.211153 0.0931023 +Mm Hs HNF1B Hepatoblasts LFB3|VHNF1|HNF1beta|MODY5|TCF2 0.005 HNF1 homeobox B protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0093985 0.00461983 +Mm Hs HHEX Hepatoblasts HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0228697 0.0395893 +Mm Hs MET Hepatoblasts HGFR|RCCP2|DFNB97 0.006 MET proto-oncogene, receptor tyrosine kinase protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0162907 0.00468399 +Mm Hs FOSL1 Hepatocytes fra-1 0.016 FOS like 1, AP-1 transcription factor subunit protein-coding gene NA Endoderm Liver 0.0 0.0 0.0278922 0.0120296 +Mm Hs EPPK1 Hepatocytes EPIPL1 0.009 epiplakin 1 protein-coding gene NA Endoderm Liver 0.0 0.15 0.00633914 0.00907044 +Mm Hs UCP2 Hepatocytes SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00507132 0.0 +Mm Hs GCK Hepatocytes MODY2 0.002 glucokinase protein-coding gene 1 Endoderm Liver 0.0 0.225 0.0 0.00186555 +Mm Hs LRP5 Hepatocytes LR3|BMND1|HBM|OPS|OPTA1|VBCH2|EVR4|LRP7|OPPG 0.003 LDL receptor related protein 5 protein-coding gene 1 Endoderm Liver 0.027027 0.025 0.00285261 0.00289482 +Mm Hs SLC10A1 Hepatocytes NTCP 0.001 solute carrier family 10 member 1 protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.0 0.0 +Mm Hs NOS2 Hepatocytes iNOS|HEP-NOS|NOS2A 0.001 nitric oxide synthase 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00158479 0.000385976 +Mm Hs ATP7B Hepatocytes WND 0.002 ATPase copper transporting beta protein-coding gene 1 Endoderm Liver 0.0 0.175 0.00190174 0.00225153 +Mm Hs HNF4A Hepatocytes NR2A1|HNF4|TCF14|MODY|MODY1 0.019 hepatocyte nuclear factor 4 alpha protein-coding gene 1 Endoderm Liver 0.0540541 0.3 0.00729002 0.0210357 +Mm Hs GJB2 Hepatocytes CX26|NSRD1|DFNB1 0.009 gap junction protein beta 2 protein-coding gene 1 Endoderm Liver 0.0 0.35 0.0120444 0.00829849 +Mm Hs FGFR4 Hepatocytes JTK2|CD334 0.003 fibroblast growth factor receptor 4 protein-coding gene 1 Endoderm Liver 0.0810811 0.15 0.00253566 0.00173689 +Mm Hs PROX1 Hepatocytes NA 0.028 prospero homeobox 1 protein-coding gene 1 Endoderm Liver 0.108108 0.25 0.00982567 0.0319074 +Mm Hs CRP Hepatocytes NA 0.002 C-reactive protein protein-coding gene 1 Endoderm Liver 0.27027 0.55 0.00126783 0.000192988 +Hs GRP Hepatocytes NA 0.0 gastrin releasing peptide protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00253566 0.0 +Mm Hs SLC2A2 Hepatocytes GLUT2 0.007 solute carrier family 2 member 2 protein-coding gene 1 Endoderm Liver 0.135135 0.0 0.000316957 0.0 +Mm Hs TFR2 Hepatocytes HFE3|TFRC2 0.003 transferrin receptor 2 protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.00760697 0.0 +Mm Hs KIF13B Hepatocytes GAKIN|KIAA0639 0.002 kinesin family member 13B protein-coding gene 1 Endoderm Liver 0.0 0.15 0.0 0.00270183 +Mm Hs LIPC Hepatocytes HTGL 0.002 lipase C, hepatic type protein-coding gene 1 Endoderm Liver 0.0540541 0.275 0.0 0.000771952 +Mm Hs VDR Hepatocytes NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00253566 0.0 +Mm Hs ASGR1 Hepatocytes CLEC4H1 0.004 asialoglycoprotein receptor 1 protein-coding gene 1 Endoderm Liver 0.351351 0.6 0.0107765 0.000450306 +Mm Hs ARG1 Hepatocytes NA 0.007 arginase 1 protein-coding gene 1 Endoderm Liver 0.216216 0.6 0.000950872 0.00566098 +Mm Hs AFP Hepatocytes FETA|HPAFP 0.007 alpha fetoprotein protein-coding gene 1 Endoderm Liver 0.0540541 0.125 0.0101426 0.00508202 +Mm Hs ALB Hepatocytes NA 0.008 albumin protein-coding gene 1 Endoderm Liver 0.972973 1.0 0.0167987 0.00122226 +Mm Hs G6PC Hepatocytes GSD1a|G6PT 0.002 glucose-6-phosphatase catalytic subunit protein-coding gene 1 Endoderm Liver 0.027027 0.425 0.0 0.00135092 +Mm Hs OTC Hepatocytes NA 0.008 ornithine carbamoyltransferase protein-coding gene 1 Endoderm Liver 0.0 0.6 0.000316957 0.00836282 +Hs SERPINA1 Hepatocytes AAT|A1A|PI1|alpha-1-antitrypsin|A1AT|alpha1AT|PI 0.016 serpin family A member 1 protein-coding gene 1 Endoderm Liver 0.972973 0.0 0.0748019 0.0 +Mm Hs UGT1A1 Hepatocytes UGT1A 0.0 UDP glucuronosyltransferase family 1 member A1 other 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs ZHX2 Hepatocytes KIAA0854 0.001 zinc fingers and homeoboxes 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs HHEX Hepatocytes HEX|HOX11L-PEN|PRHX 0.037 hematopoietically expressed homeobox protein-coding gene NA Endoderm Liver 0.108108 0.325 0.02187 0.0388549 +Mm Hs FOXA3 Hepatocytes HNF3G 0.008 forkhead box A3 protein-coding gene 1 Endoderm Liver 0.0540541 0.25 0.0044374 0.00823416 +Mm Hs FOXA2 Hepatocytes HNF3B 0.009 forkhead box A2 protein-coding gene 1 Endoderm Liver 0.027027 0.15 0.00570523 0.00958508 +Mm Hs FOXA1 Hepatocytes HNF3A 0.008 forkhead box A1 protein-coding gene 1 Endoderm Liver 0.027027 0.05 0.0104596 0.00611129 +Mm Hs CYP7A1 Hepatocytes CYP7 0.0 cytochrome P450 family 7 subfamily A member 1 protein-coding gene 1 Endoderm Liver 0.0 0.15 0.0 0.0 +Hs CYP3A7 Hepatocytes CP37|P450-HFLA 0.0 cytochrome P450 family 3 subfamily A member 7 protein-coding gene 1 Endoderm Liver 0.0540541 0.0 0.0 0.0 +Hs CYP3A4 Hepatocytes CYP3A3 0.0 cytochrome P450 family 3 subfamily A member 4 protein-coding gene 1 Endoderm Liver 0.162162 0.0 0.0 0.0 +Mm Hs CYP2E1 Hepatocytes CYP2E 0.003 cytochrome P450 family 2 subfamily E member 1 protein-coding gene 1 Endoderm Liver 0.351351 0.575 0.000316957 0.00192988 +Hs CYP2D6 Hepatocytes CPD6|P450-DB1|P450C2D|CYP2DL1|CYP2D7P2|CYP2D7BP|CYP2D8P2|CYP2D7AP 0.0 cytochrome P450 family 2 subfamily D member 6 protein-coding gene 1 Endoderm Liver 0.0810811 0.0 0.0 0.0 +Hs CYP2C9 Hepatocytes P450IIC9|CYP2C10 0.0 cytochrome P450 family 2 subfamily C member 9 protein-coding gene 1 Endoderm Liver 0.189189 0.0 0.0 0.0 +Hs CYP2C8 Hepatocytes CPC8 0.0 cytochrome P450 family 2 subfamily C member 8 protein-coding gene NA Endoderm Liver 0.243243 0.0 0.0 0.0 +Hs CYP2C19 Hepatocytes P450IIC19|CPCJ 0.0 cytochrome P450 family 2 subfamily C member 19 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Hs CYP2B6 Hepatocytes CPB6|CYPIIB6 0.0 cytochrome P450 family 2 subfamily B member 6 protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.0 0.0 +Hs CYP2A6 Hepatocytes CPA6|CYP2A3 0.0 cytochrome P450 family 2 subfamily A member 6 protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.0 0.0 +Mm Hs CYP1A2 Hepatocytes P3-450|CP12 0.001 cytochrome P450 family 1 subfamily A member 2 protein-coding gene 1 Endoderm Liver 0.027027 0.35 0.0 0.000128659 +Mm Hs CEBPA Hepatocytes C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene NA Endoderm Liver 0.0 0.375 0.0 0.0290769 +Mm Hs CDH1 Hepatocytes uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Endoderm Liver 0.0540541 0.125 0.0415214 0.0570601 +Mm Hs GPC3 Hepatocytes OCI-5|SGBS|SGBS1|SGB|DGSX|SDYS 0.059 glypican 3 protein-coding gene 1 Endoderm Liver 0.0540541 0.075 0.0652932 0.053715 +Mm Hs AHR Hepatocytes bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Endoderm Liver 0.0 0.125 0.0114105 0.00662592 +Mm Hs CYP1A1 Hepatocytes P450DX|P1-450|P450-C|CP11 0.0 cytochrome P450 family 1 subfamily A member 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.000950872 6.43294e-05 +Mm Hs NR1I3 Hepatocytes MB67|CAR1 0.0 nuclear receptor subfamily 1 group I member 3 protein-coding gene NA Endoderm Liver 0.0 0.15 0.0 0.0 +Mm Hs CPS1 Hepatocytes NA 0.013 carbamoyl-phosphate synthase 1 protein-coding gene 1 Endoderm Liver 0.297297 0.525 0.00126783 0.0136378 +Mm Hs GLS2 Hepatocytes GA|GLS|LGA|hLGA 0.001 glutaminase 2 protein-coding gene NA Endoderm Liver 0.0 0.25 0.0 0.000257317 +Mm Hs PCK1 Hepatocytes PEPCK-C 0.008 phosphoenolpyruvate carboxykinase 1 protein-coding gene 1 Endoderm Liver 0.162162 0.65 0.0139461 0.00585397 +Mm FCNA Hepatocytes NA 0.007 ficolin A protein coding gene NA Endoderm Liver 0.0 0.0 0.0 0.00849148 +Mm Hs TAT Hepatocytes NA 0.002 tyrosine aminotransferase protein-coding gene 1 Endoderm Liver 0.378378 0.0 0.0 0.0 +Mm Hs WT1 Hepatocytes WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0228209 0.0 +Mm Hs PRRG4 Hepatocytes TMG4 0.005 proline rich and Gla domain 4 protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.014897 0.00366677 +Mm Hs SULT1A1 Hepatocytes P-PST|STP1 0.012 sulfotransferase family 1A member 1 protein-coding gene 1 Endoderm Liver 0.189189 0.0 0.0183835 0.0 +Mm Hs APOH Hepatocytes BG|B2G1 0.004 apolipoprotein H protein-coding gene 1 Endoderm Liver 0.594595 0.9 0.000950872 0.0010936 +Mm Hs CTNNB1 Hepatocytes beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene 1 Endoderm Liver 0.135135 0.2 0.213312 0.010936 +Mm Hs ABCC3 Hepatocytes MRP3|cMOAT2|EST90757|MLP2|MOAT-D 0.01 ATP binding cassette subfamily C member 3 protein-coding gene NA Endoderm Liver 0.162162 0.25 0.0206022 0.00714056 +Mm Hs FGB Hepatocytes NA 0.009 fibrinogen beta chain protein-coding gene NA Endoderm Liver 0.702703 0.975 0.00950872 0.0043744 +Mm Hs AQP3 Hepatocytes GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Endoderm Liver 0.135135 0.0 0.0703645 0.0159537 +Mm Hs PLSCR1 Hepatocytes MMTRA1B 0.023 phospholipid scramblase 1 protein-coding gene NA Endoderm Liver 0.108108 0.2 0.0637084 0.0130589 +Mm Hs FGA Hepatocytes NA 0.005 fibrinogen alpha chain protein-coding gene NA Endoderm Liver 0.675676 0.85 0.00950872 0.000192988 +Mm Hs APOB Hepatocytes NA 0.015 apolipoprotein B protein-coding gene 1 Endoderm Liver 0.459459 0.7 0.00729002 0.0140238 +Mm Hs ANG Hepatocytes RNASE5|RAA1 0.02 angiogenin protein-coding gene 1 Endoderm Liver 0.459459 0.375 0.00697306 0.0207141 +Mm Hs ANXA13 Hepatocytes ANX13 0.013 annexin A13 protein-coding gene NA Endoderm Liver 0.027027 0.0 0.00126783 0.0153747 +Mm Hs SAT2 Hepatocytes SSAT2 0.042 spermidine/spermine N1-acetyltransferase family member 2 protein-coding gene 1 Endoderm Liver 0.243243 0.0 0.186054 0.0 +Mm Hs SFRP5 Hepatocytes SARP3 0.004 secreted frizzled related protein 5 protein-coding gene NA Endoderm Liver 0.0810811 0.0 0.000316957 0.0 +Mm Hs A1CF Hepatocytes ACF|ACF64|ACF65|APOBEC1CF 0.002 APOBEC1 complementation factor protein-coding gene NA Endoderm Liver 0.189189 0.175 0.0044374 0.000257317 +Mm Hs APOA1 Hepatocytes NA 0.032 apolipoprotein A1 protein-coding gene 1 Endoderm Liver 0.891892 1.0 0.0586371 0.0231586 +Mm Hs BNIP3 Hepatocytes Nip3 0.042 BCL2 interacting protein 3 protein-coding gene 1 Endoderm Liver 0.27027 0.25 0.161331 0.00604696 +Mm Hs FGL1 Hepatocytes HFREP-1 0.004 fibrinogen like 1 protein-coding gene 1 Endoderm Liver 0.594595 0.45 0.0044374 0.000450306 +Mm Hs PAH Hepatocytes PH 0.007 phenylalanine hydroxylase protein-coding gene 1 Endoderm Liver 0.216216 0.55 0.00538827 0.00533934 +Mm Hs SERPINA6 Hepatocytes CBG 0.003 serpin family A member 6 protein-coding gene NA Endoderm Liver 0.162162 0.0 0.000316957 0.0 +Mm Hs APOA2 Hepatocytes NA 0.013 apolipoprotein A2 protein-coding gene 1 Endoderm Liver 0.945946 1.0 0.0228209 0.00540367 +Mm Hs AZGP1 Hepatocytes ZA2G|ZAG 0.008 alpha-2-glycoprotein 1, zinc-binding protein-coding gene NA Endoderm Liver 0.486486 0.75 0.0323296 6.43294e-05 +Mm Hs FGG Hepatocytes NA 0.007 fibrinogen gamma chain protein-coding gene NA Endoderm Liver 0.702703 0.975 0.00507132 0.00340946 +Mm Hs APOC3 Hepatocytes NA 0.018 apolipoprotein C3 protein-coding gene 1 Endoderm Liver 0.972973 0.9 0.0133122 0.0152461 +Mm Hs DEFB1 Hepatocytes HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene NA Endoderm Liver 0.216216 0.0 0.0237718 0.00533934 +Mm Hs TM4SF4 Hepatocytes il-TMP 0.017 transmembrane 4 L six family member 4 protein-coding gene 1 Endoderm Liver 0.243243 0.0 0.0183835 0.0 +Mm Hs GC Hepatocytes VDBP|hDBP 0.009 GC, vitamin D binding protein protein-coding gene 1 Endoderm Liver 0.486486 0.975 0.00855784 0.00540367 +Mm Hs AMBP Hepatocytes UTI|EDC1|HI30|IATIL|ITILC|ITI|ITIL 0.013 alpha-1-microglobulin/bikunin precursor protein-coding gene 1 Endoderm Liver 0.621622 0.925 0.0066561 0.00984239 +Mm Hs ORM1 Hepatocytes NA 0.011 orosomucoid 1 protein-coding gene 1 Endoderm Liver 0.972973 0.75 0.0120444 0.00720489 +Mm Hs TTR Hepatocytes HsT2651|CTS|PALB|CTS1 0.055 transthyretin protein-coding gene 1 Endoderm Liver 0.594595 0.0 0.0671949 0.0 +Mm SERPINA1C Hepatocytes NA 0.004 serine (or cysteine) peptidase inhibitor, clade A, member 1C protein coding gene 1 Endoderm Liver NA NA NA NA +Mm GULO Hepatocytes NA 0.002 gulonolactone (L-) oxidase protein coding gene 1 Endoderm Liver 0.0 0.3 0.0 0.00135092 +Mm CYP2F2 Hepatocytes NA 0.008 cytochrome P450, family 2, subfamily f, polypeptide 2 protein coding gene 1 Endoderm Liver 0.0 0.4 0.0 0.00842715 +Mm Hs HAL Hepatocytes NA 0.001 histidine ammonia-lyase protein-coding gene 1 Endoderm Liver 0.027027 0.35 0.000316957 0.000450306 +Mm Hs ASS1 Hepatocytes CTLN1|ASS 0.048 argininosuccinate synthase 1 protein-coding gene 1 Endoderm Liver 0.243243 0.8 0.0383518 0.0466388 +Hs CYP2A7 Hepatocytes NA 0.0 cytochrome P450 family 2 subfamily A member 7 protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.0 0.0 +Hs SCD Hepatocytes FADS5|SCDOS 0.022 stearoyl-CoA desaturase protein-coding gene 1 Endoderm Liver 0.216216 0.0 0.081458 0.0 +Mm Hs HMGCS1 Hepatocytes HMGCS 0.18 3-hydroxy-3-methylglutaryl-CoA synthase 1 protein-coding gene 1 Endoderm Liver 0.0540541 0.45 0.00982567 0.221422 +Mm Hs ACSS2 Hepatocytes ACSA|AceCS|dJ1161H23.1|ACAS2 0.006 acyl-CoA synthetase short chain family member 2 protein-coding gene 1 Endoderm Liver 0.027027 0.225 0.00570523 0.00623995 +Mm Hs TM7SF2 Hepatocytes ANG1|DHCR14A|NET47 0.01 transmembrane 7 superfamily member 2 protein-coding gene 1 Endoderm Liver 0.135135 0.0 0.0278922 0.0 +Mm Hs SEC16B Hepatocytes RGPR|PGPR-p117|Sec16S|LZTR2 0.001 SEC16 homolog B, endoplasmic reticulum export factor protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs SLBP Hepatocytes NA 0.042 stem-loop binding protein protein-coding gene 1 Endoderm Liver 0.0540541 0.0 0.139144 0.0 +Mm Hs RND3 Hepatocytes RhoE|Rho8|ARHE 0.049 Rho family GTPase 3 protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.102377 0.0 +Mm Hs BCHE Hepatocytes CHE2 0.003 butyrylcholinesterase protein-coding gene 1 Endoderm Liver 0.108108 0.275 0.00412044 0.00173689 +Mm Hs GHR Hepatocytes GHBP 0.019 growth hormone receptor protein-coding gene 1 Endoderm Liver 0.0 0.5 0.000633914 0.0217433 +Mm Hs ALDH6A1 Hepatocytes MMSDH 0.009 aldehyde dehydrogenase 6 family member A1 protein-coding gene 1 Endoderm Liver 0.189189 0.35 0.0110935 0.00771952 +Mm Hs MASP2 Hepatocytes MASP1P1 0.001 mannan binding lectin serine peptidase 2 protein-coding gene 1 Endoderm Liver 0.189189 0.25 0.0 0.0 +Hs AKR1C1 Hepatocytes DDH|MBAB|DD1|HAKRC|DDH1 0.005 aldo-keto reductase family 1 member C1 protein-coding gene 1 Endoderm Liver 0.297297 0.0 0.0253566 0.0 +Hs HPR Hepatocytes NA 0.0 haptoglobin-related protein protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.000316957 0.0 +Mm Hs HAMP Hepatocytes LEAP-1|HEPC|HFE2B|LEAP1 0.002 hepcidin antimicrobial peptide protein-coding gene 1 Endoderm Liver 0.189189 0.825 0.00190174 0.000192988 +Mm Hs GLUL Hepatocytes GLNS 0.298 glutamate-ammonia ligase protein-coding gene 1 Endoderm Liver 0.189189 0.25 0.301743 0.305436 +Mm Hs ACLY Hepatocytes ATPCL|CLATP|ACL 0.087 ATP citrate lyase protein-coding gene 1 Endoderm Liver 0.0540541 0.325 0.059588 0.0916693 +Mm Hs ASL Hepatocytes NA 0.017 argininosuccinate lyase protein-coding gene 1 Endoderm Liver 0.108108 0.525 0.0136292 0.0159537 +Mm MUP3 Hepatocytes NA 0.002 major urinary protein 3 protein coding gene 1 Endoderm Liver 0.0 0.875 0.0 0.000450306 +Mm Hs TMEM97 Hepatocytes MAC30 0.068 transmembrane protein 97 protein-coding gene 1 Endoderm Liver 0.216216 0.0 0.0957211 0.0 +Mm Hs CP Hepatocytes NA 0.03 ceruloplasmin protein-coding gene 1 Endoderm Liver 0.135135 0.55 0.00507132 0.0348665 +Mm Hs SLPI Hepatocytes HUSI-I|BLPI|HUSI|WAP4|WFDC4 0.048 secretory leukocyte peptidase inhibitor protein-coding gene 1 Endoderm Liver 0.297297 0.0 0.0925515 0.0 +Mm Hs ACAT2 Hepatocytes NA 0.149 acetyl-CoA acetyltransferase 2 protein-coding gene 1 Endoderm Liver 0.0 0.3 0.00570523 0.183532 +Mm Hs TM4SF5 Hepatocytes NA 0.022 transmembrane 4 L six family member 5 protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.00126783 0.0 +Mm Hs MSMO1 Hepatocytes DESP4|ERG25|SC4MOL 0.104 methylsterol monooxygenase 1 protein-coding gene 1 Endoderm Liver 0.216216 0.375 0.0874802 0.107044 +Mm Hs LEPR Hepatocytes OBR|CD295 0.005 leptin receptor protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.00760697 0.00431007 +Mm Hs RCAN1 Hepatocytes DSCR1 0.025 regulator of calcineurin 1 protein-coding gene 1 Endoderm Liver 0.0540541 0.0 0.0320127 0.0 +Mm Hs AR Hepatocytes AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene 1 Endoderm Liver 0.0540541 0.075 0.00126783 0.015825 +Mm Hs PLIN1 Hepatocytes PLIN 0.0 perilipin 1 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.000450306 +Mm Hs RPP25L Hepatocytes bA296L22.5|MGC29635|C9orf23 0.039 ribonuclease P/MRP subunit p25 like protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.029794 0.0 +Mm Hs HSD11B1 Hepatocytes SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene 1 Endoderm Liver 0.135135 0.575 0.00824089 0.0230942 +Mm Hs APOM Hepatocytes ApoM|G3a|NG20 0.01 apolipoprotein M protein-coding gene 1 Endoderm Liver 0.189189 0.825 0.0164818 0.00643294 +Mm Hs TKFC Hepatocytes DKFZP586B1621|NET45|DAK 0.014 triokinase and FMN cyclase protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0066561 0.0 +Mm Hs G0S2 Hepatocytes NA 0.04 G0/G1 switch 2 protein-coding gene 1 Endoderm Liver 0.027027 0.3 0.0456418 0.037118 +Mm Hs PON3 Hepatocytes NA 0.01 paraoxonase 3 protein-coding gene 1 Endoderm Liver 0.0810811 0.225 0.00919176 0.00997105 +Hs C1ORF53 Hepatocytes NA 0.001 chromosome 1 open reading frame 53 protein-coding gene 1 Endoderm Liver 0.027027 0.0 0.00570523 0.0 +Mm Hs TTC36 Hepatocytes HBP21 0.002 tetratricopeptide repeat domain 36 protein-coding gene 1 Endoderm Liver 0.0810811 0.0 0.0 0.0 +Mm Hs GOLT1A Hepatocytes FLJ42654|MGC62027 0.0 golgi transport 1A protein-coding gene 1 Endoderm Liver 0.0810811 0.0 0.00158479 0.0 +Mm Hs FST Hepatocytes NA 0.02 follistatin protein-coding gene 1 Endoderm Liver 0.0 0.025 0.0361331 0.0153104 +Mm Hs MCC Hepatocytes NA 0.004 MCC, WNT signaling pathway regulator protein-coding gene 1 Endoderm Liver 0.0 0.15 0.00507132 0.0032808 +Mm Hs AQP9 Hepatocytes SSC1|HsT17287 0.003 aquaporin 9 protein-coding gene 1 Endoderm Liver 0.0810811 0.325 0.0022187 0.00257317 +Mm Hs GSTA2 Hepatocytes GST2 0.007 glutathione S-transferase alpha 2 protein-coding gene 1 Endoderm Liver 0.0540541 0.2 0.00919176 0.00604696 +Mm Hs NNT Hepatocytes NA 0.001 nicotinamide nucleotide transhydrogenase protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.00316957 0.0 +Mm Hs SAA4 Hepatocytes C-SAA|CSAA 0.001 serum amyloid A4, constitutive protein-coding gene 1 Endoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs MRPS18C Hepatocytes MRPS18-1|CGI-134|FLJ11146|FLJ22967 0.14 mitochondrial ribosomal protein S18C protein-coding gene 1 Endoderm Liver 0.027027 0.275 0.0152139 0.168414 +Mm Hs OCIAD1 Hepatocytes FLJ20455|TPA018|OCIA|Asrij 0.337 OCIA domain containing 1 protein-coding gene 1 Endoderm Liver 0.0810811 0.25 0.274168 0.350724 +Mm Hs APOA5 Hepatocytes RAP3|APOA-V 0.001 apolipoprotein A5 protein-coding gene 1 Endoderm Liver 0.162162 0.275 0.0 0.0 +Mm Hs ENTPD5 Hepatocytes NTPDase-5|CD39L4|PCPH 0.006 ectonucleoside triphosphate diphosphohydrolase 5 protein-coding gene 1 Endoderm Liver 0.0 0.3 0.000633914 0.00611129 +Mm Hs C4B Hepatocytes CPAMD3|C4F|C4B1|C4B3|CH 0.011 complement C4B (Chido blood group) protein-coding gene 1 Endoderm Liver 0.0810811 0.4 0.000316957 0.0124156 +Mm Hs EID2 Hepatocytes EID-2|MGC20452|CRI2 0.004 EP300 interacting inhibitor of differentiation 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00190174 0.00353812 +Hs TP53INP2 Hepatocytes FLJ21759|FLJ23500|DKFZp434B2411|DKFZp434O0827|dJ1181N3.1|PINH|DOR|C20orf110 0.002 tumor protein p53 inducible nuclear protein 2 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00982567 0.0 +Mm Hs ATIC Hepatocytes PURH|AICARFT|IMPCHASE 0.048 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase protein-coding gene 1 Endoderm Liver 0.027027 0.1 0.0602219 0.0409778 +Mm Hs SERPINH1 Hepatocytes HSP47|colligen|CBP1|CBP2|SERPINH2 0.219 serpin family H member 1 protein-coding gene 1 Endoderm Liver 0.0540541 0.0 0.156894 0.0 +Mm Hs SAMD5 Hepatocytes dJ875H10.1 0.009 sterile alpha motif domain containing 5 protein-coding gene 1 Endoderm Liver 0.0 0.0 0.00126783 0.0 +Mm Hs GRB14 Hepatocytes NA 0.039 growth factor receptor bound protein 14 protein-coding gene 1 Endoderm Liver 0.0 0.2 0.00285261 0.0472821 +Mm Hs ABCD3 Hepatocytes PMP70|ZWS2 0.041 ATP binding cassette subfamily D member 3 protein-coding gene 1 Endoderm Liver 0.0540541 0.475 0.0088748 0.0481184 +Mm Hs RHOB Hepatocytes RhoB|RHOH6|MST081|ARH6|ARHB 0.23 ras homolog family member B protein-coding gene 1 Endoderm Liver 0.27027 0.0 0.15309 0.0 +Mm Hs EPB41L4B Hepatocytes EHM2 0.009 erythrocyte membrane protein band 4.1 like 4B protein-coding gene 1 Endoderm Liver 0.027027 0.2 0.0022187 0.0104214 +Mm Hs GPAT4 Hepatocytes DKFZp586M1819|LPAAT-zeta|TSARG7|AGPAT6 0.033 glycerol-3-phosphate acyltransferase 4 protein-coding gene 1 Endoderm Liver 0.027027 0.2 0.0104596 0.038469 +Mm Hs SPTBN1 Hepatocytes NA 0.276 spectrin beta, non-erythrocytic 1 protein-coding gene 1 Endoderm Liver 0.0810811 0.0 0.119493 0.0 +Mm Hs SDC2 Hepatocytes fibroglycan|SYND2|CD362|HSPG|HSPG1 0.078 syndecan 2 protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.117908 0.0 +Mm Hs PHLDA1 Hepatocytes TDAG51|DT1P1B11|PHRIP 0.139 pleckstrin homology like domain family A member 1 protein-coding gene 1 Endoderm Liver 0.027027 0.275 0.119176 0.142554 +Mm Hs WTAP Hepatocytes KIAA0105|MGC3925|Mum2 0.159 WT1 associated protein protein-coding gene 1 Endoderm Liver 0.108108 0.0 0.277655 0.0 +Mm Hs ACADM Hepatocytes MCAD|MCADH|ACAD1 0.072 acyl-CoA dehydrogenase medium chain protein-coding gene 1 Endoderm Liver 0.162162 0.55 0.0757528 0.0676102 +Mm Hs GJA5 His bundle cells CX40 0.002 gap junction protein alpha 5 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00156642 0.00166827 +Mm Hs GJC1 His bundle cells CX45|GJA7 0.026 gap junction protein gamma 1 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0112782 0.0297722 +Mm Hs KCNK3 His bundle cells K2p3.1|TASK|TASK-1 0.005 potassium two pore domain channel subfamily K member 3 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00156642 0.00641643 +Mm Hs PAX6 Immature neurons D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.014411 0.0589707 +Mm Hs PCLO Immature neurons KIAA0559|DKFZp779G1236|ACZ 0.039 piccolo presynaptic cytomatrix protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00501253 0.0455595 +Mm Hs CUX2 Immature neurons KIAA0293|CDP2|CUTL2 0.024 cut like homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0302233 +Mm Hs SLC12A5 Immature neurons KIAA1176|KCC2 0.048 solute carrier family 12 member 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs POMC Immature neurons POC|ACTH|NPP|LPH 0.008 proopiomelanocortin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0238095 0.00500513 +Mm Hs STIM2 Immature neurons NA 0.036 stromal interaction molecule 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0131579 0.0 +Mm Hs RAX Immature neurons RX 0.006 retina and anterior neural fold homeobox protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CUL5 Immature neurons VACM-1 0.057 cullin 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0291353 0.0618583 +Mm Hs HIVEP2 Immature neurons MBP-2|HIV-EP2|MIBP1|ZAS2|Schnurri-2|ZNF40B 0.055 human immunodeficiency virus type I enhancer binding protein 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00250627 0.0684035 +Mm Hs FUT9 Immature neurons Fuc-TIX 0.039 fucosyltransferase 9 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0018797 0.0479979 +Mm Hs TBR1 Immature neurons NA 0.018 T-box, brain 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs PROX1 Immature neurons NA 0.028 prospero homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0109649 0.032405 +Mm Hs NTRK3 Immature neurons TRKC 0.044 neurotrophic receptor tyrosine kinase 3 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00908521 0.0531314 +Mm Hs RND2 Immature neurons Rho7|RhoN|ARHN 0.044 Rho family GTPase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0213033 0.0 +Mm Hs FEZF2 Immature neurons FLJ10142|FKSG36|TOF|FEZL|Zfp312|ZNF312 0.008 FEZ family zinc finger 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.00975359 +Mm Hs SOX5 Immature neurons L-SOX5|MGC35153 0.009 SRY-box 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0203634 0.0 +Mm Hs ROBO1 Immature neurons DUTT1|FLJ21882|SAX3 0.006 roundabout guidance receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.0 +Mm Hs EPHA7 Immature neurons Hek11 0.008 EPH receptor A7 protein-coding gene 0 Ectoderm Brain 0.0 1.0 0.00845865 0.00827772 +Mm Hs EPHA3 Immature neurons HEK|HEK4|ETK1 0.018 EPH receptor A3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0229723 +Mm Hs YY2 Immature neurons ZNF631 0.001 YY2 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs SLC1A1 Immature neurons EAAC1|EAAT3 0.013 solute carrier family 1 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs NOTCH3 Immature neurons CASIL|CADASIL 0.02 notch 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.014411 0.0220739 +Mm Hs NOTCH1 Immature neurons TAN1 0.007 notch 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.00763604 +Mm Hs LHX6 Immature neurons LHX6.1 0.011 LIM homeobox 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00438596 0.013347 +Mm Hs NES Immature neurons FLJ21841 0.048 nestin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0510652 0.0441478 +Mm Hs RBFOX3 Immature neurons FOX-3|NeuN|HRNBP3 0.04 RNA binding fox-1 homolog 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109649 0.0 +Mm Hs CREB1 Immature neurons NA 0.016 cAMP responsive element binding protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0413534 0.00975359 +Mm Hs NEUROD1 Immature neurons BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.023183 0.0429286 +Mm Hs ASCL1 Immature neurons HASH1|bHLHa46 0.007 achaete-scute family bHLH transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00532581 0.00725103 +Mm Hs NTRK1 Immature neurons TRKA|MTC 0.004 neurotrophic receptor tyrosine kinase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00474846 +Mm Hs SYN1 Immature neurons NA 0.028 synapsin I protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs NF1 Immature neurons NA 0.029 neurofibromin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0350877 0.0285549 +Mm Hs BCL2 Immature neurons Bcl-2|PPP1R50 0.043 BCL2, apoptosis regulator protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0516555 +Mm Hs SLC6A5 Immature neurons NA 0.0 solute carrier family 6 member 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs FOXD2 Immature neurons FREAC9|FKHL17 0.001 forkhead box D2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00250627 0.000770021 +Mm Hs ICAM5 Immature neurons TLCN 0.006 intercellular adhesion molecule 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00737936 +Mm Hs SSTR2 Immature neurons NA 0.028 somatostatin receptor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0115915 0.0 +Mm Hs NEUROG2 Immature neurons Atoh4|Math4A|ngn-2|bHLHa8|NGN2 0.016 neurogenin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0203414 +Mm Hs FOXI1 Intercalated cells FREAC6|FKHL10 0.001 forkhead box I1 protein-coding gene 1 Mesoderm Kidney 0.0 0.833333 0.0 0.000321192 +Mm Hs SLC26A11 Intercalated cells NA 0.0 solute carrier family 26 member 11 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00093985 0.0 +Mm Hs CLCNKB Intercalated cells hClC-Kb 0.002 chloride voltage-gated channel Kb protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0 0.00173444 +Mm Hs SLC4A1 Intercalated cells RTA1A|CD233|FR|SW|WR|EPB3|AE1|DI|WD 0.009 solute carrier family 4 member 1 (Diego blood group) protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0338346 0.0 +Mm Hs SLC26A4 Intercalated cells PDS|DFNB4 0.001 solute carrier family 26 member 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00093985 0.0 +Mm Hs ATP6V1B1 Intercalated cells RTA1B|ATP6B1 0.002 ATPase H+ transporting V1 subunit B1 protein-coding gene 1 Mesoderm Kidney 0.0 0.888889 0.00125313 0.00154172 +Mm Hs SLC4A8 Intercalated cells NA 0.007 solute carrier family 4 member 8 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0103383 0.0 +Mm Hs AQP6 Intercalated cells AQP2L 0.001 aquaporin 6 protein-coding gene 1 Mesoderm Kidney 0.0 0.555556 0.0 6.42385e-05 +Mm Hs ATP6V1C2 Intercalated cells VMA5|ATP6C2 0.003 ATPase H+ transporting V1 subunit C2 protein-coding gene 1 Mesoderm Kidney 0.0 0.888889 0.00125313 0.00231258 +Mm Hs ATP6V1G3 Intercalated cells ATP6G3 0.001 ATPase H+ transporting V1 subunit G3 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0 0.000192715 +Mm Hs ATP6V0D2 Intercalated cells FLJ38708|VMA6|ATP6D2 0.007 ATPase H+ transporting V0 subunit d2 protein-coding gene 1 Mesoderm Kidney 0.0 0.944444 0.000313283 0.00693775 +Mm Hs OXGR1 Intercalated cells P2RY15|P2Y15|aKGR|GPR99|GPR80 0.001 oxoglutarate receptor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.777778 0.0 0.0 +Mm Hs RHCG Intercalated cells RHGK|PDRC2|SLC42A3|C15orf6 0.002 Rh family C glycoprotein protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00219298 0.0 +Mm Hs TMEM213 Intercalated cells NA 0.005 transmembrane protein 213 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626566 0.0 +Mm Hs EGF Intercalated cells NA 0.002 epidermal growth factor protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00218411 +Mm Hs FXYD2 Intercalated cells MGC12372|ATP1G1|HOMG2 0.025 FXYD domain containing ion transport regulator 2 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.00438596 0.0294854 +Mm Hs AVPR1A Intercalated cells AVPR1 0.001 arginine vasopressin receptor 1A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00109205 +Mm Hs CLCNKA Intercalated cells hClC-Ka 0.0 chloride voltage-gated channel Ka protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.000449669 +Mm Hs RHBG Intercalated cells SLC42A2 0.002 Rh family B glycoprotein (gene/pseudogene) protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs DMRT2 Intercalated cells NA 0.001 doublesex and mab-3 related transcription factor 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313283 0.000578146 +Mm Hs P2RY14 Intercalated cells KIAA0001|GPR105 0.012 purinergic receptor P2Y14 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00344612 0.0141967 +Mm Hs AP1S3 Intercalated cells NA 0.003 adaptor related protein complex 1 subunit sigma 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00344612 0.00269801 +Mm Hs INSRR Intercalated cells IRR 0.001 insulin receptor related receptor protein-coding gene 1 Mesoderm Kidney 0.0 0.277778 0.0 0.000449669 +Mm Hs JAG1 Intercalated cells AHD|AWS|HJ1|CD339|AGS|JAGL1 0.027 jagged 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.111111 0.0238095 0.0283292 +Mm Hs ADGRF5 Intercalated cells DKFZp564O1923|KIAA0758|GPR116 0.047 adhesion G protein-coupled receptor F5 protein-coding gene 1 Mesoderm Kidney 0.0 0.555556 0.0178571 0.0540245 +Mm Hs CALB1 Interneurons CALB 0.019 calbindin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.149733 0.00125313 0.0220158 +Mm Hs CCK Interneurons NA 0.033 cholecystokinin protein-coding gene 1 Ectoderm Brain 0.0 0.73262 0.00344612 0.0300688 +Mm Hs CHAT Interneurons NA 0.001 choline O-acetyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.00534759 0.0 0.00155864 +Mm Hs VSX2 Interneurons RET1|HOX10|CHX10 0.004 visual system homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs EN1 Interneurons NA 0.003 engrailed homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00376672 +Mm Hs ETV1 Interneurons ER81 0.037 ETS variant 1 protein-coding gene 1 Ectoderm Brain 0.0 0.128342 0.00814536 0.0440317 +Mm Hs EVX1 Interneurons NA 0.0 even-skipped homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00250627 6.49435e-05 +Mm Hs GAD1 Interneurons GAD 0.03 glutamate decarboxylase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.15508 0.00344612 0.0358488 +Mm Hs ISL1 Interneurons Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0588235 0.0134712 0.031043 +Mm Hs LHX1 Interneurons LIM-1 0.011 LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.0127289 +Mm Hs LHX5 Interneurons NA 0.01 LIM homeobox 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.0122094 +Mm Hs LHX3 Interneurons NA 0.001 LIM homeobox 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.000844266 +Mm Hs LHX6 Interneurons LHX6.1 0.011 LIM homeobox 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0213904 0.00438596 0.0132485 +Mm Hs GRM1 Interneurons GPRC1A|mGlu1|MGLUR1|PPP1R85 0.004 glutamate metabotropic receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.139037 0.0 0.00337706 +Mm Hs NPY Interneurons PYY4 0.015 neuropeptide Y protein-coding gene 1 Ectoderm Brain 0.0 0.0481283 0.0056391 0.0166905 +Mm Hs OPRM1 Interneurons MOR1 0.0 opioid receptor mu 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00281955 0.0 +Mm Hs GRIN2D Interneurons GluN2D|EB11|NR2D|NMDAR2D 0.002 glutamate ionotropic receptor NMDA type subunit 2D protein-coding gene 1 Ectoderm Brain 0.0 0.0160428 0.0 0.00181842 +Mm Hs NOS1 Interneurons nNOS 0.004 nitric oxide synthase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0213904 0.0 0.00383167 +Mm Hs PVALB Interneurons D22S749 0.005 parvalbumin protein-coding gene 1 Ectoderm Brain 0.0 0.0320856 0.00344612 0.0055202 +Mm Hs PAX2 Interneurons NA 0.002 paired box 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.00168853 +Mm Hs SST Interneurons SMST 0.027 somatostatin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.047619 0.0 +Mm Hs TACR1 Interneurons SPR|NK1R|TAC1R 0.001 tachykinin receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs VIP Interneurons NA 0.003 vasoactive intestinal peptide protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CRHR1 Interneurons CRF-R|CRF1|CRHR 0.002 corticotropin releasing hormone receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.026738 0.0 0.00175347 +Mm Hs PACSIN1 Interneurons SDPI 0.04 protein kinase C and casein kinase substrate in neurons 1 protein-coding gene NA Ectoderm Brain 0.0 0.545455 0.0 0.0439667 +Mm Hs SYN1 Interneurons NA 0.028 synapsin I protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs FGF12 Interneurons FHF1|FGF12B 0.014 fibroblast growth factor 12 protein-coding gene NA Ectoderm Brain 0.0 0.160428 0.00438596 0.0153916 +Mm Hs NXPH1 Interneurons NA 0.022 neurexophilin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0748663 0.000313283 0.0271464 +Mm Hs SYT7 Interneurons IPCA-7|SYT-VII|MGC150517|PCANAP7 0.024 synaptotagmin 7 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00626566 0.0 +Mm Hs PTPRO Interneurons PTPU2|GLEPP1|PTP-U2|PTP-oc|NPHS6 0.011 protein tyrosine phosphatase, receptor type O protein-coding gene 1 Ectoderm Brain 0.0 0.0695187 0.0075188 0.011495 +Mm Hs DLGAP1 Interneurons GKAP|SAPAP1|DAP-1 0.036 DLG associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.764706 0.00219298 0.0359138 +Mm Hs GNG4 Interneurons NA 0.013 G protein subunit gamma 4 protein-coding gene NA Ectoderm Brain 0.0 0.0748663 0.0175439 0.0110404 +Mm Hs HAP1 Interneurons hHLP1|HIP5 0.041 huntingtin associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.144385 0.000626566 0.0498766 +Mm Hs SHISA8 Interneurons Orf26|C22orf17 0.004 shisa family member 8 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PCBP3 Interneurons FLJ44028|PCBP3-OT1|PCBP3OT 0.02 poly(rC) binding protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0855615 0.00250627 0.0237693 +Mm Hs ABAT Interneurons GABAT 0.032 4-aminobutyrate aminotransferase protein-coding gene NA Ectoderm Brain 0.0 0.213904 0.00344612 0.0364982 +Mm Hs PCP4L1 Interneurons IQM1 0.044 Purkinje cell protein 4 like 1 protein-coding gene NA Ectoderm Brain 0.0 0.149733 0.0 0.0541629 +Mm Hs GAL Interneurons GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene NA Ectoderm Brain 0.0 0.026738 0.0184837 0.0110404 +Mm Hs TH Interneurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs SYNPR Interneurons MGC26651 0.022 synaptoporin protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs TRH Interneurons NA 0.002 thyrotropin releasing hormone protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ADCY8 Interneurons HBAC1|AC8|ADCY3 0.001 adenylate cyclase 8 protein-coding gene NA Ectoderm Brain 0.0 0.0320856 0.0 0.000389661 +Mm Hs CTGF Interneurons IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene NA Ectoderm Brain 0.0 0.0160428 0.0996241 0.0124042 +Mm Hs EML5 Interneurons HuEMAP-2 0.01 echinoderm microtubule associated protein like 5 protein-coding gene NA Ectoderm Brain 0.0 0.0160428 0.0 0.0120145 +Mm Hs TMEM132D Interneurons KIAA1944|MOLT|PPP1R153 0.0 transmembrane protein 132D protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs BACE1 Interneurons BACE 0.022 beta-secretase 1 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.0037594 0.0256527 +Mm Hs CACNG2 Interneurons stargazin|MGC138502|MGC138504 0.014 calcium voltage-gated channel auxiliary subunit gamma 2 protein-coding gene NA Ectoderm Brain 0.0 0.219251 0.0 0.0151968 +Mm Hs ISCA1 Interneurons MGC4276|ISA1|hIscA|HBLD2 0.05 iron-sulfur cluster assembly 1 protein-coding gene NA Ectoderm Brain 0.0 0.117647 0.115288 0.0324068 +Mm Hs LPGAT1 Interneurons KIAA0205|FAM34A1|NET8|FAM34A 0.043 lysophosphatidylglycerol acyltransferase 1 protein-coding gene NA Ectoderm Brain 0.0 0.385027 0.0222431 0.0442915 +Mm Hs NAT14 Interneurons KLP1 0.015 N-acetyltransferase 14 (putative) protein-coding gene NA Ectoderm Brain 0.0 0.256684 0.00657895 0.0133784 +Mm Hs SLC12A5 Interneurons KIAA1176|KCC2 0.048 solute carrier family 12 member 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs DEPTOR Interneurons DEP.6|FLJ12428|DEPDC6 0.012 DEP domain containing MTOR interacting protein protein-coding gene NA Ectoderm Brain 0.0 0.0481283 0.00281955 0.0135732 +Mm Hs SLC22A15 Interneurons FLIPT1 0.017 solute carrier family 22 member 15 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PDE4A Interneurons DPDE2 0.013 phosphodiesterase 4A protein-coding gene NA Ectoderm Brain 0.0 0.213904 0.00125313 0.0135082 +Mm Hs CACNA1I Interneurons Cav3.3 0.0 calcium voltage-gated channel subunit alpha1 I protein-coding gene NA Ectoderm Brain 0.0 0.0106952 0.0 0.000454604 +Mm Hs FRYL Interneurons DKFZp686E205|AF4p12|MOR2|KIAA0826 0.03 FRY like transcription coactivator protein-coding gene NA Ectoderm Brain 0.0 0.0748663 0.0291353 0.0304585 +Mm CAR11 Interneurons NA 0.023 carbonic anhydrase 11 protein coding gene NA Ectoderm Brain 0.0 0.513369 0.0 0.0230549 +Mm Hs SURF1 Interneurons NA 0.061 SURF1, cytochrome c oxidase assembly factor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.118421 0.0 +Mm Hs TRIM9 Interneurons SPRING|RNF91 0.023 tripartite motif containing 9 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs KCNC1 Interneurons Kv3.1 0.03 potassium voltage-gated channel subfamily C member 1 protein-coding gene NA Ectoderm Brain 0.0 0.224599 0.000313283 0.035654 +Mm Hs RAB3B Interneurons NA 0.023 RAB3B, member RAS oncogene family protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0191103 0.0 +Mm Hs CDK17 Interneurons PCTAIRE2|PCTK2 0.023 cyclin dependent kinase 17 protein-coding gene NA Ectoderm Brain 0.0 0.229947 0.0128446 0.0238343 +Mm Hs RGS17 Interneurons RGSZ2|RGS-17 0.031 regulator of G protein signaling 17 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs ABCC5 Interneurons MRP5|SMRP|EST277145|MOAT-C 0.044 ATP binding cassette subfamily C member 5 protein-coding gene NA Ectoderm Brain 0.0 0.171123 0.00438596 0.0525393 +Mm Hs RAB26 Interneurons NA 0.002 RAB26, member RAS oncogene family protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs VLDLR Interneurons CARMQ1|CHRMQ1|VLDLRCH 0.025 very low density lipoprotein receptor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs CACNG7 Interneurons NA 0.002 calcium voltage-gated channel auxiliary subunit gamma 7 protein-coding gene NA Ectoderm Brain 0.0 0.0802139 0.0 0.00214314 +Mm Hs INAFM1 Interneurons PRR24 0.021 InaF motif containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.0162907 0.0212365 +Mm Hs BRINP1 Interneurons FAM5A|DBCCR1 0.013 BMP/retinoic acid inducible neural specific 1 protein-coding gene NA Ectoderm Brain 0.0 0.454545 0.000313283 0.0116249 +Mm Hs PIANP Interneurons DKFZp547D2210|PANP|C12orf53 0.023 PILR alpha associated neural protein protein-coding gene NA Ectoderm Brain 0.0 0.390374 0.0 0.0244837 +Mm Hs CPLX1 Interneurons CPX-I 0.026 complexin 1 protein-coding gene NA Ectoderm Brain 0.0 0.427807 0.0 0.0277309 +Mm Hs SHISA6 Interneurons FLJ45455 0.002 shisa family member 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DHRS3 Interneurons retSDR1|Rsdr1|RDH17|SDR16C1 0.082 dehydrogenase/reductase 3 protein-coding gene NA Ectoderm Brain 0.0 0.0160428 0.14411 0.0700091 +Mm Hs GRIA4 Interneurons GluA4|GLURD|GLUR4 0.014 glutamate ionotropic receptor AMPA type subunit 4 protein-coding gene NA Ectoderm Brain 0.0 0.0641711 0.00344612 0.0159761 +Mm Hs NRSN2 Interneurons dJ1103G7.6|C20orf98 0.032 neurensin 2 protein-coding gene NA Ectoderm Brain 0.0 0.208556 0.000626566 0.0374075 +Mm Hs CDHR1 Interneurons KIAA1775|CORD15|RP65|PCDH21 0.003 cadherin related family member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0748663 0.0 0.00279257 +Mm Hs ABR Interneurons MDB 0.031 ABR, RhoGEF and GTPase activating protein protein-coding gene NA Ectoderm Brain 0.0 0.513369 0.000626566 0.0322769 +Mm Hs NRN1 Interneurons NRN 0.021 neuritin 1 protein-coding gene NA Ectoderm Brain 0.0 0.534759 0.0100251 0.0168204 +Mm Hs HIVEP2 Interneurons MBP-2|HIV-EP2|MIBP1|ZAS2|Schnurri-2|ZNF40B 0.055 human immunodeficiency virus type I enhancer binding protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.486631 0.00250627 0.0633849 +Mm Hs NXPH4 Interneurons NPH4 0.003 neurexophilin 4 protein-coding gene NA Ectoderm Brain 0.0 0.0320856 0.00156642 0.0025328 +Mm Hs CDH4 Interneurons NA 0.017 cadherin 4 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.000313283 0.0200026 +Mm Hs CHST1 Interneurons KSGal6ST 0.032 carbohydrate sulfotransferase 1 protein-coding gene NA Ectoderm Brain 0.0 0.572192 0.0131579 0.0311729 +Mm Hs SHISA9 Interneurons NA 0.004 shisa family member 9 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs EOMES Interneurons TBR2 0.021 eomesodermin protein-coding gene NA Ectoderm Brain 0.0 0.0427807 0.00219298 0.0259125 +Mm Hs NMB Interneurons MGC2277|MGC3936|MGC17211 0.013 neuromedin B protein-coding gene NA Ectoderm Brain 0.0 0.0588235 0.0256892 0.00733862 +Mm Hs LY6G6E Interneurons G6e|C6orf22 0.002 lymphocyte antigen 6 family member G6E other NA Ectoderm Brain 0.0 0.026738 0.0 0.00240291 +Mm Hs CALN1 Interneurons CABP8 0.018 calneuron 1 protein-coding gene NA Ectoderm Brain 0.0 0.454545 0.000313283 0.0169503 +Mm Hs CASK Interneurons LIN2|CAGH39|FGS4|TNRC8 0.043 calcium/calmodulin dependent serine protein kinase protein-coding gene NA Ectoderm Brain 0.0 0.390374 0.00219298 0.0496818 +Mm Hs CACNA1E Interneurons Cav2.3|BII|CACH6|CACNL1A6 0.023 calcium voltage-gated channel subunit alpha1 E protein-coding gene NA Ectoderm Brain 0.0 0.449198 0.0018797 0.0228601 +Mm Hs FAM81A Interneurons MGC26690 0.028 family with sequence similarity 81 member A protein-coding gene NA Ectoderm Brain 0.0 0.550802 0.0 0.0292895 +Mm Hs CAMKV Interneurons MGC8407|VACAMKL 0.024 CaM kinase like vesicle associated protein-coding gene NA Ectoderm Brain 0.0 0.534759 0.00313283 0.0232498 +Mm Hs ARHGAP21 Interneurons KIAA1424|ARHGAP10 0.019 Rho GTPase activating protein 21 protein-coding gene NA Ectoderm Brain 0.0 0.0320856 0.0134712 0.0205221 +Mm Hs DDN Interneurons KIAA0749 0.007 dendrin protein-coding gene NA Ectoderm Brain 0.0 0.315508 0.00125313 0.00474088 +Mm Hs SV2B Interneurons KIAA0735|HsT19680 0.009 synaptic vesicle glycoprotein 2B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs FRRS1L Interneurons CG-6|C9orf4 0.028 ferric chelate reductase 1 like protein-coding gene NA Ectoderm Brain 0.0 0.684492 0.00125313 0.0259774 +Mm Hs ACSL4 Interneurons ACS4|LACS4|FACL4|MRX63|MRX68 0.035 acyl-CoA synthetase long chain family member 4 protein-coding gene NA Ectoderm Brain 0.0 0.160428 0.016604 0.0383816 +Mm Hs CAMK4 Interneurons CaMK-GR 0.027 calcium/calmodulin dependent protein kinase IV protein-coding gene NA Ectoderm Brain 0.0 0.55615 0.0325815 0.0198078 +Mm Hs NPTXR Interneurons NA 0.02 neuronal pentraxin receptor protein-coding gene NA Ectoderm Brain 0.0 0.417112 0.0 0.0200675 +Mm Hs LINGO1 Interneurons FLJ14594|LERN1|LRRN6A 0.019 leucine rich repeat and Ig domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.582888 0.0018797 0.0166905 +Mm Hs HPCAL4 Interneurons HLP4|DKFZp761G122 0.013 hippocalcin like 4 protein-coding gene NA Ectoderm Brain 0.0 0.411765 0.00093985 0.0111053 +Mm Hs LMO3 Interneurons Rhom-3|RBTNL2 0.01 LIM domain only 3 protein-coding gene NA Ectoderm Brain 0.0 0.229947 0.00720551 0.00805299 +Mm Hs LYPD1 Interneurons MGC29643|LYPDC1 0.005 LY6/PLAUR domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0909091 0.0100251 0.00285751 +Mm Hs CHN1 Interneurons ARHGAP2|n-chimerin|DURS2 0.035 chimerin 1 protein-coding gene NA Ectoderm Brain 0.0 0.582888 0.0328947 0.0288999 +Mm Hs NRGN Interneurons NA 0.031 neurogranin protein-coding gene NA Ectoderm Brain 0.0 0.486631 0.0109649 0.0290297 +Mm Hs SLC17A7 Interneurons BNPI|VGLUT1 0.012 solute carrier family 17 member 7 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CAMK2A Interneurons KIAA0968|CAMKA 0.026 calcium/calmodulin dependent protein kinase II alpha protein-coding gene NA Ectoderm Brain 0.0 0.657754 0.0 0.024159 +Mm Hs PRKCB Interneurons PRKCB2|PKCB|PRKCB1 0.046 protein kinase C beta protein-coding gene NA Ectoderm Brain 0.0 0.588235 0.0294486 0.0426679 +Mm Hs NCALD Interneurons NA 0.035 neurocalcin delta protein-coding gene NA Ectoderm Brain 0.0 0.550802 0.00125313 0.0376672 +Mm Hs RAB15 Interneurons NA 0.019 RAB15, member RAS oncogene family protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs FBXW11 Interneurons KIAA0696|Fbw1b|BTRCP2|BTRC2|Hos|Fbw11|FBXW1B 0.017 F-box and WD repeat domain containing 11 protein-coding gene NA Ectoderm Brain 0.0 0.0588235 0.0100251 0.0181842 +Mm Hs ADCY1 Interneurons AC1|DFNB44 0.017 adenylate cyclase 1 protein-coding gene NA Ectoderm Brain 0.0 0.465241 0.00125313 0.0148721 +Mm Hs FBXO11 Interneurons FBX11|UBR6 0.013 F-box protein 11 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.000626566 0.0162359 +Mm Hs IGSF21 Interneurons MGC15730|RP11-121A23.1 0.004 immunoglobin superfamily member 21 protein-coding gene NA Ectoderm Brain 0.0 0.0748663 0.000626566 0.00370178 +Mm Hs SRGAP3 Interneurons KIAA0411|MEGAP|WRP|ARHGAP14|SRGAP2 0.018 SLIT-ROBO Rho GTPase activating protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0100251 0.0 +Mm Hs NTNG1 Interneurons KIAA0976|Lmnt1 0.015 netrin G1 protein-coding gene NA Ectoderm Brain 0.0 0.283422 0.00407268 0.0146772 +Mm Hs MAGEE1 Interneurons KIAA1587|DAMAGE 0.021 MAGE family member E1 protein-coding gene NA Ectoderm Brain 0.0 0.160428 0.0 0.0242239 +Mm Hs SCAMP1 Interneurons SCAMP37 0.041 secretory carrier membrane protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0134712 0.0 +Mm Hs PSD3 Interneurons KIAA0942|HCA67|EFA6R|DKFZp761K1423|EFA6D 0.022 pleckstrin and Sec7 domain containing 3 protein-coding gene NA Ectoderm Brain 0.0 0.513369 0.0244361 0.0159112 +Mm Hs RORA Interneurons RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0140977 0.0 +Mm Hs DCAF7 Interneurons HAN11|SWAN-1|WDR68 0.05 DDB1 and CUL4 associated factor 7 protein-coding gene NA Ectoderm Brain 0.0 0.101604 0.0980576 0.0348097 +Mm Hs VGF Interneurons SCG7|SgVII 0.021 VGF nerve growth factor inducible protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0125313 0.0 +Mm Hs EID2 Interneurons EID-2|MGC20452|CRI2 0.004 EP300 interacting inhibitor of differentiation 2 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.0018797 0.00292246 +Mm Hs RGMA Interneurons RGM|RGMa 0.008 repulsive guidance molecule BMP co-receptor a protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0203634 0.0 +Mm Hs SCRT1 Interneurons DKFZp547F072|ZNF898 0.004 scratch family transcriptional repressor 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs POU2F2 Interneurons OTF2 0.034 POU class 2 homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0374332 0.0191103 0.0363034 +Mm Hs NBEA Interneurons KIAA1544|BCL8B|FLJ10197|LYST2 0.032 neurobeachin protein-coding gene NA Ectoderm Brain 0.0 0.31016 0.00469925 0.0354591 +Mm Hs SRGAP1 Interneurons KIAA1304|ARHGAP13 0.025 SLIT-ROBO Rho GTPase activating protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0802005 0.0 +Mm Hs FCHSD2 Interneurons KIAA0769|SH3MD3 0.003 FCH and double SH3 domains 2 protein-coding gene NA Ectoderm Brain 0.0 0.0481283 0.00156642 0.00240291 +Mm Hs SLC16A1 Interneurons NA 0.039 solute carrier family 16 member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0494987 0.0 +Mm Hs SLC36A1 Interneurons LYAAT-1|TRAMD3 0.006 solute carrier family 36 member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00438596 0.0 +Mm Hs ATG12 Interneurons APG12|APG12L 0.046 autophagy related 12 protein-coding gene NA Ectoderm Brain 0.0 0.0641711 0.106203 0.0249383 +Mm Hs SLC17A6 Interneurons DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs AGAP1 Interneurons KIAA1099|GGAP1|CENTG2 0.024 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 protein-coding gene NA Ectoderm Brain 0.0 0.0962567 0.0037594 0.0288999 +Mm Hs ZDHHC22 Interneurons C14orf59 0.008 zinc finger DHHC-type containing 22 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ACBD5 Interneurons DKFZp434A2417|KIAA1996 0.02 acyl-CoA binding domain containing 5 protein-coding gene NA Ectoderm Brain 0.0 0.0695187 0.0109649 0.0222107 +Mm Hs AQP4 Interneurons MIWC 0.024 aquaporin 4 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.00595238 0.0290947 +Mm Hs TMEM163 Interneurons DKFZP566N034|SV31 0.027 transmembrane protein 163 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs ZDHHC17 Interneurons HIP14|HYPH|KIAA0946 0.01 zinc finger DHHC-type containing 17 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm KITL Interneurons NA 0.041 kit ligand protein coding gene NA Ectoderm Brain 0.0 0.13369 0.0 0.0499416 +Mm Hs ZIC4 Interneurons NA 0.006 Zic family member 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs NEFM Interneurons NFM|NF-M|NEF3 0.028 neurofilament medium protein-coding gene NA Ectoderm Brain 0.0 0.13369 0.0200501 0.0270814 +Mm Hs L1CAM Interneurons CD171|HSAS1|SPG1|HSAS|MIC5 0.018 L1 cell adhesion molecule protein-coding gene NA Ectoderm Brain 0.0 0.176471 0.00156642 0.0194831 +Mm Hs IDS Interneurons SIDS 0.039 iduronate 2-sulfatase protein-coding gene NA Ectoderm Brain 0.0 0.245989 0.0836466 0.0262372 +Mm Hs DNM3 Interneurons KIAA0820 0.043 dynamin 3 protein-coding gene NA Ectoderm Brain 0.0 0.229947 0.00313283 0.0515002 +Mm Hs DNAJC6 Interneurons KIAA0473|PARK19 0.018 DnaJ heat shock protein family (Hsp40) member C6 protein-coding gene NA Ectoderm Brain 0.0 0.31016 0.00156642 0.0190934 +Mm Hs ADGRA1 Interneurons KIAA1828|GPR123 0.008 adhesion G protein-coupled receptor A1 protein-coding gene NA Ectoderm Brain 0.0 0.187166 0.0 0.0085076 +Mm Hs DZANK1 Interneurons FLJ10600|dJ568F9.2|FLJ30892|bA189K21.8|ANKRD64|C20orf84|C20orf12 0.015 double zinc ribbon and ankyrin repeat domains 1 protein-coding gene NA Ectoderm Brain 0.0 0.197861 0.000626566 0.0169503 +Mm Hs SCN2B Interneurons NA 0.035 sodium voltage-gated channel beta subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs HSPA12A Interneurons FLJ13874|KIAA0417 0.013 heat shock protein family A (Hsp70) member 12A protein-coding gene NA Ectoderm Brain 0.0 0.235294 0.0 0.0131186 +Mm Hs SYT13 Interneurons KIAA1427 0.029 synaptotagmin 13 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00689223 0.0 +Mm Hs RAMP3 Interneurons NA 0.014 receptor activity modifying protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0147243 0.0 +Mm Hs LYNX1 Interneurons SLURP2 0.019 Ly6/neurotoxin 1 protein-coding gene NA Ectoderm Brain 0.0 0.497326 0.0 0.0181842 +Mm Hs KCNA2 Interneurons Kv1.2 0.019 potassium voltage-gated channel subfamily A member 2 protein-coding gene NA Ectoderm Brain 0.0 0.358289 0.0 0.0203273 +Mm Hs OXR1 Interneurons TLDC3 0.046 oxidation resistance 1 protein-coding gene NA Ectoderm Brain 0.0 0.374332 0.0451128 0.0439018 +Mm Hs DISP2 Interneurons DISPB|KIAA1742|HsT16908|LINC00594|C15orf36 0.03 dispatched RND transporter family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.449198 0.000313283 0.0320821 +Mm Hs PCSK2 Interneurons SPC2|NEC2 0.032 proprotein convertase subtilisin/kexin type 2 protein-coding gene NA Ectoderm Brain 0.0 0.481283 0.0247494 0.0294194 +Mm Hs SHOX2 Interneurons SHOT|OG12X|OG12 0.006 short stature homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs SCN8A Interneurons Nav1.6|NaCh6|PN4|CerIII|CIAT 0.025 sodium voltage-gated channel alpha subunit 8 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs AAK1 Interneurons KIAA1048|DKFZp686K16132 0.044 AP2 associated kinase 1 protein-coding gene NA Ectoderm Brain 0.0 0.529412 0.0335213 0.0414989 +Mm Hs GABRA4 Interneurons NA 0.005 gamma-aminobutyric acid type A receptor alpha4 subunit protein-coding gene NA Ectoderm Brain 0.0 0.171123 0.00093985 0.00428627 +Mm Hs NRIP3 Interneurons C11orf14 0.021 nuclear receptor interacting protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.235294 0.0322682 0.0163658 +Mm Hs HLF Interneurons MGC33822 0.02 HLF, PAR bZIP transcription factor protein-coding gene NA Ectoderm Brain 0.0 0.245989 0.0 0.0219509 +Mm Hs PRKCD Interneurons NA 0.042 protein kinase C delta protein-coding gene NA Ectoderm Brain 0.0 0.0481283 0.00783208 0.0484479 +Mm Hs PTPN3 Interneurons PTPH1 0.004 protein tyrosine phosphatase, non-receptor type 3 protein-coding gene NA Ectoderm Brain 0.0 0.0962567 0.00250627 0.00324717 +Mm Hs KCNC2 Interneurons Kv3.2 0.005 potassium voltage-gated channel subfamily C member 2 protein-coding gene NA Ectoderm Brain 0.0 0.117647 0.0 0.00545525 +Mm Hs CDKL5 Interneurons EIEE2|CFAP247|STK9 0.009 cyclin dependent kinase like 5 protein-coding gene NA Ectoderm Brain 0.0 0.454545 0.00093985 0.00629952 +Mm Hs CCDC136 Interneurons KIAA1793|NAG6|DKFZP434G156 0.027 coiled-coil domain containing 136 protein-coding gene NA Ectoderm Brain 0.0 0.13369 0.0382206 0.0244837 +Mm Hs KCNMA1 Interneurons KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene NA Ectoderm Brain 0.0 0.652406 0.0184837 0.0411742 +Mm Hs SPOCK3 Interneurons testican-3 0.036 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00783208 0.0 +Mm Hs PTPN4 Interneurons PTPMEG 0.004 protein tyrosine phosphatase, non-receptor type 4 protein-coding gene NA Ectoderm Brain 0.0 0.112299 0.00313283 0.00357189 +Mm Hs PDP1 Interneurons PDP|PDH|PPM2A|PPM2C 0.007 pyruvate dehyrogenase phosphatase catalytic subunit 1 protein-coding gene NA Ectoderm Brain 0.0 0.106952 0.0175439 0.00344201 +Mm Hs RGS7BP Interneurons R7BP 0.034 regulator of G protein signaling 7 binding protein protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PLCB4 Interneurons NA 0.026 phospholipase C beta 4 protein-coding gene NA Ectoderm Brain 0.0 0.203209 0.00281955 0.0288999 +Mm Hs GABBR2 Interneurons HG20|GABABR2|GPRC3B|GPR51 0.023 gamma-aminobutyric acid type B receptor subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.534759 0.00657895 0.0200675 +Mm Hs ELMO1 Interneurons KIAA0281|ELMO-1 0.026 engulfment and cell motility 1 protein-coding gene NA Ectoderm Brain 0.0 0.299465 0.0056391 0.0277958 +Mm Hs ADARB1 Interneurons ADAR2|DRADA2|ADAR2g|DRABA2|RED1|hRED1|ADAR2a-L1|ADAR2a-L2|ADAR2a-L3|ADAR2a|ADAR2b|ADAR2c|ADAR2d 0.011 adenosine deaminase, RNA specific B1 protein-coding gene NA Ectoderm Brain 0.0 0.165775 0.0 0.0122743 +Mm Hs ILDR2 Interneurons C1orf32 0.018 immunoglobulin like domain containing receptor 2 protein-coding gene NA Ectoderm Brain 0.0 0.26738 0.000626566 0.0201325 +Mm Hs AKAP8L Interneurons NAKAP95|HAP95 0.027 A-kinase anchoring protein 8 like protein-coding gene NA Ectoderm Brain 0.0 0.0802139 0.0379073 0.0238992 +Mm Hs SPTY2D1 Interneurons FLJ39441|DKFZp686I068|Spt2 0.009 SPT2 chromatin protein domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs PCF11 Interneurons KIAA0824 0.038 PCF11, cleavage and polyadenylation factor subunit protein-coding gene NA Ectoderm Brain 0.0 0.0641711 0.039787 0.0380569 +Mm Hs PARM1 Interneurons DKFZP564O0823|Cipar1|WSC4 0.02 prostate androgen-regulated mucin-like protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0962567 0.018797 0.0198727 +Mm Hs PITX2 Interneurons IGDS|Brx1|Otlx2|IRID2|IHG2|RIEG|RIEG1|RGS 0.01 paired like homeodomain 2 protein-coding gene NA Ectoderm Brain 0.0 0.0320856 0.0109649 0.00837771 +Mm Hs PITX1 Interneurons POTX|BFT 0.009 paired like homeodomain 1 protein-coding gene NA Ectoderm Brain 0.0 0.0320856 0.00657895 0.00883232 +Mm Hs CLDN9 Interneurons NA 0.003 claudin 9 protein-coding gene NA Ectoderm Brain 0.0 0.0374332 0.0 0.00396155 +Mm Hs TCEAL3 Interneurons MGC15737|WEX8 0.041 transcription elongation factor A like 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0592105 0.0 +None FIGF Interneurons NA 0.006 NA NA NA Ectoderm Brain 0.0 0.0320856 0.0 0.00681907 +Mm Hs KCNK9 Interneurons K2p9.1|TASK3|TASK-3 0.004 potassium two pore domain channel subfamily K member 9 protein-coding gene NA Ectoderm Brain 0.0 0.0534759 0.0 0.00441616 +Mm Hs TSHB Interneurons NA 0.001 thyroid stimulating hormone beta protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs RORB Interneurons RZRB|NR1F2|ROR-BETA 0.023 RAR related orphan receptor B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.012218 0.0 +Mm Hs GATA2 Interneurons NFE1B 0.02 GATA binding protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.0481283 0.0134712 0.0214963 +Mm Hs TIMELESS Interneurons hTIM 0.01 timeless circadian regulator protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0075188 0.0 +Mm Hs CXCL14 Interneurons BRAK|NJAC|bolekine|Kec|MIP-2g|BMAC|SCYB14 0.049 C-X-C motif chemokine ligand 14 protein-coding gene 1 Ectoderm Brain 0.0 0.122995 0.0426065 0.0474088 +Mm Hs APOC3 Interneurons NA 0.018 apolipoprotein C3 protein-coding gene NA Ectoderm Brain 0.0 0.0427807 0.0244361 0.01721 +Mm CES1D Interneurons NA 0.016 carboxylesterase 1D protein coding gene NA Ectoderm Brain 0.0 0.0427807 0.0 0.0198078 +Mm Hs CGA Interneurons GPHa|GPHA1|FSHA|LHA|TSHA 0.003 glycoprotein hormones, alpha polypeptide protein-coding gene NA Ectoderm Brain 0.0 0.0427807 0.00845865 0.000974152 +Mm Hs ADORA2A Interneurons RDC8|ADORA2 0.01 adenosine A2a receptor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0127289 +Mm Hs RPRML Interneurons MGC43894 0.011 reprimo like protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CACNB1 Interneurons CACNLB1 0.003 calcium voltage-gated channel auxiliary subunit beta 1 protein-coding gene NA Ectoderm Brain 0.0 0.0213904 0.0 0.00389661 +Mm Hs KCNQ5 Interneurons Kv7.5 0.001 potassium voltage-gated channel subfamily Q member 5 protein-coding gene NA Ectoderm Brain 0.0 0.00534759 0.000313283 0.000974152 +Mm Hs PRKCG Interneurons PKCC|MGC57564|PKCG|SCA14 0.005 protein kinase C gamma protein-coding gene 1 Ectoderm Brain 0.0 0.278075 0.0 0.00266268 +Mm Hs GABRA5 Interneurons NA 0.005 gamma-aminobutyric acid type A receptor alpha5 subunit protein-coding gene 1 Ectoderm Brain 0.0 0.0909091 0.0 0.00571503 +Mm Hs PAX6 Interneurons D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0534759 0.014411 0.0590336 +Mm Hs PNOC Interneurons PPNOC|N/OFQ|NOP 0.009 prepronociceptin protein-coding gene 1 Ectoderm Brain 0.0 0.0320856 0.00093985 0.00967658 +Mm Hs HTR3A Interneurons 5-HT3R|5-HT3A 0.007 5-hydroxytryptamine receptor 3A protein-coding gene 1 Ectoderm Brain 0.0 0.0106952 0.0 0.00902715 +Mm Hs RELN Interneurons RL|PRO1598 0.018 reelin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs CALB2 Interneurons CAL2 0.03 calbindin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.117647 0.00281955 0.0364982 +Mm Hs PDE1A Interneurons NA 0.018 phosphodiesterase 1A protein-coding gene 1 Ectoderm Brain 0.0 0.235294 0.0216165 0.0150019 +Mm Hs ADGRL2 Interneurons KIAA0786|LEC1|LPHH1|LPHN2 0.021 adhesion G protein-coupled receptor L2 protein-coding gene 1 Ectoderm Brain 0.0 0.0213904 0.00407268 0.0254579 +Mm Hs KCNIP2 Interneurons KCHIP2 0.008 potassium voltage-gated channel interacting protein 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0695187 0.000626566 0.00928692 +Mm Hs RGS10 Interneurons NA 0.143 regulator of G protein signaling 10 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.180451 0.0 +Mm Hs NOV Interneurons IGFBP9|CCN3 0.004 nephroblastoma overexpressed protein-coding gene 1 Ectoderm Brain 0.0 0.0802139 0.00469925 0.00376672 +Mm Hs CPNE5 Interneurons CPN5|COPN5|KIAA1599 0.008 copine 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0427807 0.00093985 0.00974153 +Mm Hs SLC5A7 Interneurons hCHT|CHT1 0.002 solute carrier family 5 member 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CRH Interneurons CRH1 0.001 corticotropin releasing hormone protein-coding gene 1 Ectoderm Brain 0.0 0.0160428 0.000626566 0.00110404 +Mm Hs GDA Interneurons NA 0.039 guanine deaminase protein-coding gene 1 Ectoderm Brain 0.0 0.427807 0.0018797 0.0431225 +Mm Hs SEMA3E Interneurons M-SemaK|KIAA0331|coll-5|SEMAH 0.005 semaphorin 3E protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DLX1 Interneurons NA 0.036 distal-less homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0534759 0.0 0.0447461 +Mm Hs DLX2 Interneurons TES-1 0.031 distal-less homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.0375373 +Mm Hs DLX5 Interneurons NA 0.019 distal-less homeobox 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.0227302 +Mm Hs ARX Interneurons ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.0238992 +Mm Hs NDNF Interneurons FLJ23191|C4orf31 0.017 neuron derived neurotrophic factor protein-coding gene 1 Ectoderm Brain 0.0 0.0374332 0.00626566 0.0203273 +Mm Hs FOXI1 Ionocytes FREAC6|FKHL10 0.001 forkhead box I1 protein-coding gene 1 Mesoderm Lungs 0.0 1.0 0.0 0.001091 +Mm Hs CFTR Ionocytes ABC35|TNR-CFTR|CFTR/MRP|CF|ABCC7 0.003 cystic fibrosis transmembrane conductance regulator protein-coding gene 1 Mesoderm Lungs 0.0 1.0 0.00657895 0.00269542 +Mm Hs ASCL3 Ionocytes bHLHa42|HASH3|Sgn1 0.0 achaete-scute family bHLH transcription factor 3 protein-coding gene 1 Mesoderm Lungs 0.0 1.0 0.0 6.41766e-05 +Mm CYP2F2 Ionocytes NA 0.008 cytochrome P450, family 2, subfamily f, polypeptide 2 protein coding gene NA Mesoderm Lungs 0.0 0.0 0.0 0.00943396 +Mm Hs SCGB1A1 Ionocytes CC10|CCSP|CC16|UGB 0.028 secretoglobin family 1A member 1 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.0109649 0.0 +Mm Hs FOXN4 Ionocytes NA 0.0 forkhead box N4 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0 0.000320883 +Mm Hs TFCP2L1 Ionocytes LBP-9|CRTR1 0.008 transcription factor CP2 like 1 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.00313283 0.0 +Mm Hs SLC12A2 Ionocytes NKCC1|BSC|BSC2|PPP1R141 0.074 solute carrier family 12 member 2 protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0501253 0.0 +Mm Hs CLCNKB Ionocytes hClC-Kb 0.002 chloride voltage-gated channel Kb protein-coding gene 1 Mesoderm Lungs 0.0 0.0 0.0 0.00288795 +Mm Hs KCNMA1 Ionocytes KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene 1 Mesoderm Lungs 0.0 1.0 0.0184837 0.048325 +Mm Hs SLC9A4 Ionocytes NHE4 0.0 solute carrier family 9 member A4 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs SLC9A7 Ionocytes NHE7 0.0 solute carrier family 9 member A7 protein-coding gene NA Mesoderm Lungs 0.0 0.0 0.00125313 0.0 +Mm Hs TRPV4 Juxtaglomerular cells OTRPC4|TRP12|VROAC|VRL-2|VR-OAC|CMT2C 0.002 transient receptor potential cation channel subfamily V member 4 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Hs REN Juxtaglomerular cells NA 0.0 renin protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00219298 0.0 +Mm Hs TH Juxtaglomerular cells DYT5b 0.002 tyrosine hydroxylase protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0018797 0.0 +Mm REN1 Juxtaglomerular cells NA 0.0 renin 1 structural protein coding gene 1 Mesoderm Kidney NA NA NA NA +Mm AKR1B7 Juxtaglomerular cells NA 0.001 aldo-keto reductase family 1, member B7 protein coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.00102683 +Mm Hs ACTA2 Juxtaglomerular cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.0194236 0.0386985 +Mm Hs MYH11 Juxtaglomerular cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene NA Mesoderm Kidney 0.0 0.666667 0.0162907 0.0148248 +Mm Hs CNN1 Juxtaglomerular cells Sm-Calp 0.012 calponin 1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.0285088 0.0087922 +Hs CALML5 Keratinocytes CLSP 0.001 calmodulin like 5 protein-coding gene 1 Mesoderm Skin 0.5 0.0 0.00377121 0.0 +Hs CD24 Keratinocytes CD24A 0.039 CD24 molecule protein-coding gene 1 Mesoderm Skin 0.6 0.0 0.190761 0.0 +Mm Hs FLG Keratinocytes NA 0.0 filaggrin protein-coding gene 1 Mesoderm Skin 0.0 0.0275229 0.0 0.0 +Mm Hs KPRP Keratinocytes C1orf45 0.0 keratinocyte proline rich protein protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs ICAM1 Keratinocytes CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA Mesoderm Skin 0.0 0.100917 0.00597109 0.00936935 +Mm Hs IVL Keratinocytes NA 0.001 involucrin protein-coding gene 1 Mesoderm Skin 0.1 0.0458716 0.0 0.00135694 +Mm Hs TGM1 Keratinocytes TGASE|TGK|LI|LI1|ICR2 0.002 transglutaminase 1 protein-coding gene 1 Mesoderm Skin 0.1 0.0 0.00157134 0.0 +Mm Hs KRT1 Keratinocytes KRT1A 0.006 keratin 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0733945 0.00471402 0.00633239 +Mm Hs KRT5 Keratinocytes KRT5A|EBS2 0.019 keratin 5 protein-coding gene 1 Mesoderm Skin 0.6 0.963303 0.0427404 0.0084001 +Mm Hs KRT14 Keratinocytes EBS3|EBS4 0.019 keratin 14 protein-coding gene 1 Mesoderm Skin 0.6 0.908257 0.0179133 0.0129232 +Mm Hs KRT16 Keratinocytes NEPPK 0.005 keratin 16 protein-coding gene NA Mesoderm Skin 0.4 0.605505 0.00722816 0.000323081 +Mm Hs KRT17 Keratinocytes PCHC1 0.025 keratin 17 protein-coding gene 1 Mesoderm Skin 1.0 0.733945 0.071653 0.0106617 +Mm Hs LAMA5 Keratinocytes NA 0.008 laminin subunit alpha 5 protein-coding gene NA Mesoderm Skin 0.0 0.100917 0.0122564 0.00710778 +Mm Hs LCN2 Keratinocytes NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Mesoderm Skin 0.3 0.0642202 0.0559397 0.0416128 +Mm Hs PLEC Keratinocytes PLTN|EBS1|PLEC1 0.056 plectin protein-coding gene 1 Mesoderm Skin 0.0 0.733945 0.030484 0.0580253 +Hs PI3 Keratinocytes ESI|SKALP|ELAFIN|WAP3|WFDC14|cementoin 0.003 peptidase inhibitor 3 protein-coding gene NA Mesoderm Skin 0.3 0.0 0.0201131 0.0 +Mm Hs SPRR1A Keratinocytes NA 0.004 small proline rich protein 1A protein-coding gene 1 Mesoderm Skin 0.2 0.0 0.000314268 0.0 +Mm Hs SPRR1B Keratinocytes GADD33|SPRR1 0.002 small proline rich protein 1B protein-coding gene 1 Mesoderm Skin 0.3 0.0 0.00439975 0.0 +Mm Hs GJB3 Keratinocytes CX31|EKV 0.008 gap junction protein beta 3 protein-coding gene 1 Mesoderm Skin 0.2 0.137615 0.00942803 0.00710778 +Mm Hs IRF3 Keratinocytes NA 0.019 interferon regulatory factor 3 protein-coding gene 1 Mesoderm Skin 0.0 0.165138 0.0188561 0.0153787 +Mm Hs LAMC2 Keratinocytes nicein-100kDa|kalinin-105kDa|BM600-100kDa|EBR2|LAMB2T|LAMNB2|EBR2A 0.012 laminin subunit gamma 2 protein-coding gene 1 Mesoderm Skin 0.0 0.412844 0.0226273 0.00723701 +Mm Hs SIRT7 Keratinocytes NA 0.025 sirtuin 7 protein-coding gene 1 Mesoderm Skin 0.2 0.0 0.014142 0.0 +Mm Hs RIPK4 Keratinocytes DIK|ANKK2|RIP4|PKK|ANKRD3 0.005 receptor interacting serine/threonine kinase 4 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs REL Keratinocytes I-Rel|c-Rel 0.03 REL proto-oncogene, NF-kB subunit protein-coding gene 1 Mesoderm Skin 0.3 0.0 0.0367693 0.0 +Mm Hs IL13RA1 Keratinocytes IL-13Ra|NR4|CD213a1 0.016 interleukin 13 receptor subunit alpha 1 protein-coding gene 1 Mesoderm Skin 0.1 0.311927 0.0289126 0.0113078 +Mm Hs SGPP1 Keratinocytes NA 0.011 sphingosine-1-phosphate phosphatase 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000628536 0.0 +Mm Hs PKP3 Keratinocytes NA 0.021 plakophilin 3 protein-coding gene 1 Mesoderm Skin 0.2 0.761468 0.0282841 0.0139571 +Mm Hs PKP1 Keratinocytes B6P 0.006 plakophilin 1 protein-coding gene 1 Mesoderm Skin 0.2 0.770642 0.00439975 0.00174464 +Mm Hs ANXA8 Keratinocytes ANX8 0.008 annexin A8 protein-coding gene NA Mesoderm Skin 0.0 0.798165 0.00157134 0.00355389 +Mm Hs TRIM29 Keratinocytes FLJ36085 0.009 tripartite motif containing 29 protein-coding gene 1 Mesoderm Skin 0.2 0.0 0.00817096 0.0 +Mm Hs DSC3 Keratinocytes CDHF3|DSC|DSC1|DSC2|DSC4 0.006 desmocollin 3 protein-coding gene 1 Mesoderm Skin 0.2 0.752294 0.00534255 0.000581546 +Mm Hs FST Keratinocytes NA 0.02 follistatin protein-coding gene 1 Mesoderm Skin 0.0 0.0917431 0.0358265 0.0147971 +Mm Hs AQP3 Keratinocytes GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Mesoderm Skin 0.6 0.798165 0.0694532 0.0104032 +Mm Hs KRT15 Keratinocytes K15|CK15|K1CO 0.022 keratin 15 protein-coding gene 1 Mesoderm Skin 0.7 0.908257 0.0458831 0.0110494 +Mm Hs S100A14 Keratinocytes BCMP84 0.03 S100 calcium binding protein A14 protein-coding gene 1 Mesoderm Skin 0.7 0.0 0.0949089 0.0 +Mm Hs DMKN Keratinocytes ZD52F10 0.032 dermokine protein-coding gene 1 Mesoderm Skin 0.3 0.825688 0.0637964 0.0138279 +Mm Hs ENTPD2 Keratinocytes NTPDase-2|CD39L1 0.012 ectonucleoside triphosphate diphosphohydrolase 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000942803 0.0146679 +Mm Hs FGF5 Keratinocytes NA 0.002 fibroblast growth factor 5 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.00754243 0.00155079 +Mm Hs NGFR Keratinocytes TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene 1 Mesoderm Skin 0.0 0.00917431 0.00219987 0.00743086 +Mm Hs TFAP2A Keratinocytes AP-2|TFAP2|AP2TF 0.023 transcription factor AP-2 alpha protein-coding gene 1 Mesoderm Skin 0.2 0.0 0.0194846 0.0 +Mm Hs LGALS7 Keratinocytes TP53I1|LGALS7A 0.016 galectin 7 protein-coding gene 1 Mesoderm Skin 0.2 0.899083 0.00282841 0.012794 +Mm Hs CXCL1 Keratinocytes SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene NA Mesoderm Skin 0.3 0.0458716 0.0449403 0.0304342 +Mm Hs CCL2 Keratinocytes MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Skin 0.1 0.00917431 0.0647392 0.0320496 +Mm Hs SFN Keratinocytes YWHAS 0.051 stratifin protein-coding gene 1 Mesoderm Skin 0.5 0.0 0.0776241 0.0 +Mm Hs KRT10 Keratinocytes K10|CK10|KPP 0.099 keratin 10 protein-coding gene 1 Mesoderm Skin 0.6 0.458716 0.386864 0.0258465 +Mm Hs SBSN Keratinocytes UNQ698|HLAR698 0.003 suprabasin protein-coding gene 1 Mesoderm Skin 0.2 0.0 0.000314268 0.0 +Mm Hs KRT84 Keratinocytes Hb-4|KRTHB4 0.001 keratin 84 protein-coding gene 1 Mesoderm Skin 0.0 0.12844 0.0 0.0 +Mm Hs KRT36 Keratinocytes KRTHA6 0.002 keratin 36 protein-coding gene 1 Mesoderm Skin 0.0 0.293578 0.0 0.000193849 +Mm Hs OSR1 Kidney progenitor cells NA 0.011 odd-skipped related transciption factor 1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.00156691 0.0126436 +Mm Hs PAX2 Kidney progenitor cells NA 0.002 paired box 2 protein-coding gene NA Mesoderm Kidney 1.0 0.75 0.00313381 0.00147616 +Mm Hs EYA1 Kidney progenitor cells NA 0.001 EYA transcriptional coactivator and phosphatase 1 protein-coding gene NA Mesoderm Kidney 1.0 0.75 0.00125353 0.00121943 +Mm Hs WT1 Kidney progenitor cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene NA Mesoderm Kidney 1.0 0.0 0.0222501 0.0 +Mm Hs SIX2 Kidney progenitor cells NA 0.001 SIX homeobox 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00188029 0.0 +Mm Hs SALL1 Kidney progenitor cells Hsal1|ZNF794|TBS 0.004 spalt like transcription factor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs CITED1 Kidney progenitor cells MSG1 0.023 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 protein-coding gene NA Mesoderm Kidney 1.0 1.0 0.0156691 0.0243245 +Mm Hs TNF Kupffer cells TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00125313 0.0 +Hs LYZ Kupffer cells NA 0.008 lysozyme protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0407268 0.0 +Mm Hs MPO Kupffer cells NA 0.023 myeloperoxidase protein-coding gene NA Mesoderm Liver 0.0 0.0 0.0206767 0.0231467 +Mm Hs VSIG4 Kupffer cells Z39IG 0.005 V-set and immunoglobulin domain containing 4 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0134712 0.0 +Mm Hs PROK2 Kupffer cells PK2|BV8|MIT1|KAL4 0.003 prokineticin 2 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00438596 0.00237896 +Mm Hs STARD5 Kupffer cells MGC10327 0.006 StAR related lipid transfer domain containing 5 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs MSR1 Kupffer cells SCARA1|CD204|SR-AI|SR-AII|SR-AIII|SR-A 0.012 macrophage scavenger receptor 1 protein-coding gene 1 Mesoderm Liver 0.0 0.625 0.0109649 0.0108018 +Mm Hs TLR9 Kupffer cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs PPARA Kupffer cells hPPAR|NR1C1|PPAR 0.001 peroxisome proliferator activated receptor alpha protein-coding gene NA Mesoderm Liver 0.0 0.0 0.00250627 0.000707259 +Mm Hs TREM1 Kupffer cells TREM-1|CD354 0.003 triggering receptor expressed on myeloid cells 1 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00125313 0.0 +Mm Hs SLC11A1 Kupffer cells NRAMP|NRAMP1 0.017 solute carrier family 11 member 1 protein-coding gene NA Mesoderm Liver 0.0 0.0 0.00657895 0.0 +Mm Hs TLR4 Kupffer cells hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.000313283 0.0 +Mm Hs MMP13 Kupffer cells CLG3 0.003 matrix metallopeptidase 13 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0 0.00334341 +Mm Hs CD14 Kupffer cells NA 0.051 CD14 molecule protein-coding gene 1 Mesoderm Liver 0.0 0.25 0.0266291 0.0551019 +Mm Hs VDR Kupffer cells NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00250627 0.0 +Mm Hs CHIT1 Kupffer cells CHIT|CHI3 0.003 chitinase 1 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00125313 0.00392207 +Mm Hs OSM Kupffer cells MGC20461 0.007 oncostatin M protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0 0.00842281 +Mm Hs PPARD Kupffer cells NUC1|NUCII|FAAR|NR1C2 0.009 peroxisome proliferator activated receptor delta protein-coding gene NA Mesoderm Liver 0.0 0.0 0.0018797 0.0104803 +Mm Hs CLEC4F Kupffer cells FLJ39110|KCLR 0.003 C-type lectin domain family 4 member F protein-coding gene 1 Mesoderm Liver 0.0 0.96875 0.0 0.00160741 +Mm Hs ADGRE1 Kupffer cells TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene 1 Mesoderm Liver 0.0 0.96875 0.000626566 0.0394136 +Mm Hs IL1B Kupffer cells IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene NA Mesoderm Liver 0.0 0.21875 0.0253759 0.0273259 +Mm Hs SLC40A1 Kupffer cells MTP1|IREG1|FPN1|HFE4|SLC11A3 0.033 solute carrier family 40 member 1 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.035401 0.0 +Hs G6PD Kupffer cells G6PD1 0.011 glucose-6-phosphate dehydrogenase protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0466792 0.0 +Mm FCNA Kupffer cells NA 0.007 ficolin A protein coding gene 1 Mesoderm Liver 0.0 0.96875 0.0 0.00649392 +Mm Hs TIMD4 Kupffer cells NA 0.006 T cell immunoglobulin and mucin domain containing 4 protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0238095 0.0 +Mm Hs MNDA Kupffer cells PYHIN3 0.019 myeloid cell nuclear differentiation antigen protein-coding gene NA Mesoderm Liver 0.0 0.1875 0.0460526 0.0127307 +Mm Hs SLC15A3 Kupffer cells PHT2|hPTR3 0.016 solute carrier family 15 member 3 protein-coding gene NA Mesoderm Liver 0.0 0.0 0.0075188 0.0 +Mm Hs DNASE1L3 Kupffer cells DNAS1L3|LSD 0.015 deoxyribonuclease 1 like 3 protein-coding gene 1 Mesoderm Liver 0.0 0.53125 0.0100251 0.0151739 +Mm Hs MARCO Kupffer cells SCARA2|SR-A6 0.003 macrophage receptor with collagenous structure protein-coding gene 1 Mesoderm Liver 0.0 0.4375 0.00407268 0.00225037 +Mm EAR2 Kupffer cells NA 0.009 eosinophil-associated, ribonuclease A family, member 2 protein coding gene 1 Mesoderm Liver 0.0 0.4375 0.0 0.00990163 +Mm Hs HFE Kupffer cells HLA-H 0.017 homeostatic iron regulator protein-coding gene 1 Mesoderm Liver 0.0 0.5 0.000313283 0.0203819 +Mm Hs CD38 Kupffer cells NA 0.016 CD38 molecule protein-coding gene 1 Mesoderm Liver 0.0 0.5625 0.0140977 0.014981 +Mm ADGRE4 Kupffer cells NA 0.004 adhesion G protein-coupled receptor E4 protein coding gene 1 Mesoderm Liver 0.0 0.59375 0.0 0.00379348 +Mm Hs CD163 Kupffer cells MM130|SCARI1 0.005 CD163 molecule protein-coding gene 1 Mesoderm Liver 0.0 0.5 0.00720551 0.00327911 +Mm Hs CCR5 Kupffer cells CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene 1 Mesoderm Liver 0.0 0.625 0.0 0.0171028 +Mm Hs CLEC1B Kupffer cells CLEC2 0.003 C-type lectin domain family 1 member B protein-coding gene 1 Mesoderm Liver 0.0 0.75 0.00093985 0.001736 +Mm SIGLECF Kupffer cells NA 0.002 sialic acid binding Ig-like lectin F protein coding gene 1 Mesoderm Liver NA NA NA NA +Mm Hs CLEC4G Kupffer cells UNQ431|LSECtin 0.001 C-type lectin domain family 4 member G protein-coding gene 1 Mesoderm Liver 0.0 0.09375 0.000313283 0.000707259 +Mm Hs GPIHBP1 Kupffer cells LOC338328|GPI-HBP1 0.017 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 protein-coding gene 1 Mesoderm Liver 0.0 0.09375 0.00469925 0.0194818 +Mm Hs FOLR2 Kupffer cells NA 0.001 folate receptor beta protein-coding gene 1 Mesoderm Liver 0.0 0.03125 0.0037594 0.000257185 +Mm Hs PLTP Kupffer cells BPIFE 0.009 phospholipid transfer protein protein-coding gene 1 Mesoderm Liver 0.0 0.03125 0.0260025 0.0051437 +Hs FTL Kupffer cells MGC71996|NBIA3 0.178 ferritin light chain protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.938596 0.0 +Mm Hs IRF7 Kupffer cells NA 0.033 interferon regulatory factor 7 protein-coding gene 1 Mesoderm Liver 0.0 0.78125 0.0285088 0.0307336 +Mm Hs SPIC Kupffer cells MGC40611|SPI-C 0.002 Spi-C transcription factor protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.0 0.0 +Mm Hs CSF1R Kupffer cells C-FMS|CSFR|CD115|FMS 0.064 colony stimulating factor 1 receptor protein-coding gene 1 Mesoderm Liver 0.0 0.96875 0.0178571 0.074005 +Mm Hs C1QC Kupffer cells C1QG 0.066 complement C1q C chain protein-coding gene 1 Mesoderm Liver 0.0 1.0 0.0169173 0.0771555 +Mm Hs C1QA Kupffer cells NA 0.07 complement C1q A chain protein-coding gene 1 Mesoderm Liver 0.0 1.0 0.0241228 0.0804346 +Mm Hs C1QB Kupffer cells NA 0.071 complement C1q B chain protein-coding gene 1 Mesoderm Liver 0.0 1.0 0.0191103 0.0814634 +Mm Hs CLEC4E Kupffer cells mincle|CLECSF9 0.006 C-type lectin domain family 4 member E protein-coding gene 1 Mesoderm Liver 0.0 0.0 0.00250627 0.00610815 +Mm Hs ACHE Langerhans cells YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00476493 0.0195701 +Hs CD1A Langerhans cells NA 0.0 CD1a molecule protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Hs FCGR1A Langerhans cells CD64|CD64A 0.001 Fc fragment of IgG receptor Ia protein-coding gene NA Mesoderm Skin 0.0227273 0.0 0.00349428 0.0 +Hs HLA-DMA Langerhans cells D6S222E|RING6 0.022 major histocompatibility complex, class II, DM alpha protein-coding gene NA Mesoderm Skin 0.909091 0.0 0.112452 0.0 +Hs HLA-DMB Langerhans cells D6S221E|RING7 0.009 major histocompatibility complex, class II, DM beta protein-coding gene NA Mesoderm Skin 0.522727 0.0 0.0374841 0.0 +Hs HLA-DQA1 Langerhans cells HLA-DQA 0.01 major histocompatibility complex, class II, DQ alpha 1 protein-coding gene NA Mesoderm Skin 0.772727 0.0 0.0412961 0.0 +Hs HLA-DQA2 Langerhans cells HLA-DXA 0.003 major histocompatibility complex, class II, DQ alpha 2 protein-coding gene NA Mesoderm Skin 0.136364 0.0 0.0114358 0.0 +Hs HLA-DQB1 Langerhans cells HLA-DQB 0.012 major histocompatibility complex, class II, DQ beta 1 protein-coding gene NA Mesoderm Skin 0.795455 0.0 0.0546379 0.0 +Hs HLA-DQB2 Langerhans cells HLA-DXB 0.0 major histocompatibility complex, class II, DQ beta 2 protein-coding gene NA Mesoderm Skin 0.0227273 0.0 0.00158831 0.0 +Hs HLA-DQB3 Langerhans cells D6S205|D6S205E|DVB|DQB3|HLA-DVB 0.0 major histocompatibility complex, class II, DQ beta 3 other NA Mesoderm Skin 0.0 0.0 0.0 0.0 +Hs HLA-DRA Langerhans cells HLA-DRA1 0.039 major histocompatibility complex, class II, DR alpha protein-coding gene NA Mesoderm Skin 1.0 0.0 0.201398 0.0 +Hs HLA-DRB1 Langerhans cells HLA-DR1B 0.033 major histocompatibility complex, class II, DR beta 1 protein-coding gene NA Mesoderm Skin 1.0 0.0 0.168679 0.0 +Hs HLA-DRB5 Langerhans cells NA 0.011 major histocompatibility complex, class II, DR beta 5 protein-coding gene NA Mesoderm Skin 0.477273 0.0 0.0568615 0.0 +Hs HLA-DRB6 Langerhans cells NA 0.002 major histocompatibility complex, class II, DR beta 6 (pseudogene) pseudogene NA Mesoderm Skin 0.227273 0.0 0.0108005 0.0 +Hs HLA-DRB9 Langerhans cells D6S206|D6S206E|HLA-DRB1L|HLA-DR1BL 0.0 major histocompatibility complex, class II, DR beta 9 (pseudogene) pseudogene NA Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs CD207 Langerhans cells Langerin|CLEC4K 0.001 CD207 molecule protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00147578 +Mm Hs EHF Langerhans cells ESE3|ESEJ 0.024 ETS homologous factor protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0520966 0.0193134 +Mm Hs PRKCB Langerhans cells PRKCB2|PKCB|PRKCB1 0.046 protein kinase C beta protein-coding gene 1 Mesoderm Skin 0.227273 0.0 0.0266836 0.049214 +Mm Hs AHR Langerhans cells bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Mesoderm Skin 0.0227273 0.0 0.0111182 0.00692974 +Mm Hs GPNMB Langerhans cells NMB|HGFIN 0.013 glycoprotein nmb protein-coding gene 1 Mesoderm Skin 0.318182 0.0 0.0257306 0.00943215 +Mm Hs EPCAM Langerhans cells Ly74|TROP1|GA733-2|EGP34|EGP40|EGP-2|KSA|CD326|Ep-CAM|HEA125|KS1/4|MK-1|MH99|MOC31|323/A3|17-1A|TACST-1|CO-17A|M4S1|MIC18|TACSTD1 0.117 epithelial cell adhesion molecule protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.17122 0.104203 +Mm Hs CD80 Langerhans cells B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.000192493 +Mm Hs PTPRC Langerhans cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Skin 0.454545 0.0 0.212834 0.106192 +Mm Hs TLR2 Langerhans cells TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000952986 0.0 +Mm Hs TLR4 Langerhans cells hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000317662 0.0 +Mm Hs TLR9 Langerhans cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Hs FCGR2A Langerhans cells CD32A|IGFR2|CDw32|FCGR2A1 0.002 Fc fragment of IgG receptor IIa protein-coding gene 1 Mesoderm Skin 0.0681818 0.0 0.00889454 0.0 +Mm Hs CCR6 Langerhans cells CKR-L3|GPR-CY4|CMKBR6|GPR29|DRY-6|DCR2|BN-1|CD196|STRL22 0.001 C-C motif chemokine receptor 6 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00186076 +Mm DEFB3 Langerhans cells NA 0.0 defensin beta 3 protein coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs CLDN1 Langerhans cells SEMP1|ILVASC 0.01 claudin 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0289072 0.00564646 +Mm Hs HSD11B2 Leydig cells SDR9C3 0.004 hydroxysteroid 11-beta dehydrogenase 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0109718 0.0026968 +Mm Hs MAFB Leydig cells KRML 0.053 MAF bZIP transcription factor B protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0592477 0.0529087 +Mm Hs ALDH1A1 Leydig cells RALDH1|PUMB1|ALDH1 0.039 aldehyde dehydrogenase 1 family member A1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.909091 0.0880878 0.0281238 +Mm Hs SLC9A8 Leydig cells KIAA0939|NHE8 0.001 solute carrier family 9 member A8 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs KISS1 Leydig cells NA 0.001 KiSS-1 metastasis suppressor protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00344828 0.0 +Mm Hs PDE8A Leydig cells HsT19550 0.015 phosphodiesterase 8A protein-coding gene 1 Mesoderm Reproductive 0.0 0.0909091 0.00376176 0.0181071 +Mm Hs LEP Leydig cells OBS 0.0 leptin protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs CXCL10 Leydig cells IFI10|IP-10|crg-2|mob-1|C7|gIP-10|INP10|SCYB10 0.009 C-X-C motif chemokine ligand 10 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0100313 0.00892513 +Mm Hs PTCH1 Leydig cells BCNS|NBCCS|PTCH 0.012 patched 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.181818 0.0191223 0.0109156 +Mm Hs GATA4 Leydig cells NA 0.008 GATA binding protein 4 protein-coding gene NA Mesoderm Reproductive 0.0 0.181818 0.00470219 0.00783357 +Mm Hs ACSBG1 Leydig cells BGM|FLJ30320|MGC14352|BG1|KIAA0631|hBG1|hsBG 0.023 acyl-CoA synthetase bubblegum family member 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.909091 0.0 0.0279954 +Mm Hs INHA Leydig cells NA 0.006 inhibin subunit alpha protein-coding gene NA Mesoderm Reproductive 1.0 0.727273 0.0128527 0.00449467 +Mm Hs HSD3B1 Leydig cells SDR11E1|HSDB3|HSD3B 0.001 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.818182 0.000626959 0.000770515 +Mm Hs DHCR7 Leydig cells SLOS 0.018 7-dehydrocholesterol reductase protein-coding gene NA Mesoderm Reproductive 1.0 0.181818 0.015674 0.0152819 +Mm Hs CALB2 Leydig cells CAL2 0.03 calbindin 2 protein-coding gene NA Mesoderm Reproductive 1.0 0.0 0.00219436 0.0374984 +Mm Hs CYP17A1 Leydig cells P450C17|CPT7|S17AH|CYP17 0.001 cytochrome P450 family 17 subfamily A member 1 protein-coding gene 1 Mesoderm Reproductive 1.0 0.636364 0.00125392 0.000642096 +Mm Hs CYP11A1 Leydig cells P450SCC|CYP11A 0.005 cytochrome P450 family 11 subfamily A member 1 protein-coding gene 1 Mesoderm Reproductive 1.0 0.818182 0.00344828 0.00494414 +Mm Hs IGF1 Leydig cells IGF1A|IGFI|IGF-I|IGF 0.044 insulin like growth factor 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.181818 0.00282132 0.0542571 +Mm Hs INSL3 Leydig cells RLF|MGC119818|MGC119819|RLNL 0.001 insulin like 3 protein-coding gene 1 Mesoderm Reproductive 1.0 0.545455 0.000940439 0.000192629 +Mm Hs NR5A2 Leydig cells FTZ-F1beta|hB1F|FTZ-F1|hB1F-2|B1F2|LRH1|FTF 0.003 nuclear receptor subfamily 5 group A member 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00031348 0.00372416 +Mm Hs LHCGR Leydig cells LHR|LCGR|LGR2|HHG 0.0 luteinizing hormone/choriogonadotropin receptor protein-coding gene 1 Mesoderm Reproductive 1.0 0.272727 0.0 0.000321048 +Mm Hs MLANA Leydig cells NA 0.002 melan-A protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.00166945 +Mm Hs RLN1 Leydig cells NA 0.0 relaxin 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Hs RLN2 Leydig cells RLXH2|bA12D24.1.1|bA12D24.1.2 0.001 relaxin 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00658307 0.0 +Mm Hs RLN3 Leydig cells ZINS4|RXN3 0.0 relaxin 3 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs TAC1 Leydig cells NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00532915 0.0 +Mm Hs STAR Leydig cells StAR|STARD1 0.001 steroidogenic acute regulatory protein protein-coding gene 1 Mesoderm Reproductive 0.5 0.0 0.0 0.0 +Mm Hs THBS2 Leydig cells TSP2 0.01 thrombospondin 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0031348 0.0 +Mm Hs PTGDS Leydig cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Mesoderm Reproductive 1.0 0.181818 0.0576802 0.0550276 +Mm Hs LCN2 Leydig cells NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.181818 0.0567398 0.041672 +Mm Hs HSD17B3 Leydig cells SDR12C2 0.002 hydroxysteroid 17-beta dehydrogenase 3 protein-coding gene 1 Mesoderm Reproductive 1.0 0.181818 0.00219436 0.0019905 +Mm Hs ASS1 Leydig cells CTLN1|ASS 0.048 argininosuccinate synthase 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.363636 0.0407524 0.0483498 +Mm Hs PRLR Leydig cells NA 0.013 prolactin receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.727273 0.0106583 0.0133556 +Mm REN1 Leydig cells NA 0.0 renin 1 structural protein coding gene NA Mesoderm Reproductive NA NA NA NA +Mm AKR1CL Leydig cells NA 0.005 aldo-keto reductase family 1, member C-like protein coding gene NA Mesoderm Reproductive 0.0 1.0 0.0 0.00545781 +Mm Hs CYP26B1 Leydig cells P450RAI-2 0.005 cytochrome P450 family 26 subfamily B member 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.454545 0.00125392 0.0053936 +Mm Hs IGF2 Leydig cells FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.046395 0.000898934 +Mm Hs IGFBP5 Leydig cells NA 0.075 insulin like growth factor binding protein 5 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.09279 0.0701169 +Mm Hs CFD Leydig cells ADN|DF|PFD 0.018 complement factor D protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0987461 0.00115577 +Mm Hs DLK1 Leydig cells FA1|pG2|Pref-1|ZOG|Delta1 0.055 delta like non-canonical Notch ligand 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.272727 0.0460815 0.0578528 +Mm Hs IGFBP3 Leydig cells IBP3|BP-53 0.031 insulin like growth factor binding protein 3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0592477 0.0256196 +Mm Hs INHBA Leydig cells NA 0.013 inhibin subunit beta A protein-coding gene 1 Mesoderm Reproductive 0.0 0.636364 0.00815047 0.0129061 +Mm Hs VIT Leydig cells NA 0.005 vitrin protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000626959 0.0 +Mm Hs ALDH1A3 Leydig cells RALDH3|ALDH6 0.008 aldehyde dehydrogenase 1 family member A3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0347962 0.00327469 +Mm Hs NOS1 Leydig cells nNOS 0.004 nitric oxide synthase 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0040452 +Mm Hs EDNRA Leydig cells ET-A|ETA-R|hET-AR 0.013 endothelin receptor type A protein-coding gene 1 Mesoderm Reproductive 0.0 0.0909091 0.0100313 0.014704 +Mm Hs SMOC2 Leydig cells SMAP2 0.026 SPARC related modular calcium binding 2 protein-coding gene 1 Mesoderm Reproductive 1.0 0.0 0.0172414 0.0 +Mm Hs ADAM21 Leydig cells ADAM31 0.001 ADAM metallopeptidase domain 21 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00344828 0.000192629 +Mm Hs ESRRG Leydig cells NR3B3|ERRg|ERR-gamma 0.002 estrogen related receptor gamma protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00438871 0.0019905 +Mm Hs GPRC6A Leydig cells bA86F4.3 0.0 G protein-coupled receptor class C group 6 member A protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs GJA1 Leydig cells CX43|ODOD|SDTY3|ODDD|GJAL 0.1 gap junction protein alpha 1 protein-coding gene 1 Mesoderm Reproductive 1.0 0.454545 0.0626959 0.106909 +Mm Hs GAS6 Leydig cells AXSF|FLJ34709|DKFZp666G247|AXLLG 0.1 growth arrest specific 6 protein-coding gene 1 Mesoderm Reproductive 0.0 0.727273 0.0435737 0.114165 +Mm Hs SULT1E1 Leydig cells STE 0.002 sulfotransferase family 1E member 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00595611 0.0 +Mm Hs CYP19A1 Leydig cells ARO|P-450AROM|CPV1|ARO1|CYAR|aromatase|CYP19 0.0 cytochrome P450 family 19 subfamily A member 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00219436 0.0 +Mm Hs PLAUR Leydig cells URKR|UPAR|CD87 0.052 plasminogen activator, urokinase receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.10721 0.0393605 +Mm Hs FABP9 Leydig cells PERF|T-FABP|PERF15 0.008 fatty acid binding protein 9 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0909091 0.0 0.00988828 +Mm Hs CLDN16 Loop of Henle cells PCLN1|HOMG3 0.0 claudin 16 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs CLDN8 Loop of Henle cells NA 0.004 claudin 8 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.000626763 0.0044915 +Mm Hs UMOD Loop of Henle cells NA 0.0 uromodulin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs FABP4 Loop of Henle cells A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0103416 0.0332371 +Mm Hs AQP1 Loop of Henle cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0178627 0.0424767 +Mm Hs CLDN10 Loop of Henle cells OSP-L|CPETRL3 0.028 claudin 10 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.023817 0.0302214 +Mm Hs CLDN19 Loop of Henle cells NA 0.001 claudin 19 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626763 0.0008983 +Mm Hs SLC12A1 Loop of Henle cells NKCC2 0.001 solute carrier family 12 member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626763 0.0 +Mm Hs DEFB1 Loop of Henle cells HBD-1|DEFB-1|DEFB101|HBD1|BD1|MGC51822 0.009 defensin beta 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0260107 0.00532563 +Mm Hs CLCNKA Loop of Henle cells hClC-Ka 0.0 chloride voltage-gated channel Ka protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00044915 +Mm Hs TRPM7 Loop of Henle cells CHAK1|LTRPC7|TRP-PLIK 0.031 transient receptor potential cation channel subfamily M member 7 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00595425 0.0 +Mm Hs CDH6 Loop of Henle cells NA 0.01 cadherin 6 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0184895 0.0078922 +Mm Hs LCN2 Loop of Henle cells NGAL|24p3 0.043 lipocalin 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.056722 0.0417709 +Mm Hs DKK1 Loop of Henle cells SK|DKK-1 0.006 dickkopf WNT signaling pathway inhibitor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0247571 0.00141161 +Mm Hs DACH1 Loop of Henle cells DACH 0.013 dachshund family transcription factor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0275776 0.0111646 +Mm Hs SLC12A3 Loop of Henle cells NCCT 0.001 solute carrier family 12 member 3 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC11A2 Loop of Henle cells DCT1|NRAMP2 0.007 solute carrier family 11 member 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00658101 0.0 +Mm Hs ARVCF Loop of Henle cells NA 0.005 ARVCF, delta catenin family member protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.00603144 +Mm Hs RGS5 Loop of Henle cells NA 0.043 regulator of G protein signaling 5 protein-coding gene 1 Mesoderm Kidney NA NA NA NA +Mm Hs COX4I2 Loop of Henle cells COXIV-2|COX4B|dJ857M17.2|COX4-2|COX4L2 0.018 cytochrome c oxidase subunit 4I2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00720777 0.0213025 +Mm Hs CYP4B1 Loop of Henle cells NA 0.018 cytochrome P450 family 4 subfamily B member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0128486 0.019121 +Mm Hs PARVB Loop of Henle cells CGI-56 0.036 parvin beta protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.050141 0.0334937 +Mm Hs SH3RF2 Loop of Henle cells FLJ23654|RNF158|Hepp1|POSHER|PPP1R39 0.008 SH3 domain containing ring finger 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0250705 0.0 +Mm Hs HEY2 Loop of Henle cells bHLHb32|HERP1|HESR2 0.004 hes related family bHLH transcription factor with YRPW motif 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0150423 0.00153994 +Mm Hs NKAIN4 Loop of Henle cells bA261N11.2|FAM77A|C20orf58 0.036 sodium/potassium transporting ATPase interacting 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00908806 0.0420918 +Mm Hs ADAMTS5 Loop of Henle cells ADMP-2|ADAMTS11 0.016 ADAM metallopeptidase with thrombospondin type 1 motif 5 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0144155 0.016811 +Mm Hs CXCL1 Loop of Henle cells SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0454403 0.0305422 +Mm Hs GEM Loop of Henle cells NA 0.038 GTP binding protein overexpressed in skeletal muscle protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0360389 0.0395252 +Mm Hs FGA Loop of Henle cells NA 0.005 fibrinogen alpha chain protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.017236 0.00237408 +Mm Hs PLA2G7 Loop of Henle cells LDL-PLA2 0.048 phospholipase A2 group VII protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0115951 0.0564004 +Mm Hs THBS1 Loop of Henle cells TSP1|THBS|TSP|THBS-1|TSP-1 0.04 thrombospondin 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0517079 0.0 +Mm Hs ENC1 Loop of Henle cells PIG10|ENC-1|TP53I10|KLHL37|NRPB 0.073 ectodermal-neural cortex 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0200564 0.0854026 +Mm Hs SPSB1 Loop of Henle cells SSB-1 0.006 splA/ryanodine receptor domain and SOCS box containing 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00282043 0.0 +Mm Hs ARID5A Loop of Henle cells MRF-1|RP11-363D14 0.017 AT-rich interaction domain 5A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0253839 0.0146295 +Mm Hs CD40 Loop of Henle cells Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.013162 0.0108438 +Mm Hs SLC14A2 Loop of Henle cells HUT2 0.005 solute carrier family 14 member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs NRGN Loop of Henle cells NA 0.031 neurogranin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0109683 0.0345204 +Mm Hs RNF182 Loop of Henle cells MGC33993 0.03 ring finger protein 182 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313381 0.0 +Mm Hs PCSK9 Loop of Henle cells NARC-1|FH3|HCHOLA3 0.005 proprotein convertase subtilisin/kexin type 9 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313381 0.00590311 +Mm Hs DRAM1 Loop of Henle cells FLJ11259|DRAM 0.012 DNA damage regulated autophagy modulator 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0166092 0.0108438 +Mm Hs ARC Loop of Henle cells KIAA0278|Arg3.1 0.005 activity regulated cytoskeleton associated protein protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00376058 0.00571062 +Mm Hs NEK6 Loop of Henle cells SID6-1512 0.027 NIMA related kinase 6 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0272642 0.0238691 +Mm Hs CDKN1C Loop of Henle cells P57|BWCR|BWS 0.097 cyclin dependent kinase inhibitor 1C protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0470072 0.108566 +Mm Hs CALCRL Loop of Henle cells CGRPR|CRLR 0.017 calcitonin receptor like receptor protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0247571 0.0160411 +Mm Hs SMARCD3 Loop of Henle cells BAF60C|CRACD3 0.004 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.017236 0.0 +Mm Hs KCNT1 Loop of Henle cells KCa4.1|KIAA1422|SLACK|Slo2.2 0.002 potassium sodium-activated channel subfamily T member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00205326 +Mm Hs PTGS2 Loop of Henle cells NA 0.009 prostaglandin-endoperoxide synthase 2 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0134754 0.00840552 +Mm Hs IRX2 Loop of Henle cells NA 0.012 iroquois homeobox 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00626763 0.0131537 +Mm Hs PPP1R1B Loop of Henle cells DARPP-32|FLJ20940 0.026 protein phosphatase 1 regulatory inhibitor subunit 1B protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0162958 0.0285531 +Mm Hs LIPG Loop of Henle cells EDL 0.003 lipase G, endothelial type protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00188029 0.00327238 +Mm Hs TNNI1 Loop of Henle cells NA 0.009 troponin I1, slow skeletal type protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00908806 0.0 +Mm Hs LRRC66 Loop of Henle cells NA 0.0 leucine rich repeat containing 66 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00044915 +Mm Hs IGF1 Loop of Henle cells IGF1A|IGFI|IGF-I|IGF 0.044 insulin like growth factor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00282043 0.0543471 +Mm Hs FGFR2 Luminal epithelial cells CEK3|TK14|TK25|ECT1|K-SAM|CD332|KGFR|BEK|JWS 0.034 fibroblast growth factor receptor 2 protein-coding gene 1 Ectoderm Mammary gland 0.0 1.0 0.0157381 0.0379527 +Mm Hs FGG Luminal epithelial cells NA 0.007 fibrinogen gamma chain protein-coding gene 1 Ectoderm Mammary gland 0.0 0.769231 0.01322 0.00526586 +Mm Hs KRT18 Luminal epithelial cells NA 0.126 keratin 18 protein-coding gene 1 Ectoderm Mammary gland 0.8 1.0 0.235127 0.0920241 +Hs ANKRD30A Luminal epithelial cells NY-BR-1 0.001 ankyrin repeat domain 30A protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00409191 0.0 +Mm Hs SLPI Luminal epithelial cells HUSI-I|BLPI|HUSI|WAP4|WFDC4 0.048 secretory leukocyte peptidase inhibitor protein-coding gene 1 Ectoderm Mammary gland 0.866667 0.0 0.0912811 0.0 +Mm Hs PROM1 Luminal epithelial cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene 1 Ectoderm Mammary gland 0.0 0.769231 0.00723953 0.0235679 +Mm Hs KRT19 Luminal epithelial cells K19|CK19|K1CS|MGC15366 0.088 keratin 19 protein-coding gene 1 Ectoderm Mammary gland 0.666667 1.0 0.168398 0.0646674 +Mm Hs SYTL2 Luminal epithelial cells FLJ20163|FLJ21219|KIAA1597|exophilin-4|CHR11SYT|SLP2|SGA72M|MGC102768|PPP1R151 0.019 synaptotagmin like 2 protein-coding gene 1 Ectoderm Mammary gland 0.0666667 0.0 0.0050362 0.0 +Mm Hs CD74 Luminal epithelial cells DHLAG 0.169 CD74 molecule protein-coding gene 1 Ectoderm Mammary gland 0.733333 0.0769231 0.361977 0.125225 +Mm Hs AGR2 Luminal epithelial cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene 1 Ectoderm Mammary gland 0.933333 0.0 0.0692477 0.0125225 +Mm Hs LTF Luminal epithelial cells HLF2 0.016 lactotransferrin protein-coding gene 1 Ectoderm Mammary gland 0.0666667 0.0 0.00598048 0.0183663 +Mm Hs SAA2 Luminal epithelial cells NA 0.006 serum amyloid A2 protein-coding gene 1 Ectoderm Mammary gland 0.266667 0.0 0.037142 0.0 +Mm Hs KRT23 Luminal epithelial cells K23|DKFZP434G032|HAIK1|CK23|MGC26158 0.014 keratin 23 protein-coding gene 1 Ectoderm Mammary gland 0.333333 0.0 0.0563425 0.00552273 +Hs SERPINB4 Luminal epithelial cells PI11|LEUPIN|SCCA-2|SCCA2 0.001 serpin family B member 4 protein-coding gene 1 Ectoderm Mammary gland 0.466667 0.0 0.00377715 0.0 +Hs SERPINB3 Luminal epithelial cells T4-A|HsT1196|SCC 0.001 serpin family B member 3 protein-coding gene 1 Ectoderm Mammary gland 0.533333 0.0 0.00377715 0.0 +Mm Hs WFDC2 Luminal epithelial cells HE4|WAP5|dJ461P17.6|EDDM4 0.056 WAP four-disulfide core domain 2 protein-coding gene 1 Ectoderm Mammary gland 0.733333 0.0 0.0912811 0.0 +Mm Hs LCN2 Luminal epithelial cells NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Ectoderm Mammary gland 0.8 0.153846 0.0531948 0.0416774 +Mm Hs BTG1 Luminal epithelial cells APRO2 0.333 BTG anti-proliferation factor 1 protein-coding gene 1 Ectoderm Mammary gland 0.866667 1.0 0.666667 0.257963 +Mm Hs CLDN4 Luminal epithelial cells CPE-R|WBSCR8|hCPE-R|CPETR|CPETR1 0.047 claudin 4 protein-coding gene 1 Ectoderm Mammary gland 0.8 1.0 0.125275 0.0278705 +Mm Hs ANXA1 Luminal epithelial cells ANX1|LPC1 0.161 annexin A1 protein-coding gene 1 Ectoderm Mammary gland 0.8 1.0 0.357885 0.118289 +Mm Hs HMGA1 Luminal epithelial cells HMGIY 0.084 high mobility group AT-hook 1 protein-coding gene 1 Ectoderm Mammary gland 0.733333 0.153846 0.292729 0.0269715 +Mm Hs STC2 Luminal epithelial cells STC-2 0.01 stanniocalcin 2 protein-coding gene 1 Ectoderm Mammary gland 0.0666667 0.0 0.0122757 0.0 +Mm Hs AREG Luminal epithelial cells SDGF|AREGB 0.031 amphiregulin protein-coding gene 1 Ectoderm Mammary gland 0.2 1.0 0.100094 0.0136142 +Mm Hs TNFSF10 Luminal epithelial cells TRAIL|Apo-2L|TL2|CD253 0.014 TNF superfamily member 10 protein-coding gene 1 Ectoderm Mammary gland 0.6 0.0 0.0620082 0.0 +Hs SERPINA1 Luminal epithelial cells AAT|A1A|PI1|alpha-1-antitrypsin|A1AT|alpha1AT|PI 0.016 serpin family A member 1 protein-coding gene 1 Ectoderm Mammary gland 0.0666667 0.0 0.0853006 0.0 +Mm Hs PIP Luminal epithelial cells GCDFP-15|GCDFP15|GPIP4 0.001 prolactin induced protein protein-coding gene 1 Ectoderm Mammary gland 0.266667 0.0 0.000629525 0.00147701 +Mm Hs ATP7B Luminal epithelial cells WND 0.002 ATPase copper transporting beta protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00188857 0.00269715 +Mm Hs HIF1A Luminal epithelial cells MOP1|HIF-1alpha|PASD8|HIF1|bHLHe78 0.089 hypoxia inducible factor 1 subunit alpha protein-coding gene 1 Ectoderm Mammary gland 0.533333 0.769231 0.0997797 0.0850886 +Mm Hs FGFR4 Luminal epithelial cells JTK2|CD334 0.003 fibroblast growth factor receptor 4 protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00346239 0.00211919 +Mm Hs DDR1 Luminal epithelial cells RTK6|CD167|NTRK4|PTK3A|EDDR1 0.051 discoidin domain receptor tyrosine kinase 1 protein-coding gene 1 Ectoderm Mammary gland 0.466667 0.230769 0.0431224 0.0547136 +Mm Hs CEBPD Luminal epithelial cells CRP3|CELF|C/EBP-delta|NF-IL6-beta 0.122 CCAAT enhancer binding protein delta protein-coding gene 1 Ectoderm Mammary gland 0.866667 0.307692 0.182562 0.108464 +Mm Hs PGR Luminal epithelial cells NR3C3 0.003 progesterone receptor protein-coding gene 1 Ectoderm Mammary gland 0.0 1.0 0.00661001 0.0010917 +Mm Hs KRT8 Luminal epithelial cells K8|CK8|CYK8|K2C8|KO 0.12 keratin 8 protein-coding gene 1 Ectoderm Mammary gland 0.933333 1.0 0.207743 0.0923452 +Mm Hs UXT Luminal epithelial cells ART-27|STAP1 0.004 ubiquitously expressed prefoldin like chaperone protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00849858 0.0 +Mm Hs PTH1R Luminal epithelial cells PTHR1 0.019 parathyroid hormone 1 receptor protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.0050362 0.0234395 +Mm Hs CD9 Luminal epithelial cells BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Ectoderm Mammary gland 0.933333 1.0 0.267863 0.365656 +Mm Hs AR Luminal epithelial cells AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00188857 0.0159902 +Mm Hs AQP3 Luminal epithelial cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Ectoderm Mammary gland 0.866667 0.461538 0.0673591 0.0155407 +Mm Hs ATP2C2 Luminal epithelial cells KIAA0703|SPCA2 0.001 ATPase secretory pathway Ca2+ transporting 2 protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00440667 0.00102749 +Mm Hs WNT5A Luminal epithelial cells hWNT5A 0.015 Wnt family member 5A protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.00818382 0.0 +Mm Hs SLC12A2 Luminal epithelial cells NKCC1|BSC|BSC2|PPP1R141 0.074 solute carrier family 12 member 2 protein-coding gene 1 Ectoderm Mammary gland 0.0666667 0.0 0.0500472 0.0 +Mm Hs ESR1 Luminal epithelial cells NR3A1|Era|ER-alpha|ESR 0.004 estrogen receptor 1 protein-coding gene 1 Ectoderm Mammary gland 0.0 0.538462 0.000944287 0.00417416 +Mm Hs AQP5 Luminal epithelial cells NA 0.018 aquaporin 5 protein-coding gene 1 Ectoderm Mammary gland 0.4 1.0 0.0402896 0.0131647 +Mm Hs RUNX1 Luminal epithelial cells PEBP2A2|AMLCR1|AML1|CBFA2 0.054 runt related transcription factor 1 protein-coding gene 1 Ectoderm Mammary gland 0.133333 0.0 0.0308467 0.0 +Mm Hs CDH1 Luminal epithelial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Ectoderm Mammary gland 0.533333 1.0 0.0393453 0.0564475 +Mm Hs MUC1 Luminal epithelial cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Ectoderm Mammary gland 0.666667 0.0 0.0299024 0.0125225 +Mm Hs ANPEP Luminal epithelial cells gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Ectoderm Mammary gland 0.0 0.0 0.0129053 0.0168893 +Hs KLK3 Luminal epithelial cells NA 0.002 kallikrein related peptidase 3 protein-coding gene 1 Ectoderm Mammary gland 0.266667 0.0 0.00944287 0.0 +Mm Hs AKT1 Luteal cells RAC|PKB|PRKBA|AKT 0.055 AKT serine/threonine kinase 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0093985 0.0655243 +Mm Hs LHCGR Luteal cells LHR|LCGR|LGR2|HHG 0.0 luteinizing hormone/choriogonadotropin receptor protein-coding gene 1 Mesoderm Reproductive 0.0 1.0 0.000626566 0.000320883 +Mm Hs HSD3B1 Luteal cells SDR11E1|HSDB3|HSD3B 0.001 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.000626566 0.00115518 +Mm Hs CYP11A1 Luteal cells P450SCC|CYP11A 0.005 cytochrome P450 family 11 subfamily A member 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.00407268 0.00532666 +Mm Hs EPHX2 Luteal cells NA 0.009 epoxide hydrolase 2 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.0056391 0.00994738 +Mm Hs SFRP4 Luteal cells frpHE|FRP-4|FRPHE|FRZB-2 0.006 secreted frizzled related protein 4 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00720551 0.0 +Mm Hs PLIN5 Luteal cells LSDP5|LSDA5|OXPAT|MLDP 0.001 perilipin 5 protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.000626566 0.000962649 +Mm Hs BHMT Luteal cells BHMT1 0.003 betaine--homocysteine S-methyltransferase protein-coding gene NA Mesoderm Reproductive 0.0 0.666667 0.00219298 0.00333718 +Mm Hs PGAM1 Luteal cells PGAMA 0.037 phosphoglycerate mutase 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.0842732 0.0245155 +Mm Hs CHKA Luteal cells CKI 0.019 choline kinase alpha protein-coding gene NA Mesoderm Reproductive 0.0 0.666667 0.0225564 0.0191888 +Mm Hs ADAMTS1 Luteal cells C3-C5|METH1|KIAA1346 0.053 ADAM metallopeptidase with thrombospondin type 1 motif 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.666667 0.0560777 0.0542934 +Mm Hs SLC16A2 Luteal cells XPCT|MCT8|DXS128|AHDS|MRX22 0.023 solute carrier family 16 member 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00344612 0.0 +Mm Hs PMPCB Luteal cells MPPB|MPPP52 0.062 peptidase, mitochondrial processing beta subunit protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.0946115 0.0517905 +Mm Hs SDC1 Luteal cells CD138|syndecan|SYND1|SDC 0.046 syndecan 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0463659 0.0 +Mm Hs BCAT1 Luteal cells BCT1 0.024 branched chain amino acid transaminase 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.056391 0.0171993 +Mm Hs RORA Luteal cells RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0140977 0.0 +Mm Hs AIF1L Luteal cells IBA2|FLJ12783|C9orf58 0.01 allograft inflammatory factor 1 like protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.0222431 0.00673854 +Mm Hs DHCR7 Luteal cells SLOS 0.018 7-dehydrocholesterol reductase protein-coding gene NA Mesoderm Reproductive 0.0 0.333333 0.0162907 0.0153382 +Mm Hs EPDR1 Luteal cells MERP-1|MERP1|UCC1|EPDR 0.022 ependymin related 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.00657895 0.0263124 +Mm Hs AVPI1 Luteal cells VIP32|PP5395|VIT32 0.053 arginine vasopressin induced 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.666667 0.0266291 0.0589141 +Mm Hs GAMT Luteal cells PIG2|TP53I2 0.051 guanidinoacetate N-methyltransferase protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.0661028 0.0456937 +Mm Hs PRLR Luteal cells NA 0.013 prolactin receptor protein-coding gene 1 Mesoderm Reproductive 0.0 1.0 0.0106516 0.0136696 +Mm Hs TMEM86A Luteal cells FLJ90119 0.018 transmembrane protein 86A protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00093985 0.0 +Mm Hs CITED4 Luteal cells NA 0.01 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.0159774 0.00949814 +Mm DYNLT1A Luteal cells NA 0.023 dynein light chain Tctex-type 1A protein coding gene NA Mesoderm Reproductive 0.0 0.666667 0.0 0.0282377 +Mm Hs GAPDH Luteal cells GAPD 0.052 glyceraldehyde-3-phosphate dehydrogenase protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.10589 0.0320241 +Mm Hs FKBP5 Luteal cells FKBP51|FKBP54|Ptg-10 0.018 FK506 binding protein 5 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.0303885 0.0146323 +Mm Hs ME1 Luteal cells NA 0.031 malic enzyme 1 protein-coding gene NA Mesoderm Reproductive 0.0 1.0 0.00626566 0.0365165 +Mm Hs ITGAL Macrophages CD11A 0.013 integrin subunit alpha L protein-coding gene 1 Mesoderm Immune system 0.0 0.141414 0.00408805 0.0106693 +Mm Hs ITGAM Macrophages CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.5 0.29495 0.00125786 0.0216037 +Mm Hs CD14 Macrophages NA 0.051 CD14 molecule protein-coding gene 1 Mesoderm Immune system 0.416667 0.749495 0.0251572 0.0327369 +Mm Hs FUT4 Macrophages FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00072896 +Hs FCGR3A Macrophages CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene 1 Mesoderm Immune system 0.583333 0.0 0.0333333 0.0 +Mm Hs CD33 Macrophages SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Immune system 0.166667 0.179798 0.0119497 0.0119284 +Hs FCGR1A Macrophages CD64|CD64A 0.001 Fc fragment of IgG receptor Ia protein-coding gene 1 Mesoderm Immune system 0.333333 0.0 0.00251572 0.0 +Mm Hs CD80 Macrophages B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0020202 0.0 0.000132538 +Hs LILRB4 Macrophages LIR-5|ILT3|HM18|LIR5|CD85k 0.002 leukocyte immunoglobulin like receptor B4 protein-coding gene 1 Mesoderm Immune system 0.5 0.0 0.0122642 0.0 +Mm Hs CD86 Macrophages B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.25 0.490909 0.0113208 0.014049 +Mm Hs CD163 Macrophages MM130|SCARI1 0.005 CD163 molecule protein-coding gene 1 Mesoderm Immune system 0.25 0.0989899 0.00628931 0.00119284 +Mm Hs CCR5 Macrophages CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.0 0.0123923 +Mm Hs TLR2 Macrophages TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000943396 0.0 +Mm Hs TLR4 Macrophages hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000314465 0.0 +Mm Hs ADGRE1 Macrophages TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene 1 Mesoderm Immune system 0.0 0.654545 0.000628931 0.0212061 +Mm Hs GPR34 Macrophages NA 0.026 G protein-coupled receptor 34 protein-coding gene 1 Mesoderm Immune system 0.333333 0.157576 0.00377358 0.0276342 +Mm CCL9 Macrophages NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Mesoderm Immune system 0.0 0.634343 0.0 0.0247846 +Mm Hs TREM2 Macrophages TREM-2|Trem2a|Trem2b|Trem2c 0.042 triggering receptor expressed on myeloid cells 2 protein-coding gene 1 Mesoderm Immune system 0.75 0.0 0.00377358 0.0 +Mm Hs FABP4 Macrophages A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0484848 0.0100629 0.0327369 +Mm Hs S100A8 Macrophages P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.0795598 0.0 +Mm WFDC17 Macrophages NA 0.037 WAP four-disulfide core domain 17 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs CPM Macrophages NA 0.015 carboxypeptidase M protein-coding gene 1 Mesoderm Immune system 0.416667 0.0 0.013522 0.0159708 +Mm Hs CHIT1 Macrophages CHIT|CHI3 0.003 chitinase 1 protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.000314465 0.00404241 +Mm Hs F13A1 Macrophages F13A 0.021 coagulation factor XIII A chain protein-coding gene 1 Mesoderm Immune system 0.0833333 0.515152 0.00408805 0.00709079 +Mm H2-DMA Macrophages NA 0.065 histocompatibility 2, class II, locus DMa protein coding gene 1 Mesoderm Immune system 0.0 0.6 0.0 0.0600398 +Mm Hs CX3CR1 Macrophages CMKDR1|V28|GPR13|CMKBRL1 0.039 C-X3-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.490909 0.00220126 0.0337309 +Mm Hs CXCL16 Macrophages SR-PSOX|CXCLG16|SRPSOX 0.048 C-X-C motif chemokine ligand 16 protein-coding gene 1 Mesoderm Immune system 0.666667 0.519192 0.063522 0.0299536 +Mm Hs TGFBR1 Macrophages ALK-5|ALK5|TBRI|TBR-i|MSSE|ESS1 0.031 transforming growth factor beta receptor 1 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.0100629 0.0 +Mm Hs SLAMF9 Macrophages CD2F-10|CD84-H1|SF2001 0.01 SLAM family member 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000628931 0.0 +Mm MGL2 Macrophages NA 0.008 macrophage galactose N-acetyl-galactosamine specific lectin 2 protein coding gene 1 Mesoderm Immune system 0.0 0.220202 0.0 0.00284957 +Mm Hs SCIMP Macrophages DTFT5783|UNQ5783|FLJ32580|MGC163426|MGC163428|C17orf87 0.008 SLP adaptor and CSK interacting membrane protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00157233 0.0 +Mm Hs LILRA5 Macrophages ILT11|LIR9|CD85f|LILRB7 0.007 leukocyte immunoglobulin like receptor A5 protein-coding gene 1 Mesoderm Immune system 0.0 0.119192 0.0103774 0.00218688 +Mm CLEC4A2 Macrophages NA 0.034 C-type lectin domain family 4, member a2 protein coding gene 1 Mesoderm Immune system 0.0 0.660606 0.0 0.0212061 +Mm CCL12 Macrophages NA 0.013 chemokine (C-C motif) ligand 12 protein coding gene 1 Mesoderm Immune system 0.0 0.319192 0.0 0.00576541 +Mm Hs CD83 Macrophages HB15|BL11 0.045 CD83 molecule protein-coding gene 1 Mesoderm Immune system 0.666667 0.563636 0.0361635 0.0306163 +Mm Hs C3AR1 Macrophages C3AR|AZ3B 0.022 complement C3a receptor 1 protein-coding gene 1 Mesoderm Immune system 0.25 0.519192 0.00534591 0.010338 +Mm Hs STAB1 Macrophages KIAA0246|STAB-1|FEEL-1|CLEVER-1|FELE-1|FEX1|SCARH2 0.018 stabilin 1 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0 0.00220126 0.0 +Mm Hs MRC1 Macrophages CLEC13D|CD206|bA541I19.1|CLEC13DL|MRC1L1 0.029 mannose receptor C-type 1 protein-coding gene 1 Mesoderm Immune system 0.416667 0.585859 0.0081761 0.0166335 +Mm Hs PARP14 Macrophages KIAA1268|pART8 0.018 poly(ADP-ribose) polymerase family member 14 protein-coding gene 1 Mesoderm Immune system 0.416667 0.050505 0.0421384 0.00861498 +None SEPP1 Macrophages NA 0.029 NA NA 1 Mesoderm Immune system NA NA NA NA +Mm Hs FGD2 Macrophages ZFYVE4 0.017 FYVE, RhoGEF and PH domain containing 2 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.2 0.0113208 0.0124586 +Mm FCGR1 Macrophages NA 0.023 Fc receptor, IgG, high affinity I protein coding gene 1 Mesoderm Immune system 0.0 0.484848 0.0 0.0128562 +Mm Hs RAB7B Macrophages MGC9726|MGC16212 0.013 RAB7B, member RAS oncogene family protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.00125786 0.0 +Mm Hs RBPJ Macrophages IGKJRB|RBPJK|KBF2|RBP-J|CBF1|IGKJRB1|RBPSUH 0.051 recombination signal binding protein for immunoglobulin kappa J region protein-coding gene 1 Mesoderm Immune system 0.666667 0.0 0.163522 0.0 +Mm Hs SLCO2B1 Macrophages OATP-B|OATP2B1|SLC21A9 0.021 solute carrier organic anion transporter family member 2B1 protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.00314465 0.0 +Mm Hs NAAA Macrophages ASAHL 0.025 N-acylethanolamine acid amidase protein-coding gene 1 Mesoderm Immune system 0.0 0.208081 0.0141509 0.0220013 +Mm Hs MARCH1 Macrophages FLJ20668|MARCH-I|RNF171 0.005 membrane associated ring-CH-type finger 1 protein-coding gene 1 Mesoderm Immune system 0.333333 0.020202 0.00471698 0.00384361 +Mm Hs EGLN3 Macrophages PHD3|HIFPH3 0.012 egl-9 family hypoxia inducible factor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.00808081 0.0150943 0.00960901 +Hs JAML Macrophages Gm638|AMICA|AMICA1 0.005 junction adhesion molecule like protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0 0.0289308 0.0 +Mm Hs FGL2 Macrophages pT49|T49 0.03 fibrinogen like 2 protein-coding gene 1 Mesoderm Immune system 0.25 0.177778 0.0349057 0.0231942 +Mm CCL6 Macrophages NA 0.043 chemokine (C-C motif) ligand 6 protein coding gene 1 Mesoderm Immune system 0.0 0.670707 0.0 0.0325381 +Mm Hs GPNMB Macrophages NMB|HGFIN 0.013 glycoprotein nmb protein-coding gene 1 Mesoderm Immune system 0.75 0.0949495 0.027044 0.00662691 +Mm Hs CLEC4D Macrophages Mpcl|CD368|MCL|Dectin-3|CLECSF8 0.007 C-type lectin domain family 4 member D protein-coding gene 1 Mesoderm Immune system 0.0 0.0848485 0.0 0.00510272 +Mm Hs ADAM8 Macrophages CD156|MS2|CD156a 0.01 ADAM metallopeptidase domain 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0929293 0.00566038 0.00801856 +Mm Hs ARL11 Macrophages ARLTS1|FLJ33930 0.004 ADP ribosylation factor like GTPase 11 protein-coding gene 1 Mesoderm Immune system 0.0 0.0727273 0.0 0.0019218 +Mm Hs MMP12 Macrophages HME 0.003 matrix metallopeptidase 12 protein-coding gene 1 Mesoderm Immune system 0.0 0.0707071 0.00188679 0.00072896 +Mm Hs LYVE1 Macrophages LYVE-1|XLKD1 0.012 lymphatic vessel endothelial hyaluronan receptor 1 protein-coding gene 1 Mesoderm Immune system 0.25 0.169697 0.00440252 0.00848244 +Mm Hs PLTP Macrophages BPIFE 0.009 phospholipid transfer protein protein-coding gene 1 Mesoderm Immune system 0.333333 0.0181818 0.0248428 0.00477137 +Mm Hs VSIG4 Macrophages Z39IG 0.005 V-set and immunoglobulin domain containing 4 protein-coding gene 1 Mesoderm Immune system 0.666667 0.0 0.0110063 0.0 +Mm Hs MS4A4A Macrophages CD20L1|MS4A7 0.002 membrane spanning 4-domains A4A protein-coding gene 1 Mesoderm Immune system 0.583333 0.020202 0.00534591 0.000132538 +Hs MS4A6A Macrophages CD20L3|MS4A6 0.007 membrane spanning 4-domains A6A protein-coding gene 1 Mesoderm Immune system 0.333333 0.0 0.0389937 0.0 +Mm Hs FPR1 Macrophages FPR|FMLP 0.003 formyl peptide receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.030303 0.00314465 0.00185553 +Mm Hs CD180 Macrophages RP105|Ly78|LY64 0.012 CD180 molecule protein-coding gene 1 Mesoderm Immune system 0.0833333 0.131313 0.000628931 0.0104042 +Mm RETNLA Macrophages NA 0.004 resistin like alpha protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs GDF15 Macrophages PLAB|MIC-1|PDF|NAG-1|PTGFB 0.014 growth differentiation factor 15 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0181818 0.0566038 0.00258449 +Mm Hs RAB20 Macrophages FLJ20429 0.017 RAB20, member RAS oncogene family protein-coding gene 1 Mesoderm Immune system 0.416667 0.0 0.00628931 0.0 +Mm Hs HFE Macrophages HLA-H 0.017 homeostatic iron regulator protein-coding gene 1 Mesoderm Immune system 0.0 0.436364 0.000314465 0.00775348 +Mm Hs TNF Macrophages TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125786 0.0 +Mm Hs CCR2 Macrophages CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.282828 0.0 0.0178926 +Mm Hs SNX20 Macrophages SLIC-1|SLIC1 0.02 sorting nexin 20 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125786 0.0 +Mm CD209A Macrophages NA 0.003 CD209a antigen protein coding gene 1 Mesoderm Immune system 0.0 0.0525253 0.0 0.00238569 +Mm Hs FMNL1 Macrophages C17orf1B|FMNL 0.022 formin like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.224242 0.00660377 0.0198144 +Mm Hs GPR132 Macrophages G2A 0.009 G protein-coupled receptor 132 protein-coding gene 1 Mesoderm Immune system 0.0 0.0767677 0.000314465 0.00861498 +Mm Hs SLAMF7 Macrophages CRACC|19A|CS1|CD319 0.013 SLAM family member 7 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.00691824 0.0 +Mm Hs NCEH1 Macrophages KIAA1363|NCEH|AADACL1 0.025 neutral cholesterol ester hydrolase 1 protein-coding gene 1 Mesoderm Immune system 0.416667 0.0787879 0.00660377 0.027833 +Mm Hs CCL24 Macrophages Ckb-6|MPIF-2|eotaxin-2|MPIF2|SCYA24 0.011 C-C motif chemokine ligand 24 protein-coding gene 1 Mesoderm Immune system 0.0 0.319192 0.0 0.00390987 +Mm Hs C5AR1 Macrophages C5A|C5AR|CD88|C5R1 0.027 complement C5a receptor 1 protein-coding gene 1 Mesoderm Immune system 0.583333 0.543434 0.0119497 0.0133863 +Mm Hs CD300A Macrophages Irp60|CMRF35H|CMRF-35-H9|IRC1|IRC2|IGSF12 0.023 CD300a molecule protein-coding gene 1 Mesoderm Immune system 0.166667 0.50101 0.00786164 0.0100729 +Mm Hs CXCL2 Macrophages SCYB2|GROb|MIP-2a|MGSA-b|CINC-2a|GRO2 0.041 C-X-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.511111 0.0566038 0.0225977 +Mm Hs CCL7 Macrophages MCP-3|NC28|FIC|MARC|MCP3|SCYA6|SCYA7 0.017 C-C motif chemokine ligand 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.258586 0.000314465 0.0139165 +Mm Hs CCL2 Macrophages MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Immune system 0.5 0.408081 0.0632075 0.0195494 +Mm Hs IL1B Macrophages IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene 1 Mesoderm Immune system 0.166667 0.40202 0.0248428 0.0154407 +Mm Hs IRF5 Macrophages NA 0.028 interferon regulatory factor 5 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.549495 0.0 0.0173625 +Mm Hs AHR Macrophages bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0161616 0.0113208 0.00662691 +Mm Hs MYO1G Macrophages HA-2 0.022 myosin IG protein-coding gene 1 Mesoderm Immune system 0.0 0.226263 0.0238994 0.0129225 +Mm Hs DUSP5 Macrophages HVH3 0.032 dual specificity phosphatase 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0888889 0.0496855 0.0265076 +Mm Hs GPR171 Macrophages H963 0.016 G protein-coupled receptor 171 protein-coding gene 1 Mesoderm Immune system 0.0 0.0161616 0.0207547 0.015507 +Mm Hs CCR7 Macrophages BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.020202 0.0421384 0.0111332 +Mm Hs DNASE1L3 Macrophages DNAS1L3|LSD 0.015 deoxyribonuclease 1 like 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.111111 0.0100629 0.0131213 +Mm Hs CXCL1 Macrophages SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0606061 0.0459119 0.029556 +Mm Hs SAMSN1 Macrophages NASH1|SASH2|SH3D6B|HACS1|SLy2 0.046 SAM domain, SH3 domain and nuclear localization signals 1 protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.0506289 0.0 +Mm Hs NR4A3 Macrophages CSMF|MINOR 0.01 nuclear receptor subfamily 4 group A member 3 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0282828 0.0119497 0.00894632 +Mm Hs CCL22 Macrophages STCP-1|ABCD-1|DC/B-CK|A-152E5.1|MGC34554|SCYA22 0.002 C-C motif chemokine ligand 22 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0181818 0.000314465 0.00159046 +Mm Hs S100A4 Macrophages P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.916667 0.0 0.369182 0.0 +Mm Hs MMP9 Macrophages CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene 1 Mesoderm Immune system 0.416667 0.020202 0.0081761 0.0168986 +Mm Hs HILPDA Macrophages FLJ21076|HIG-2|HIG2|C7orf68 0.033 hypoxia inducible lipid droplet associated protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0666667 0.0141509 0.0297548 +Mm Hs NRP2 Macrophages VEGF165R2 0.04 neuropilin 2 protein-coding gene 1 Mesoderm Immune system 0.666667 0.0848485 0.0330189 0.0399602 +Mm Hs SLC37A2 Macrophages FLJ00171 0.001 solute carrier family 37 member 2 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0 0.0 0.0 +Mm Hs CTSK Macrophages PKND|CTSO2|CTSO|PYCD 0.027 cathepsin K protein-coding gene 1 Mesoderm Immune system 0.0 0.0040404 0.0176101 0.0294897 +Mm Hs CD36 Macrophages SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Immune system 0.666667 0.232323 0.0320755 0.0379722 +Mm Hs LPCAT2 Macrophages FLJ20481|AGPAT11|LysoPAFAT|AYTL1 0.034 lysophosphatidylcholine acyltransferase 2 protein-coding gene 1 Mesoderm Immune system 0.25 0.349495 0.00377358 0.0316766 +Mm Hs HPGDS Macrophages GSTS|H-PGDS|PGD2|GSTS1-1|GSTS1 0.033 hematopoietic prostaglandin D synthase protein-coding gene 1 Mesoderm Immune system 0.333333 0.391919 0.0172956 0.0255136 +Mm Hs IFNAR2 Macrophages IFNABR 0.024 interferon alpha and beta receptor subunit 2 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.234343 0.00503145 0.0196819 +Mm Hs MS4A7 Macrophages CD20L4|CFFM4|MS4A8 0.027 membrane spanning 4-domains A7 protein-coding gene 1 Mesoderm Immune system 0.833333 0.652525 0.0292453 0.00609675 +Mm Hs SLC11A1 Macrophages NRAMP|NRAMP1 0.017 solute carrier family 11 member 1 protein-coding gene 1 Mesoderm Immune system 0.416667 0.0 0.00503145 0.0 +Mm Hs HPGD Macrophages SDR36C1 0.044 15-hydroxyprostaglandin dehydrogenase protein-coding gene 1 Mesoderm Immune system 0.0833333 0.446465 0.0191824 0.0348575 +Mm Hs CCL3 Macrophages G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Mesoderm Immune system 0.166667 0.440404 0.0072327 0.0294897 +Mm Hs CLEC7A Macrophages dectin-1|hDectin-1|CD369|SCARE2|CLECSF12 0.03 C-type lectin domain containing 7A protein-coding gene 1 Mesoderm Immune system 0.75 0.375758 0.0440252 0.0135852 +Mm Hs CD5L Macrophages Spalpha|API6 0.005 CD5 molecule like protein-coding gene 1 Mesoderm Immune system 0.0833333 0.050505 0.000628931 0.00483764 +Mm LILR4B Macrophages NA 0.016 leukocyte immunoglobulin-like receptor, subfamily B, member 4B protein coding gene 1 Mesoderm Immune system 0.0 0.339394 0.0 0.00848244 +Mm Hs CCL5 Macrophages RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.109091 0.0861635 0.0302187 +Mm Hs CYTH4 Macrophages CYT4|cytohesin-4|PSCD4 0.053 cytohesin 4 protein-coding gene 1 Mesoderm Immune system 0.333333 0.692929 0.000943396 0.0430749 +Mm CLEC4N Macrophages NA 0.02 C-type lectin domain family 4, member n protein coding gene 1 Mesoderm Immune system 0.0 0.432323 0.0 0.00994036 +Mm CD209F Macrophages NA 0.003 CD209f antigen protein coding gene 1 Mesoderm Immune system 0.0 0.109091 0.0 0.000198807 +Mm Hs CD3E Macrophages NA 0.041 CD3e molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.00808081 0.1 0.03055 +Mm Hs CD19 Macrophages NA 0.007 CD19 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00786164 0.00629556 +Mm Hs CD74 Macrophages DHLAG 0.169 CD74 molecule protein-coding gene 1 Mesoderm Immune system 0.75 0.721212 0.362264 0.105633 +Mm LYZ1 Macrophages NA 0.031 lysozyme 1 protein coding gene 1 Mesoderm Immune system 0.0 0.345455 0.0 0.027833 +Mm Hs CSF1R Macrophages C-FMS|CSFR|CD115|FMS 0.064 colony stimulating factor 1 receptor protein-coding gene 1 Mesoderm Immune system 0.5 0.925252 0.0160377 0.0479788 +Mm Hs LGALS3 Macrophages MAC-2|GALIG|LGALS2 0.164 galectin 3 protein-coding gene 1 Mesoderm Immune system 0.583333 0.650505 0.307862 0.111199 +Mm Hs CD68 Macrophages SCARD1|macrosialin|DKFZp686M18236|LAMP4 0.063 CD68 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.923232 0.0 0.0481776 +Mm Hs UCP2 Macrophages SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00503145 0.0 +Mm Hs TREML4 Macrophages TLT4 0.003 triggering receptor expressed on myeloid cells like 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs FGR Macrophages c-fgr|p55c-fgr|SRC2 0.013 FGR proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.416667 0.175758 0.0204403 0.0064281 +Mm Hs CYBB Macrophages GP91-PHOX|NOX2|CGD 0.059 cytochrome b-245 beta chain protein-coding gene 1 Mesoderm Immune system 0.916667 0.763636 0.0342767 0.0406229 +Mm Hs CD200 Macrophages MRC|OX-2 0.111 CD200 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0161616 0.022956 0.138569 +Mm Hs CD200R1 Macrophages HCRTR2|CD200R|MOX2R 0.002 CD200 receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0444444 0.0 0.00178926 +Mm Hs GATA6 Macrophages NA 0.019 GATA binding protein 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0040404 0.00471698 0.02167 +Mm H2-AB1 Macrophages NA 0.087 histocompatibility 2, class II antigen A, beta 1 protein coding gene 1 Mesoderm Immune system 0.0 0.612121 0.0 0.0872101 +Mm H2-EB1 Macrophages NA 0.066 histocompatibility 2, class II antigen E beta protein coding gene 1 Mesoderm Immune system 0.0 0.547475 0.0 0.0640159 +Mm IL4RA Macrophages NA 0.013 interleukin 4 receptor, alpha protein coding gene 1 Mesoderm Immune system 0.0 0.163636 0.0 0.012061 +Mm Hs ITGAX Macrophages CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.583333 0.0626263 0.0141509 0.00337972 +Mm LY6C1 Macrophages NA 0.054 lymphocyte antigen 6 complex, locus C1 protein coding gene 1 Mesoderm Immune system 0.0 0.0343434 0.0 0.0676607 +Mm Hs PPARG Macrophages PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0040404 0.0106918 0.00463883 +Mm SIGLECF Macrophages NA 0.002 sialic acid binding Ig-like lectin F protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs TYROBP Macrophages DAP12|PLO-SL|KARAP|PLOSL 0.149 TYRO protein tyrosine kinase binding protein protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.139623 0.0 +Mm Hs RGS1 Macrophages 1R20|IR20|BL34|IER1 0.049 regulator of G protein signaling 1 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0 0.0638365 0.0 +Mm Hs DAB2 Macrophages DOC-2 0.068 DAB2, clathrin adaptor protein protein-coding gene 1 Mesoderm Immune system 0.75 0.723232 0.045283 0.0525514 +Mm Hs P2RY6 Macrophages P2Y6 0.018 pyrimidinergic receptor P2Y6 protein-coding gene 1 Mesoderm Immune system 0.0 0.436364 0.00283019 0.0083499 +Mm Hs MAF Macrophages c-MAF 0.072 MAF bZIP transcription factor protein-coding gene 1 Mesoderm Immune system 0.833333 0.533333 0.0336478 0.0675282 +Mm LYZ2 Macrophages NA 0.124 lysozyme 2 protein coding gene 1 Mesoderm Immune system 0.0 0.989899 0.0 0.121074 +Mm Hs AIF1 Macrophages IRT-1|AIF-1|Em:AF129756.17|IBA1 0.085 allograft inflammatory factor 1 protein-coding gene 1 Mesoderm Immune system 0.916667 0.826263 0.127987 0.0518224 +Mm Hs CLEC10A Macrophages HML2|HML|CD301|CLECSF14 0.01 C-type lectin domain containing 10A protein-coding gene 1 Mesoderm Immune system 0.0 0.20404 0.0119497 0.00331345 +Mm ADGRE4 Macrophages NA 0.004 adhesion G protein-coupled receptor E4 protein coding gene 1 Mesoderm Immune system 0.0 0.0747475 0.0 0.00271703 +Mm Hs ADGRE5 Macrophages TM7LN1|CD97 0.04 adhesion G protein-coupled receptor E5 protein-coding gene 1 Mesoderm Immune system 0.25 0.307071 0.0380503 0.0320742 +Mm CLEC4A3 Macrophages NA 0.019 C-type lectin domain family 4, member a3 protein coding gene 1 Mesoderm Immune system 0.0 0.543434 0.0 0.00649437 +Mm CLEC4A1 Macrophages NA 0.017 C-type lectin domain family 4, member a1 protein coding gene 1 Mesoderm Immune system 0.0 0.521212 0.0 0.00390987 +Mm Hs SLC15A3 Macrophages PHT2|hPTR3 0.016 solute carrier family 15 member 3 protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.00660377 0.0 +Mm AKR1B3 Macrophages NA 0.025 aldo-keto reductase family 1, member B3 (aldose reductase) protein coding gene 1 Mesoderm Immune system 0.0 0.0686869 0.0 0.0286945 +Mm Hs CYP27A1 Macrophages CTX|CYP27 0.006 cytochrome P450 family 27 subfamily A member 1 protein-coding gene 1 Mesoderm Immune system 0.5 0.00808081 0.0132075 0.00377734 +Mm Hs SLC7A7 Macrophages y+LAT-1|LPI 0.007 solute carrier family 7 member 7 protein-coding gene NA Mesoderm Immune system 0.75 0.0 0.0176101 0.0 +Mm Hs RUNX3 Macrophages AML2|PEBP2A3|CBFA3 0.018 runt related transcription factor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0207547 0.0 +Mm Hs SYK Macrophages NA 0.011 spleen associated tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.416667 0.0 0.0091195 0.0 +Mm Hs CSN2 Mammary epithelial cells CASB 0.004 casein beta protein-coding gene 1 Mesoderm Mammary gland 0.0 0.709677 0.0 0.00424328 +Mm CSN1S2A Mammary epithelial cells NA 0.004 casein alpha s2-like A protein coding gene 1 Mesoderm Mammary gland 0.0 0.709677 0.0 0.00398611 +Mm Hs BTN1A1 Mammary epithelial cells BT|BTN 0.001 butyrophilin subfamily 1 member A1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.419355 0.0 0.000450045 +Mm Hs BTN2A2 Mammary epithelial cells BT2.2|BTN2.2 0.0 butyrophilin subfamily 2 member A2 protein-coding gene NA Mesoderm Mammary gland 0.0 0.0 0.0 0.0 +Hs BTN3A1 Mammary epithelial cells BT3.1|BTF5|CD277|BTN3.1 0.0 butyrophilin subfamily 3 member A1 protein-coding gene NA Mesoderm Mammary gland 0.0 0.0 0.000940439 0.0 +Mm Hs MMP14 Mammary epithelial cells MT1-MMP 0.054 matrix metallopeptidase 14 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0967742 0.0354232 0.05677 +Mm Hs TOX3 Mammary epithelial cells CAGF9|TNRC9 0.017 TOX high mobility group box family member 3 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.00376176 0.0 +Mm Hs CDH1 Mammary epithelial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.709677 0.0416928 0.0559342 +Mm Hs FFAR1 Mammary epithelial cells FFA1R|GPR40 0.002 free fatty acid receptor 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.00721003 0.00154301 +Mm Hs PYGO2 Mammary epithelial cells NA 0.002 pygopus family PHD finger 2 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.0 0.00257169 +Mm Hs SERPINB5 Mammary epithelial cells maspin|PI5 0.015 serpin family B member 5 protein-coding gene 1 Mesoderm Mammary gland 0.5 0.0 0.0203762 0.0 +Mm Hs RUNX2 Mammary epithelial cells AML3|PEBP2A1|PEBP2aA1|CCD|CBFA1|CCD1 0.008 runt related transcription factor 2 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.00877743 0.0 +Mm WAP Mammary epithelial cells NA 0.001 whey acidic protein protein coding gene 1 Mesoderm Mammary gland NA NA NA NA +Mm Hs CITED1 Mammary epithelial cells MSG1 0.023 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.129032 0.0159875 0.0243667 +Mm Hs IRF6 Mammary epithelial cells OFC6|VWS|LPS 0.015 interferon regulatory factor 6 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.225806 0.0285266 0.0132442 +Mm Hs SULT1E1 Mammary epithelial cells STE 0.002 sulfotransferase family 1E member 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.00595611 0.0 +Mm Hs KRT14 Mammary epithelial cells EBS3|EBS4 0.019 keratin 14 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.193548 0.0197492 0.0188376 +Mm Hs KDM3A Mammary epithelial cells TSGA|KIAA0742|JHMD2A|JMJD1|JMJD1A 0.006 lysine demethylase 3A protein-coding gene NA Mesoderm Mammary gland 0.0 0.0322581 0.015047 0.0048862 +Mm Hs SLC30A2 Mammary epithelial cells ZNT2 0.001 solute carrier family 30 member 2 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.0 0.0 +Mm Hs PADI2 Mammary epithelial cells KIAA0994|PDI2 0.007 peptidyl arginine deiminase 2 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.00752351 0.00720072 +Mm Hs CLDN1 Mammary epithelial cells SEMP1|ILVASC 0.01 claudin 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.129032 0.0285266 0.00540054 +Mm Hs ABCG2 Mammary epithelial cells EST157481|MXR|BCRP|ABCP|CD338 0.038 ATP binding cassette subfamily G member 2 (Junior blood group) protein-coding gene NA Mesoderm Mammary gland 0.0 0.16129 0.00470219 0.0464832 +Mm Hs PIP Mammary epithelial cells GCDFP-15|GCDFP15|GPIP4 0.001 prolactin induced protein protein-coding gene NA Mesoderm Mammary gland 0.0 0.0322581 0.00188088 0.00141443 +Mm Hs KRT5 Mammary epithelial cells KRT5A|EBS2 0.019 keratin 5 protein-coding gene 1 Mesoderm Mammary gland 1.0 0.0322581 0.0438871 0.0150444 +Mm Hs PRLR Mammary epithelial cells NA 0.013 prolactin receptor protein-coding gene 1 Mesoderm Mammary gland 0.0 0.16129 0.0106583 0.0135656 +Mm Hs CLDN4 Mammary epithelial cells CPE-R|WBSCR8|hCPE-R|CPETR|CPETR1 0.047 claudin 4 protein-coding gene NA Mesoderm Mammary gland 1.0 0.967742 0.1279 0.0268098 +Mm Hs CSN3 Mammary epithelial cells CSN10 0.004 casein kappa protein-coding gene 1 Mesoderm Mammary gland 0.0 0.903226 0.0 0.00385753 +Mm Hs CSN1S1 Mammary epithelial cells CASA 0.003 casein alpha s1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.709677 0.0 0.00295744 +Mm Hs RARRES1 Mammary epithelial cells LXNL 0.01 retinoic acid receptor responder 1 protein-coding gene NA Mesoderm Mammary gland 0.0 0.0 0.0341693 0.0 +Mm Hs KRT17 Mammary epithelial cells PCHC1 0.025 keratin 17 protein-coding gene NA Mesoderm Mammary gland 1.0 0.193548 0.0739812 0.0153658 +Mm Hs NNMT Mammary epithelial cells NA 0.017 nicotinamide N-methyltransferase protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.0605016 0.00790793 +Mm Hs ALDH1A3 Mammary epithelial cells RALDH3|ALDH6 0.008 aldehyde dehydrogenase 1 family member A3 protein-coding gene NA Mesoderm Mammary gland 0.0 0.387097 0.0347962 0.00250739 +Mm Hs SGMS2 Mammary epithelial cells MGC26963|SMS2 0.017 sphingomyelin synthase 2 protein-coding gene NA Mesoderm Mammary gland 0.0 0.0 0.015674 0.0 +Mm Hs PIEZO1 Mammary epithelial cells KIAA0233|FAM38A 0.01 piezo type mechanosensitive ion channel component 1 protein-coding gene NA Mesoderm Mammary gland 0.0 0.354839 0.0163009 0.00758647 +Mm Hs ANO1 Mammary epithelial cells TAOS2|FLJ10261|DOG1|ORAOV2|TMEM16A 0.009 anoctamin 1 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.580645 0.000940439 0.0105439 +Mm Hs WNT5B Mammary epithelial cells NA 0.003 Wnt family member 5B protein-coding gene NA Mesoderm Mammary gland 0.0 0.0 0.00188088 0.0 +Mm Hs NEDD9 Mammary epithelial cells HEF1|CAS-L|CASS2 0.013 neural precursor cell expressed, developmentally down-regulated 9 protein-coding gene NA Mesoderm Mammary gland 0.5 0.290323 0.0219436 0.0112511 +Mm Hs FOXP4 Mammary epithelial cells FLJ40908 0.01 forkhead box P4 protein-coding gene 0 Mesoderm Mammary gland 0.0 0.0967742 0.00219436 0.0117012 +Mm Hs LSR Mammary epithelial cells LISCH7|ILDR3 0.026 lipolysis stimulated lipoprotein receptor protein-coding gene NA Mesoderm Mammary gland 0.0 0.129032 0.0586207 0.0156873 +Mm Hs LIF Mammary epithelial cells CDF|HILDA 0.002 LIF, interleukin 6 family cytokine protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0967742 0.00532915 0.00090009 +Mm Hs KRT19 Mammary epithelial cells K19|CK19|K1CS|MGC15366 0.088 keratin 19 protein-coding gene 1 Mesoderm Mammary gland 1.0 1.0 0.170219 0.0635849 +Mm Hs KRT7 Mammary epithelial cells CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Mesoderm Mammary gland 1.0 0.483871 0.100627 0.0465475 +Mm Hs STAT3 Mammary epithelial cells APRF 0.099 signal transducer and activator of transcription 3 protein-coding gene 1 Mesoderm Mammary gland 0.0 0.0 0.14953 0.0 +Mm Hs KRT8 Mammary epithelial cells K8|CK8|CYK8|K2C8|KO 0.12 keratin 8 protein-coding gene 1 Mesoderm Mammary gland 1.0 1.0 0.210658 0.0912948 +Mm Hs KRT18 Mammary epithelial cells NA 0.126 keratin 18 protein-coding gene 1 Mesoderm Mammary gland 1.0 1.0 0.237304 0.0909734 +Mm WFDC18 Mammary epithelial cells NA 0.007 WAP four-disulfide core domain 18 protein coding gene 1 Mesoderm Mammary gland NA NA NA NA +Mm Hs KIT Mast cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.625 0.921053 0.000942211 0.0163376 +Mm Hs ENPP3 Mast cells PD-IBETA|gp130RB13-6|B10|CD203c|PDNP3 0.002 ectonucleotide pyrophosphatase/phosphodiesterase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0021226 +Mm Hs IL2RA Mast cells IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.125 0.0 0.0197864 0.00675371 +Hs FCER2 Mast cells CLEC4J|CD23|CD23A|FCE2 0.002 Fc fragment of IgE receptor II protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00219849 0.0 +Mm Hs IL17A Mast cells IL-17A|IL-17|CTLA8|IL17 0.0 interleukin 17A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000257284 +Mm Hs CRH Mast cells CRH1 0.001 corticotropin releasing hormone protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000628141 0.00128642 +Mm Hs HSD11B1 Mast cells SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0263158 0.00973618 0.0245063 +Mm Hs CD274 Mast cells B7-H|B7H1|PD-L1|PDL1|B7-H1|PDCD1LG1 0.004 CD274 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00408291 0.00379494 +Mm Hs CXCR2 Mast cells CMKAR2|CD182|IL8RB 0.003 C-X-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00353766 +Mm Hs CXCR4 Mast cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.198807 0.00881199 +Mm Hs CCR3 Mast cells CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00147939 +Mm Hs CCR5 Mast cells CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0183958 +Mm Hs LTC4S Mast cells MGC33147 0.037 leukotriene C4 synthase protein-coding gene 1 Mesoderm Immune system 0.375 0.0 0.00690955 0.0449604 +Mm Hs GPR34 Mast cells NA 0.026 G protein-coupled receptor 34 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00502513 0.0318389 +Mm Hs MGST2 Mast cells MGST-II 0.05 microsomal glutathione S-transferase 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.140075 0.0300379 +Mm Hs ACHE Mast cells YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00471106 0.0196179 +Mm Hs CPA3 Mast cells NA 0.009 carboxypeptidase A3 protein-coding gene 1 Mesoderm Immune system 1.0 1.0 0.00596734 0.00604618 +Mm Hs CPA1 Mast cells CPA 0.006 carboxypeptidase A1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0031407 0.007011 +Mm Hs CMA1 Mast cells NA 0.007 chymase 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.00604618 +Mm Hs HNMT Mast cells NA 0.007 histamine N-methyltransferase protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0254397 0.00218692 +Mm Hs TPSAB1 Mast cells TPSB1|TPS1|TPS2 0.002 tryptase alpha/beta 1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.00439698 0.0 +Mm Hs PTGDS Mast cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CFP Mast cells PFC 0.035 complement factor properdin protein-coding gene NA Mesoderm Immune system 0.0 0.315789 0.03549 0.0340902 +Mm Hs RAB27B Mast cells NA 0.017 RAB27B, member RAS oncogene family protein-coding gene 1 Mesoderm Immune system 0.125 0.0 0.0207286 0.0 +Mm ATP8B5 Mast cells NA 0.001 ATPase, class I, type 8B, member 5 protein coding gene NA Mesoderm Immune system 0.0 0.184211 0.0 0.000707532 +Mm Hs SLA Mast cells SLA1|SLAP-1|hSLAP 0.023 Src like adaptor protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0125628 0.0 +Mm Hs IL1RL1 Mast cells ST2|FIT-1|ST2V|DER4|IL33R 0.007 interleukin 1 receptor like 1 protein-coding gene 1 Mesoderm Immune system 0.5 1.0 0.013505 0.00302309 +Mm CSF2RB2 Mast cells NA 0.003 colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage) protein coding gene NA Mesoderm Immune system 0.0 0.5 0.0 0.00257284 +Mm Hs GNAI1 Mast cells NA 0.05 G protein subunit alpha i1 protein-coding gene 1 Mesoderm Immune system 0.0 0.184211 0.0411432 0.0540297 +Mm Hs CFD Mast cells ADN|DF|PFD 0.018 complement factor D protein-coding gene NA Mesoderm Immune system 0.0 0.0263158 0.0989322 0.00109346 +Mm Hs OSBPL8 Mast cells OSBP10|ORP8|MST120|MSTP120 0.037 oxysterol binding protein like 8 protein-coding gene 1 Mesoderm Immune system 0.125 0.657895 0.117462 0.0151155 +Mm Hs ADORA3 Mast cells NA 0.002 adenosine A3 receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.684211 0.0 0.000964816 +Mm Hs HS3ST1 Mast cells 3OST1 0.019 heparan sulfate-glucosamine 3-sulfotransferase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.447368 0.00910804 0.0201325 +Mm Hs CSF2RB Mast cells IL5RB|CD131|betaGMR|IL3RB 0.018 colony stimulating factor 2 receptor beta common subunit protein-coding gene 1 Mesoderm Immune system 0.0 0.789474 0.00282663 0.0195536 +Mm Hs DAPP1 Mast cells BAM32 0.022 dual adaptor of phosphotyrosine and 3-phosphoinositides 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.447368 0.0160176 0.0206471 +Mm Hs SLC6A4 Mast cells 5-HTT|SERT1|HTT|OCD1 0.002 solute carrier family 6 member 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125628 0.0 +Mm Hs MAOB Mast cells NA 0.009 monoamine oxidase B protein-coding gene 1 Mesoderm Immune system 0.375 0.5 0.00879397 0.0082331 +Mm LILR4B Mast cells NA 0.016 leukocyte immunoglobulin-like receptor, subfamily B, member 4B protein coding gene NA Mesoderm Immune system 0.0 0.552632 0.0 0.0176883 +Mm Hs CSRNP1 Mast cells URAX1|DKFZp566F164|FAM130B|TAIP-3|AXUD1 0.044 cysteine and serine rich nuclear protein 1 protein-coding gene NA Mesoderm Immune system 0.125 0.289474 0.0345477 0.0457966 +Mm Hs CYP11A1 Mast cells P450SCC|CYP11A 0.005 cytochrome P450 family 11 subfamily A member 1 protein-coding gene NA Mesoderm Immune system 0.0 1.0 0.00408291 0.00308741 +Mm Hs RGS1 Mast cells 1R20|IR20|BL34|IER1 0.049 regulator of G protein signaling 1 protein-coding gene NA Mesoderm Immune system 0.875 0.0 0.0618719 0.0 +Mm MRGPRB2 Mast cells NA 0.0 MAS-related GPR, member B2 protein coding gene 1 Mesoderm Immune system 0.0 0.157895 0.0 0.0 +Mm Hs PLEK Mast cells NA 0.051 pleckstrin protein-coding gene NA Mesoderm Immune system 0.0 0.210526 0.0452261 0.052486 +Mm MRGPRB1 Mast cells NA 0.0 MAS-related GPR, member B1 protein coding gene 1 Mesoderm Immune system 0.0 0.131579 0.0 0.0 +Mm Hs HDC Mast cells NA 0.019 histidine decarboxylase protein-coding gene 1 Mesoderm Immune system 0.5 1.0 0.00031407 0.0204541 +Mm MCPT4 Mast cells NA 0.001 mast cell protease 4 protein coding gene 1 Mesoderm Immune system 0.0 0.368421 0.0 6.43211e-05 +Mm Hs TPSB2 Mast cells NA 0.004 tryptase beta 2 (gene/pseudogene) protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.00471106 0.0 +Mm Hs TPH1 Mast cells TPRH|TPH 0.002 tryptophan hydroxylase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125628 0.0 +Mm Hs CD55 Mast cells TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Immune system 0.25 0.684211 0.125628 0.0180742 +Mm CD200R3 Mast cells NA 0.003 CD200 receptor 3 protein coding gene 1 Mesoderm Immune system 0.0 0.815789 0.0 0.00154371 +Mm Hs RGS13 Mast cells NA 0.003 regulator of G protein signaling 13 protein-coding gene 1 Mesoderm Immune system 0.875 0.0 0.00251256 0.0 +Mm Hs TPSG1 Mast cells TMT|PRSS31 0.003 tryptase gamma 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000942211 0.0 +Mm Hs SOCS1 Mast cells SOCS-1|SSI-1|JAB|TIP3|Cish1 0.012 suppressor of cytokine signaling 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0197864 0.0 +Mm Hs BTK Mast cells ATK|XLA|PSCTK1|AGMX1|IMD1 0.008 Bruton tyrosine kinase protein-coding gene NA Mesoderm Immune system 0.125 0.394737 0.00188442 0.00694668 +Mm Hs IL4 Mast cells BSF1|IL-4|BCGF1|BCGF-1|MGC79402 0.002 interleukin 4 protein-coding gene NA Mesoderm Immune system 0.0 0.710526 0.0 0.000964816 +Mm Hs MS4A2 Mast cells MS4A1|FCER1B|APY 0.003 membrane spanning 4-domains A2 protein-coding gene NA Mesoderm Immune system 0.75 0.289474 0.0 0.0024442 +Mm Hs VWA5A Mast cells BCSC-1|LOH11CR2A 0.011 von Willebrand factor A domain containing 5A protein-coding gene 1 Mesoderm Immune system 0.75 0.0 0.00722362 0.0 +Mm Hs FCER1A Mast cells FCE1A 0.004 Fc fragment of IgE receptor Ia protein-coding gene 1 Mesoderm Immune system 0.375 0.105263 0.0175879 0.00141506 +Mm Hs MCEMP1 Mast cells MGC132456|C19orf59 0.022 mast cell expressed membrane protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00188442 0.02605 +Mm Hs MILR1 Mast cells Allergin-1|MCA-32|C17orf60 0.012 mast cell immunoglobulin like receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.131579 0.000942211 0.0123496 +Mm Hs CCL2 Mast cells MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Immune system 0.125 0.105263 0.0646985 0.0317103 +Mm CMA2 Mast cells NA 0.0 chymase 2, mast cell protein coding gene 1 Mesoderm Immune system 0.0 0.210526 0.0 0.000128642 +Mm Hs CREB3L1 Mast cells OASIS 0.015 cAMP responsive element binding protein 3 like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.657895 0.00973618 0.0151798 +Mm Hs EDNRA Mast cells ET-A|ETA-R|hET-AR 0.013 endothelin receptor type A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0100503 0.0147939 +Mm Hs HS6ST2 Mast cells NA 0.02 heparan sulfate 6-O-sulfotransferase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.263158 0.00125628 0.0243777 +Mm Hs KCNE3 Mast cells MiRP2 0.01 potassium voltage-gated channel subfamily E regulatory subunit 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.263158 0.000628141 0.0115778 +Mm MCPT9 Mast cells NA 0.0 mast cell protease 9 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000192963 +Mm Hs MEIS2 Mast cells HsT18361 0.17 Meis homeobox 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.421053 0.0549623 0.200167 +Mm MRGPRA4 Mast cells NA 0.0 MAS-related GPR, member A4 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs MRGPRX2 Mast cells MRGX2 0.0 MAS related GPR family member X2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm OLFR920 Mast cells NA 0.0 olfactory receptor 920 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs PLAU Mast cells URK 0.01 plasminogen activator, urokinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0439699 0.00250852 +Mm Hs ADAMTS9 Mast cells KIAA1312 0.007 ADAM metallopeptidase with thrombospondin type 1 motif 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0260678 0.00360198 +Mm Hs CHST1 Mast cells KSGal6ST 0.032 carbohydrate sulfotransferase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0263158 0.013191 0.0376922 +Mm Hs COBL Mast cells KIAA0633 0.004 cordon-bleu WH2 repeat protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00031407 0.00501704 +Mm Hs CTSG Mast cells CG 0.017 cathepsin G protein-coding gene 1 Mesoderm Immune system 0.125 0.0 0.0128769 0.0169164 +Mm Hs DNM3 Mast cells KIAA0820 0.043 dynamin 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0031407 0.0537724 +Mm Hs FAM198B Mast cells FLJ38155|DKFZp434L142|ENED|C4orf18 0.011 family with sequence similarity 198 member B protein-coding gene 1 Mesoderm Immune system 0.0 0.605263 0.00502513 0.0110632 +Mm Hs GRIK2 Mast cells GluK2|MRT6|GLUR6 0.01 glutamate ionotropic receptor kainate type subunit 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00031407 0.0131215 +Mm Hs HPGDS Mast cells GSTS|H-PGDS|PGD2|GSTS1-1|GSTS1 0.033 hematopoietic prostaglandin D synthase protein-coding gene 1 Mesoderm Immune system 1.0 0.315789 0.0160176 0.0364701 +Mm Hs HS3ST3A1 Mast cells 3OST3A1|30ST3A1 0.001 heparan sulfate-glucosamine 3-sulfotransferase 3A1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00408291 0.000128642 +Mm Hs PAPSS2 Mast cells ATPSK2 0.012 3'-phosphoadenosine 5'-phosphosulfate synthase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.578947 0.0150754 0.0108059 +Mm Hs PCBD1 Mast cells DCOH|PCBD 0.084 pterin-4 alpha-carbinolamine dehydratase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.154523 0.0623271 +Mm Hs PCP4L1 Mast cells IQM1 0.044 Purkinje cell protein 4 like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0263158 0.0 0.0553805 +Mm Hs RNF128 Mast cells FLJ23516|GRAIL 0.024 ring finger protein 128, E3 ubiquitin protein ligase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00157035 0.0 +Mm SERPINB1A Mast cells NA 0.059 serine (or cysteine) peptidase inhibitor, clade B, member 1a protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs SLC29A1 Mast cells ENT1 0.063 solute carrier family 29 member 1 (Augustine blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0188442 0.0 +Mm Hs SLC45A3 Mast cells IPCA-6|prostein|IPCA-2|IPCA-8|PCANAP6|PCANAP2|PCANAP8 0.005 solute carrier family 45 member 3 protein-coding gene 1 Mesoderm Immune system 0.125 0.0 0.00157035 0.0 +Mm Hs STARD13 Mast cells GT650|DLC2|ARHGAP37|LINC00464 0.003 StAR related lipid transfer domain containing 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000942211 0.0 +Mm Hs A4GALT Mast cells A14GALT|Gb3S|P(k) 0.005 alpha 1,4-galactosyltransferase (P blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0141332 0.00302309 +Mm Hs ACER3 Mast cells FLJ11238|APHC|PHCA 0.018 alkaline ceramidase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.342105 0.0201005 0.0175597 +Mm Hs ARMCX3 Mast cells ALEX3|GASP6 0.026 armadillo repeat containing X-linked 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0819724 0.00951952 +Mm Hs ATL2 Mast cells ARL6IP2 0.013 atlastin GTPase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0789474 0.00439698 0.0153084 +Mm Hs BBS10 Mast cells FLJ23560|C12orf58 0.0 Bardet-Biedl syndrome 10 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000450248 +Mm Hs BMPR2 Mast cells BRK-3|T-ALK|BMPR3|BMPR-II|PPH1 0.056 bone morphogenetic protein receptor type 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0263158 0.0216709 0.0658005 +Mm Hs C2 Mast cells NA 0.008 complement C2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00659548 0.00887631 +Mm CAR13 Mast cells NA 0.003 carbonic anhydrase 13 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0036663 +Mm Hs CCDC141 Mast cells FLJ39502|CAMDI 0.019 coiled-coil domain containing 141 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00188442 0.0229626 +Mm Hs CCL7 Mast cells MCP-3|NC28|FIC|MARC|MCP3|SCYA6|SCYA7 0.017 C-C motif chemokine ligand 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0526316 0.00031407 0.0216119 +Mm Hs CDC42BPA Mast cells MRCKA|PK428|FLJ23347|KIAA0451|MRCK 0.035 CDC42 binding protein kinase alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0518216 0.0322249 +Mm Hs CDH9 Mast cells NA 0.001 cadherin 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00160803 +Mm Hs COPZ2 Mast cells MGC23008 0.038 coatomer protein complex subunit zeta 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.184211 0.0207286 0.0428378 +Mm MCPT2 Mast cells NA 0.0 mast cell protease 2 protein coding gene 1 Mesoderm Immune system 0.0 0.105263 0.0 0.0 +Mm ZFP9 Mast cells NA 0.001 zinc finger protein 9 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm ZFP521 Mast cells NA 0.001 zinc finger protein 521 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs ZDHHC13 Mast cells FLJ10852|FLJ10941|HIP14L 0.006 zinc finger DHHC-type containing 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0138191 0.0 +Mm Hs WDR60 Mast cells FLJ10300|FAP163 0.017 WD repeat domain 60 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0562186 0.0 +Mm Hs UNC13B Mast cells hmunc13|Unc13h2|UNC13 0.0 unc-13 homolog B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TRANK1 Mast cells LBA1|KIAA0342 0.013 tetratricopeptide repeat and ankyrin repeat containing 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000628141 0.0 +Mm Hs TIAM2 Mast cells STEF 0.005 T cell lymphoma invasion and metastasis 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00722362 0.0 +Mm Hs TCF7L1 Mast cells TCF3 0.009 transcription factor 7 like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0084799 0.0 +Mm Hs STK32B Mast cells STKG6|YANK2|STK32|HSA250839 0.004 serine/threonine kinase 32B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00722362 0.0 +Mm Hs ST6GALNAC3 Mast cells SIAT7C 0.003 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00628141 0.0 +Mm Hs SOCS2 Mast cells STATI2|SSI2|SOCS-2|SSI-2|CIS2|Cish2 0.095 suppressor of cytokine signaling 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.031407 0.0 +Mm Hs SPRED1 Mast cells FLJ33903|PPP1R147 0.026 sprouty related EVH1 domain containing 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00753769 0.0 +Mm Hs SMPX Mast cells DFNX4|DFN6 0.006 small muscle protein X-linked protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SMARCA1 Mast cells NURF140|SWI|hSNF2L|SNF2L1|SNF2L 0.015 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0414573 0.0 +Mm Hs SLC7A5 Mast cells E16|D16S469E|MPE16 0.043 solute carrier family 7 member 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.031093 0.0 +Mm Hs SLC4A4 Mast cells NBC1|HNBC1|NBC2|pNBC|hhNMC|SLC4A5 0.033 solute carrier family 4 member 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0122487 0.0 +Mm Hs SLC31A2 Mast cells hCTR2|CTR2|COPT2 0.019 solute carrier family 31 member 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SGCE Mast cells DYT11 0.028 sarcoglycan epsilon protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0166457 0.0 +Mm Hs ROR1 Mast cells NTRKR1 0.001 receptor tyrosine kinase like orphan receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00565327 0.0 +Mm Hs RNF180 Mast cells NA 0.017 ring finger protein 180 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000628141 0.0 +Hs RIOK2 Mast cells FLJ11159 0.001 RIO kinase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00376884 0.0 +Mm Hs RBFOX1 Mast cells A2BP1|FOX-1|HRNBP1 0.051 RNA binding fox-1 homolog 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00188442 0.0 +Mm Hs RAPGEF2 Mast cells PDZ-GEF1|RA-GEF|DKFZP586O1422|KIAA0313|PDZGEF1 0.003 Rap guanine nucleotide exchange factor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00251256 0.0 +Mm Hs PDE1C Mast cells Hcam3 0.007 phosphodiesterase 1C protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00565327 0.00746125 +Mm Hs PCDH7 Mast cells BH-Pcdh|PPP1R120 0.042 protocadherin 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0119347 0.0483695 +Mm Hs OPTN Mast cells FIP2|HYPL|FIP-2|TFIIIA-INTP|HIP7|GLC1E 0.025 optineurin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.093907 0.00958384 +Mm OLFR918 Mast cells NA 0.0 olfactory receptor 918 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm OLFR917 Mast cells NA 0.0 olfactory receptor 917 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm OLFR915 Mast cells NA 0.0 olfactory receptor 915 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs OAF Mast cells MGC52117 0.036 out at first homolog protein-coding gene 1 Mesoderm Immune system 0.0 0.578947 0.0285804 0.0364057 +Mm Hs NEO1 Mast cells NGN|HsT17534|IGDCC2|NTN1R2 0.02 neogenin 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00502513 0.0233486 +Mm Hs NDST2 Mast cells NST2 0.001 N-deacetylase and N-sulfotransferase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.447368 0.0 0.000771853 +Mm Hs NCEH1 Mast cells KIAA1363|NCEH|AADACL1 0.025 neutral cholesterol ester hydrolase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00816583 0.0295234 +Mm MT2 Mast cells NA 0.097 metallothionein 2 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.119509 +Mm Hs MRGPRX1 Mast cells MRGX1 0.0 MAS related GPR family member X1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs MLPH Mast cells l1Rk3|l(1)-3Rk|Slac-2a|ln|exophilin-3 0.007 melanophilin protein-coding gene 1 Mesoderm Immune system 0.125 0.0 0.0157035 0.00308741 +Mm Hs MITF Mast cells MI|bHLHe32|WS2A|WS2 0.004 melanogenesis associated transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.105263 0.00596734 0.00315173 +Mm Hs MFGE8 Mast cells SED1|EDIL1|BA46|OAcGD3S|HsT19888|MFG-E8|hP47|SPAG10 0.15 milk fat globule-EGF factor 8 protein protein-coding gene 1 Mesoderm Immune system 0.0 0.657895 0.080402 0.164919 +Mm Hs LSAMP Mast cells IGLON3 0.119 limbic system associated membrane protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00942211 0.144465 +Mm Hs LRRC66 Mast cells NA 0.0 leucine rich repeat containing 66 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000450248 +Mm Hs LIMA1 Mast cells EPLIN 0.078 LIM domain and actin binding 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.125314 0.0685663 +Mm Hs KRT4 Mast cells CK4|K4|CYK4 0.004 keratin 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0526316 0.00219849 0.00482408 +Mm Hs KDELR3 Mast cells NA 0.025 KDEL endoplasmic reticulum protein retention receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0185302 0.0263716 +Mm Hs IDS Mast cells SIDS 0.039 iduronate 2-sulfatase protein-coding gene 1 Mesoderm Immune system 0.125 0.342105 0.0835427 0.0281083 +Mm Hs HSPA13 Mast cells STCH 0.012 heat shock protein family A (Hsp70) member 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.131579 0.0109925 0.0119637 +Mm Hs HS2ST1 Mast cells KIAA0448 0.013 heparan sulfate 2-O-sulfotransferase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0526316 0.00345477 0.0155014 +Mm Hs GPM6A Mast cells GPM6 0.241 glycoprotein M6A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0235553 0.296649 +Mm Hs GP1BA Mast cells CD42b|GPIbalpha|GP1B 0.0 glycoprotein Ib platelet subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00031407 0.000128642 +Mm Hs GNAZ Mast cells NA 0.018 G protein subunit alpha z protein-coding gene 1 Mesoderm Immune system 0.0 0.631579 0.000628141 0.021226 +Mm Hs FAM84A Mast cells FLJ35392 0.026 family with sequence similarity 84 member A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0144472 0.0297807 +Mm Hs FAM129B Mast cells DKFZP434H0820|FLJ13518|FLJ22151|FLJ22298|bA356B19.6|MINERVA|C9orf88 0.024 family with sequence similarity 129 member B protein-coding gene 1 Mesoderm Immune system 0.0 0.105263 0.0235553 0.0238631 +Mm Hs EXT1 Mast cells ttv 0.016 exostosin glycosyltransferase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0172739 0.0147939 +Mm Hs ESYT3 Mast cells CHR3SYT|FAM62C 0.0 extended synaptotagmin 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000128642 +Mm Hs ENO2 Mast cells NA 0.06 enolase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.02701 0.0658005 +Mm Hs ENAH Mast cells FLJ10773|NDPP1|MENA 0.116 ENAH, actin regulator protein-coding gene 1 Mesoderm Immune system 0.0 0.447368 0.157977 0.0992474 +Mm Hs DUSP1 Mast cells HVH1|CL100|MKP-1|PTPN10 0.281 dual specificity phosphatase 1 protein-coding gene 1 Mesoderm Immune system 0.5 0.868421 0.442525 0.249566 +Mm Hs DGKI Mast cells DGK-IOTA 0.001 diacylglycerol kinase iota protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00057889 +Mm Hs DDC Mast cells AADC 0.014 dopa decarboxylase protein-coding gene 1 Mesoderm Immune system 0.0 0.263158 0.00471106 0.016016 +Mm Hs DCLK3 Mast cells KIAA1765|DCDC3C|DCAMKL3 0.001 doublecortin like kinase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00345477 0.00057889 +Mm Hs ITGA2B Megakaryocytes CD41B|CD41|PPP1R93|GP2B 0.003 integrin subunit alpha 2b protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00407268 0.00314405 +Mm Hs GP1BA Megakaryocytes CD42b|GPIbalpha|GP1B 0.0 glycoprotein Ib platelet subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.000128329 +Mm Hs ITGB3 Megakaryocytes CD61|GPIIIa|GP3A 0.001 integrin subunit beta 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.00121912 +Mm Hs MPL Megakaryocytes CD110|TPOR 0.001 MPL proto-oncogene, thrombopoietin receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00121912 +Mm Hs LAT Megakaryocytes NA 0.034 linker for activation of T cells protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0140977 0.0376003 +Mm Hs PLEK Megakaryocytes NA 0.051 pleckstrin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0451128 0.0528714 +Mm Hs S100A9 Megakaryocytes MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.103383 0.0 +Mm Hs S100A8 Megakaryocytes P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0798872 0.0 +Mm Hs PF4 Megakaryocytes SCYB4|CXCL4 0.029 platelet factor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00344612 0.035162 +Mm Hs F13A1 Megakaryocytes F13A 0.021 coagulation factor XIII A chain protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00438596 0.0232275 +Mm Hs CD9 Megakaryocytes BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.27099 0.366185 +Mm Hs EPOR Megakaryocytes NA 0.004 erythropoietin receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0147243 0.00250241 +Mm Hs CXCR4 Megakaryocytes LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.198308 0.0087905 +Mm Hs GP5 Megakaryocytes CD42d 0.001 glycoprotein V platelet protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00121912 +Mm Hs CXCR1 Megakaryocytes CDw128a|CD181|CMKAR1|IL8RA 0.0 C-X-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000128329 +Mm Hs CXCR2 Megakaryocytes CMKAR2|CD182|IL8RB 0.003 C-X-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00352903 +Mm Hs SLAMF1 Megakaryocytes CD150|SLAM 0.001 signaling lymphocytic activation molecule family member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00156642 0.0 +Mm Hs PDE6B Megakaryocytes CSNB3|rd1|RP40|CSNBAD2|PDEB 0.002 phosphodiesterase 6B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125313 0.00275906 +Mm Hs MATK Megakaryocytes HYLTK|CTK|HYL|Lsk|HHYLTK|DKFZp434N1212|MGC1708|MGC2101 0.032 megakaryocyte-associated tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0184837 0.0367661 +Mm Hs SPON2 Megakaryocytes DIL1 0.017 spondin 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0488722 0.0 +Mm Hs MKL2 Megakaryocytes NA 0.035 MKL/myocardin-like 2 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0056391 0.0424126 +Mm Hs TLR9 Megakaryocytes CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs KIF5B Megakaryocytes KNS|KNS1 0.486 kinesin family member 5B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.327068 0.52326 +Mm Hs GATA1 Megakaryocytes ERYF1|NFE1|GATA-1 0.008 GATA binding protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0178571 0.00590311 +Mm Hs FLI1 Megakaryocytes SIC-1 0.036 Fli-1 proto-oncogene, ETS transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00595238 0.0436317 +Mm Hs PROX1 Megakaryocytes NA 0.028 prospero homeobox 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0109649 0.0324671 +Mm Hs SYP Megakaryocytes MRX96 0.049 synaptophysin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00720551 0.0 +Mm Hs TSPAN9 Megakaryocytes NET-5 0.028 tetraspanin 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00313283 0.0 +Mm Hs RGS18 Megakaryocytes RGS13 0.019 regulator of G protein signaling 18 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00344612 0.0 +Mm Hs TREML1 Megakaryocytes TLT1|dJ238O23.3 0.0 triggering receptor expressed on myeloid cells like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000626566 0.0 +Mm Hs GATA2 Megakaryocytes NFE1B 0.02 GATA binding protein 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0134712 0.0218158 +Mm Hs VWF Megakaryocytes F8VWF 0.016 von Willebrand factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0266291 0.0 +Mm Hs ALOX12 Megakaryocytes 12S-LOX 0.001 arachidonate 12-lipoxygenase, 12S type protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000962464 +Mm Hs SELP Megakaryocytes CD62|PSEL|PADGEM|GMP140|CD62P|GRMP 0.003 selectin P protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125313 0.0 +Mm Hs NFATC1 Megakaryocytes NF-ATC|NFATc|NFAT2 0.006 nuclear factor of activated T cells 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00501253 0.00692974 +Mm Hs CIB1 Megakaryocytes SIP2-28|KIP 0.156 calcium and integrin binding 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.300439 0.121463 +Mm Hs PLK3 Megakaryocytes FNK|PRK 0.01 polo like kinase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0093985 0.0102663 +Mm Hs MAFG Megakaryocytes MGC13090|MGC20149 0.076 MAF bZIP transcription factor G protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0435464 0.0821303 +Mm Hs IL2RA Megakaryocytes IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0200501 0.00673725 +Mm Hs PECAM1 Megakaryocytes CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0441729 0.053513 +Mm Hs PPARG Megakaryocytes PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0109649 0.00461983 +Mm Hs IL6 Megakaryocytes IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0134712 0.00648059 +Mm Hs IL21R Megakaryocytes CD360 0.013 interleukin 21 receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0160411 +Mm Hs LRP1 Megakaryocytes CD91|LRP1A|APOER|A2MR|IGFBP3R1 0.071 LDL receptor related protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.035401 0.0773821 +Mm Hs ACHE Megakaryocytes YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00469925 0.0195701 +Mm Hs VEGFA Megakaryocytes VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0247494 0.0 +Mm Hs TGFB1 Megakaryocytes CED|TGFbeta|TGFB|DPD1 0.11 transforming growth factor beta 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0451128 0.0 +Mm Hs GP9 Megakaryocytes CD42a|GPIX 0.001 glycoprotein IX platelet protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000626566 0.000962464 +Mm Hs AHR Melanocytes bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0112782 0.00693508 +Mm Hs MC1R Melanocytes MSH-R 0.0 melanocortin 1 receptor protein-coding gene 1 Mesoderm Skin 0.0 0.0833333 0.0 0.0 +Mm Hs PMEL Melanocytes D12S53E|SI|Pmel17|gp100|SILV 0.003 premelanosome protein protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.0037594 0.00128427 +Mm Hs PTGDS Melanocytes L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.0582707 0.054389 +Mm Hs SLC45A2 Melanocytes OCA4|MATP 0.001 solute carrier family 45 member 2 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs MLANA Melanocytes NA 0.002 melan-A protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.0 0.000898992 +Mm Hs MITF Melanocytes MI|bHLHe32|WS2A|WS2 0.004 melanogenesis associated transcription factor protein-coding gene 1 Mesoderm Skin 0.0 0.833333 0.00595238 0.00276119 +Mm Hs TYR Melanocytes OCAIA|OCA1A|OCA1 0.001 tyrosinase protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs TYRP1 Melanocytes GP75|CATB|TRP|b-PROTEIN|OCA3|TYRP|CAS2 0.002 tyrosinase related protein 1 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.000626566 0.0 +Mm Hs DCT Melanocytes TYRP2 0.002 dopachrome tautomerase protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.0 0.0018622 +Mm Hs FILIP1L Melanocytes DOC-1|GIP130 0.032 filamin A interacting protein 1 like protein-coding gene NA Mesoderm Skin 0.0 0.166667 0.0385338 0.0322995 +Mm Hs GPNMB Melanocytes NMB|HGFIN 0.013 glycoprotein nmb protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.0297619 0.00866885 +Mm Hs LOXL2 Melanocytes WS9-14|LOR 0.021 lysyl oxidase like 2 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.016604 0.0209979 +Mm Hs ZC3H7A Melanocytes HSPC055|FLJ20318|ZC3HDC7|ZC3H7 0.011 zinc finger CCCH-type containing 7A protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0128446 0.0 +Mm Hs SLK Melanocytes se20-9|KIAA0204 0.038 STE20 like kinase protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0344612 0.0 +Mm SERPINB1A Melanocytes NA 0.059 serine (or cysteine) peptidase inhibitor, clade B, member 1a protein coding gene NA Mesoderm Skin NA NA NA NA +Mm Hs DKK3 Melanocytes REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene NA Mesoderm Skin 0.0 0.75 0.037594 0.034868 +Mm Hs AHNAK2 Melanocytes C14orf78 0.019 AHNAK nucleoprotein 2 protein-coding gene NA Mesoderm Skin 0.0 0.416667 0.00783208 0.02164 +Mm Hs HSPB1 Melanocytes HSP27|HSP28|Hs.76067|Hsp25|CMT2F 0.19 heat shock protein family B (small) member 1 protein-coding gene 1 Mesoderm Skin 0.0 0.25 0.442982 0.126629 +Mm Hs PAX3 Melanocytes HUP2|WS1 0.004 paired box 3 protein-coding gene 1 Mesoderm Skin 0.0 1.0 0.00407268 0.00308226 +Mm Hs TRPM1 Melanocytes LTRPC1|CSNB1C|MLSN1 0.006 transient receptor potential cation channel subfamily M member 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00438596 0.0 +Mm Hs CTNS Melanocytes CTNS-LSB|PQLC4 0.002 cystinosin, lysosomal cystine transporter protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00469925 0.00205484 +Mm Hs ENPP1 Melanocytes PC-1|NPPS|M6S1|PDNP1 0.005 ectonucleotide pyrophosphatase/phosphodiesterase 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0112782 0.0032749 +Mm Hs SOX9 Melanocytes SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0322682 0.0 +Mm Hs BNC2 Melanocytes BSN2|FLJ20043 0.007 basonuclin 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0833333 0.0103383 0.0051371 +Mm Hs MEN1 Melanocytes NA 0.006 menin 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00156642 0.00738458 +Mm Hs POMC Melanocytes POC|ACTH|NPP|LPH 0.008 proopiomelanocortin protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0238095 0.00500867 +Mm Hs TFAP2A Melanocytes AP-2|TFAP2|AP2TF 0.023 transcription factor AP-2 alpha protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0200501 0.0 +Mm Hs RAB38 Melanocytes NY-MEL-1 0.014 RAB38, member RAS oncogene family protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0106516 0.0 +Hs TP63 Melanocytes SHFM4|EEC3|p63|p73L|OFC8|KET|p73H|p53CP|TP73L|TP53L|TP53CP 0.001 tumor protein p63 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0056391 0.0 +Mm Hs CRABP1 Melanocytes CRABP|CRABPI|RBP5 0.025 cellular retinoic acid binding protein 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0833333 0.0300752 0.0233096 +Mm Hs BMI1 Melanocytes RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00532581 0.00931099 +Mm Hs PTN Melanocytes HBNF|HBGF8|NEGF1 0.313 pleiotrophin protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0905388 0.370256 +4 CCN5 Melanocytes Wisp2|Ccn5|Ctgfl 0.0 cellular communication network factor 5 NA 1 Mesoderm Skin NA NA NA NA +Hs PRKN Melanocytes PDJ|AR-JP|parkin|PARK2 0.0 parkin RBR E3 ubiquitin protein ligase protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0018797 0.0 +Mm Hs KLC2 Melanocytes FLJ12387 0.018 kinesin light chain 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0229885 +Mm Hs IL24 Melanocytes mda-7|IL10B|Mob-5|C49A|FISP|IL-24|ST16 0.0 interleukin 24 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000626566 0.0 +Mm Hs TPH2 Melanocytes NTPH|FLJ37295 0.001 tryptophan hydroxylase 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs PPARA Melanocytes hPPAR|NR1C1|PPAR 0.001 peroxisome proliferator activated receptor alpha protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00250627 0.000706351 +Mm Hs PPARD Melanocytes NUC1|NUCII|FAAR|NR1C2 0.009 peroxisome proliferator activated receptor delta protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0018797 0.0104668 +Mm Hs PPARG Melanocytes PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0109649 0.00462339 +Mm Hs PRKCA Melanocytes PKCA 0.033 protein kinase C alpha protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0153509 0.0369229 +Mm Hs FOXC1 Meningeal cells FREAC3|IGDA|IHG1|FKHL7|IRID1 0.015 forkhead box C1 protein-coding gene 1 Ectoderm Brain 0.0 0.461538 0.00720551 0.016504 +Mm Hs FOXC2 Meningeal cells MFH-1|FKHL14 0.003 forkhead box C2 protein-coding gene NA Ectoderm Brain 0.0 0.153846 0.00814536 0.00231184 +Mm Hs BMP7 Meningeal cells OP-1 0.01 bone morphogenetic protein 7 protein-coding gene NA Ectoderm Brain 0.0 0.615385 0.00595238 0.00873362 +Mm Hs ZIC1 Meningeal cells ZIC|ZNF201 0.046 Zic family member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00845865 0.0 +Mm Hs ZIC3 Meningeal cells HTX|ZNF203|HTX1 0.01 Zic family member 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs ALDH1A2 Meningeal cells RALDH2 0.011 aldehyde dehydrogenase 1 family member A2 protein-coding gene NA Ectoderm Brain 0.0 0.692308 0.0250627 0.00764192 +Mm Hs ALX4 Meningeal cells KIAA1788 0.0 ALX homeobox 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs IGF2 Meningeal cells FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0463659 0.00089905 +Mm Hs VTN Meningeal cells VN 0.029 vitronectin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00971178 0.0 +Mm Hs IGFBP2 Meningeal cells IBP2 0.129 insulin like growth factor binding protein 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.162907 0.115528 +Mm Hs DCN Meningeal cells DSPG2|SLRR1B 0.084 decorin protein-coding gene 1 Ectoderm Brain 0.0 0.846154 0.107143 0.0812356 +Mm Hs LUM Meningeal cells SLRR2D|LDC 0.051 lumican protein-coding gene 1 Ectoderm Brain 0.0 0.153846 0.0870927 0.0426406 +Mm Hs PDGFRA Meningeal cells CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene 1 Ectoderm Brain 0.0 0.0769231 0.047619 0.0439892 +Mm Hs IL33 Meningeal cells DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0206139 +Mm Hs PTGDS Meningeal cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0582707 0.0543283 +Mm Hs NNAT Meningeal cells Peg5 0.229 neuronatin protein-coding gene 1 Ectoderm Brain 0.0 0.692308 0.0460526 0.276394 +Mm Hs NOV Meningeal cells IGFBP9|CCN3 0.004 nephroblastoma overexpressed protein-coding gene 1 Ectoderm Brain 0.0 0.153846 0.00469925 0.00455947 +Mm Hs SLC47A1 Meningeal cells FLJ10847|MATE1 0.002 solute carrier family 47 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs CHGA Merkel cells NA 0.057 chromogranin A protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0379073 0.0622393 +Mm Hs KRT20 Merkel cells CK20|K20|MGC35423 0.012 keratin 20 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0150376 0.0117421 +Mm Hs FLI1 Merkel cells SIC-1 0.036 Fli-1 proto-oncogene, ETS transcription factor protein-coding gene NA Mesoderm Skin 0.0 0.0 0.00595238 0.0436317 +Hs CD99 Merkel cells MIC2 0.007 CD99 molecule (Xg blood group) protein-coding gene NA Mesoderm Skin 0.0 0.0 0.00156642 0.0 +Mm Hs GNAI1 Merkel cells NA 0.05 G protein subunit alpha i1 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.0410401 0.0543471 +Mm Hs VIL1 Merkel cells D2S1471|VIL 0.022 villin 1 protein-coding gene NA Mesoderm Skin 0.0 0.0 0.00845865 0.0 +Mm Hs PIEZO2 Merkel cells FLJ23403|FLJ23144|HsT748|HsT771|FLJ34907|FAM38B2|C18orf30|C18orf58|FAM38B 0.006 piezo type mechanosensitive ion channel component 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000626566 0.00776388 +Mm Hs ID2 Merkel cells GIG8|bHLHb26 0.354 inhibitor of DNA binding 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.348058 0.358229 +Mm Hs TRPV4 Merkel cells OTRPC4|TRP12|VROAC|VRL-2|VR-OAC|CMT2C 0.002 transient receptor potential cation channel subfamily V member 4 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs ATOH1 Merkel cells HATH1|MATH-1|Math1|bHLHa14 0.003 atonal bHLH transcription factor 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00093985 0.00282323 +Mm Hs SOX2 Merkel cells NA 0.082 SRY-box 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0288221 0.0 +Mm Hs TTF1 Merkel cells NA 0.009 transcription termination factor 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0350877 0.0 +Mm Hs POU4F3 Merkel cells BRN3C|DFNA15|DFNA42 0.002 POU class 4 homeobox 3 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00205326 +Mm Hs GFI1 Merkel cells GFI1A|GFI-1|ZNF163 0.001 growth factor independent 1 transcriptional repressor protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00128329 +Mm Hs KRT8 Merkel cells K8|CK8|CYK8|K2C8|KO 0.12 keratin 8 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.211153 0.0931023 +Mm Hs KRT18 Merkel cells NA 0.126 keratin 18 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.237782 0.0927815 +Mm Hs PDGFB Mesangial cells SSV|SIS 0.01 platelet derived growth factor subunit B protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0015674 0.0125762 +Mm Hs PDGFRB Mesangial cells JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0357367 0.0334296 +Mm Hs ACTA2 Mesangial cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0194357 0.0388835 +Mm Hs TNS1 Mesangial cells DKFZp586K0617|PPP1R155|TNS|MXRA6 0.047 tensin 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0153605 0.0 +Mm Hs SFRP2 Mesangial cells SARP1|SDF-5|FRP-2 0.009 secreted frizzled related protein 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0238245 0.0 +Mm Hs ECM1 Mesangial cells NA 0.034 extracellular matrix protein 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00940439 0.0403593 +Mm Hs ANGPT2 Mesangial cells Ang2 0.004 angiopoietin 2 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0153605 0.00186076 +Mm Hs FGF1 Mesangial cells AFGF|ECGF|ECGFA|ECGFB|HBGF1|ECGF-beta|FGF-alpha|GLIO703|FGFA 0.011 fibroblast growth factor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0031348 0.0125762 +Mm Hs CTGF Mesangial cells IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene NA Mesoderm Kidney 1.0 0.0 0.0990596 0.0124479 +Mm Hs PLAU Mesangial cells URK 0.01 plasminogen activator, urokinase protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0438871 0.00250241 +Mm Hs GATA3 Mesangial cells HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0194357 0.0297722 +Mm Hs LEF1 Mesangial cells TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00940439 0.0277831 +Mm Hs MRC1 Mesangial cells CLEC13D|CD206|bA541I19.1|CLEC13DL|MRC1L1 0.029 mannose receptor C-type 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00971787 0.0347129 +Mm Hs PML Mesangial cells MYL|TRIM19|RNF71 0.007 promyelocytic leukemia protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00783699 0.00660892 +Mm Hs OGT Mesangial cells O-GLCNAC|HRNT1|MGC22921|FLJ23071|OGT1 0.039 O-linked N-acetylglucosamine (GlcNAc) transferase protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0206897 0.044145 +Mm Hs NOCT Mesangial cells CCR4L|Ccr4c|NOC|CCRN4L 0.016 nocturnin protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0205326 +Mm Hs NCOA2 Mesangial cells TIF2|NCoA-2|KAT13C|bHLHe75 0.004 nuclear receptor coactivator 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0031348 0.00417068 +Mm Hs PER3 Mesangial cells NA 0.025 period circadian regulator 3 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00031348 0.0314405 +Mm Hs PLA2R1 Mesangial cells PLA2G1R|PLA2IR|PLA2-R|CLEC13C 0.003 phospholipase A2 receptor 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0128527 0.000513314 +Mm Hs TRIP4 Mesangial cells HsT17391 0.009 thyroid hormone receptor interactor 4 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00658307 0.0 +Mm Hs AMOTL2 Mesangial cells LCCP 0.021 angiomotin like 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.015047 0.0216234 +Mm Hs LATS2 Mesangial cells NA 0.008 large tumor suppressor kinase 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00909091 0.00846968 +Mm Hs YAP1 Mesangial cells YAP65 0.021 Yes associated protein 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0197492 0.0 +Mm Hs LRP5 Mesangial cells LR3|BMND1|HBM|OPS|OPTA1|VBCH2|EVR4|LRP7|OPPG 0.003 LDL receptor related protein 5 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0031348 0.00295156 +Mm Hs MIB1 Mesangial cells DIP-1|MIB|KIAA1323|ZZANK2|ZZZ6 0.017 mindbomb E3 ubiquitin protein ligase 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00971787 0.0184151 +Mm Hs NOSTRIN Mesangial cells MGC20702 0.025 nitric oxide synthase trafficking protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0238245 0.0261149 +Mm Hs ADAMTSL4 Mesangial cells DKFZP434K1772|TSRC1 0.003 ADAMTS like 4 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0015674 0.00327238 +Mm Hs EMILIN1 Mesangial cells DKFZp586M121|gp115 0.028 elastin microfibril interfacer 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0297806 0.027719 +Mm Hs ITGA8 Mesangial cells NA 0.005 integrin subunit alpha 8 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.00783699 0.00429901 +Mm Hs DYRK1A Mesangial cells DYRK1|DYRK|MNBH 0.012 dual specificity tyrosine phosphorylation regulated kinase 1A protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00689655 0.0135387 +Mm Hs ARID5B Mesangial cells FLJ21150|MRF2 0.084 AT-rich interaction domain 5B protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.151097 0.071094 +Mm Hs CCR7 Mesangial cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0420063 0.0114212 +Mm Hs FN1 Mesangial cells CIG|LETS|GFND2|FINC 0.091 fibronectin 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0987461 0.0869426 +Mm Hs PAWR Mesangial cells par-4 0.024 pro-apoptotic WT1 regulator protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0874608 0.00725056 +Mm Hs PTN Mesangial cells HBNF|HBGF8|NEGF1 0.313 pleiotrophin protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0899687 0.369971 +Mm Hs SERPINE2 Mesangial cells PNI|nexin|PI7 0.134 serpin family E member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0661442 0.0 +Mm Hs TBX18 Mesangial cells NA 0.004 T-box 18 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00031348 0.0 +Mm Hs TEK Mesangial cells TIE2|TIE-2|VMCM1|CD202b|VMCM 0.02 TEK receptor tyrosine kinase protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00188088 0.0 +Mm Hs THY1 Mesangial cells CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0322884 0.0 +Mm Hs MYL9 Mesangial cells MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.159875 0.0633943 +Mm Hs TPM2 Mesangial cells NEM4|AMCD1 0.075 tropomyosin 2 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.146395 0.0 +Mm Hs CALD1 Mesangial cells H-CAD|L-CAD 0.186 caldesmon 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.268339 0.165544 +Mm Hs HOPX Mesangial cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0912226 0.022265 +Mm Hs NR4A2 Mesangial cells TINUR|NOT|RNR1|HZF-3|NURR1 0.033 nuclear receptor subfamily 4 group A member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0780564 0.0255374 +Mm Hs ACTN1 Mesangial cells NA 0.091 actinin alpha 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.130094 0.0797562 +Mm Hs AKAP12 Mesangial cells AKAP250|SSeCKS 0.098 A-kinase anchoring protein 12 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.138871 0.0866859 +Mm Hs ROCK1 Mesangial cells p160ROCK 0.149 Rho associated coiled-coil containing protein kinase 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.13511 0.0 +Mm Hs SH3BGRL Mesangial cells MGC117402 0.325 SH3 domain binding glutamate rich protein like protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.294357 0.0 +Mm Hs RASD1 Mesangial cells DEXRAS1 0.013 ras related dexamethasone induced 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0326019 0.0 +Mm Hs SNCG Mesangial cells BCSG1|SR|persyn 0.03 synuclein gamma protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0382445 0.0 +Mm Hs FILIP1L Mesangial cells DOC-1|GIP130 0.032 filamin A interacting protein 1 like protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.037931 0.032403 +Mm Hs FLNA Mesangial cells FLN1|FLN|OPD2|OPD1 0.108 filamin A protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.138245 0.0956047 +Mm Hs MEF2C Mesangial cells NA 0.163 myocyte enhancer factor 2C protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0924765 0.178248 +Mm Hs CSTB Mesangial cells CST6|PME|EPM1|STFB 0.37 cystatin B protein-coding gene 1 Mesoderm Kidney 0.5 0.0 0.505016 0.333975 +Mm Hs SMARCA5 Mesangial cells hSNF2H|hISWI 0.218 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.129467 0.0 +Mm Hs PDE3A Mesangial cells CGI-PDE 0.01 phosphodiesterase 3A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626959 0.0120629 +Mm Hs MAP3K20 Mesangial cells MLTKalpha|MLTKbeta|ZAK|MLTK|MLK7 0.022 mitogen-activated protein kinase kinase kinase 20 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0275862 0.0202117 +Mm Hs CALB2 Mesothelial cells CAL2 0.03 calbindin 2 protein-coding gene NA Mesoderm Epithelium 1.0 0.0 0.00219436 0.0375442 +Mm Hs MUC16 Mesothelial cells FLJ14303 0.001 mucin 16, cell surface associated protein-coding gene NA Mesoderm Epithelium 1.0 0.4 0.0015674 0.000192864 +Mm Hs KRT5 Mesothelial cells KRT5A|EBS2 0.019 keratin 5 protein-coding gene NA Mesoderm Epithelium 1.0 0.0 0.0438871 0.0151077 +Mm Hs KRT6A Mesothelial cells CK6C|K6C|CK6D|K6D|KRT6C|KRT6D 0.007 keratin 6A protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0112853 0.00694311 +Mm Hs DES Mesothelial cells CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene NA Mesoderm Epithelium 0.0 0.0666667 0.00940439 0.023208 +Mm Hs CDH1 Mesothelial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0416928 0.0573449 +Mm Hs HAS2 Mesothelial cells NA 0.003 hyaluronan synthase 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0119122 0.000514304 +Mm Hs KRT7 Mesothelial cells CK7|K2C7 0.056 keratin 7 protein-coding gene NA Mesoderm Epithelium 1.0 0.733333 0.100627 0.0460945 +Mm Hs ME1 Mesothelial cells NA 0.031 malic enzyme 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00626959 0.0367727 +Mm Hs ME2 Mesothelial cells NA 0.043 malic enzyme 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0272727 0.0456445 +Mm Hs MSLN Mesothelial cells MPF 0.004 mesothelin protein-coding gene 1 Mesoderm Epithelium 1.0 0.966667 0.000626959 0.00347155 +Mm Hs THBD Mesothelial cells CD141 0.022 thrombomodulin protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0131661 0.0 +Mm Hs WT1 Mesothelial cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.0 0.0219436 0.0 +Mm Hs LRRN4 Mesothelial cells dJ1056H1.1|NLRR4|C20orf75 0.002 leucine rich repeat neuronal 4 protein-coding gene 1 Mesoderm Epithelium 0.0 0.933333 0.0 0.000385728 +Mm Hs IL17RE Mesothelial cells FLJ23658 0.003 interleukin 17 receptor E protein-coding gene NA Mesoderm Epithelium 0.0 0.133333 0.000940439 0.00347155 +Mm Hs LOX Mesothelial cells NA 0.017 lysyl oxidase protein-coding gene NA Mesoderm Epithelium 0.0 0.333333 0.015047 0.0162649 +Mm OASL2 Mesothelial cells NA 0.011 2'-5' oligoadenylate synthetase-like 2 protein coding gene NA Mesoderm Epithelium 0.0 0.2 0.0 0.012729 +Mm Hs KCNAB1 Mesothelial cells AKR6A3|KCNA1B|hKvBeta3|Kvb1.3|hKvb3 0.006 potassium voltage-gated channel subfamily A member regulatory beta subunit 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0666667 0.00031348 0.00713597 +Mm Hs PKHD1L1 Mesothelial cells NA 0.001 PKHD1 like 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.466667 0.00125392 0.000450016 +Mm Hs SULF1 Mesothelial cells KIAA1077|SULF-1|hSulf-1 0.013 sulfatase 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.0 0.0169279 0.0 +Mm Hs DUSP5 Mesothelial cells HVH3 0.032 dual specificity phosphatase 5 protein-coding gene NA Mesoderm Epithelium 0.0 0.0666667 0.0495298 0.0284153 +Mm Hs MIR22HG Mesothelial cells MGC14376|DKFZp686O06159|C17orf91 0.021 MIR22 host gene non-coding RNA NA Mesoderm Epithelium 1.0 0.1 0.0326019 0.0190935 +Mm Hs COBLL1 Mesothelial cells KIAA0977 0.013 cordon-bleu WH2 repeat protein like 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.166667 0.0169279 0.0117647 +Mm Hs ST3GAL1 Mesothelial cells ST3O|SIATFL|ST3GalA.1|SIAT4A 0.013 ST3 beta-galactoside alpha-2,3-sialyltransferase 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.015674 0.0 +Mm Hs FBXO33 Mesothelial cells Fbx33 0.008 F-box protein 33 protein-coding gene NA Mesoderm Epithelium 0.0 0.1 0.0119122 0.00739312 +Mm Hs FZD1 Mesothelial cells DKFZp564G072 0.01 frizzled class receptor 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.1 0.00282132 0.0120861 +Mm Hs RASL11A Mesothelial cells NA 0.012 RAS like family 11 member A protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00031348 0.0 +Mm Hs CDON Mesothelial cells ORCAM|CDO|CDON1 0.005 cell adhesion associated, oncogene regulated protein-coding gene NA Mesoderm Epithelium 0.0 0.4 0.0 0.00552877 +Mm Hs BCL3 Mesothelial cells D19S37|BCL4 0.012 B cell CLL/lymphoma 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.0333333 0.00877743 0.013179 +Mm Hs ACKR3 Mesothelial cells GPR159|CMKOR1|CXCR7 0.01 atypical chemokine receptor 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.1 0.00658307 0.0112504 +Mm Hs NPR1 Mesothelial cells GUCY2A|ANPa|ANPRA|NPRA 0.009 natriuretic peptide receptor 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.2 0.00188088 0.0108647 +Mm Hs PCSK6 Mesothelial cells SPC4|PACE4 0.007 proprotein convertase subtilisin/kexin type 6 protein-coding gene NA Mesoderm Epithelium 0.0 0.1 0.0 0.00835744 +Mm Hs DPP4 Mesothelial cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene NA Mesoderm Epithelium 0.0 0.633333 0.0131661 0.0201221 +Mm Hs RND1 Mesothelial cells Rho6|ARHS|RHOS 0.007 Rho family GTPase 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.00501567 0.0 +Mm Hs GBP2 Mesothelial cells NA 0.02 guanylate binding protein 2 protein-coding gene NA Mesoderm Epithelium 0.5 0.566667 0.0394984 0.0145291 +Mm C1RA Mesothelial cells NA 0.015 complement component 1, r subcomponent A protein coding gene NA Mesoderm Epithelium 0.0 0.633333 0.0 0.0178078 +Mm Hs MEDAG Mesothelial cells FLJ14834|AWMS3|MEDA-4|C13orf33 0.007 mesenteric estrogen dependent adipogenesis protein-coding gene NA Mesoderm Epithelium 1.0 0.1 0.00877743 0.00649309 +Mm Hs AR Mesothelial cells AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene NA Mesoderm Epithelium 0.0 0.266667 0.00188088 0.0154934 +Mm Hs LGALS7 Mesothelial cells TP53I1|LGALS7A 0.016 galectin 7 protein-coding gene NA Mesoderm Epithelium 0.0 0.533333 0.00344828 0.0180006 +Mm GSTT1 Mesothelial cells NA 0.022 glutathione S-transferase theta 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.4 0.0 0.0272581 +Mm Hs ANO1 Mesothelial cells TAOS2|FLJ10261|DOG1|ORAOV2|TMEM16A 0.009 anoctamin 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.466667 0.000940439 0.0108004 +Mm Hs GSTA3 Mesothelial cells NA 0.014 glutathione S-transferase alpha 3 protein-coding gene NA Mesoderm Epithelium 0.0 0.566667 0.000940439 0.0164577 +Mm Hs OSR1 Mesothelial cells NA 0.011 odd-skipped related transciption factor 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.366667 0.0015674 0.0122147 +Mm Hs TWSG1 Mesothelial cells TSG 0.02 twisted gastrulation BMP signaling modulator 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.0 0.0304075 0.0 +Mm MMP23 Mesothelial cells NA 0.012 matrix metallopeptidase 23 protein coding gene NA Mesoderm Epithelium 0.0 0.633333 0.0 0.0141434 +Mm Hs ADGRD1 Mesothelial cells DKFZp434B1272|PGR25|GPR133 0.004 adhesion G protein-coupled receptor D1 protein-coding gene NA Mesoderm Epithelium 0.0 0.266667 0.00721003 0.00250723 +Mm Hs CRLS1 Mesothelial cells dJ967N21.6|CLS1|C20orf155 0.022 cardiolipin synthase 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.6 0.0507837 0.0111218 +Mm Hs FLNC Mesothelial cells ABPL|FLN2 0.01 filamin C protein-coding gene NA Mesoderm Epithelium 0.0 0.0666667 0.00250784 0.0102861 +Mm Hs PTGS2 Mesothelial cells NA 0.009 prostaglandin-endoperoxide synthase 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.0666667 0.0137931 0.00829315 +Mm Hs C2 Mesothelial cells NA 0.008 complement C2 protein-coding gene NA Mesoderm Epithelium 0.0 0.8 0.00658307 0.00732883 +Mm Hs FMO2 Mesothelial cells NA 0.014 flavin containing monooxygenase 2 protein-coding gene NA Mesoderm Epithelium 0.0 0.566667 0.00376176 0.0149791 +Mm Hs FMOD Mesothelial cells SLRR2E 0.009 fibromodulin protein-coding gene NA Mesoderm Epithelium 0.0 0.533333 0.00595611 0.00810029 +Mm Hs FGF1 Mesothelial cells AFGF|ECGF|ECGFA|ECGFB|HBGF1|ECGF-beta|FGF-alpha|GLIO703|FGFA 0.011 fibroblast growth factor 1 protein-coding gene NA Mesoderm Epithelium 0.0 0.233333 0.0031348 0.0121504 +Mm TRIM30C Mesothelial cells NA 0.001 tripartite motif-containing 30C protein coding gene NA Mesoderm Epithelium NA NA NA NA +Mm Hs EFEMP1 Mesothelial cells S1-5|FBLN3|MTLV|DHRD|FBNL 0.021 EGF containing fibulin extracellular matrix protein 1 protein-coding gene NA Mesoderm Epithelium 1.0 0.9 0.0413793 0.0149148 +Mm Hs FRAS1 Mesothelial cells FLJ22031|FLJ14927|KIAA1500 0.003 Fraser extracellular matrix complex subunit 1 protein-coding gene 1 Mesoderm Epithelium 0.0 0.2 0.00219436 0.00199293 +Mm Hs RSPO1 Mesothelial cells FLJ40906|RSPONDIN 0.007 R-spondin 1 protein-coding gene 1 Mesoderm Epithelium 1.0 0.0 0.0 0.0 +Mm Hs RARRES2 Mesothelial cells TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene NA Mesoderm Epithelium 1.0 0.0 0.0780564 0.0 +Mm Hs GP2 Microfold cells ZAP75 0.001 glycoprotein 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.0008983 +Mm Hs SPIB Microfold cells SPI-B 0.01 Spi-B transcription factor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00877193 0.0 +Mm Hs PGLYRP1 Microfold cells TAG7|PGRP|PGRP-S|PGRPS|TNFSF3L|PGLYRP 0.062 peptidoglycan recognition protein 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0754572 +Mm CCL9 Microfold cells NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.044145 +Mm Hs EHF Microfold cells ESE3|ESEJ 0.024 ETS homologous factor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0513784 0.0193134 +Mm Hs ANXA5 Microfold cells ENX2|ANX5 0.299 annexin A5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.370614 0.282708 +Mm Hs SOX8 Microfold cells NA 0.028 SRY-box 8 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.0 +Mm Hs MIER3 Microfold cells FLJ35954|DKFZp686L09111|DKFZp781I1119 0.004 MIER family member 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219298 0.00468399 +Mm Hs NFIC Microfold cells CTF|NF-I|CTF5|NFI 0.079 nuclear factor I C protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.100564 0.074238 +Mm SERPINB6A Microfold cells NA 0.107 serine (or cysteine) peptidase inhibitor, clade B, member 6a protein coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs CXCL16 Microfold cells SR-PSOX|CXCLG16|SRPSOX 0.048 C-X-C motif chemokine ligand 16 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0657895 0.0454925 +Mm Hs CTSD Microfold cells CLN10|CPSD 0.349 cathepsin D protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.260652 0.367918 +Mm Hs CCL20 Microfold cells LARC|MIP-3a|exodus-1|ST38|CKb4|SCYA20 0.005 C-C motif chemokine ligand 20 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0260025 0.0008983 +Mm Hs CTSH Microfold cells ACC-4|ACC-5|ACC4|ACC5|CPSB 0.147 cathepsin H protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.109023 0.154187 +Mm CCL6 Microfold cells NA 0.043 chemokine (C-C motif) ligand 6 protein coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0528072 +Mm Hs MARCKSL1 Microfold cells F52|MacMARCKS 0.505 MARCKS like 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.331767 0.537568 +Mm Hs RAC2 Microfold cells EN-7 0.172 Rac family small GTPase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.18515 0.0 +Mm Hs TNFAIP2 Microfold cells B94|EXOC3L3 0.027 TNF alpha induced protein 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0404135 0.0 +Mm Hs FABP5 Microfold cells E-FABP|PA-FABP|KFABP 0.354 fatty acid binding protein 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.218358 0.389028 +Mm Hs GJB2 Microfold cells CX26|NSRD1|DFNB1 0.009 gap junction protein beta 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0119048 0.00917549 +Mm Hs MFGE8 Microfold cells SED1|EDIL1|BA46|OAcGD3S|HsT19888|MFG-E8|hP47|SPAG10 0.15 milk fat globule-EGF factor 8 protein protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0802005 0.166121 +Mm Hs CYBA Microfold cells p22-PHOX 0.358 cytochrome b-245 alpha chain protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.457393 0.331537 +Mm Hs TMPRSS2 Microfold cells PRSS10 0.017 transmembrane serine protease 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0216165 0.0 +Mm Hs AHR Microfold cells bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0112782 0.00692974 +Mm Hs MTF1 Microfold cells NA 0.009 metal regulatory transcription factor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0103383 0.00962464 +Mm Hs RELB Microfold cells REL-B 0.015 RELB proto-oncogene, NF-kB subunit protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.016604 0.0 +Mm Hs TULP4 Microfold cells TUSP|KIAA1397 0.104 tubby like protein 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0319549 0.0 +Mm Hs ONECUT2 Microfold cells OC-2 0.012 one cut homeobox 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00344612 0.0131537 +Mm Hs FOSL2 Microfold cells FRA2|FLJ23306 0.045 FOS like 2, AP-1 transcription factor subunit protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0347744 0.0476099 +Mm Hs IRF6 Microfold cells OFC6|VWS|LPS 0.015 interferon regulatory factor 6 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0285088 0.013667 +Mm Hs IRF2 Microfold cells NA 0.03 interferon regulatory factor 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0125313 0.0340712 +Mm ZFP553 Microfold cells NA 0.002 zinc finger protein 553 protein coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs NFIB Microfold cells NFI-RED|NFIB2|NFIB3 0.29 nuclear factor I B protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0911654 0.340969 +Mm Hs FOXP4 Microfold cells FLJ40908 0.01 forkhead box P4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219298 0.0118704 +Mm Hs ITGAM Microglia CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Ectoderm Brain 0.0 0.356818 0.00313283 0.0207989 +Mm Hs ITGAX Microglia CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0162907 0.00541433 +Mm Hs C5AR1 Microglia C5A|C5AR|CD88|C5R1 0.027 complement C5a receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.111364 0.0140977 0.027864 +Mm Hs CX3CR1 Microglia CMKDR1|V28|GPR13|CMKBRL1 0.039 C-X3-C motif chemokine receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.988636 0.00219298 0.020931 +Mm Hs P2RY12 Microglia P2Y12|SP1999|HORK3 0.025 purinergic receptor P2Y12 protein-coding gene 1 Ectoderm Brain 0.0 0.968182 0.0 0.00462199 +Mm Hs P2RX7 Microglia P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0159091 0.00877193 0.00310333 +Mm Hs CD40 Microglia Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0131579 0.0111588 +Mm Hs TREM2 Microglia TREM-2|Trem2a|Trem2b|Trem2c 0.042 triggering receptor expressed on myeloid cells 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.0 +Mm Hs TMEM119 Microglia NA 0.031 transmembrane protein 119 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.0 +Mm Hs GPR34 Microglia NA 0.026 G protein-coupled receptor 34 protein-coding gene 1 Ectoderm Brain 0.0 0.915909 0.00501253 0.00607461 +Mm Hs TFF3 Microglia HITF|ITF 0.022 trefoil factor 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0451128 0.0 +Mm CBR2 Microglia NA 0.027 carbonyl reductase 2 protein coding gene 1 Ectoderm Brain 0.0 0.00909091 0.0 0.0340707 +Mm ZEB2OS Microglia NA 0.007 zinc finger E-box binding homeobox 2, opposite strand antisense lncRNA gene 1 Ectoderm Brain NA NA NA NA +Mm Hs SALL1 Microglia Hsal1|ZNF794|TBS 0.004 spalt like transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CSF3R Microglia GCSFR|CD114 0.012 colony stimulating factor 3 receptor protein-coding gene NA Ectoderm Brain 0.0 0.170455 0.0213033 0.0062727 +Mm Hs TCIRG1 Microglia TIRC7|OC-116|OC116|ATP6N1C|Atp6i|a3|ATP6V0A3 0.011 T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00595238 0.0 +Mm Hs SUSD3 Microglia MGC26847 0.018 sushi domain containing 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0253759 0.0 +Mm Hs GPR183 Microglia EBI2 0.019 G protein-coupled receptor 183 protein-coding gene 1 Ectoderm Brain 0.0 0.111364 0.0488722 0.00970617 +Mm Hs VAV1 Microglia VAV 0.016 vav guanine nucleotide exchange factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs SLC2A5 Microglia GLUT5 0.012 solute carrier family 2 member 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0131579 0.0 +Mm Hs IL21R Microglia CD360 0.013 interleukin 21 receptor protein-coding gene NA Ectoderm Brain 0.0 0.125 0.0 0.0128755 +Mm Hs IL10RA Microglia HIL-10R|CDW210A|CD210a|CD210|IL10R 0.011 interleukin 10 receptor subunit alpha protein-coding gene NA Ectoderm Brain 0.0 0.159091 0.0075188 0.00779135 +Mm Hs PTAFR Microglia NA 0.018 platelet activating factor receptor protein-coding gene NA Ectoderm Brain 0.0 0.129545 0.00657895 0.0180258 +Mm Hs LAG3 Microglia CD223 0.011 lymphocyte activating 3 protein-coding gene 1 Ectoderm Brain 0.0 0.211364 0.0106516 0.00574447 +Mm IL6RA Microglia NA 0.018 interleukin 6 receptor, alpha protein coding gene 1 Ectoderm Brain 0.0 0.229545 0.0 0.016243 +Mm Hs ENTPD1 Microglia NTPDase-1|ATPDase|SPG64|CD39 0.014 ectonucleoside triphosphate diphosphohydrolase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.193182 0.00657895 0.0100363 +Mm Hs ADRB2 Microglia ADRBR|B2AR|ADRB2R 0.016 adrenoceptor beta 2 protein-coding gene 1 Ectoderm Brain 0.0 0.152273 0.0100251 0.0142621 +Mm Hs TMEM173 Microglia FLJ38577|NET23|MPYS|STING|MITA 0.012 transmembrane protein 173 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00501253 0.0 +Mm Hs TBXAS1 Microglia CYP5|CYP5A1|THAS|TXS|TXAS 0.013 thromboxane A synthase 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs P2RY6 Microglia P2Y6 0.018 pyrimidinergic receptor P2Y6 protein-coding gene 1 Ectoderm Brain 0.0 0.202273 0.00281955 0.0167052 +Mm Hs P2RY13 Microglia FKSG77|P2Y13|GPR94|GPR86 0.008 purinergic receptor P2Y13 protein-coding gene 1 Ectoderm Brain 0.0 0.325 0.00125313 0.000858369 +Mm Hs CEBPA Microglia C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene 1 Ectoderm Brain 0.0 0.193182 0.0 0.0252228 +Mm Hs CD180 Microglia RP105|Ly78|LY64 0.012 CD180 molecule protein-coding gene 1 Ectoderm Brain 0.0 0.181818 0.00093985 0.00937603 +Mm Hs MYO1F Microglia NA 0.031 myosin IF protein-coding gene NA Ectoderm Brain 0.0 0.0863636 0.0281955 0.0289865 +Mm FCRLS Microglia NA 0.038 Fc receptor-like S, scavenger receptor protein coding gene 1 Ectoderm Brain 0.0 0.938636 0.0 0.0220535 +Mm Hs OLFML3 Microglia HNOEL-iso|OLF44 0.053 olfactomedin like 3 protein-coding gene 1 Ectoderm Brain 0.0 0.8 0.031015 0.0365137 +Mm SIGLECH Microglia NA 0.021 sialic acid binding Ig-like lectin H protein coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs S100A8 Microglia P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0798872 0.0 +Mm Hs LTC4S Microglia MGC33147 0.037 leukotriene C4 synthase protein-coding gene 1 Ectoderm Brain 0.0 0.8 0.00783208 0.0229119 +Mm Hs TGFBR1 Microglia ALK-5|ALK5|TBRI|TBR-i|MSSE|ESS1 0.031 transforming growth factor beta receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0 +Mm Hs S100A9 Microglia MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.103383 0.0 +Mm Hs LPCAT2 Microglia FLJ20481|AGPAT11|LysoPAFAT|AYTL1 0.034 lysophosphatidylcholine acyltransferase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.743182 0.00469925 0.0213932 +Mm Hs ITGB5 Microglia NA 0.047 integrin subunit beta 5 protein-coding gene 1 Ectoderm Brain 0.0 0.731818 0.0150376 0.0358534 +Mm Hs LAIR1 Microglia CD305 0.027 leukocyte associated immunoglobulin like receptor 1 protein-coding gene NA Ectoderm Brain 0.0 0.454545 0.0159774 0.0178277 +Mm Hs SPHK1 Microglia SPHK 0.016 sphingosine kinase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0369674 0.0 +Mm Hs COLEC12 Microglia SRCL|CL-P1|SCARA4 0.025 collectin subfamily member 12 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0119048 0.0285903 +Mm Hs ALDH1A2 Microglia RALDH2 0.011 aldehyde dehydrogenase 1 family member A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0250627 0.00845163 +Mm Hs AEBP1 Microglia ACLP 0.044 AE binding protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0335213 0.048927 +Mm Hs PTGDS Microglia L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene NA Ectoderm Brain 0.0 0.0386364 0.0582707 0.0555959 +Mm Hs CCR5 Microglia CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene 1 Ectoderm Brain 0.0 0.284091 0.0 0.0106306 +Mm Hs SLCO2B1 Microglia OATP-B|OATP2B1|SLC21A9 0.021 solute carrier organic anion transporter family member 2B1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00407268 0.0 +Mm Hs PTGS1 Microglia PGHS-1|PTGHS 0.029 prostaglandin-endoperoxide synthase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.465909 0.0037594 0.0235061 +Mm Hs APBB1IP Microglia INAG1|RIAM 0.052 amyloid beta precursor protein binding family B member 1 interacting protein protein-coding gene 1 Ectoderm Brain 0.0 0.343182 0.02099 0.0505117 +Mm Hs CYFIP1 Microglia KIAA0068|P140SRA-1|SHYC 0.051 cytoplasmic FMR1 interacting protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.513636 0.0159774 0.0467481 +Mm Hs CYTH4 Microglia CYT4|cytohesin-4|PSCD4 0.053 cytohesin 4 protein-coding gene 1 Ectoderm Brain 0.0 0.722727 0.00219298 0.0445692 +Mm Hs MERTK Microglia mer|RP38|c-Eyk|Tyro12 0.016 MER proto-oncogene, tyrosine kinase protein-coding gene 1 Ectoderm Brain 0.0 0.293182 0.00093985 0.0118851 +Mm Hs MAFB Microglia KRML 0.053 MAF bZIP transcription factor B protein-coding gene 1 Ectoderm Brain 0.0 0.418182 0.0592105 0.0422582 +Mm Hs HPGDS Microglia GSTS|H-PGDS|PGD2|GSTS1-1|GSTS1 0.033 hematopoietic prostaglandin D synthase protein-coding gene 1 Ectoderm Brain 0.0 0.736364 0.0184837 0.0168372 +Mm Hs BIN2 Microglia BRAP-1 0.06 bridging integrator 2 protein-coding gene NA Ectoderm Brain 0.0 0.388636 0.0463659 0.0527567 +Mm FCGR1 Microglia NA 0.023 Fc receptor, IgG, high affinity I protein coding gene 1 Ectoderm Brain 0.0 0.340909 0.0 0.0187521 +None FAM105A Microglia NA 0.045 NA NA 1 Ectoderm Brain 0.0 0.538636 0.0272556 0.0352592 +Mm Hs CMTM6 Microglia FLJ20396|CKLFSF6 0.051 CKLF like MARVEL transmembrane domain containing 6 protein-coding gene NA Ectoderm Brain 0.0 0.465909 0.0504386 0.0387587 +Mm Hs CCL4 Microglia MIP-1-beta|Act-2|AT744.1|SCYA4 0.049 C-C motif chemokine ligand 4 protein-coding gene 1 Ectoderm Brain 0.0 0.556818 0.0557644 0.0342027 +Mm Hs CCL3 Microglia G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Ectoderm Brain 0.0 0.565909 0.00783208 0.0273358 +Mm Hs CCRL2 Microglia CRAM-B|CKRX|CRAM-A|ACKR5 0.018 C-C motif chemokine receptor like 2 protein-coding gene 1 Ectoderm Brain 0.0 0.120455 0.00156642 0.0191482 +Mm Hs UCP2 Microglia SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00501253 0.0 +Mm Hs CLEC3B Microglia TNA 0.021 C-type lectin domain family 3 member B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0275338 +Mm Hs MRC2 Microglia KIAA0709|ENDO180|CLEC13E|CD280 0.012 mannose receptor C type 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0213033 0.0112909 +Mm Hs CLEC10A Microglia HML2|HML|CD301|CLECSF14 0.01 C-type lectin domain containing 10A protein-coding gene 1 Ectoderm Brain 0.0 0.00681818 0.0119048 0.0097722 +Mm Hs PF4 Microglia SCYB4|CXCL4 0.029 platelet factor 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0636364 0.00344612 0.0343348 +Mm CTS3 Microglia NA 0.0 cathepsin 3 protein coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.000132057 +Mm FCGR3 Microglia NA 0.073 Fc receptor, IgG, low affinity III protein coding gene 1 Ectoderm Brain 0.0 0.936364 0.0 0.0635193 +Mm Hs CD53 Microglia TSPAN25|MOX44 0.153 CD53 molecule protein-coding gene 1 Ectoderm Brain 0.0 0.877273 0.121867 0.137207 +Mm Hs FOS Microglia c-fos 0.395 Fos proto-oncogene, AP-1 transcription factor subunit protein-coding gene 1 Ectoderm Brain 0.0 0.609091 0.495927 0.374117 +Mm Hs EGR1 Microglia TIS8|G0S30|NGFI-A|KROX-24|ZIF-268|AT225|ZNF225 0.202 early growth response 1 protein-coding gene 1 Ectoderm Brain 0.0 0.397727 0.187657 0.202971 +Mm Hs AIF1 Microglia IRT-1|AIF-1|Em:AF129756.17|IBA1 0.085 allograft inflammatory factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.929545 0.130952 0.0516342 +Mm Hs CTSS Microglia NA 0.129 cathepsin S protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.134398 0.101222 +Mm Hs CSF1R Microglia C-FMS|CSFR|CD115|FMS 0.064 colony stimulating factor 1 receptor protein-coding gene 1 Ectoderm Brain 0.0 0.997727 0.0178571 0.0490591 +Mm Hs SKI Microglia NA 0.034 SKI proto-oncogene protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs C1QB Microglia NA 0.071 complement C1q B chain protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0191103 0.0567184 +Mm Hs RGS1 Monocytes 1R20|IR20|BL34|IER1 0.049 regulator of G protein signaling 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0644346 0.0 +Hs APOBEC3A Monocytes PHRBN 0.001 apolipoprotein B mRNA editing enzyme catalytic subunit 3A protein-coding gene 1 Mesoderm Immune system 0.192308 0.0 0.0028427 0.0 +Mm Hs CD7 Monocytes LEU-9|TP41|Tp40 0.03 CD7 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.104548 0.0161083 +Mm Hs TET2 Monocytes FLJ20032|KIAA1546 0.008 tet methylcytosine dioxygenase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00442198 0.0 +Mm Hs CD40 Monocytes Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Immune system 0.0769231 0.666667 0.0126342 0.0107175 +Mm Hs DYSF Monocytes FER1L1|LGMD2B 0.002 dysferlin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00315856 0.00147606 +Mm Hs CMKLR1 Monocytes RVER1 0.003 chemerin chemokine-like receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000315856 0.00314465 +Mm Hs MEFV Monocytes FMF|TRIM20 0.0 MEFV, pyrin innate immunity regulator protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00019253 +Mm Hs HCK Monocytes JTK9 0.031 HCK proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0384615 0.666667 0.0227416 0.0336285 +Hs FCGR3B Monocytes CD16b 0.0 Fc fragment of IgG receptor IIIb protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs PADI4 Monocytes PDI5|PDI4|PADI5 0.005 peptidyl arginine deiminase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000947568 0.00545501 +Mm Hs GHSR Monocytes NA 0.0 growth hormone secretagogue receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs ITGAX Monocytes CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.0384615 0.0 0.0161087 0.00526248 +Mm Hs SELE Monocytes ESEL|CD62E|ELAM1|ELAM 0.001 selectin E protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00536955 0.0 +Mm Hs TLR4 Monocytes hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000315856 0.0 +Mm Hs AR Monocytes AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00189514 0.01598 +Mm Hs CXCR4 Monocytes LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.269231 0.666667 0.197726 0.00866384 +Mm Hs CD86 Monocytes B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.0769231 0.666667 0.0116867 0.029072 +Mm Hs CCR2 Monocytes CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0263124 +Mm Hs TNFRSF14 Monocytes HVEM|ATAR|LIGHTR|HVEA|CD270 0.019 TNF receptor superfamily member 14 protein-coding gene 1 Mesoderm Immune system 0.0384615 0.0 0.0243209 0.0 +Hs ADA2 Monocytes ADGF|IDGFL|CECR1 0.002 adenosine deaminase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0129501 0.0 +Mm Hs MGMT Monocytes NA 0.027 O-6-methylguanine-DNA methyltransferase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0862287 0.0100116 +Mm Hs CD14 Monocytes NA 0.051 CD14 molecule protein-coding gene 1 Mesoderm Immune system 0.269231 0.666667 0.0246368 0.0553844 +Mm Hs CD33 Monocytes SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0126342 0.0172635 +Mm Hs ITGAM Monocytes CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00315856 0.0302914 +Mm Hs ACE Monocytes ACE1|CD143|DCP1 0.022 angiotensin I converting enzyme protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0259002 0.0216275 +Mm Hs FUT4 Monocytes FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000705943 +Mm Hs ICAM1 Monocytes CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00600126 0.0100116 +Mm Hs SELL Monocytes LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene 1 Mesoderm Immune system 0.269231 0.0 0.0584334 0.0 +Mm Hs CD163 Monocytes MM130|SCARI1 0.005 CD163 molecule protein-coding gene 1 Mesoderm Immune system 0.0769231 0.0 0.00663298 0.00429983 +Hs FCGR1A Monocytes CD64|CD64A 0.001 Fc fragment of IgG receptor Ia protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00379027 0.0 +Mm Hs FCGR2B Monocytes CD32B 0.031 Fc fragment of IgG receptor IIb protein-coding gene 1 Mesoderm Immune system 0.0 0.666667 0.00473784 0.0359389 +Mm Hs ACP5 Monocytes HPAP 0.033 acid phosphatase 5, tartrate resistant protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0183196 0.0365807 +Mm Hs MRC1 Monocytes CLEC13D|CD206|bA541I19.1|CLEC13DL|MRC1L1 0.029 mannose receptor C-type 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00979154 0.0347195 +Mm Hs TNF Monocytes TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00126342 0.0 +Mm Hs PLAU Monocytes URK 0.01 plasminogen activator, urokinase protein-coding gene NA Mesoderm Immune system 0.153846 0.0 0.0429564 0.00250289 +Hs GBP1 Monocytes NA 0.004 guanylate binding protein 1 protein-coding gene 1 Mesoderm Immune system 0.384615 0.0 0.0224258 0.0 +Hs OAS1 Monocytes OIASI|IFI-4|OIAS 0.005 2'-5'-oligoadenylate synthetase 1 protein-coding gene 1 Mesoderm Immune system 0.692308 0.0 0.0161087 0.0 +Mm Hs IRF7 Monocytes NA 0.033 interferon regulatory factor 7 protein-coding gene 1 Mesoderm Immune system 0.538462 1.0 0.0243209 0.0320883 +Mm Hs PLSCR1 Monocytes MMTRA1B 0.023 phospholipid scramblase 1 protein-coding gene 1 Mesoderm Immune system 0.692308 0.0 0.0590651 0.0135413 +Mm Hs MX1 Monocytes IFI-78K|MxA 0.008 MX dynamin like GTPase 1 protein-coding gene 1 Mesoderm Immune system 0.692308 1.0 0.0170562 0.00378642 +Mm Hs IL1RN Monocytes ICIL-1RA|IL1F3|IL-1RN|MGC10430 0.013 interleukin 1 receptor antagonist protein-coding gene 1 Mesoderm Immune system 0.269231 1.0 0.0176879 0.0112309 +Hs HLA-DRA Monocytes HLA-DRA1 0.039 major histocompatibility complex, class II, DR alpha protein-coding gene NA Mesoderm Immune system 0.576923 0.0 0.209413 0.0 +Mm Hs IFIT1 Monocytes GARG-16|G10P1|IFI56|IFNAI1 0.015 interferon induced protein with tetratricopeptide repeats 1 protein-coding gene 1 Mesoderm Immune system 0.692308 1.0 0.0104232 0.013092 +Mm Hs IDO1 Monocytes IDO|INDO 0.003 indoleamine 2,3-dioxygenase 1 protein-coding gene 1 Mesoderm Immune system 0.192308 0.0 0.00852811 0.00128353 +Mm Hs IFIT3 Monocytes ISG60|RIG-G|CIG-49|IFI60|GARG-49|IRG2|IFIT4 0.014 interferon induced protein with tetratricopeptide repeats 3 protein-coding gene 1 Mesoderm Immune system 0.692308 1.0 0.0164245 0.0112309 +Mm Hs TNFSF10 Monocytes TRAIL|Apo-2L|TL2|CD253 0.014 TNF superfamily member 10 protein-coding gene NA Mesoderm Immune system 0.653846 0.0 0.0596968 0.0 +Mm Hs CXCL10 Monocytes IFI10|IP-10|crg-2|mob-1|C7|gIP-10|INP10|SCYB10 0.009 C-X-C motif chemokine ligand 10 protein-coding gene 1 Mesoderm Immune system 0.461538 1.0 0.00631712 0.00872802 +Mm Hs S100A9 Monocytes MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Immune system 0.576923 0.0 0.0994946 0.0 +Mm Hs S100A8 Monocytes P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.384615 0.0 0.0773847 0.0 +Mm Hs S100A4 Monocytes P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.5 0.0 0.370183 0.0 +Mm Hs CLEC7A Monocytes dectin-1|hDectin-1|CD369|SCARE2|CLECSF12 0.03 C-type lectin domain containing 7A protein-coding gene 1 Mesoderm Immune system 0.269231 1.0 0.0448515 0.0249005 +Mm Hs CSF3R Monocytes GCSFR|CD114 0.012 colony stimulating factor 3 receptor protein-coding gene 1 Mesoderm Immune system 0.230769 0.333333 0.0195831 0.0108458 +Mm Hs MNDA Monocytes PYHIN3 0.019 myeloid cell nuclear differentiation antigen protein-coding gene 1 Mesoderm Immune system 0.461538 1.0 0.0426406 0.0128995 +Hs MS4A6A Monocytes CD20L3|MS4A6 0.007 membrane spanning 4-domains A6A protein-coding gene 1 Mesoderm Immune system 0.346154 0.0 0.0375869 0.0 +Mm Hs ZFP36L2 Monocytes ERF2|RNF162C|TIS11D|BRF2 0.103 ZFP36 ring finger protein like 2 protein-coding gene NA Mesoderm Immune system 0.384615 0.0 0.418509 0.0 +Mm Hs LTA4H Monocytes NA 0.053 leukotriene A4 hydrolase protein-coding gene NA Mesoderm Immune system 0.153846 0.0 0.0735944 0.0431267 +Mm Hs CLEC12A Monocytes CLL-1|MICL|CD371|DCAL-2 0.009 C-type lectin domain family 12 member A protein-coding gene 1 Mesoderm Immune system 0.115385 0.0 0.00821226 0.00757284 +Mm Hs CD48 Monocytes BLAST|mCD48|hCD48|SLAMF2|BCM1 0.076 CD48 molecule protein-coding gene 1 Mesoderm Immune system 0.269231 0.333333 0.114972 0.0653318 +Mm Hs PRTN3 Monocytes PR-3|ACPA|C-ANCA|AGP7|MBT|P29 0.026 proteinase 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0113708 0.0276601 +Hs FCGR3A Monocytes CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene 1 Mesoderm Immune system 0.0384615 0.0 0.0353759 0.0 +Mm Hs VCAN Monocytes PG-M|CSPG2 0.056 versican protein-coding gene 1 Mesoderm Immune system 0.307692 0.0 0.0950726 0.0 +Mm LY6C2 Monocytes NA 0.039 lymphocyte antigen 6 complex, locus C2 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0448595 +Mm Hs IFITM3 Monocytes 1-8U|DSPA2b 0.33 interferon induced transmembrane protein 3 protein-coding gene 1 Mesoderm Immune system 0.461538 1.0 0.419141 0.304005 +Mm Hs FN1 Monocytes CIG|LETS|GFND2|FINC 0.091 fibronectin 1 protein-coding gene 1 Mesoderm Immune system 0.0769231 0.0 0.0994946 0.0869593 +Mm Hs ADGRE1 Monocytes TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000631712 0.0413297 +Mm Hs CD44 Monocytes IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Immune system 0.5 1.0 0.2988 0.0876011 +Mm Hs CSF1R Monocytes C-FMS|CSFR|CD115|FMS 0.064 colony stimulating factor 1 receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.666667 0.0180038 0.0757284 +Mm Hs CX3CR1 Monocytes CMKDR1|V28|GPR13|CMKBRL1 0.039 C-X3-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00221099 0.0482608 +Mm Hs ITGAL Monocytes CD11A 0.013 integrin subunit alpha L protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00410613 0.0148248 +Mm LY6C1 Monocytes NA 0.054 lymphocyte antigen 6 complex, locus C1 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0664228 +Mm LY6G Monocytes NA 0.007 lymphocyte antigen 6 complex, locus G protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0090489 +Mm Hs PECAM1 Monocytes CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0445357 0.0535233 +Mm Hs PTPRC Monocytes T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Immune system 0.615385 1.0 0.212887 0.10602 +Mm Hs SPN Monocytes LSN|CD43|GPL115 0.029 sialophorin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0511687 0.0 +Mm Hs PSAP Monocytes GLBA 0.588 prosaposin protein-coding gene 1 Mesoderm Immune system 0.615385 1.0 0.497473 0.610191 +Hs FCN1 Monocytes FCNM 0.007 ficolin 1 protein-coding gene 1 Mesoderm Immune system 0.461538 0.0 0.0322173 0.0 +Hs LYZ Monocytes NA 0.008 lysozyme protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs RHOC Monocytes RhoC|ARH9|ARHC 0.205 ras homolog family member C protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs PILRA Monocytes FDF03 0.016 paired immunoglobin like type 2 receptor alpha protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs NFKBIZ Monocytes MAIL|FLJ34463|INAP 0.08 NFKB inhibitor zeta protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs NAAA Monocytes ASAHL 0.025 N-acylethanolamine acid amidase protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs LY6E Monocytes TSA-1|RIG-E|SCA-2 0.345 lymphocyte antigen 6 family member E protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs LYN Monocytes JTK8 0.062 LYN proto-oncogene, Src family tyrosine kinase protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs MS4A7 Monocytes CD20L4|CFFM4|MS4A8 0.027 membrane spanning 4-domains A7 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CEBPB Monocytes NFIL6|IL6DBP|C/EBP-beta|TCF5 0.138 CCAAT enhancer binding protein beta protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CD68 Monocytes SCARD1|macrosialin|DKFZp686M18236|LAMP4 0.063 CD68 molecule protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs IFI30 Monocytes IFI-30|GILT|IP30|MGC32056|IP-30 0.078 IFI30, lysosomal thiol reductase protein-coding gene NA Mesoderm Immune system NA NA NA NA +Hs S100A12 Monocytes CGRP|CAAF1|CAGC|ENRAGE 0.003 S100 calcium binding protein A12 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Hs SERPINA1 Monocytes AAT|A1A|PI1|alpha-1-antitrypsin|A1AT|alpha1AT|PI 0.016 serpin family A member 1 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs RGS2 Monocytes G0S8 0.128 regulator of G protein signaling 2 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs LST1 Monocytes B144|D6S49E 0.082 leukocyte specific transcript 1 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs SPI1 Monocytes PU.1|SPI-A|SFPI1|SPI-1 0.094 Spi-1 proto-oncogene protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs TYMP Monocytes MNGIE|ECGF1 0.011 thymidine phosphorylase protein-coding gene NA Mesoderm Immune system NA NA NA NA +Hs CSTA Monocytes STF1|STFA 0.012 cystatin A protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs FGL2 Monocytes pT49|T49 0.03 fibrinogen like 2 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs PYCARD Monocytes CARD5|ASC 0.147 PYD and CARD domain containing protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs LYST Monocytes CHS 0.015 lysosomal trafficking regulator protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CCL3 Monocytes G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs IL1B Monocytes IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CFP Monocytes PFC 0.035 complement factor properdin protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs CD36 Monocytes SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs ISL1 Motor neurons Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0134712 0.0313763 +Mm Hs MNX1 Motor neurons HB9|HOXHB9|SCRA1|HLXB9 0.0 motor neuron and pancreas homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ISL2 Motor neurons FLJ10160 0.004 ISL LIM homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00519731 +Mm Hs CHAT Motor neurons NA 0.001 choline O-acetyltransferase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00160411 +Mm Hs VSX2 Motor neurons RET1|HOX10|CHX10 0.004 visual system homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs EN1 Motor neurons NA 0.003 engrailed homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00372153 +Mm Hs EVX1 Motor neurons NA 0.0 even-skipped homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00250627 6.41643e-05 +Mm Hs EVX2 Motor neurons NA 0.0 even-skipped homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs FGF1 Motor neurons AFGF|ECGF|ECGFA|ECGFB|HBGF1|ECGF-beta|FGF-alpha|GLIO703|FGFA 0.011 fibroblast growth factor 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00313283 0.0125762 +Mm Hs LHX3 Motor neurons NA 0.001 LIM homeobox 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.000834135 +Mm Hs NKX6-1 Motor neurons Nkx6.1|NKX6A 0.006 NK6 homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0103383 0.00526147 +Mm Hs NGFR Motor neurons TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00219298 0.00744305 +Mm REG2 Motor neurons NA 0.0 regenerating islet-derived 2 protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs SIM1 Motor neurons bHLHe14 0.0 SIM bHLH transcription factor 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs TLR2 Müller cells TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00093985 0.0 +Mm Hs IL6 Müller cells IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0134712 0.0064885 +Mm Hs CNR2 Müller cells CB2 0.0 cannabinoid receptor 2 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0 6.42426e-05 +Mm Hs VEGFA Müller cells VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0247494 0.0 +Mm Hs SLC38A5 Müller cells SN2|JM24 0.02 solute carrier family 38 member 5 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0228697 0.0 +Mm Hs SLC38A3 Müller cells SN1 0.018 solute carrier family 38 member 3 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00125313 0.0 +Mm Hs IL33 Müller cells DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Ectoderm Eye 0.0 0.578947 0.0106516 0.0199152 +Mm Hs RDH10 Müller cells SDR16C4 0.012 retinol dehydrogenase 10 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0181704 0.0 +Mm Hs SLITRK2 Müller cells KIAA1854|SLITL1|TMEM257|CXorf1 0.006 SLIT and NTRK like family member 2 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00156642 0.0 +Mm Hs SYNPR Müller cells MGC26651 0.022 synaptoporin protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00093985 0.0 +Mm ABCA8A Müller cells NA 0.01 ATP-binding cassette, sub-family A (ABC1), member 8a protein coding gene 1 Ectoderm Eye 0.0 0.684211 0.0 0.0111782 +Mm Hs CROT Müller cells NA 0.009 carnitine O-octanoyltransferase protein-coding gene NA Ectoderm Eye 0.0 0.684211 0.00469925 0.0095079 +Mm Hs CRYM Müller cells DFNA40 0.015 crystallin mu protein-coding gene NA Ectoderm Eye 0.0 0.736842 0.00156642 0.0181164 +Mm CAR14 Müller cells NA 0.002 carbonic anhydrase 14 protein coding gene 1 Ectoderm Eye 0.0 0.789474 0.0 0.00199152 +Mm Hs COL9A1 Müller cells NA 0.006 collagen type IX alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.00657895 0.00513941 +Mm Hs SIX3OS1 Müller cells NA 0.005 SIX homeobox 3, opposite strand 1 unclassified non-coding RNA ge NA Ectoderm Eye NA NA NA NA +Mm Hs DAPL1 Müller cells NA 0.009 death associated protein like 1 protein-coding gene NA Ectoderm Eye 0.0 1.0 0.00783208 0.00835154 +Mm Hs AQP4 Müller cells MIWC 0.024 aquaporin 4 protein-coding gene 1 Ectoderm Eye 0.0 0.842105 0.00595238 0.0283952 +Mm Hs RLBP1 Müller cells CRALBP 0.028 retinaldehyde binding protein 1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs DKK3 Müller cells REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.037594 0.0342413 +Mm Hs VSX2 Müller cells RET1|HOX10|CHX10 0.004 visual system homeobox 2 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs COL1A1 Müller cells NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0999373 0.073365 +Mm Hs COL2A1 Müller cells STL1|SEDC|AOM 0.009 collagen type II alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.473684 0.0119048 0.00642426 +Mm Hs COL3A1 Müller cells EDS4A 0.086 collagen type III alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0993108 0.0813311 +Mm Hs COL4A2 Müller cells FLJ22259|DKFZp686I14213 0.094 collagen type IV alpha 2 chain protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0811404 0.0963639 +Mm Hs COL5A1 Müller cells NA 0.028 collagen type V alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0357143 0.0249904 +Mm Hs COL6A1 Müller cells NA 0.063 collagen type VI alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0902256 0.0556341 +Mm Hs COL11A1 Müller cells STL2|CO11A1|COLL6 0.009 collagen type XI alpha 1 chain protein-coding gene 1 Ectoderm Eye 0.0 0.105263 0.00971178 0.00860851 +Mm Hs GLUL Müller cells GLNS 0.298 glutamate-ammonia ligase protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.300439 0.304446 +Mm Hs CLU Müller cells SGP-2|SP-40|TRPM-2|KUB1|CLU2|CLI|APOJ 0.168 clusterin protein-coding gene 1 Ectoderm Eye 0.0 0.947368 0.216165 0.161891 +Mm Hs S100A16 Müller cells S100F|DT1P1A7|MGC17528 0.192 S100 calcium binding protein A16 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.179198 0.0 +Mm Hs SOX2 Müller cells NA 0.082 SRY-box 2 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0288221 0.0 +Mm Hs APOE Müller cells AD2 0.343 apolipoprotein E protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.132519 0.388668 +Mm Hs DBI Müller cells ACBD1 0.597 diazepam binding inhibitor, acyl-CoA binding protein protein-coding gene 1 Ectoderm Eye 0.0 0.947368 0.468358 0.621483 +Mm Hs GNAI2 Müller cells GNAI2B 0.46 G protein subunit alpha i2 protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.18609 0.520429 +Mm Hs GPR37 Müller cells EDNRBL|hET(B)R-LP|PAELR 0.034 G protein-coupled receptor 37 protein-coding gene 1 Ectoderm Eye 0.0 0.736842 0.00469925 0.0402801 +Mm Hs KCNJ2 Müller cells Kir2.1|IRK1|LQT7 0.002 potassium voltage-gated channel subfamily J member 2 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00971178 0.00025697 +Mm Hs KCNJ10 Müller cells Kir4.1|Kir1.2 0.046 potassium voltage-gated channel subfamily J member 10 protein-coding gene 1 Ectoderm Eye 0.0 0.105263 0.00219298 0.0565977 +Mm Hs SPC25 Müller cells MGC22228|AD024|SPBC25 0.062 SPC25, NDC80 kinetochore complex component protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0216165 0.0 +Mm Hs ITM2B Müller cells BRI|E25B|E3-16|BRICD2B|BRI2 0.854 integral membrane protein 2B protein-coding gene 1 Ectoderm Eye 0.0 1.0 0.736216 0.890852 +Mm Hs ATG4B Müller cells Apg4B|KIAA0943|DKFZp586D1822|APG4B 0.025 autophagy related 4B cysteine peptidase protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0394737 0.0213928 +Hs CA2 Müller cells Car2|CA-II|CAII 0.011 carbonic anhydrase 2 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0648496 0.0 +Mm Hs ZBED4 Müller cells KIAA0637 0.0 zinc finger BED-type containing 4 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.000626566 0.0 +Mm Hs PRDX6 Müller cells AOP2|KIAA0106|1-Cys|NSGPx|PRX|aiPLA2|MGC46173 0.396 peroxiredoxin 6 protein-coding gene 1 Ectoderm Eye 0.0 0.947368 0.473684 0.369523 +Mm Hs SLC1A3 Müller cells EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0109649 0.0 +Mm Hs HES1 Müller cells FLJ20408|HES-1|Hes1|bHLHb39|HRY 0.129 hes family bHLH transcription factor 1 protein-coding gene 1 Ectoderm Eye 0.0 0.947368 0.145677 0.126622 +Mm Hs KIT Müller cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00250627 0.0185661 +Mm Hs CRB1 Müller cells LCA8|RP12 0.0 crumbs 1, cell polarity complex component protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs ANXA4 Müller cells ANX4 0.06 annexin A4 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0736216 0.0565977 +Mm Hs CD44 Müller cells IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.300439 0.0878839 +Mm GSTT1 Müller cells NA 0.022 glutathione S-transferase theta 1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0280098 +Mm Hs GSTM5 Müller cells NA 0.201 glutathione S-transferase mu 5 protein-coding gene 1 Ectoderm Eye 0.0 0.105263 0.00532581 0.250096 +Mm Hs SLC6A1 Müller cells GAT1|GABATR|GABATHG 0.043 solute carrier family 6 member 1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00313283 0.0 +Mm Hs SFTPA1 Müller cells SP-A|SP-A1|COLEC4|SFTP1 0.015 surfactant protein A1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0178571 0.0 +Mm Hs ITGAM Myeloid-derived suppressor cells CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene NA mesoderm Immune system 0.0 0.0 0.00313283 0.0302855 +Mm Hs FUT4 Myeloid-derived suppressor cells FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.000705807 +Mm Hs CD33 Myeloid-derived suppressor cells SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0125313 0.0172602 +Hs CEACAM8 Myeloid-derived suppressor cells CD66b|CGM6 0.0 carcinoembryonic antigen related cell adhesion molecule 8 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs IL4R Myeloid-derived suppressor cells CD124 0.002 interleukin 4 receptor protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0103383 0.0 +Mm Hs CCR2 Myeloid-derived suppressor cells CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.0263073 +Hs CD1D Myeloid-derived suppressor cells NA 0.0 CD1d molecule protein-coding gene NA mesoderm Immune system 0.0 0.0 0.00093985 0.0 +Hs FCGR3A Myeloid-derived suppressor cells CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene NA mesoderm Immune system 0.0 0.0 0.035401 0.0 +Mm Hs ICAM1 Myeloid-derived suppressor cells CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.00595238 0.0100096 +Mm Hs CD80 Myeloid-derived suppressor cells B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.000192493 +Mm Hs CXCR1 Myeloid-derived suppressor cells CDw128a|CD181|CMKAR1|IL8RA 0.0 C-X-C motif chemokine receptor 1 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.000128329 +Mm Hs ADGRE1 Myeloid-derived suppressor cells TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.000626566 0.0413218 +None GR1 Myeloid-derived suppressor cells NA 0.0 NA NA NA mesoderm Immune system NA NA NA NA +Mm LY6G Myeloid-derived suppressor cells NA 0.007 lymphocyte antigen 6 complex, locus G protein coding gene NA mesoderm Immune system 0.0 0.0 0.0 0.00904716 +Mm Hs S100A9 Myeloid-derived suppressor cells MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 mesoderm Immune system 0.0 0.0 0.103383 0.0 +Mm Hs S100A4 Myeloid-derived suppressor cells P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 mesoderm Immune system 0.0 0.0 0.371241 0.0 +Mm Hs S100A8 Myeloid-derived suppressor cells P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene NA mesoderm Immune system 0.0 0.0 0.0798872 0.0 +Mm Hs MYOG Myoblasts bHLHc3|MYF4 0.002 myogenin protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0714286 0.000313283 0.00160555 +Mm Hs LIF Myoblasts CDF|HILDA 0.002 LIF, interleukin 6 family cytokine protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00532581 0.00109177 +Mm Hs NGF Myoblasts NGFB 0.003 nerve growth factor protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.000626566 0.00346799 +Mm Hs IGF2 Myoblasts FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0714286 0.0463659 0.000834885 +Mm Hs ANGPT2 Myoblasts Ang2 0.004 angiopoietin 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0159774 0.00186244 +Mm Hs ACHE Myoblasts YT 0.016 acetylcholinesterase (Cartwright blood group) protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00469925 0.0195877 +Mm Hs ADAM12 Myoblasts MCMPMltna|MLTN 0.007 ADAM metallopeptidase domain 12 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00626566 0.00764241 +Mm Hs TPM2 Myoblasts NEM4|AMCD1 0.075 tropomyosin 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.14693 0.0 +Mm Hs ENO3 Myoblasts NA 0.01 enolase 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.142857 0.000313283 0.0105966 +Mm Hs DES Myoblasts CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Skeletal muscle 0.0 1.0 0.0093985 0.0224135 +Mm Hs CDH15 Myoblasts CDH3 0.003 cadherin 15 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.714286 0.00156642 0.00244043 +Mm Hs CAPN1 Myoblasts muCANP|muCL|CANPL1 0.018 calpain 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0479323 0.0107251 +Mm Hs MYF6 Myoblasts MRF4|bHLHc4 0.0 myogenic factor 6 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.000128444 +Mm Hs MYF5 Myoblasts bHLHc2 0.001 myogenic factor 5 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 1.0 0.0 0.00102755 +Mm Hs MYOD1 Myoblasts MYOD|bHLHc1|MYF3 0.004 myogenic differentiation 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.714286 0.000626566 0.00269732 +Mm Hs PAX3 Myoblasts HUP2|WS1 0.004 paired box 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00407268 0.00385332 +Mm Hs PAX7 Myoblasts Hup1 0.001 paired box 7 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.5 0.00093985 0.000449554 +Mm Hs TBX3 Myoblasts TBX3-ISO|XHL|UMS 0.024 T-box 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0303885 0.0 +Mm Hs TTN Myoblasts CMPD4|FLJ32040|TMD|CMH9|LGMD2J|MYLK5|CMD1G 0.007 titin protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0112782 0.0 +Mm Hs MUSK Myoblasts NA 0.002 muscle associated receptor tyrosine kinase protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.928571 0.0 0.00192666 +Mm Hs FLNC Myoblasts ABPL|FLN2 0.01 filamin C protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.571429 0.00250627 0.00989018 +Mm Hs FGFR4 Myoblasts JTK2|CD334 0.003 fibroblast growth factor receptor 4 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.857143 0.00344612 0.00134866 +Mm Hs STK40 Myoblasts MGC4796|SgK495 0.015 serine/threonine kinase 40 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0213033 0.0 +Mm Hs CXCL1 Myoblasts SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.642857 0.0457393 0.0299917 +Mm Hs TNFRSF12A Myoblasts FN14|TweakR|CD266 0.084 TNF receptor superfamily member 12A protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.150689 0.0 +Mm Hs ARL4D Myoblasts ARF4L 0.014 ADP ribosylation factor like GTPase 4D protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.5 0.0363409 0.00751397 +Mm Hs CCL2 Myoblasts MCP1|MCP-1|MCAF|SMC-CF|GDCF-2|HC11|MGC9434|SCYA2 0.037 C-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0714286 0.0648496 0.0318541 +Mm Hs MYD88 Myoblasts NA 0.013 myeloid differentiation primary response 88 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.00877193 0.0139362 +Mm Hs BRAF Myoblasts BRAF1 0.025 B-Raf proto-oncogene, serine/threonine kinase protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0714286 0.0159774 0.0277439 +Mm Hs EGFR Myoblasts ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.285714 0.0222431 0.0125233 +Mm Hs ZBTB16 Myoblasts PLZF|ZNF145 0.007 zinc finger and BTB domain containing 16 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0119048 0.0 +Mm Hs SIX1 Myoblasts DFNA23 0.014 SIX homeobox 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0269424 0.0 +Mm Hs PDZRN3 Myoblasts KIAA1095|SEMACAP3|LNX3 0.003 PDZ domain containing ring finger 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00156642 0.00276154 +Mm Hs ACTC1 Myocytes CMD1R|ACTC 0.011 actin, alpha, cardiac muscle 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.444444 0.0134712 0.00821777 +Mm Hs FHL2 Myocytes SLIM3|DRAL 0.043 four and a half LIM domains 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.10401 0.0285696 +Mm Hs ACTA1 Myocytes NEM3|ACTA 0.004 actin, alpha 1, skeletal muscle protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.888889 0.00250627 0.00365948 +Mm Hs TNNI1 Myocytes NA 0.009 troponin I1, slow skeletal type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00908521 0.0 +Mm Hs TNNI2 Myocytes NA 0.005 troponin I2, fast skeletal type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00344612 0.0 +Mm Hs TNNT1 Myocytes ANM|STNT|TNTS|FLJ98147|MGC104241|NEM5 0.014 troponin T1, slow skeletal type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0222431 0.0 +Mm Hs TNNT3 Myocytes DKFZp779M2348 0.001 troponin T3, fast skeletal type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.0 +Mm Hs TNNC1 Myocytes TNNC 0.005 troponin C1, slow skeletal and cardiac type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00093985 0.0 +Mm Hs TNNC2 Myocytes NA 0.0 troponin C2, fast skeletal type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00250627 0.0 +Mm Hs ACTN2 Myocytes NA 0.005 actinin alpha 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.222222 0.0 0.00635593 +Mm Hs ACTN3 Myocytes NA 0.001 actinin alpha 3 (gene/pseudogene) protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.777778 0.000313283 0.000256805 +Mm Hs ANKRD1 Myocytes C-193|ALRP|CVARP|MCARP 0.007 ankyrin repeat domain 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.00783208 0.00642013 +Mm Hs ANKRD2 Myocytes ARPP 0.0 ankyrin repeat domain 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0 0.0 +Mm Hs CAPZA3 Myocytes Gsg3|CAPPA3 0.007 capping actin protein of muscle Z-line subunit alpha 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0266291 0.00353107 +Mm Hs CLOCK Myocytes KIAA0334|KAT13D|bHLHe8 0.017 clock circadian regulator protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0350877 0.0136749 +Mm Hs DES Myocytes CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene NA Mesoderm Skeletal muscle 0.0 1.0 0.0093985 0.0227273 +Mm Hs DMD Myocytes DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85 0.012 dystrophin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.00469925 0.0142527 +Mm Hs IL4 Myocytes BSF1|IL-4|BCGF1|BCGF-1|MGC79402 0.002 interleukin 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.00269646 +Mm Hs ITGA7 Myocytes NA 0.003 integrin subunit alpha 7 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.00156642 0.00353107 +Mm Hs LAMA2 Myocytes LAMM 0.007 laminin subunit alpha 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.012218 0.00654854 +Mm Hs LAMB1 Myocytes NA 0.051 laminin subunit beta 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0463659 0.0523883 +Mm Hs LDB1 Myocytes NLI|CLIM2 0.015 LIM domain binding 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00093985 0.0187468 +Mm Hs LDB3 Myocytes PDLIM6|KIAA0613|ZASP|CMD1C 0.004 LIM domain binding 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.666667 0.00219298 0.00333847 +Mm Hs MSTN Myocytes GDF8 0.002 myostatin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.00237545 +Mm Hs MYH1 Myocytes MYHSA1|MYHa|MyHC-2X/D|MGC133384 0.0 myosin heavy chain 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0 0.0 +Mm Hs MYH4 Myocytes MYH2B|MyHC-2B|MyHC-IIb 0.0 myosin heavy chain 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.0 0.0 +Mm Hs MYH7 Myocytes CMD1S|CMH1|MPD1 0.001 myosin heavy chain 7 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.000313283 0.00166923 +Mm Hs MYH8 Myocytes MyHC-peri|MyHC-pn 0.0 myosin heavy chain 8 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0 0.0 +Mm Hs NBR1 Myocytes KIAA0049|1A1-3B|M17S2 0.026 NBR1, autophagy cargo receptor protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.222222 0.0457393 0.0226631 +Mm Hs NEB Myocytes NEB177D|NEM2 0.004 nebulin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.444444 0.000626566 0.00333847 +Mm Hs NID1 Myocytes entactin|NID 0.057 nidogen 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0175439 0.0683744 +Mm Hs NID2 Myocytes NA 0.001 nidogen 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.000770416 +Mm Hs TMOD4 Myocytes Sk-Tmod 0.0 tropomodulin 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs TPM2 Myocytes NEM4|AMCD1 0.075 tropomyosin 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.14693 0.0 +Mm Hs TTN Myocytes CMPD4|FLJ32040|TMD|CMH9|LGMD2J|MYLK5|CMD1G 0.007 titin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0112782 0.0 +Mm Hs MYF5 Myocytes bHLHc2 0.001 myogenic factor 5 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.00192604 +Mm Hs MYF6 Myocytes MRF4|bHLHc4 0.0 myogenic factor 6 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.222222 0.000313283 0.0 +Mm Hs MYOD1 Myocytes MYOD|bHLHc1|MYF3 0.004 myogenic differentiation 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.444444 0.000626566 0.00308166 +Mm Hs MYOG Myocytes bHLHc3|MYF4 0.002 myogenin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.000313283 0.00147663 +Mm Hs SIX1 Myocytes DFNA23 0.014 SIX homeobox 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0269424 0.0 +Mm Hs SIX4 Myocytes AREC3 0.001 SIX homeobox 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs PAX3 Myocytes HUP2|WS1 0.004 paired box 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00407268 0.00385208 +Mm Hs PAX7 Myocytes Hup1 0.001 paired box 7 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00093985 0.000898819 +Mm Hs ADAM12 Myocytes MCMPMltna|MLTN 0.007 ADAM metallopeptidase domain 12 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00626566 0.00763996 +Mm Hs ARHGAP26 Myocytes GRAF|KIAA0621|OPHN1L|OPHN1L1 0.016 Rho GTPase activating protein 26 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0112782 0.017527 +Mm Hs CAV3 Myocytes VIP-21|LGMD1C|VIP21|LQT9 0.001 caveolin 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.0 0.00141243 +Mm Hs CDH15 Myocytes CDH3 0.003 cadherin 15 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.444444 0.00156642 0.00282486 +Mm Hs CMKLR1 Myocytes RVER1 0.003 chemerin chemokine-like receptor 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.00314587 +Mm Hs CXCR4 Myocytes LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.198308 0.00879558 +Mm Hs DLL1 Myocytes NA 0.003 delta like canonical Notch ligand 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00501253 0.00263225 +Mm Hs DOCK1 Myocytes DOCK180|ced5 0.01 dedicator of cytokinesis 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0018797 0.0128403 +Mm Hs DOCK5 Myocytes FLJ21034 0.009 dedicator of cytokinesis 5 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0369674 0.00211864 +Mm Hs FLNC Myocytes ABPL|FLN2 0.01 filamin C protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.444444 0.00250627 0.0101438 +Mm IL4RA Myocytes NA 0.013 interleukin 4 receptor, alpha protein coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.016885 +Mm Hs IQSEC1 Myocytes KIAA0763|GEP100|BRAG2|ARF-GEP100 0.054 IQ motif and Sec7 domain 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.222222 0.00093985 0.0674114 +Mm Hs ITGA3 Myocytes CD49c|VLA3a|VCA-2|GAP-B3|MSK18 0.012 integrin subunit alpha 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0197368 0.00905239 +Mm Hs MMP2 Myocytes TBE-1|CLG4|CLG4A 0.045 matrix metallopeptidase 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0676692 0.038585 +Mm Hs MMP9 Myocytes CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00971178 0.0170134 +Mm Hs MRC1 Myocytes CLEC13D|CD206|bA541I19.1|CLEC13DL|MRC1L1 0.029 mannose receptor C-type 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00971178 0.0347329 +Mm Hs MYH14 Myocytes FLJ13881|KIAA2034|MHC16|MYH17|DFNA4 0.019 myosin heavy chain 14 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00125313 0.0230483 +Mm Hs NOTCH3 Myocytes CASIL|CADASIL 0.02 notch 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.014411 0.0220853 +Mm Hs NPHS1 Myocytes CNF|NPHN 0.002 NPHS1, nephrin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00689223 0.00102722 +Mm OLFR599 Myocytes NA 0.0 olfactory receptor 599 protein coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs PLD1 Myocytes NA 0.004 phospholipase D1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00219298 0.0046867 +Mm Hs PRKCQ Myocytes NA 0.007 protein kinase C theta protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.00911659 +Mm Hs PTGIR Myocytes NA 0.001 prostaglandin I2 receptor protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00219298 0.000770416 +Mm Hs PTK2 Myocytes FAK|FADK|FAK1|PPP1R71 0.033 protein tyrosine kinase 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0648496 0.0249743 +Mm Hs PXN Myocytes NA 0.021 paxillin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.222222 0.0153509 0.0208012 +Mm Hs SULF1 Myocytes KIAA1077|SULF-1|hSulf-1 0.013 sulfatase 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0175439 0.0 +Mm Hs TRIO Myocytes ARHGEF23 0.028 trio Rho guanine nucleotide exchange factor protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00814536 0.0 +Mm Hs WASHC1 Myocytes FLJ00038|FAM39E|WASH1 0.013 WASH complex subunit 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.0 +Mm Hs WIPF1 Myocytes WIP|WASPIP 0.02 WAS/WASL interacting protein family member 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0460526 0.0 +Mm Hs NPPA Myocytes ANP|PND 0.0 natriuretic peptide A protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.000321007 +Mm Hs NPPB Myocytes NA 0.003 natriuretic peptide B protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0018797 0.00243965 +Mm Hs EDN1 Myocytes ET1 0.01 endothelin 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0379073 0.0048793 +Mm Hs GATA4 Myocytes NA 0.008 GATA binding protein 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00469925 0.00796097 +Mm Hs GATA5 Myocytes bB379O24.1|GATAS 0.002 GATA binding protein 5 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00125313 0.00128403 +Mm Hs MEF2A Myocytes RSRFC4|RSRFC9 0.064 myocyte enhancer factor 2A protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.333333 0.00877193 0.077491 +Mm Hs MEF2B Myocytes RSRFR2 0.001 myocyte enhancer factor 2B protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.00179764 +Mm Hs MEF2D Myocytes NA 0.002 myocyte enhancer factor 2D protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.00219298 0.00237545 +Mm Hs POPDC2 Myocytes NA 0.002 popeye domain containing 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.111111 0.0 0.00186184 +Mm Hs CHODL Myocytes FLJ12627|PRED12|MT75|C21orf68 0.004 chondrolectin protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00125313 0.00430149 +Mm Hs MYLPF Myocytes HUMMLC2B|MYL11 0.006 myosin light chain, phosphorylatable, fast skeletal muscle protein-coding gene NA Mesoderm Skeletal muscle 0.0 1.0 0.00125313 0.00590652 +Mm Hs MYL1 Myocytes NA 0.003 myosin light chain 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.888889 0.000626566 0.00237545 +Mm Hs CKM Myocytes CKMM 0.003 creatine kinase, M-type protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.555556 0.00219298 0.00301746 +Mm Hs TCAP Myocytes T-cap|TELE|telethonin|CMD1N|LGMD2G 0.003 titin-cap protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs MYOZ1 Myocytes FATZ|MYOZ 0.0 myozenin 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.555556 0.0 0.0 +Mm Hs PYGM Myocytes NA 0.002 glycogen phosphorylase, muscle associated protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.777778 0.000313283 0.00243965 +Mm Hs ENO3 Myocytes NA 0.01 enolase 3 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.888889 0.000313283 0.010208 +Mm Hs THBS4 Myocytes NA 0.002 thrombospondin 4 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00313283 0.0 +Mm Hs SFN Myoepithelial cells YWHAS 0.051 stratifin protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0790216 0.0 +Mm Hs ACTA2 Myoepithelial cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene NA Mesoderm Smooth muscle 0.333333 1.0 0.0191283 0.0351691 +Mm Hs CNN1 Myoepithelial cells Sm-Calp 0.012 calponin 1 protein-coding gene NA Mesoderm Smooth muscle 1.0 0.966667 0.0275949 0.0052818 +Hs CA3 Myoepithelial cells Car3|CAIII 0.0 carbonic anhydrase 3 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00250862 0.0 +Mm Hs MME Myoepithelial cells CALLA|CD10 0.017 membrane metalloendopeptidase protein-coding gene NA Mesoderm Smooth muscle 0.0 0.383333 0.0269677 0.013591 +Mm Hs CD109 Myoepithelial cells FLJ38569|DKFZp762L1111|CPAMD7 0.006 CD109 molecule protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00219505 0.00637681 +Mm Hs KRT14 Myoepithelial cells EBS3|EBS4 0.019 keratin 14 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.933333 0.0197554 0.0156522 +Mm Hs KRT17 Myoepithelial cells PCHC1 0.025 keratin 17 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.916667 0.0746315 0.0122383 +Mm Hs EGFR Myoepithelial cells ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene NA Mesoderm Smooth muscle 0.0 0.1 0.022264 0.0124316 +Mm Hs SERPINB5 Myoepithelial cells maspin|PI5 0.015 serpin family B member 5 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0206961 0.0 +Hs TP63 Myoepithelial cells SHFM4|EEC3|p63|p73L|OFC8|KET|p73H|p53CP|TP73L|TP53L|TP53CP 0.001 tumor protein p63 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0056444 0.0 +Mm Hs NGFR Myoepithelial cells TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00219505 0.00747182 +Mm Hs CDH3 Myoepithelial cells CDHP|PCAD 0.006 cadherin 3 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.2 0.0112888 0.00309179 +Mm Hs MYH11 Myoepithelial cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene NA Mesoderm Smooth muscle 1.0 0.916667 0.0153653 0.0114654 +Mm Hs FST Myoepithelial cells NA 0.02 follistatin protein-coding gene NA Mesoderm Smooth muscle 0.0 0.483333 0.0357479 0.0135266 +Mm Hs ACTG2 Myoepithelial cells ACTSG|ACTL3|ACTA3 0.011 actin, gamma 2, smooth muscle, enteric protein-coding gene 1 Mesoderm Smooth muscle 1.0 0.716667 0.0197554 0.0068277 +Mm Hs MDFI Myoepithelial cells I-mfa 0.02 MyoD family inhibitor protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0833333 0.0332393 0.0137842 +Mm Hs PXN Myoepithelial cells NA 0.021 paxillin protein-coding gene NA Mesoderm Smooth muscle 0.0 0.233333 0.0153653 0.0200966 +Mm Hs LAMB3 Myoepithelial cells nicein-125kDa|kalinin-140kDa|BM600-125kDa|LAMNB1 0.017 laminin subunit beta 3 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.483333 0.0536218 0.00760064 +Mm Hs LAMC2 Myoepithelial cells nicein-100kDa|kalinin-105kDa|BM600-100kDa|EBR2|LAMB2T|LAMNB2|EBR2A 0.012 laminin subunit gamma 2 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.466667 0.0225776 0.00830918 +Mm Hs GRWD1 Myoepithelial cells WDR28|GRWD|RRB1 0.017 glutamate rich WD repeat containing 1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.166667 0.0122295 0.0150081 +Mm Hs SPHK1 Myoepithelial cells SPHK 0.016 sphingosine kinase 1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0370022 0.0 +Mm Hs SMIM3 Myoepithelial cells MSTP150|NID67|C5orf62 0.017 small integral membrane protein 3 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0197554 0.0 +Mm Hs KRT5 Myoepithelial cells KRT5A|EBS2 0.019 keratin 5 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.916667 0.0445281 0.0115942 +Mm Hs MYLK Myoepithelial cells smMLCK|MYLK1|MLCK1 0.047 myosin light chain kinase protein-coding gene 1 Mesoderm Smooth muscle 1.0 0.866667 0.0545626 0.0436071 +Mm Hs MYL9 Myoepithelial cells MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Smooth muscle 1.0 1.0 0.159611 0.0597746 +Mm Hs CDH11 Myofibroblasts CAD11 0.039 cadherin 11 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.5 0.0516917 0.0361384 +Mm Hs DES Myofibroblasts CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene NA Mesoderm Smooth muscle 0.0 0.5 0.0093985 0.023108 +Mm Hs PALLD Myofibroblasts KIAA0992|SIH002|CGI-151 0.053 palladin, cytoskeletal associated protein protein-coding gene NA Mesoderm Smooth muscle 0.0 0.333333 0.10213 0.0423647 +Mm Hs ACTA2 Myofibroblasts ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene 1 Mesoderm Smooth muscle 0.0 1.0 0.0194236 0.0385134 +Mm Hs GFAP Myofibroblasts FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0056391 0.014956 +Mm Hs TNS1 Myofibroblasts DKFZp586K0617|PPP1R155|TNS|MXRA6 0.047 tensin 1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0153509 0.0 +Mm Hs CALD1 Myofibroblasts H-CAD|L-CAD 0.186 caldesmon 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 1.0 0.268797 0.165222 +Mm Hs MYL9 Myofibroblasts MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Smooth muscle 0.0 1.0 0.160401 0.0630336 +Mm Hs TAGLN Myofibroblasts SM22|WS3-10|TAGLN1|DKFZp686P11128 0.01 transgelin protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.000626566 0.0 +Mm Hs IL12RB2 Natural killer T cells NA 0.0 interleukin 12 receptor subunit beta 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000192493 +Mm Hs IL17RA Natural killer T cells hIL-17R|IL-17RA|CDw217|CD217|IL17R 0.014 interleukin 17 receptor A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0056391 0.0164902 +Mm Hs IL12RB1 Natural killer T cells CD212|IL12RB 0.0 interleukin 12 receptor subunit beta 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 6.41643e-05 +Mm Hs KLRB1 Natural killer T cells CD161|NKR-P1|NKR-P1A|hNKR-P1A|CLEC5B 0.008 killer cell lectin like receptor B1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.047619 0.000705807 +Mm Hs RORA Natural killer T cells RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0140977 0.0 +Mm Hs ITGB2 Natural killer T cells CD18|MFI7 0.07 integrin subunit beta 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.111216 0.0605069 +Mm Hs EGR1 Natural killer T cells TIS8|G0S30|NGFI-A|KROX-24|ZIF-268|AT225|ZNF225 0.202 early growth response 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.187657 0.20847 +Mm Hs MAP3K8 Natural killer T cells Tpl-2|c-COT|MEKK8|ESTF 0.014 mitogen-activated protein kinase kinase kinase 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0473058 0.00763555 +Mm Hs NR4A1 Natural killer T cells N10|NAK-1|NGFIB|NUR77|HMR|GFRP1 0.083 nuclear receptor subfamily 4 group A member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00469925 0.101829 +Mm Hs GZMB Natural killer T cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0604637 0.00834135 +Mm Hs TNFRSF8 Natural killer T cells KI-1|CD30|D1S166E 0.0 TNF receptor superfamily member 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs PRF1 Natural killer T cells PFP|HPLH2 0.009 perforin 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0307018 0.00474816 +Mm Hs IL2RB Natural killer T cells CD122|IL15RB 0.02 interleukin 2 receptor subunit beta protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.018797 0.0195059 +Mm Hs ZBTB16 Natural killer T cells PLZF|ZNF145 0.007 zinc finger and BTB domain containing 16 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0119048 0.0 +Mm Hs TBX21 Natural killer T cells TBLYM|T-bet 0.0 T-box 21 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs GATA3 Natural killer T cells HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0200501 0.0297722 +Mm Hs NCAM1 Natural killer T cells NCAM|CD56 0.351 neural cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0297619 0.43112 +Mm Hs S1PR1 Natural killer T cells edg-1|D1S3362|CD363 0.044 sphingosine-1-phosphate receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0112782 0.0 +Mm Hs STYK1 Natural killer T cells SuRTK106|DKFZp761P1010|NOK 0.002 serine/threonine/tyrosine kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TCF7 Natural killer T cells TCF-1 0.03 transcription factor 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0363409 0.0 +Mm Hs SLAMF7 Natural killer T cells CRACC|19A|CS1|CD319 0.013 SLAM family member 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0075188 0.0 +Mm ZFP683 Natural killer T cells NA 0.0 zinc finger protein 683 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs CXCR4 Natural killer T cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.198308 0.0087905 +Mm Hs CD44 Natural killer T cells IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.300439 0.0877767 +Mm Hs SOX1 Neural stem/precursor cells NA 0.002 SRY-box 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PROM1 Neural stem/precursor cells AC133|CD133|RP41|CORD12|PROML1|STGD4 0.021 prominin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00720551 0.0242319 +Mm Hs IGF1R Neural stem/precursor cells JTK13|CD221|IGFIR|MGC18216|IGFR 0.076 insulin like growth factor 1 receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0740741 0.047619 0.0812444 +Mm Hs SP8 Neural stem/precursor cells NA 0.007 Sp8 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs GFAP Neural stem/precursor cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.0149762 +Mm Hs RBM3 Neural stem/precursor cells IS1-RNPL 0.127 RNA binding motif protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.516917 0.0 +Mm Hs SOX3 Neural stem/precursor cells PHP 0.002 SRY-box 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00501253 0.0 +Mm Hs S100B Neural stem/precursor cells S100beta 0.066 S100 calcium binding protein B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.033208 0.0 +Mm Hs SLC1A3 Neural stem/precursor cells EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109649 0.0 +Mm Hs NEUROD4 Neural stem/precursor cells Atoh3|ATH-3|MATH-3|bHLHa4 0.006 neuronal differentiation 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.00771307 +Mm Hs NEUROG1 Neural stem/precursor cells AKA|Math4C|ngn1|bHLHa6|NEUROD3 0.001 neurogenin 1 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.00093985 0.000899859 +Mm Hs NEUROG2 Neural stem/precursor cells Atoh4|Math4A|ngn-2|bHLHa8|NGN2 0.016 neurogenin 2 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.00093985 0.0202468 +Mm Hs NHLH1 Neural stem/precursor cells NSCL|NSCL1|bHLHa35 0.002 nescient helix-loop-helix 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00313283 0.000899859 +Mm Hs PPP1R17 Neural stem/precursor cells GSBS|C7orf16 0.002 protein phosphatase 1 regulatory subunit 17 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00156642 0.00141406 +Mm Hs TMTC4 Neural stem/precursor cells FLJ14624|FLJ22153 0.006 transmembrane and tetratricopeptide repeat containing 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs EOMES Neural stem/precursor cells TBR2 0.021 eomesodermin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.0261602 +Mm Hs PLEKHH2 Neural stem/precursor cells KIAA2028|PLEKHH1L 0.003 pleckstrin homology, MyTH4 and FERM domain containing H2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0056391 0.00250675 +Mm Hs TLR3 Neural stem/precursor cells CD283 0.003 toll like receptor 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00720551 0.0 +Mm Hs PARP12 Neural stem/precursor cells FLJ22693|PARP-12|ZC3H1|ZC3HDC1 0.005 poly(ADP-ribose) polymerase family member 12 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00720551 0.0050135 +Mm Hs P2RX7 Neural stem/precursor cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00877193 0.00347088 +Mm Hs INAFM2 Neural stem/precursor cells OGU1|LINC00984 0.007 InaF motif containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00720551 0.0073917 +Mm Hs ISG15 Neural stem/precursor cells IFI15|G1P2 0.061 ISG15 ubiquitin-like modifier protein-coding gene NA Ectoderm Brain 0.0 0.0 0.130013 0.0404936 +Mm Hs IGFBP3 Neural stem/precursor cells IBP3|BP-53 0.031 insulin like growth factor binding protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0592105 0.025646 +Mm Hs IFIT1 Neural stem/precursor cells GARG-16|G10P1|IFI56|IFNAI1 0.015 interferon induced protein with tetratricopeptide repeats 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0159774 0.0133051 +Mm Hs IFI44 Neural stem/precursor cells MTAP44|TLDC5 0.007 interferon induced protein 44 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.012218 0.00456357 +Mm Hs MGAT5 Neural stem/precursor cells GNT-V|MGAT5A 0.046 alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase protein-coding gene NA Ectoderm Brain 0.0 0.037037 0.000313283 0.0550842 +Mm Hs PBK Neural stem/precursor cells TOPK|FLJ14385|Nori-3|CT84 0.06 PDZ binding kinase protein-coding gene NA Ectoderm Brain 0.0 0.185185 0.0432331 0.062026 +Mm Hs DLX2 Neural stem/precursor cells TES-1 0.031 distal-less homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.925926 0.00657895 0.0355444 +Mm Hs CBX3 Neural stem/precursor cells HP1Hs-gamma 0.114 chromobox 3 protein-coding gene NA Ectoderm Brain 0.0 0.222222 0.327694 0.0596478 +Mm Hs RND3 Neural stem/precursor cells RhoE|Rho8|ARHE 0.049 Rho family GTPase 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.101504 0.0 +Mm Hs DLX5 Neural stem/precursor cells NA 0.019 distal-less homeobox 5 protein-coding gene NA Ectoderm Brain 0.0 0.814815 0.0056391 0.0210824 +Mm Hs SP9 Neural stem/precursor cells ZNF990 0.02 Sp9 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs POU3F4 Neural stem/precursor cells BRN4|OTF9|DFNX2|DFN3 0.004 POU class 3 homeobox 4 protein-coding gene 1 Ectoderm Brain 0.0 0.555556 0.00219298 0.00353516 +Mm DYNLT1C Neural stem/precursor cells NA 0.008 dynein light chain Tctex-type 1C protein coding gene 1 Ectoderm Brain 0.0 0.0740741 0.0 0.0106055 +Mm Hs BARHL2 Neural stem/precursor cells NA 0.004 BarH like homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.0 0.00507777 +Mm Hs LHX9 Neural stem/precursor cells NA 0.004 LIM homeobox 9 protein-coding gene NA Ectoderm Brain 0.0 0.037037 0.00250627 0.00507777 +Mm Hs SHOX2 Neural stem/precursor cells SHOT|OG12X|OG12 0.006 short stature homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs DBX1 Neural stem/precursor cells NA 0.0 developing brain homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.0 6.42756e-05 +Mm Hs DLL3 Neural stem/precursor cells SCDO1 0.009 delta like canonical Notch ligand 3 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.0153509 0.00662039 +Mm Hs PITX2 Neural stem/precursor cells IGDS|Brx1|Otlx2|IRID2|IHG2|RIEG|RIEG1|RGS 0.01 paired like homeodomain 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0109649 0.00867721 +Mm Hs OTX1 Neural stem/precursor cells NA 0.0 orthodenticle homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.000321378 +Mm Hs ARX Neural stem/precursor cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Ectoderm Brain 0.0 0.814815 0.00219298 0.0222394 +Mm Hs NXPH1 Neural stem/precursor cells NA 0.022 neurexophilin 1 protein-coding gene NA Ectoderm Brain 0.0 0.0740741 0.000313283 0.0276385 +Mm Hs TOX3 Neural stem/precursor cells CAGF9|TNRC9 0.017 TOX high mobility group box family member 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs ASCL2 Neural stem/precursor cells HASH2|bHLHa45 0.005 achaete-scute family bHLH transcription factor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0075188 0.00482067 +Mm Hs HES5 Neural stem/precursor cells bHLHb38 0.036 hes family bHLH transcription factor 5 protein-coding gene 1 Ectoderm Brain 0.0 0.222222 0.00125313 0.041972 +Mm Hs HOPX Neural stem/precursor cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.091792 0.0223036 +Mm Hs NEUROD1 Neural stem/precursor cells BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0740741 0.023183 0.0429361 +Mm Hs PRSS56 Neural stem/precursor cells NA 0.002 serine protease 56 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00199254 +Mm Hs SOX9 Neural stem/precursor cells SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0322682 0.0 +Mm Hs ALDOC Neural stem/precursor cells NA 0.078 aldolase, fructose-bisphosphate C protein-coding gene 1 Ectoderm Brain 0.0 0.037037 0.00093985 0.0968634 +Mm Hs APOE Neural stem/precursor cells AD2 0.343 apolipoprotein E protein-coding gene 1 Ectoderm Brain 0.0 0.296296 0.132519 0.389574 +Mm Hs ID4 Neural stem/precursor cells bHLHb27 0.093 inhibitor of DNA binding 4, HLH protein protein-coding gene 1 Ectoderm Brain 0.0 0.555556 0.0642231 0.100977 +Mm Hs SOX2 Neural stem/precursor cells NA 0.082 SRY-box 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0288221 0.0 +Mm Hs DCX Neural stem/precursor cells SCLH|DC|LISX|DBCN|XLIS 0.112 doublecortin protein-coding gene 1 Ectoderm Brain 0.0 0.703704 0.016604 0.135043 +Mm Hs CCND2 Neural stem/precursor cells NA 0.232 cyclin D2 protein-coding gene 1 Ectoderm Brain 0.0 0.925926 0.0964912 0.261345 +Mm Hs DLX1 Neural stem/precursor cells NA 0.036 distal-less homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.925926 0.0 0.0433218 +Mm Hs S100A6 Neural stem/precursor cells 2A9|PRA|CABP|CACY 0.317 S100 calcium binding protein A6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.659774 0.0 +Mm Hs NTNG1 Neuroblasts KIAA0976|Lmnt1 0.015 netrin G1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00407268 0.017903 +Mm Hs TSHZ1 Neuroblasts NY-CO-33|SDCCAG33 0.015 teashirt zinc finger homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.0 +Mm Hs SP9 Neuroblasts ZNF990 0.02 Sp9 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs SP8 Neuroblasts NA 0.007 Sp8 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PROK2 Neuroblasts PK2|BV8|MIT1|KAL4 0.003 prokineticin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00438596 0.00237423 +Mm Hs ASCL1 Neuroblasts HASH1|bHLHa46 0.007 achaete-scute family bHLH transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00532581 0.00725103 +Mm Hs DLL3 Neuroblasts SCDO1 0.009 delta like canonical Notch ligand 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0153509 0.00673768 +Mm Hs SALL3 Neuroblasts ZNF796 0.006 spalt like transcription factor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs DRAXIN Neuroblasts FLJ34999|Draxin|Neucrin|C1orf187 0.008 dorsal inhibitory axon guidance protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00657895 0.00840606 +Mm Hs ERBB4 Neuroblasts ALS19|HER4 0.009 erb-b2 receptor tyrosine kinase 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00438596 0.0103311 +Mm Hs TRIM32 Neuroblasts HT2A|TATIP|BBS11|LGMD2H 0.035 tripartite motif containing 32 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs IGFBPL1 Neuroblasts bA113O24.1 0.14 insulin like growth factor binding protein like 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.000626566 0.175308 +Mm Hs EOMES Neuroblasts TBR2 0.021 eomesodermin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.0261165 +Mm Hs PBX1 Neuroblasts NA 0.175 PBX homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.077381 0.19982 +Mm Hs CUX2 Neuroblasts KIAA0293|CDP2|CUTL2 0.024 cut like homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0302233 +Mm Hs ISL1 Neuroblasts Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0134712 0.0313783 +Mm Hs PHF1 Neuroblasts MTF2L2|TDRD19C 0.009 PHD finger protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0372807 0.00256674 +Mm Hs NEUROG1 Neuroblasts AKA|Math4C|ngn1|bHLHa6|NEUROD3 0.001 neurogenin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.00102669 +Mm Hs NKX6-1 Neuroblasts Nkx6.1|NKX6A 0.006 NK6 homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0103383 0.00526181 +Mm Hs NEUROG2 Neuroblasts Atoh4|Math4A|ngn-2|bHLHa8|NGN2 0.016 neurogenin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0203414 +Mm Hs MAPK7 Neuroblasts BMK1|ERK5|PRKM7 0.002 mitogen-activated protein kinase 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.00205339 +Mm Hs PROKR2 Neuroblasts GPR73b|PKR2|GPRg2|dJ680N4.3|GPR73L1|KAL3 0.0 prokineticin receptor 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00038501 +Mm Hs POU6F2 Neuroblasts RPF-1 0.002 POU class 6 homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00275924 +Mm Hs ITGA6 Neuroblasts CD49f 0.059 integrin subunit alpha 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0501253 0.0616016 +Mm Hs EFNA2 Neuroblasts ELF-1|LERK6|EPLG6 0.002 ephrin A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00256674 +Mm Hs DCX Neuroblasts SCLH|DC|LISX|DBCN|XLIS 0.112 doublecortin protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.016604 0.135973 +Mm Hs CCKAR Neuroblasts NA 0.001 cholecystokinin A receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00173255 +Mm Hs CCKBR Neuroblasts NA 0.0 cholecystokinin B receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.000128337 +Mm Hs GRM5 Neuroblasts MGLUR5|GPRC1E|mGlu5|PPP1R86 0.033 glutamate metabotropic receptor 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0420303 +Mm Hs EZH2 Neuroblasts EZH1|ENX-1|KMT6|KMT6A 0.137 enhancer of zeste 2 polycomb repressive complex 2 subunit protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0682957 0.152336 +Mm Hs DLX2 Neuroblasts TES-1 0.031 distal-less homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00657895 0.0370252 +Mm Hs MARK2 Neuroblasts Par1b|PAR-1B|EMK1 0.04 microtubule affinity regulating kinase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00971178 0.0470996 +Mm Hs LRP8 Neuroblasts APOER2|MCI1|LRP-8|HSZ75190 0.029 LDL receptor related protein 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0367685 +Mm Hs VLDLR Neuroblasts CARMQ1|CHRMQ1|VLDLRCH 0.025 very low density lipoprotein receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs DAB1 Neuroblasts NA 0.045 DAB1, reelin adaptor protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.056789 +Mm Hs NCAN Neuroblasts CSPG3 0.209 neurocan protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0018797 0.261422 +Mm Hs EPHA4 Neuroblasts Hek8|TYRO1 0.076 EPH receptor A4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00407268 0.0940067 +Mm Hs TACC3 Neuroblasts ERIC1 0.058 transforming acidic coiled-coil containing protein 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0432331 0.0 +Mm Hs EGFR Neuroblasts ERBB1|ERBB 0.014 epidermal growth factor receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0222431 0.0127695 +Mm Hs TUBB3 Neuroblasts beta-4|CFEOM3|CFEOM3A|FEOM3 0.196 tubulin beta 3 class III protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SIRT1 Neuroblasts SIR2L1 0.003 sirtuin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0 +Mm Hs NCAM1 Neuroblasts NCAM|CD56 0.351 neural cell adhesion molecule 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0297619 0.431083 +Mm Hs NEUROD1 Neuroblasts BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.023183 0.0429928 +Mm Hs SCGN Neuroblasts SECRET|DJ501N12.8|SEGN|CALBL 0.014 secretagogin, EF-hand calcium binding protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0297619 0.0 +Hs KLK3 Neuroblasts NA 0.002 kallikrein related peptidase 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0106516 0.0 +Mm Hs NES Neuroblasts FLJ21841 0.048 nestin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0510652 0.0441478 +Mm Hs WT1 Neuroblasts WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0225564 0.0 +Mm Hs ZBED4 Neuroblasts KIAA0637 0.0 zinc finger BED-type containing 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs PROS1 Neuroblasts PROS 0.024 protein S protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0037594 0.0286833 +Mm Hs CNR1 Neuroblasts CB1K5|CB-R|CB1|CANN6|CB1A|CNR 0.065 cannabinoid receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00250627 0.0813013 +Mm Hs PPP1R1B Neuroendocrine cells DARPP-32|FLJ20940 0.026 protein phosphatase 1 regulatory inhibitor subunit 1B protein-coding gene NA Ectoderm Brain 0.0 0.689655 0.0162907 0.0260836 +Mm Hs CLASP2 Neuroendocrine cells KIAA0627 0.064 cytoplasmic linker associated protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.12069 0.0125313 0.0768339 +Mm Hs MKL2 Neuroendocrine cells NA 0.035 MKL/myocardin-like 2 protein coding gene NA Ectoderm Brain 0.0 0.155172 0.0056391 0.0419914 +Mm Hs FXYD7 Neuroendocrine cells NA 0.024 FXYD domain containing ion transport regulator 7 protein-coding gene NA Ectoderm Brain 0.0 0.258621 0.00093985 0.0292394 +Mm Hs DPF1 Neuroendocrine cells neuro-d4|NEUD4|BAF45b 0.016 double PHD fingers 1 protein-coding gene NA Ectoderm Brain 0.0 0.12069 0.0018797 0.0183551 +Mm Hs PENK Neuroendocrine cells NA 0.02 proenkephalin protein-coding gene NA Ectoderm Brain 0.0 0.310345 0.0275689 0.0185483 +Mm Hs GRM5 Neuroendocrine cells MGLUR5|GPRC1E|mGlu5|PPP1R86 0.033 glutamate metabotropic receptor 5 protein-coding gene NA Ectoderm Brain 0.0 0.758621 0.0 0.0393508 +Mm Hs SFXN5 Neuroendocrine cells BBG-TCC|SLC56A5 0.023 sideroflexin 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00689223 0.0 +Mm Hs TAC1 Neuroendocrine cells NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs CCDC85C Neuroendocrine cells NA 0.007 coiled-coil domain containing 85C protein-coding gene NA Ectoderm Brain 0.0 0.0862069 0.0 0.0081149 +Mm Hs ATXN1 Neuroendocrine cells D6S504E|ATX1|SCA1 0.033 ataxin 1 protein-coding gene NA Ectoderm Brain 0.0 0.172414 0.00783208 0.0389 +Mm Hs GPR88 Neuroendocrine cells NA 0.006 G protein-coupled receptor 88 protein-coding gene NA Ectoderm Brain 0.0 0.637931 0.0 0.00470149 +Mm Hs PDE10A Neuroendocrine cells NA 0.024 phosphodiesterase 10A protein-coding gene NA Ectoderm Brain 0.0 0.689655 0.00281955 0.0276293 +Mm Hs SST Neuroendocrine cells SMST 0.027 somatostatin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.047619 0.0 +Mm Hs CXCL14 Neuroendocrine cells BRAK|NJAC|bolekine|Kec|MIP-2g|BMAC|SCYB14 0.049 C-X-C motif chemokine ligand 14 protein-coding gene NA Ectoderm Brain 0.0 0.310345 0.0426065 0.0473369 +Mm Hs NPY Neuroendocrine cells PYY4 0.015 neuropeptide Y protein-coding gene 1 Ectoderm Brain 0.0 0.206897 0.0056391 0.0163586 +Mm Hs NRGN Neuroendocrine cells NA 0.031 neurogranin protein-coding gene NA Ectoderm Brain 0.0 0.465517 0.0109649 0.0329104 +Mm Hs SCN2B Neuroendocrine cells NA 0.035 sodium voltage-gated channel beta subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs ABHD2 Neuroendocrine cells LABH2 0.06 abhydrolase domain containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.155172 0.0416667 0.0652412 +Mm Hs SPOCK1 Neuroendocrine cells testican-1|TIC1|SPOCK 0.025 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0181704 0.0 +Mm Hs NEGR1 Neuroendocrine cells KILON|MGC46680|Ntra|IGLON4 0.034 neuronal growth regulator 1 protein-coding gene NA Ectoderm Brain 0.0 0.224138 0.00407268 0.0417338 +Mm Hs DUSP26 Neuroendocrine cells MGC1136 0.04 dual specificity phosphatase 26 protein-coding gene NA Ectoderm Brain 0.0 0.103448 0.012218 0.0475301 +Mm Hs ARHGDIG Neuroendocrine cells RHOGDI-3 0.038 Rho GDP dissociation inhibitor gamma protein-coding gene NA Ectoderm Brain 0.0 0.310345 0.00344612 0.04592 +Mm Hs CCK Neuroendocrine cells NA 0.033 cholecystokinin protein-coding gene 1 Ectoderm Brain 0.0 0.137931 0.00344612 0.0381271 +Mm Hs PRSS12 Neuroendocrine cells BSSP-3|MRT1 0.003 serine protease 12 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.0032846 +Mm Hs SERPINI1 Neuroendocrine cells PI12 0.023 serpin family I member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0238095 0.0 +Mm Hs NKX2-2 Neuroendocrine cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0103383 0.000644039 +Mm Hs ENO2 Neurons NA 0.06 enolase 2 protein-coding gene 1 Ectoderm Brain 1.0 0.692564 0.024191 0.0271724 +Mm Hs RBFOX3 Neurons FOX-3|NeuN|HRNBP3 0.04 RNA binding fox-1 homolog 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109959 0.0 +Mm Hs CHAT Neurons NA 0.001 choline O-acetyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0244173 0.0 0.000204304 +Mm Hs TH Neurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene 1 Ectoderm Brain 0.222222 0.0 0.00125668 0.0 +Mm Hs CALB1 Neurons CALB 0.019 calbindin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.216426 0.00125668 0.0117134 +Mm Hs CALB2 Neurons CAL2 0.03 calbindin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.139845 0.00282752 0.0311904 +Mm Hs ISL1 Neurons Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0610433 0.0135093 0.029556 +Mm Hs EPO Neurons EP 0.0 erythropoietin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CSF3 Neurons MGC45931|GCSF|G-CSF|C17orf33 0.003 colony stimulating factor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00973924 0.00197494 +Mm Hs NEFH Neurons NA 0.009 neurofilament heavy protein-coding gene 1 Ectoderm Brain 0.444444 0.0588235 0.00251335 0.00769545 +Mm Hs NEFM Neurons NFM|NF-M|NEF3 0.028 neurofilament medium protein-coding gene 1 Ectoderm Brain 0.666667 0.147614 0.0182218 0.0210433 +Mm Hs DLG4 Neurons PSD-95|PSD95|SAP90|SAP-90 0.022 discs large MAGUK scaffold protein 4 protein-coding gene 1 Ectoderm Brain 0.0 0.281909 0.000314169 0.0124625 +Mm Hs SLC12A5 Neurons KIAA1176|KCC2 0.048 solute carrier family 12 member 5 protein-coding gene 1 Ectoderm Brain 0.666667 0.0 0.00188501 0.0 +Mm Hs GABRA1 Neurons EJM5 0.027 gamma-aminobutyric acid type A receptor alpha1 subunit protein-coding gene 1 Ectoderm Brain 0.111111 0.336293 0.0 0.0135522 +Mm Hs AQP1 Neurons CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0179076 0.0450831 +Mm Hs IFIT3 Neurons ISG60|RIG-G|CIG-49|IFI60|GARG-49|IRG2|IFIT4 0.014 interferon induced protein with tetratricopeptide repeats 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0219918 0.012122 +Mm Hs SLC11A1 Neurons NRAMP|NRAMP1 0.017 solute carrier family 11 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00659755 0.0 +Mm Hs TFF3 Neurons HITF|ITF 0.022 trefoil factor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0452403 0.0 +Mm Hs SLC1A1 Neurons EAAC1|EAAT3 0.013 solute carrier family 1 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00157085 0.0 +Mm Hs CXCL1 Neurons SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0458687 0.0324162 +Mm Hs CXCR5 Neurons MDR15|CD185|BLR1 0.001 C-X-C motif chemokine receptor 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00108962 +Mm Hs AIM2 Neurons PYHIN4 0.002 absent in melanoma 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00157085 0.00183874 +Mm Hs MATN2 Neurons NA 0.017 matrilin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0099889 0.0179076 0.0182512 +Mm Hs SLC36A4 Neurons PAT4|FLJ38932 0.006 solute carrier family 36 member 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00754006 0.0 +Mm Hs PRPH Neurons PRPH1|NEF4 0.011 peripherin protein-coding gene 1 Ectoderm Brain 0.0 0.00554939 0.024191 0.00912558 +Mm Hs MECP2 Neurons RTT|MRX16|MRX79 0.011 methyl-CpG binding protein 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0588235 0.0122526 0.00708254 +Mm Hs RIN1 Neurons NA 0.0 Ras and Rab interactor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125668 0.0 +Mm Hs OMP Neurons NA 0.001 olfactory marker protein protein-coding gene 1 Ectoderm Brain 0.0 0.00110988 0.0 0.00170253 +Mm Hs PTPN11 Neurons BPTP3|SH-PTP2|SHP-2|PTP2C|SHP2|NS1 0.05 protein tyrosine phosphatase, non-receptor type 11 protein-coding gene 1 Ectoderm Brain 0.111111 0.110988 0.0326736 0.0511441 +Mm Hs GHSR Neurons NA 0.0 growth hormone secretagogue receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs NPY Neurons PYY4 0.015 neuropeptide Y protein-coding gene 1 Ectoderm Brain 0.0 0.126526 0.00565504 0.0103514 +Mm Hs AGRP Neurons Agrt|ART|ASIP2 0.001 agouti related neuropeptide protein-coding gene 1 Ectoderm Brain 0.0 0.0210877 0.0 0.000408608 +Mm Hs RESP18 Neurons NA 0.062 regulated endocrine specific protein 18 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs STX1A Neurons HPC-1|p35-1|STX1 0.013 syntaxin 1A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00659755 0.0 +Mm Hs SCN2B Neurons NA 0.035 sodium voltage-gated channel beta subunit 2 protein-coding gene 1 Ectoderm Brain 0.222222 0.0 0.0 0.0 +Mm Hs DISP2 Neurons DISPB|KIAA1742|HsT16908|LINC00594|C15orf36 0.03 dispatched RND transporter family member 2 protein-coding gene NA Ectoderm Brain 0.111111 0.419534 0.0 0.0136203 +Mm Hs CBARP Neurons MGC40084|DOS|BARP|C19orf26 0.035 CACN subunit beta associated regulatory protein protein-coding gene NA Ectoderm Brain 0.0 0.491676 0.00314169 0.0157995 +Mm Hs B3GAT2 Neurons GlcAT-S 0.003 beta-1,3-glucuronyltransferase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.017758 0.0 0.00326886 +Mm Hs FMO1 Neurons NA 0.012 flavin containing monooxygenase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000314169 0.0151185 +Mm Hs FBLN2 Neurons NA 0.025 fibulin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0197926 0.0286026 +Mm Hs SHISA2 Neurons bA398O19.2|PRO28631|WGAR9166|hShisa|C13orf13|TMEM46 0.011 shisa family member 2 protein-coding gene 1 Ectoderm Brain 0.111111 0.0 0.0329877 0.0 +Mm Hs LUZP2 Neurons NA 0.037 leucine zipper protein 2 protein-coding gene 1 Ectoderm Brain 0.0 0.036626 0.00471254 0.0461727 +Mm Hs SCRG1 Neurons SCRG-1 0.037 stimulator of chondrogenesis 1 protein-coding gene 1 Ectoderm Brain 0.111111 0.0 0.0169651 0.0 +Mm Hs FAM181B Neurons LOC220382|MGC33846 0.018 family with sequence similarity 181 member B protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000314169 0.0245165 +Mm Hs IGF1 Neurons IGF1A|IGFI|IGF-I|IGF 0.044 insulin like growth factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0643729 0.00282752 0.053732 +Mm CD59A Neurons NA 0.033 CD59a antigen protein coding gene 1 Ectoderm Brain 0.0 0.0332963 0.0 0.0418823 +Mm Hs CTXN2 Neurons NA 0.015 cortexin 2 protein-coding gene NA Ectoderm Brain 0.0 0.235294 0.0 0.0050395 +Mm Hs TMEM130 Neurons DKFZp761L1417|FLJ42643 0.04 transmembrane protein 130 protein-coding gene NA Ectoderm Brain 0.666667 0.0 0.0 0.0 +Mm Hs DZANK1 Neurons FLJ10600|dJ568F9.2|FLJ30892|bA189K21.8|ANKRD64|C20orf84|C20orf12 0.015 double zinc ribbon and ankyrin repeat domains 1 protein-coding gene NA Ectoderm Brain 0.0 0.259711 0.000628338 0.00435849 +Mm Hs ACSL4 Neurons ACS4|LACS4|FACL4|MRX63|MRX68 0.035 acyl-CoA synthetase long chain family member 4 protein-coding gene NA Ectoderm Brain 0.111111 0.158713 0.0163368 0.0325524 +Mm Hs CLSTN3 Neurons CSTN3|KIAA0726|CDHR14 0.033 calsyntenin 3 protein-coding gene NA Ectoderm Brain 0.666667 0.54828 0.000628338 0.00953419 +Mm Hs ARHGDIG Neurons RHOGDI-3 0.038 Rho GDP dissociation inhibitor gamma protein-coding gene NA Ectoderm Brain 0.222222 0.371809 0.00282752 0.0269681 +Mm Hs HAP1 Neurons hHLP1|HIP5 0.041 huntingtin associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.609323 0.000628338 0.0167529 +Mm Hs NRSN2 Neurons dJ1103G7.6|C20orf98 0.032 neurensin 2 protein-coding gene NA Ectoderm Brain 0.0 0.550499 0.000628338 0.00810406 +Mm Hs ABAT Neurons GABAT 0.032 4-aminobutyrate aminotransferase protein-coding gene NA Ectoderm Brain 0.222222 0.336293 0.00282752 0.0203623 +Mm Hs HDAC11 Neurons NA 0.032 histone deacetylase 11 protein-coding gene NA Ectoderm Brain 0.0 0.344062 0.018536 0.017502 +Mm Hs SLC30A9 Neurons HUEL|ZNT9|GAC63|C4orf1 0.04 solute carrier family 30 member 9 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0254477 0.0 +Mm Hs SCAMP1 Neurons SCAMP37 0.041 secretory carrier membrane protein 1 protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.0125668 0.0 +Mm Hs MAGEE1 Neurons KIAA1587|DAMAGE 0.021 MAGE family member E1 protein-coding gene NA Ectoderm Brain 0.0 0.285239 0.0 0.0099428 +Mm Hs NCALD Neurons NA 0.035 neurocalcin delta protein-coding gene NA Ectoderm Brain 0.0 0.341842 0.00125668 0.025538 +Mm Hs COPG1 Neurons COPG 0.039 coatomer protein complex subunit gamma 1 protein-coding gene NA Ectoderm Brain 0.0 0.36182 0.0150801 0.0258104 +Mm Hs KCNC1 Neurons Kv3.1 0.03 potassium voltage-gated channel subfamily C member 1 protein-coding gene NA Ectoderm Brain 0.111111 0.45505 0.0 0.0123263 +Mm Hs FBXW7 Neurons AGO|FLJ11071|SEL-10|SEL10|FBW7|CDC4|FBXW6 0.038 F-box and WD repeat domain containing 7 protein-coding gene NA Ectoderm Brain 0.0 0.27192 0.0373861 0.0232907 +Mm Hs GABRG2 Neurons NA 0.024 gamma-aminobutyric acid type A receptor gamma2 subunit protein-coding gene NA Ectoderm Brain 0.333333 0.341842 0.000314169 0.0105557 +Mm Hs NMT1 Neurons NMT 0.028 N-myristoyltransferase 1 protein-coding gene NA Ectoderm Brain 0.0 0.0688124 0.0251335 0.0261509 +Mm Hs ARID4A Neurons RBP1|RBP-1|RBBP1 0.051 AT-rich interaction domain 4A protein-coding gene NA Ectoderm Brain 0.666667 0.174251 0.0436695 0.0464451 +Mm Hs ZRSR1 Neurons NA 0.005 zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1 protein coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs RGS17 Neurons RGSZ2|RGS-17 0.031 regulator of G protein signaling 17 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.00314169 0.0 +Mm Hs TMEM91 Neurons FLJ27310|IFITMD6|DSPC3 0.011 transmembrane protein 91 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0116243 0.0 +Mm Hs CDK5 Neurons PSSALRE 0.026 cyclin dependent kinase 5 protein-coding gene NA Ectoderm Brain 0.111111 0.145394 0.00659755 0.0230183 +Mm Hs SAFB Neurons HET|SAFB1 0.061 scaffold attachment factor B protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.0628338 0.0 +Mm Hs RNF220 Neurons FLJ10597|C1orf164 0.044 ring finger protein 220 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0175935 0.0 +Mm Hs RASGRF1 Neurons CDC25L|GRF55|H-GRF55|GNRP|PP13187|GRF1 0.023 Ras protein specific guanine nucleotide releasing factor 1 protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.00219918 0.0 +Mm Hs TCEAL6 Neurons WEX2 0.015 transcription elongation factor A like 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000942507 0.0 +Mm Hs TMEM179 Neurons FLJ42486|TMEM179A|C14orf90 0.03 transmembrane protein 179 protein-coding gene NA Ectoderm Brain 0.111111 0.0 0.0 0.0 +Mm Hs NICN1 Neurons MGC12936 0.022 nicolin 1 protein-coding gene NA Ectoderm Brain 0.0 0.216426 0.0 0.0160719 +Mm PNMAL1 Neurons NA 0.017 PNMA-like 1 protein coding gene NA Ectoderm Brain 0.0 0.299667 0.0 0.00469899 +Mm Hs NAPG Neurons NA 0.033 NSF attachment protein gamma protein-coding gene NA Ectoderm Brain 0.111111 0.347392 0.020421 0.0163443 +Mm Hs CMIP Neurons NA 0.031 c-Maf inducing protein protein-coding gene NA Ectoderm Brain 0.333333 0.205327 0.0254477 0.0224734 +Mm Hs ZMYND11 Neurons BS69 0.036 zinc finger MYND-type containing 11 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.0103676 0.0 +Mm Hs RHBDD2 Neurons NPD007|RHBDL7 0.026 rhomboid domain containing 2 protein-coding gene NA Ectoderm Brain 1.0 0.0 0.0810556 0.0 +Mm Hs ST8SIA3 Neurons SIAT8C 0.017 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PQBP1 Neurons RENS1|MRXS8|SHS|MRX55|MRX2|MRXS3 0.06 polyglutamine binding protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.134295 0.0870248 0.0433806 +Mm Hs MATK Neurons HYLTK|CTK|HYL|Lsk|HHYLTK|DKFZp434N1212|MGC1708|MGC2101 0.032 megakaryocyte-associated tyrosine kinase protein-coding gene NA Ectoderm Brain 0.0 0.418424 0.018536 0.0133479 +Mm Hs TRO Neurons MAGE-D3|KIAA1114|MAGED3 0.032 trophinin protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125668 0.0 +Mm CKMT1 Neurons NA 0.051 creatine kinase, mitochondrial 1, ubiquitous protein coding gene NA Ectoderm Brain 0.0 0.314095 0.0 0.0471942 +Mm Hs AKAP8L Neurons NAKAP95|HAP95 0.027 A-kinase anchoring protein 8 like protein-coding gene NA Ectoderm Brain 0.0 0.166482 0.0380145 0.0158676 +Mm Hs DUSP26 Neurons MGC1136 0.04 dual specificity phosphatase 26 protein-coding gene NA Ectoderm Brain 0.222222 0.390677 0.0116243 0.0266957 +Mm Hs SYT5 Neurons NA 0.033 synaptotagmin 5 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.00345586 0.0 +Mm Hs GAD1 Neurons GAD 0.03 glutamate decarboxylase 1 protein-coding gene NA Ectoderm Brain 0.333333 0.423973 0.00251335 0.0135522 +Mm Hs FLYWCH1 Neurons DKFZp761A132 0.022 FLYWCH-type zinc finger 1 protein-coding gene NA Ectoderm Brain 0.0 0.228635 0.00282752 0.0148461 +Mm Hs RIT2 Neurons RIBA|RIN 0.029 Ras like without CAAX 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000314169 0.0 +Mm Hs TCEAL5 Neurons WEX4 0.025 transcription elongation factor A like 5 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.00816839 0.0 +Mm Hs PNCK Neurons MGC45419|CaMK1b 0.021 pregnancy up-regulated nonubiquitous CaM kinase protein-coding gene NA Ectoderm Brain 0.0 0.342952 0.0 0.00708254 +Mm Hs TMEM59L Neurons BSMAP|C19orf4 0.046 transmembrane protein 59 like protein-coding gene NA Ectoderm Brain 0.888889 0.0 0.00754006 0.0 +Mm Hs TCEAL3 Neurons MGC15737|WEX8 0.041 transcription elongation factor A like 3 protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.0584354 0.0 +Mm Hs GPRASP2 Neurons GASP2|FLJ37327 0.033 G protein-coupled receptor associated sorting protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.573807 0.0 0.00926178 +Mm Hs MAP7D2 Neurons FLJ14503 0.039 MAP7 domain containing 2 protein-coding gene NA Ectoderm Brain 0.222222 0.487236 0.0263902 0.0155271 +Mm Hs MIAT Neurons FLJ25967|Rncr2|gomafu|NCRNA00066|LINC00066|lncRNA-MIAT|C22orf35 0.02 myocardial infarction associated transcript non-coding RNA NA Ectoderm Brain 0.666667 0.173141 0.0144518 0.00939798 +Mm Hs RB1CC1 Neurons KIAA0203|Cc1|DRAGOU14|FIP200|ATG17|PPP1R131 0.058 RB1 inducible coiled-coil 1 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.0945649 0.0 +Mm Hs PABPN1 Neurons PAB2|OPMD 0.05 poly(A) binding protein nuclear 1 protein-coding gene NA Ectoderm Brain 0.0 0.211987 0.103362 0.0236993 +Mm Hs GRIA3 Neurons GluA3|GLURC|MRX94|GLUR3 0.02 glutamate ionotropic receptor AMPA type subunit 3 protein-coding gene NA Ectoderm Brain 0.0 0.228635 0.00219918 0.0104876 +Mm Hs NBEA Neurons KIAA1544|BCL8B|FLJ10197|LYST2 0.032 neurobeachin protein-coding gene NA Ectoderm Brain 0.111111 0.263041 0.00439837 0.0249932 +Mm Hs SFSWAP Neurons SFRS8 0.025 splicing factor SWAP protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0135093 0.0 +Mm Hs WDR60 Neurons FLJ10300|FAP163 0.017 WD repeat domain 60 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0562363 0.0 +Mm MIRG Neurons NA 0.014 miRNA containing gene lincRNA gene NA Ectoderm Brain 0.0 0.240844 0.0 0.00360937 +Mm Hs SCN1A Neurons Nav1.1|GEFSP2|SMEI|SCN1|FEB3 0.018 sodium voltage-gated channel alpha subunit 1 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.00125668 0.0 +Mm Hs RNPC3 Neurons KIAA1839|FLJ20008|RBM40 0.02 RNA binding region (RNP1, RRM) containing 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00219918 0.0 +Mm Hs HOXC8 Neurons HOX3A 0.005 homeobox C8 protein-coding gene NA Ectoderm Brain 0.0 0.00776915 0.00314169 0.0051757 +Mm Hs RERE Neurons KIAA0458|DNB1|ATN1L 0.049 arginine-glutamic acid dipeptide repeats protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.0386428 0.0 +Mm Hs SCN8A Neurons Nav1.6|NaCh6|PN4|CerIII|CIAT 0.025 sodium voltage-gated channel alpha subunit 8 protein-coding gene NA Ectoderm Brain 0.222222 0.0 0.0 0.0 +Mm Hs TRIP11 Neurons CEV14|Trip230|GMAP-210|GMAP210 0.037 thyroid hormone receptor interactor 11 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0430412 0.0 +Mm Hs EML5 Neurons HuEMAP-2 0.01 echinoderm microtubule associated protein like 5 protein-coding gene NA Ectoderm Brain 0.0 0.114317 0.0 0.00578861 +Mm Hs KMT2C Neurons KIAA1506|HALR|MLL3 0.037 lysine methyltransferase 2C protein-coding gene NA Ectoderm Brain 0.222222 0.0688124 0.0493245 0.0322119 +Mm Hs AAK1 Neurons KIAA1048|DKFZp686K16132 0.044 AP2 associated kinase 1 protein-coding gene NA Ectoderm Brain 0.555556 0.470588 0.0320452 0.0213838 +Mm Hs SAFB2 Neurons KIAA0138 0.024 scaffold attachment factor B2 protein-coding gene NA Ectoderm Brain 0.111111 0.0 0.0486962 0.0 +Mm Hs SACS Neurons ARSACS|KIAA0730|DKFZp686B15167|DNAJC29|SPAX6|PPP1R138 0.005 sacsin molecular chaperone protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00471254 0.0 +Mm Hs RYR2 Neurons ARVC2|VTSIP|ARVD2 0.008 ryanodine receptor 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CSPP1 Neurons FLJ22490|CSPP|JBTS21 0.018 centrosome and spindle pole associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.0532741 0.0263902 0.0153909 +Mm Hs GRIA4 Neurons GluA4|GLURD|GLUR4 0.014 glutamate ionotropic receptor AMPA type subunit 4 protein-coding gene NA Ectoderm Brain 0.333333 0.154273 0.00251335 0.00810406 +Mm Hs CHD6 Neurons KIAA1335|FLJ22369|dJ620E11.1|RIGB 0.044 chromodomain helicase DNA binding protein 6 protein-coding gene NA Ectoderm Brain 0.0 0.305216 0.0267044 0.0307818 +Mm ZFP445 Neurons NA 0.02 zinc finger protein 445 protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs ZCCHC7 Neurons FLJ22611|AIR1 0.034 zinc finger CCHC-type containing 7 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0345586 0.0 +Mm Hs GPATCH8 Neurons KIAA0553|GPATC8 0.048 G-patch domain containing 8 protein-coding gene NA Ectoderm Brain 0.0 0.298557 0.00942507 0.0433806 +Mm Hs PCLO Neurons KIAA0559|DKFZp779G1236|ACZ 0.039 piccolo presynaptic cytomatrix protein protein-coding gene NA Ectoderm Brain 0.333333 0.503885 0.0040842 0.0174339 +Mm Hs SYNE1 Neurons SYNE-1B|KIAA0796|8B|Nesprin-1|enaptin|MYNE1|CPG2|dJ45H2.2|SCAR8|ARCA1|Nesp1|C6orf98 0.05 spectrin repeat containing nuclear envelope protein 1 protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.0144518 0.0 +Mm Hs PROX1 Neurons NA 0.028 prospero homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.054384 0.0109959 0.0311223 +Mm Hs NRGN Neurons NA 0.031 neurogranin protein-coding gene 1 Ectoderm Brain 0.111111 0.17869 0.0106817 0.0256742 +Mm Hs PPP1R14C Neurons NY-BR-81|KEPI 0.026 protein phosphatase 1 regulatory inhibitor subunit 14C protein-coding gene NA Ectoderm Brain 0.0 0.0588235 0.00596921 0.0299646 +Mm UBE2D2A Neurons NA 0.014 ubiquitin-conjugating enzyme E2D 2A protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs SYNPR Neurons MGC26651 0.022 synaptoporin protein-coding gene NA Ectoderm Brain 0.333333 0.0 0.0 0.0 +Mm Hs CCDC28B Neurons MGC1203|RP4-622L5.5 0.02 coiled-coil domain containing 28B protein-coding gene NA Ectoderm Brain 0.222222 0.0332963 0.018536 0.0195451 +Mm Hs KCNK1 Neurons K2p1.1|TWIK-1 0.042 potassium two pore domain channel subfamily K member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0765816 0.027961 0.0445383 +Mm Hs CNRIP1 Neurons DKFZP566K1924|CRIP1|CRIP1a|CRIP1b|C2orf32 0.031 cannabinoid receptor interacting protein 1 protein-coding gene NA Ectoderm Brain 0.222222 0.200888 0.022306 0.0230864 +Mm Hs FRRS1L Neurons CG-6|C9orf4 0.028 ferric chelate reductase 1 like protein-coding gene NA Ectoderm Brain 0.222222 0.379578 0.000628338 0.0126668 +Mm Hs FAM69B Neurons MGC20262|C9orf136 0.034 family with sequence similarity 69 member B protein-coding gene NA Ectoderm Brain 0.0 0.287458 0.000628338 0.0277853 +Mm Hs GPR162 Neurons A-2|GRCA 0.019 G protein-coupled receptor 162 protein-coding gene NA Ectoderm Brain 0.0 0.231964 0.000314169 0.011441 +Mm Hs CACNG2 Neurons stargazin|MGC138502|MGC138504 0.014 calcium voltage-gated channel auxiliary subunit gamma 2 protein-coding gene NA Ectoderm Brain 0.0 0.190899 0.0 0.00701444 +Mm Hs SPOCK3 Neurons testican-3 0.036 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 protein-coding gene NA Ectoderm Brain 0.555556 0.0 0.00628338 0.0 +Mm Hs RGS7BP Neurons R7BP 0.034 regulator of G protein signaling 7 binding protein protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DNM3 Neurons KIAA0820 0.043 dynamin 3 protein-coding gene NA Ectoderm Brain 0.777778 0.449501 0.000942507 0.0293517 +Mm Hs TMEM191C Neurons NA 0.031 transmembrane protein 191C protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0201068 0.0 +Mm Hs SLC6A17 Neurons NA 0.023 solute carrier family 6 member 17 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DNER Neurons UNQ26|bet 0.046 delta/notch like EGF repeat containing protein-coding gene NA Ectoderm Brain 1.0 0.45616 0.0153943 0.0297603 +Mm Hs GRM5 Neurons MGLUR5|GPRC1E|mGlu5|PPP1R86 0.033 glutamate metabotropic receptor 5 protein-coding gene NA Ectoderm Brain 0.0 0.469478 0.0 0.0157995 +Mm Hs CNTNAP2 Neurons Caspr2|KIAA0868 0.037 contactin associated protein like 2 protein-coding gene NA Ectoderm Brain 0.333333 0.320755 0.0229343 0.023495 +Mm Hs CPLX1 Neurons CPX-I 0.026 complexin 1 protein-coding gene NA Ectoderm Brain 0.0 0.294118 0.0 0.0164805 +Mm Hs SLC32A1 Neurons VGAT|bA122O1.1|VIAAT 0.026 solute carrier family 32 member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00157085 0.0 +Mm Hs DLGAP1 Neurons GKAP|SAPAP1|DAP-1 0.036 DLG associated protein 1 protein-coding gene NA Ectoderm Brain 0.444444 0.340733 0.000942507 0.0264914 +Mm Hs PPP1R9A Neurons Neurabin-I|KIAA1222|FLJ20068 0.044 protein phosphatase 1 regulatory subunit 9A protein-coding gene NA Ectoderm Brain 0.222222 0.469478 0.00439837 0.0283302 +Mm Hs GNL3L Neurons FLJ10613|GNL3B 0.053 G protein nucleolar 3 like protein-coding gene NA Ectoderm Brain 0.0 0.645949 0.000314169 0.0305775 +Mm Hs ZCCHC12 Neurons FLJ16123|SIZN|SIZN1|PNMA7A 0.038 zinc finger CCHC-type containing 12 protein-coding gene NA Ectoderm Brain 0.111111 0.0 0.0 0.0 +Mm Hs ATP6V1H Neurons CGI-11|VMA13|SFDalpha|SFDbeta 0.031 ATPase H+ transporting V1 subunit H protein-coding gene NA Ectoderm Brain 0.444444 0.119867 0.0282752 0.0262871 +Mm Hs HPCA Neurons NA 0.015 hippocalcin protein-coding gene NA Ectoderm Brain 0.333333 0.149834 0.00251335 0.00967039 +Mm Hs CHN1 Neurons ARHGAP2|n-chimerin|DURS2 0.035 chimerin 1 protein-coding gene NA Ectoderm Brain 0.555556 0.284129 0.0314169 0.0202942 +Mm Hs CPNE6 Neurons NA 0.006 copine 6 protein-coding gene NA Ectoderm Brain 0.0 0.0732519 0.0 0.00292836 +Mm Hs PDE1A Neurons NA 0.018 phosphodiesterase 1A protein-coding gene NA Ectoderm Brain 0.111111 0.122087 0.0213635 0.0112367 +Mm Hs GNAI1 Neurons NA 0.05 G protein subunit alpha i1 protein-coding gene NA Ectoderm Brain 0.222222 0.319645 0.0405278 0.0380686 +Mm Hs CCK Neurons NA 0.033 cholecystokinin protein-coding gene NA Ectoderm Brain 0.0 0.189789 0.00345586 0.0292155 +Mm Hs RIMS3 Neurons RIM3|NIM3 0.008 regulating synaptic membrane exocytosis 3 protein-coding gene NA Ectoderm Brain 0.111111 0.0 0.0 0.0 +Mm Hs OGFOD1 Neurons KIAA1612|FLJ10826|TPA1 0.006 2-oxoglutarate and iron dependent oxygenase domain containing 1 protein-coding gene NA Ectoderm Brain 0.0 0.0743618 0.00973924 0.000749115 +Mm Hs CELF6 Neurons BRUNOL6 0.014 CUGBP Elav-like family member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.206437 0.0 0.00612912 +Mm Hs DTD1 Neurons DUEB|MGC119131|MGC41905|bA379J5.3|bA555E18.1|pqn-68|C20orf88|HARS2 0.062 D-tyrosyl-tRNA deacylase 1 protein-coding gene NA Ectoderm Brain 0.222222 0.306326 0.105247 0.0313266 +Mm Hs PRMT2 Neurons MGC111373|HRMT1L1 0.052 protein arginine methyltransferase 2 protein-coding gene NA Ectoderm Brain 0.333333 0.236404 0.113729 0.0224734 +Mm Hs AVP Neurons ADH|ARVP 0.004 arginine vasopressin protein-coding gene 1 Ectoderm Brain 0.0 0.0443951 0.0103676 0.000476709 +Mm Hs RORA Neurons RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene 1 Ectoderm Brain 0.333333 0.0 0.0131951 0.0 +Mm Hs VGF Neurons SCG7|SgVII 0.021 VGF nerve growth factor inducible protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0125668 0.0 +Mm Hs PCSK2 Neurons SPC2|NEC2 0.032 proprotein convertase subtilisin/kexin type 2 protein-coding gene 1 Ectoderm Brain 0.111111 0.280799 0.0245052 0.0197494 +Mm Hs CHODL Neurons FLJ12627|PRED12|MT75|C21orf68 0.004 chondrolectin protein-coding gene 1 Ectoderm Brain 0.0 0.0199778 0.00125668 0.00333697 +Mm Hs NECAB2 Neurons EFCBP2 0.011 N-terminal EF-hand calcium binding protein 2 protein-coding gene 1 Ectoderm Brain 0.111111 0.108768 0.00188501 0.00749115 +Mm TAC2 Neurons NA 0.005 tachykinin 2 protein coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs KCNMA1 Neurons KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene 1 Ectoderm Brain 0.111111 0.441731 0.0182218 0.0243803 +Mm Hs CACNB3 Neurons CACNLB3 0.032 calcium voltage-gated channel auxiliary subunit beta 3 protein-coding gene NA Ectoderm Brain 0.111111 0.119867 0.00157085 0.0345955 +Mm Hs NWD2 Neurons KIAA1239 0.003 NACHT and WD repeat domain containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0288568 0.0 0.00211114 +Mm Hs ZIC1 Neurons ZIC|ZNF201 0.046 Zic family member 1 protein-coding gene NA Ectoderm Brain 0.111111 0.0 0.00816839 0.0 +Mm Hs TESC Neurons FLJ20607|CHP3 0.032 tescalcin protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0782281 0.0 +Mm Hs NECAB3 Neurons XB51|dJ63M2.4|dJ63M2.5|EFCBP3|SYTIP2|APBA2BP 0.005 N-terminal EF-hand calcium binding protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.0133185 0.0160226 0.00143013 +Mm Hs NRN1 Neurons NRN 0.021 neuritin 1 protein-coding gene NA Ectoderm Brain 0.111111 0.119867 0.00973924 0.0170934 +Mm Hs GABBR2 Neurons HG20|GABABR2|GPRC3B|GPR51 0.023 gamma-aminobutyric acid type B receptor subunit 2 protein-coding gene NA Ectoderm Brain 0.555556 0.221976 0.0050267 0.0142332 +Mm Hs SLC17A7 Neurons BNPI|VGLUT1 0.012 solute carrier family 17 member 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm CAR10 Neurons NA 0.021 carbonic anhydrase 10 protein coding gene NA Ectoderm Brain 0.0 0.104329 0.0 0.0216562 +Mm Hs DGKB Neurons KIAA0718|DGK-BETA|DAGK2 0.01 diacylglycerol kinase beta protein-coding gene NA Ectoderm Brain 0.0 0.154273 0.0 0.00388178 +Mm Hs CACNB4 Neurons EJM4 0.017 calcium voltage-gated channel auxiliary subunit beta 4 protein-coding gene NA Ectoderm Brain 0.222222 0.163152 0.000314169 0.0126668 +Mm Hs CTTNBP2 Neurons KIAA1758|Orf4|CORTBP2|C7orf8 0.032 cortactin binding protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.0665927 0.00628338 0.0370471 +Mm Hs PPP1R1B Neurons DARPP-32|FLJ20940 0.026 protein phosphatase 1 regulatory inhibitor subunit 1B protein-coding gene 1 Ectoderm Brain 0.111111 0.045505 0.0160226 0.0275129 +Mm Hs PCP4 Neurons PEP-19 0.083 Purkinje cell protein 4 protein-coding gene 1 Ectoderm Brain 0.333333 0.529412 0.018536 0.0704849 +Mm Hs MEG3 Neurons GTL2|NCRNA00023|LINC00023|onco-lncRNA-83 0.288 maternally expressed 3 non-coding RNA 1 Ectoderm Brain 0.666667 0.99889 0.113729 0.294198 +Mm Hs BEX2 Neurons DJ79P11.1 0.311 brain expressed X-linked 2 protein-coding gene 1 Ectoderm Brain 1.0 0.90455 0.0807414 0.337102 +Mm Hs BEX1 Neurons NA 0.17 brain expressed X-linked 1 protein-coding gene 1 Ectoderm Brain 1.0 0.583796 0.0983349 0.158131 +Mm Hs NDN Neurons HsT16328 0.233 necdin, MAGE family member protein-coding gene 1 Ectoderm Brain 0.222222 0.739179 0.083569 0.241011 +Mm Hs CAMK2N1 Neurons NA 0.108 calcium/calmodulin dependent protein kinase II inhibitor 1 protein-coding gene 1 Ectoderm Brain 0.666667 0.574917 0.0420986 0.0958186 +Mm Hs PNISR Neurons FLJ14752|bA98I9.2|DKFZp564B0769|SRrp130|C6orf111|SFRS18 0.553 PNN interacting serine and arginine rich protein protein-coding gene 1 Ectoderm Brain 0.666667 0.893452 0.5765 0.526764 +Mm Hs SNHG11 Neurons LINC00101|C20orf198 0.111 small nucleolar RNA host gene 11 non-coding RNA 1 Ectoderm Brain 0.0 0.0 0.00628338 0.0 +Mm Hs STMN2 Neurons SCG10|SCGN10 0.209 stathmin 2 protein-coding gene 1 Ectoderm Brain 0.666667 0.0 0.0490104 0.0 +Mm Hs PTK2B Neurons CAKB|PYK2|RAFTK|PTK|CADTK|FAK2 0.014 protein tyrosine kinase 2 beta protein-coding gene 1 Ectoderm Brain 0.0 0.0943396 0.00157085 0.0115091 +Mm Hs DDN Neurons KIAA0749 0.007 dendrin protein-coding gene 1 Ectoderm Brain 0.0 0.0621532 0.00125668 0.0051757 +Mm Hs ICAM5 Neurons TLCN 0.006 intercellular adhesion molecule 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0843507 0.0 0.00265595 +Mm Hs GNG2 Neurons NA 0.142 G protein subunit gamma 2 protein-coding gene 1 Ectoderm Brain 0.111111 0.281909 0.0333019 0.163716 +Mm Hs SNAP25 Neurons SNAP-25|RIC-4|RIC4|SEC9|bA416N4.2|dJ1068F16.2|SNAP 0.112 synaptosome associated protein 25 protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0194785 0.0 +Mm Hs VSNL1 Neurons VILIP|HPCAL3|HUVISL1|VILIP-1 0.049 visinin like 1 protein-coding gene 1 Ectoderm Brain 0.777778 0.0 0.00534087 0.0 +Mm Hs PACSIN1 Neurons SDPI 0.04 protein kinase C and casein kinase substrate in neurons 1 protein-coding gene 1 Ectoderm Brain 0.0 0.538291 0.0 0.0200218 +Mm Hs CACNA2D1 Neurons lncRNA-N3|CACNL2A|CACNA2|MHS3|LINC01112 0.039 calcium voltage-gated channel auxiliary subunit alpha2delta 1 protein-coding gene 1 Ectoderm Brain 0.111111 0.26859 0.0103676 0.0330291 +Mm Hs SGIP1 Neurons DKFZp761D221 0.047 SH3 domain GRB2 like endophilin interacting protein 1 protein-coding gene 1 Ectoderm Brain 0.222222 0.0 0.00125668 0.0 +Mm Hs ATP6V0A1 Neurons a1|VPP1|ATP6N1|ATP6N1A 0.047 ATPase H+ transporting V0 subunit a1 protein-coding gene 1 Ectoderm Brain 0.666667 0.54162 0.00282752 0.0285345 +Mm Hs MYO5A Neurons MYO5|MYR12|MYH12 0.045 myosin VA protein-coding gene 1 Ectoderm Brain 0.666667 0.429523 0.00219918 0.0316671 +Mm Hs DYNC1I1 Neurons DNCIC1|DNCI1 0.022 dynein cytoplasmic 1 intermediate chain 1 protein-coding gene 1 Ectoderm Brain 0.777778 0.167592 0.000314169 0.0183193 +Mm Hs PRUNE2 Neurons BMCC1|BNIPXL|A214N16.3|bA214N16.3|C9orf65|KIAA0367 0.033 prune homolog 2 protein-coding gene 1 Ectoderm Brain 0.0 0.315205 0.00722589 0.0234269 +Mm Hs CACNA2D2 Neurons KIAA0558 0.027 calcium voltage-gated channel auxiliary subunit alpha2delta 2 protein-coding gene 1 Ectoderm Brain 0.0 0.301887 0.00125668 0.0179107 +Mm Hs SLC17A6 Neurons DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000314169 0.0 +Mm Hs TUBB3 Neurons beta-4|CFEOM3|CFEOM3A|FEOM3 0.196 tubulin beta 3 class III protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ELAVL3 Neurons HUC|PLE21|DKFZp547J036|HUCL|MGC20653 0.235 ELAV like RNA binding protein 3 protein-coding gene 1 Ectoderm Brain 0.666667 0.793563 0.0179076 0.260147 +Mm Hs MME Neutrophils CALLA|CD10 0.017 membrane metalloendopeptidase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0270525 0.0153021 +Mm Hs ITGAM Neutrophils CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.0 0.508532 0.00314564 0.0211222 +Mm Hs ITGAX Neutrophils CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0163573 0.00536228 +Mm Hs CD14 Neutrophils NA 0.051 CD14 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.180887 0.026738 0.0530997 +Mm Hs FUT4 Neutrophils FUC-TIV|CD15|ELFT 0.001 fucosyltransferase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00071933 +Hs FCGR3A Neutrophils CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0355458 0.0 +Mm Hs PECAM1 Neutrophils CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0443536 0.0545383 +Mm Hs CD33 Neutrophils SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.170648 0.0125826 0.0143212 +Mm Hs SELL Neutrophils LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0603964 0.0 +Hs CEACAM8 Neutrophils CD66b|CGM6 0.0 carcinoembryonic antigen related cell adhesion molecule 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs C5AR1 Neutrophils C5A|C5AR|CD88|C5R1 0.027 complement C5a receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.31058 0.0141554 0.0248496 +Mm Hs CXCR1 Neutrophils CDw128a|CD181|CMKAR1|IL8RA 0.0 C-X-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000130787 +Mm Hs CXCR2 Neutrophils CMKAR2|CD182|IL8RB 0.003 C-X-C motif chemokine receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.156997 0.0 0.000588543 +Hs JAML Neutrophils Gm638|AMICA|AMICA1 0.005 junction adhesion molecule like protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0292545 0.0 +Mm Hs TLR2 Neutrophils TIL4|CD282 0.014 toll like receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000943693 0.0 +Mm Hs MYLK Neutrophils smMLCK|MYLK1|MLCK1 0.047 myosin light chain kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0556779 0.047672 +Mm Hs S100A9 Neutrophils MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Immune system 0.307692 0.0 0.102548 0.0 +Mm Hs MPO Neutrophils NA 0.023 myeloperoxidase protein-coding gene 1 Mesoderm Immune system 1.0 0.590444 0.0166719 0.0122286 +Mm CCL6 Neutrophils NA 0.043 chemokine (C-C motif) ligand 6 protein coding gene 1 Mesoderm Immune system 0.0 0.235495 0.0 0.0493068 +Hs CD24 Neutrophils CD24A 0.039 CD24 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.192828 0.0 +Mm Hs CEACAM1 Neutrophils BGP1|CD66a|BGP 0.024 carcinoembryonic antigen related cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.290102 0.0191884 0.0208606 +Hs FCGR1A Neutrophils CD64|CD64A 0.001 Fc fragment of IgG receptor Ia protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00377477 0.0 +Mm Hs CRP Neutrophils NA 0.002 C-reactive protein protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0044039 0.00163484 +Mm Hs LCN2 Neutrophils NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.897611 0.0569361 0.0253727 +Hs DEFA1 Neutrophils HNP-1|DEF1|DEFA2 0.0 defensin alpha 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm DEFA2 Neutrophils NA 0.003 defensin, alpha, 2 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0041852 +Mm Hs DEFA3 Neutrophils HNP-3 0.002 defensin alpha 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00294272 +Mm Hs LTF Neutrophils HLF2 0.016 lactotransferrin protein-coding gene 1 Mesoderm Immune system 0.0 0.733788 0.00629129 0.00464295 +Hs LYZ Neutrophils NA 0.008 lysozyme protein-coding gene 1 Mesoderm Immune system 0.615385 0.0 0.0383768 0.0 +Mm Hs ELANE Neutrophils NE|HNE|HLE|ELA2 0.019 elastase, neutrophil expressed protein-coding gene 1 Mesoderm Immune system 1.0 0.631399 0.00629129 0.00732409 +Mm Hs S100A8 Neutrophils P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.538462 0.0 0.078012 0.0 +Mm RETNLG Neutrophils NA 0.014 resistin like gamma protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs IL1B Neutrophils IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene 1 Mesoderm Immune system 0.0 0.150171 0.0254797 0.0253727 +Mm NGP Neutrophils NA 0.02 neutrophilic granule protein protein coding gene 1 Mesoderm Immune system 0.0 0.83959 0.0 0.00941669 +Mm Hs CXCL2 Neutrophils SCYB2|GROb|MIP-2a|MGSA-b|CINC-2a|GRO2 0.041 C-X-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.16041 0.0569361 0.0357703 +Mm Hs HP Neutrophils NA 0.044 haptoglobin protein-coding gene 1 Mesoderm Immune system 0.0 0.952218 0.0251651 0.0297541 +Mm Hs CCL3 Neutrophils G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0580205 0.00786411 0.0422443 +Mm CCL9 Neutrophils NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Mesoderm Immune system 0.0 0.136519 0.0 0.0423751 +Mm Hs HDC Neutrophils NA 0.019 histidine decarboxylase protein-coding gene 1 Mesoderm Immune system 0.0 0.460751 0.00157282 0.014452 +Mm Hs MMP8 Neutrophils CLG1 0.004 matrix metallopeptidase 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.211604 0.0 0.00124248 +Mm STFA2L1 Neutrophils NA 0.001 stefin A2 like 1 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs LRG1 Neutrophils LRG 0.026 leucine rich alpha-2-glycoprotein 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.692833 0.00346021 0.0188988 +Mm Hs OSM Neutrophils MGC20461 0.007 oncostatin M protein-coding gene 1 Mesoderm Immune system 0.0 0.146758 0.0 0.00575464 +Mm Hs MMP9 Neutrophils CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.262799 0.00975149 0.012294 +Mm Hs PILRA Neutrophils FDF03 0.016 paired immunoglobin like type 2 receptor alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.303754 0.01447 0.0117055 +Mm Hs CLEC4D Neutrophils Mpcl|CD368|MCL|Dectin-3|CLECSF8 0.007 C-type lectin domain family 4 member D protein-coding gene 1 Mesoderm Immune system 0.0 0.153584 0.0 0.00483913 +Mm Hs CLEC4E Neutrophils mincle|CLECSF9 0.006 C-type lectin domain family 4 member E protein-coding gene 1 Mesoderm Immune system 0.0 0.163823 0.00251651 0.0030735 +Mm TREM3 Neutrophils NA 0.013 triggering receptor expressed on myeloid cells 3 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs ASPRV1 Neutrophils Taps|SASPase|FLJ25084 0.001 aspartic peptidase retroviral like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0443686 0.0 0.00111169 +Mm Hs CCRL2 Neutrophils CRAM-B|CKRX|CRAM-A|ACKR5 0.018 C-C motif chemokine receptor like 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0614334 0.00157282 0.0212529 +Mm Hs CCR1 Neutrophils MIP1aR|CD191|SCYAR1|CMKBR1 0.014 C-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.201365 0.00534759 0.010463 +Mm Hs NCF1 Neutrophils p47phox|NOXO2|NCF1A|SH3PXD1A 0.038 neutrophil cytosolic factor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.744027 0.0 0.0321737 +Mm LY6G Neutrophils NA 0.007 lymphocyte antigen 6 complex, locus G protein coding gene 1 Mesoderm Immune system 0.0 0.477816 0.0 6.53937e-05 +Mm Hs TREM1 Neutrophils TREM-1|CD354 0.003 triggering receptor expressed on myeloid cells 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125826 0.0 +Mm Hs SORL1 Neutrophils gp250|LR11|SorLA|SorLA-1|C11orf32 0.034 sortilin related receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.012268 0.0 +Mm Hs ARG2 Neutrophils NA 0.001 arginase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0102389 0.000314564 0.00137327 +Mm Hs BST1 Neutrophils CD157 0.008 bone marrow stromal cell antigen 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0273038 0.00629129 0.008305 +Mm MRGPRA2B Neutrophils NA 0.003 MAS-related GPR, member A2B protein coding gene 1 Mesoderm Immune system 0.0 0.174061 0.0 0.000196181 +Mm Hs IL1R2 Neutrophils CD121b|IL1RB 0.007 interleukin 1 receptor type 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.204778 0.00723498 0.00281193 +Mm Hs CFP Neutrophils PFC 0.035 complement factor properdin protein-coding gene NA Mesoderm Immune system 0.0 0.156997 0.0355458 0.0324353 +Mm Hs ADAM8 Neutrophils CD156|MS2|CD156a 0.01 ADAM metallopeptidase domain 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.191126 0.00566216 0.0072587 +Mm Hs CD177 Neutrophils PRV1|HNA2A|NB1 0.011 CD177 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.593857 0.00377477 0.00124248 +Mm Hs PTGS2 Neutrophils NA 0.009 prostaglandin-endoperoxide synthase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0614334 0.0138408 0.00738948 +Mm Hs OAS3 Neutrophils NA 0.003 2'-5'-oligoadenylate synthetase 3 protein-coding gene NA Mesoderm Immune system 0.0 0.00341297 0.00817867 0.000588543 +Mm Hs PRTN3 Neutrophils PR-3|ACPA|C-ANCA|AGP7|MBT|P29 0.026 proteinase 3 protein-coding gene 1 Mesoderm Immune system 1.0 0.607509 0.00723498 0.0165446 +Hs AZU1 Neutrophils AZU|CAP37|AZAMP|NAZC|HUMAZUR 0.002 azurocidin 1 protein-coding gene NA Mesoderm Immune system 1.0 0.0 0.0088078 0.0 +Mm Hs CTSG Neutrophils CG 0.017 cathepsin G protein-coding gene 1 Mesoderm Immune system 1.0 0.532423 0.00912237 0.00699712 +Hs SERPINB1 Neutrophils EI|PI2|anti-elastase|ELANH2 0.029 serpin family B member 1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.155709 0.0 +Mm Hs CAMP Neutrophils CAP18|FALL39|FALL-39|LL37 0.022 cathelicidin antimicrobial peptide protein-coding gene NA Mesoderm Immune system 0.0 0.83959 0.000314564 0.0103976 +Mm CAR1 Neutrophils NA 0.006 carbonic anhydrase 1 protein coding gene 1 Mesoderm Immune system 0.0 0.00341297 0.0 0.00745488 +Mm Hs SLC1A5 Neutrophils AAAT|ASCT2|RDRC|M7V1 0.038 solute carrier family 1 member 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0465555 0.0 +Mm CHIL3 Neutrophils NA 0.022 chitinase-like 3 protein coding gene 1 Mesoderm Immune system 0.0 0.767918 0.0 0.0119016 +Mm Hs SNX20 Neutrophils SLIC-1|SLIC1 0.02 sorting nexin 20 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00125826 0.0 +Mm Hs ADPGK Neutrophils DKFZp434B195|ADP-GK 0.015 ADP dependent glucokinase protein-coding gene 1 Mesoderm Immune system 0.0 0.549488 0.0103806 0.00582004 +Mm Hs PSTPIP1 Neutrophils PSTPIP|CD2BP1L|CD2BP1|CD2BP1S|H-PIP|PAPAS 0.014 proline-serine-threonine phosphatase interacting protein 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.372014 0.00251651 0.00889354 +Mm Hs LYST Neutrophils CHS 0.015 lysosomal trafficking regulator protein-coding gene 1 Mesoderm Immune system 0.0769231 0.327645 0.0320856 0.00536228 +Mm Hs DOCK8 Neutrophils FLJ00026|FLJ00152|ZIR8|FLJ00346 0.015 dedicator of cytokinesis 8 protein-coding gene NA Mesoderm Immune system 0.0 0.211604 0.0160428 0.0109207 +Mm Hs S100A4 Neutrophils P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.692308 0.0 0.369928 0.0 +Mm Hs NLRP3 Neutrophils AGTAVPRL|AII|AVP|FCAS|FCU|NALP3|PYPAF1|MWS|CLR1.1|C1orf7|CIAS1 0.004 NLR family pyrin domain containing 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0375427 0.000943693 0.00457756 +Mm Hs CSF3R Neutrophils GCSFR|CD114 0.012 colony stimulating factor 3 receptor protein-coding gene 1 Mesoderm Immune system 0.230769 0.21843 0.0204467 0.00693173 +Mm Hs ITGAM NK cells CD11b|CR3A|CD11B 0.025 integrin subunit alpha M protein-coding gene 1 Mesoderm Immune system 0.0 0.0106383 0.00320718 0.0304048 +Mm Hs ITGAX NK cells CD11c|CD11C 0.007 integrin subunit alpha X protein-coding gene 1 Mesoderm Immune system 0.0945946 0.0212766 0.0144323 0.00516429 +Hs FCGR3A NK cells CD16a 0.006 Fc fragment of IgG receptor IIIa protein-coding gene 1 Mesoderm Immune system 0.0675676 0.0 0.0346376 0.0 +Mm Hs CD69 NK cells CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.527027 0.0212766 0.101347 0.00729456 +Mm Hs KLRD1 NK cells CD94 0.02 killer cell lectin like receptor D1 protein-coding gene 1 Mesoderm Immune system 0.594595 0.914894 0.0256575 0.0111678 +Mm Hs IL2RB NK cells CD122|IL15RB 0.02 interleukin 2 receptor subunit beta protein-coding gene 1 Mesoderm Immune system 0.243243 0.904255 0.0134702 0.0141372 +Mm Hs KLRB1 NK cells CD161|NKR-P1|NKR-P1A|hNKR-P1A|CLEC5B 0.008 killer cell lectin like receptor B1 protein-coding gene 1 Mesoderm Immune system 0.418919 0.0 0.0388069 0.00071009 +Mm Hs CD244 NK cells 2B4|NAIL|NKR2B4|Nmrk|SLAMF4 0.002 CD244 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.138298 0.0 0.00167839 +Mm Hs KLRK1 NK cells NKG2D|KLR|NKG2-D|CD314|D12S2489E 0.009 killer cell lectin like receptor K1 protein-coding gene 1 Mesoderm Immune system 0.0 0.93617 0.0 0.00432509 +Mm Hs SLAMF7 NK cells CRACC|19A|CS1|CD319 0.013 SLAM family member 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00769724 0.0 +Hs SIGLEC7 NK cells SIGLEC-7|p75/AIRM1|QA79|CD328|SIGLEC19P|SIGLECP2 0.0 sialic acid binding Ig like lectin 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs NCR1 NK cells NK-p46|NKP46|CD335|LY94 0.004 natural cytotoxicity triggering receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.797872 0.0 0.000451875 +Mm KLRA1 NK cells NA 0.0 killer cell lectin-like receptor, subfamily A, member 1 protein coding gene 1 Mesoderm Immune system 0.0 0.0425532 0.0 6.45536e-05 +Mm Hs SLAMF6 NK cells KALI|NTBA|KALIb|Ly108|SF2000|NTB-A|CD352 0.003 SLAM family member 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs KIT NK cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00256575 0.018656 +Mm Hs CD27 NK cells S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0106383 0.0234124 0.0158156 +Mm Hs KLRC1 NK cells NKG2-A|NKG2-B|CD159a|NKG2 0.004 killer cell lectin like receptor C1 protein-coding gene 1 Mesoderm Immune system 0.216216 0.319149 0.00384862 0.000839197 +Hs KLRF1 NK cells CLEC5C|NKp80 0.003 killer cell lectin like receptor F1 protein-coding gene 1 Mesoderm Immune system 0.256757 0.0 0.0150738 0.0 +Hs GNLY NK cells NKG5|LAG-2|D2S69E|TLA519|LAG2 0.013 granulysin protein-coding gene 1 Mesoderm Immune system 0.851351 0.0 0.0635022 0.0 +Mm Hs NKG7 NK cells GMP-17 0.056 natural killer cell granule protein 7 protein-coding gene 1 Mesoderm Immune system 0.945946 1.0 0.0878768 0.0401523 +Hs IL32 NK cells NK4|TAIF|TAIFb|TAIFd 0.036 interleukin 32 protein-coding gene NA Mesoderm Immune system 0.824324 0.0 0.190186 0.0 +Hs GZMH NK cells CGL-2|CCP-X|CSP-C|CTSGL2 0.005 granzyme H protein-coding gene 1 Mesoderm Immune system 0.527027 0.0 0.0195638 0.0 +Hs FGFBP2 NK cells NA 0.005 fibroblast growth factor binding protein 2 protein-coding gene 1 Mesoderm Immune system 0.459459 0.0 0.0186017 0.0 +Mm Hs GZMM NK cells MET1|LMET1 0.007 granzyme M protein-coding gene 1 Mesoderm Immune system 0.486486 0.0 0.0343169 0.000258214 +Mm Hs CTSW NK cells NA 0.026 cathepsin W protein-coding gene 1 Mesoderm Immune system 0.702703 0.925532 0.0465042 0.0139436 +Mm Hs HMBOX1 NK cells HNF1LA|PBHNF|FLJ21616|HOT1 0.008 homeobox containing 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0150738 0.00723 +Mm FASL NK cells NA 0.001 Fas ligand (TNF superfamily, member 6) protein coding gene 1 Mesoderm Immune system 0.0 0.159574 0.0 0.000580982 +Mm Hs AHR NK cells bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0115459 0.00697179 +Mm Hs PRF1 NK cells PFP|HPLH2 0.009 perforin 1 protein-coding gene 1 Mesoderm Immune system 0.310811 0.702128 0.0240539 0.000516429 +Mm Hs CCL4 NK cells MIP-1-beta|Act-2|AT744.1|SCYA4 0.049 C-C motif chemokine ligand 4 protein-coding gene 1 Mesoderm Immune system 0.581081 0.595745 0.043297 0.0456394 +Mm Hs SEMA6D NK cells KIAA1479|FLJ11598 0.026 semaphorin 6D protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00160359 0.0 +Mm Hs FHL2 NK cells SLIM3|DRAL 0.043 four and a half LIM domains 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.106479 0.0287909 +Mm Hs CD2 NK cells NA 0.04 CD2 molecule protein-coding gene 1 Mesoderm Immune system 0.513514 0.723404 0.0840282 0.0254341 +Mm Hs CD7 NK cells LEU-9|TP41|Tp40 0.03 CD7 molecule protein-coding gene 1 Mesoderm Immune system 0.432432 0.62766 0.0958948 0.0123943 +Mm Hs CD3G NK cells NA 0.048 CD3g molecule protein-coding gene 1 Mesoderm Immune system 0.351351 0.0744681 0.0782553 0.0405397 +Mm Hs CD33 NK cells SIGLEC3|SIGLEC-3|FLJ00391 0.017 CD33 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0128287 0.0173649 +Mm Hs DPP4 NK cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0134702 0.0214318 +Mm Hs LAT NK cells NA 0.034 linker for activation of T cells protein-coding gene 1 Mesoderm Immune system 0.0135135 0.0212766 0.0141116 0.0376993 +Mm Hs PCDH15 NK cells CDHR15|USH1F|DFNB23 0.006 protocadherin related 15 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00192431 0.00671358 +Mm Hs CCL5 NK cells RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Immune system 0.891892 0.968085 0.0667094 0.027048 +Mm Hs GZMA NK cells HFSP|CTLA3 0.026 granzyme A protein-coding gene 1 Mesoderm Immune system 0.905405 0.787234 0.0458627 0.0136854 +Mm Hs GZMB NK cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 0.513514 0.670213 0.0497114 0.00432509 +Mm KLRE1 NK cells NA 0.005 killer cell lectin-like receptor family E member 1 protein coding gene 1 Mesoderm Immune system 0.0 0.861702 0.0 0.00071009 +Mm KLRA4 NK cells NA 0.002 killer cell lectin-like receptor, subfamily A, member 4 protein coding gene NA Mesoderm Immune system 0.0 0.404255 0.0 6.45536e-05 +Mm Hs CMA1 NK cells NA 0.007 chymase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.234043 0.0 0.0071009 +Mm KLRB1C NK cells NA 0.005 killer cell lectin-like receptor subfamily B member 1C protein coding gene 1 Mesoderm Immune system 0.0 0.829787 0.0 0.00071009 +Mm Hs DUSP2 NK cells PAC-1 0.042 dual specificity phosphatase 2 protein-coding gene 1 Mesoderm Immune system 0.5 0.797872 0.0493906 0.0343425 +Mm Hs TXK NK cells TKL|PSCTK5|BTKL|RLK|PTK4 0.003 TXK tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0675676 0.0 0.000641437 0.0 +Mm KLRA8 NK cells NA 0.003 killer cell lectin-like receptor, subfamily A, member 8 protein coding gene 1 Mesoderm Immune system 0.0 0.5 0.0 0.000129107 +Mm Hs DOK2 NK cells p56dok-2|Dok-2 0.022 docking protein 2 protein-coding gene 1 Mesoderm Immune system 0.0810811 0.606383 0.0259782 0.0173004 +Mm Hs CST7 NK cells NA 0.028 cystatin F protein-coding gene 1 Mesoderm Immune system 0.878378 0.340426 0.0500321 0.0167839 +Mm KLRA7 NK cells NA 0.001 killer cell lectin-like receptor, subfamily A, member 7 protein coding gene 1 Mesoderm Immune system 0.0 0.265957 0.0 0.000129107 +Mm KLRA9 NK cells NA 0.002 killer cell lectin-like receptor subfamily A, member 9 protein coding gene 1 Mesoderm Immune system 0.0 0.37234 0.0 0.000129107 +Mm Hs HSD11B1 NK cells SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene NA Mesoderm Immune system 0.0 0.244681 0.00994227 0.0231747 +Mm Hs KLRC2 NK cells NKG2-C|CD159c 0.003 killer cell lectin like receptor C2 protein-coding gene 1 Mesoderm Immune system 0.0945946 0.478723 0.000962155 0.000322768 +Mm KLRB1B NK cells NA 0.002 killer cell lectin-like receptor subfamily B member 1B protein coding gene 1 Mesoderm Immune system 0.0 0.138298 0.0 0.00154929 +Mm Hs SAMD3 NK cells bA73O6.2|FLJ34032 0.001 sterile alpha motif domain containing 3 protein-coding gene 1 Mesoderm Immune system 0.027027 0.0 0.000320718 0.0 +Mm KLRB1A NK cells NA 0.001 killer cell lectin-like receptor subfamily B member 1A protein coding gene 1 Mesoderm Immune system 0.0 0.106383 0.0 0.000258214 +Mm Hs TBX21 NK cells TBLYM|T-bet 0.0 T-box 21 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm KLRB1F NK cells NA 0.001 killer cell lectin-like receptor subfamily B member 1F protein coding gene 1 Mesoderm Immune system 0.0 0.180851 0.0 0.000193661 +Mm Hs CHSY1 NK cells KIAA0990|CSS1 0.007 chondroitin sulfate synthase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0425532 0.00545221 0.00774643 +Hs XCL2 NK cells SCM-1b|SCYC2 0.002 X-C motif chemokine ligand 2 protein-coding gene 1 Mesoderm Immune system 0.297297 0.0 0.00384862 0.0 +Mm Hs TRDC NK cells NA 0.011 T cell receptor delta constant other NA Mesoderm Immune system 0.351351 0.0 0.0179602 0.0 +Mm Hs CXCR4 NK cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.554054 0.0531915 0.189865 0.00852108 +Mm Hs IL18R1 NK cells IL1RRP|IL-1Rrp|CD218a 0.013 interleukin 18 receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.319149 0.000641437 0.0149119 +Mm KLRA3 NK cells NA 0.0 killer cell lectin-like receptor, subfamily A, member 3 protein coding gene 1 Mesoderm Immune system 0.0 0.0425532 0.0 0.0 +Mm Hs SERPINB9 NK cells CAP3|PI9 0.018 serpin family B member 9 protein-coding gene 1 Mesoderm Immune system 0.027027 0.0 0.033034 0.0 +Mm Hs DOCK2 NK cells KIAA0209 0.014 dedicator of cytokinesis 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.106383 0.000962155 0.0167839 +Mm Hs SH2D2A NK cells TSAd|F2771 0.009 SH2 domain containing 2A protein-coding gene 1 Mesoderm Immune system 0.0405405 0.0 0.0131495 0.0 +Mm MS4A4B NK cells NA 0.023 membrane-spanning 4-domains, subfamily A, member 4B protein coding gene 1 Mesoderm Immune system 0.0 0.893617 0.0 0.0223355 +Mm Hs S100A4 NK cells P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.851351 0.0 0.359846 0.0 +Mm Hs XCL1 NK cells LPTN|ATAC|SCM-1a|SCM-1|LTN|SCYC1 0.006 X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Immune system 0.297297 0.0 0.00320718 0.0 +Mm Hs GZMK NK cells TRYP2|PRSS 0.001 granzyme K protein-coding gene 1 Mesoderm Immune system 0.0 0.0106383 0.000320718 0.00148473 +Mm Hs IFNG NK cells NA 0.003 interferon gamma protein-coding gene 1 Mesoderm Immune system 0.0810811 0.0319149 0.0109044 0.00154929 +Mm Hs CCL3 NK cells G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Mesoderm Immune system 0.0540541 0.393617 0.00673509 0.0404106 +Mm Hs CSF2 NK cells GM-CSF|GMCSF 0.002 colony stimulating factor 2 protein-coding gene 1 Mesoderm Immune system 0.027027 0.0 0.00898012 0.000774643 +Mm Hs IL2RG NK cells CD132|SCIDX1|IMD4|CIDX 0.04 interleukin 2 receptor subunit gamma protein-coding gene 1 Mesoderm Immune system 0.594595 0.255319 0.103271 0.0236912 +Mm Hs TGFB1 NK cells CED|TGFbeta|TGFB|DPD1 0.11 transforming growth factor beta 1 protein-coding gene 1 Mesoderm Immune system 0.121622 0.0 0.043297 0.0 +Mm CTLA2A NK cells NA 0.067 cytotoxic T lymphocyte-associated protein 2 alpha protein coding gene 1 Mesoderm Immune system 0.0 0.595745 0.0 0.0788845 +Hs KIR2DL1 NK cells cl-42|nkat1|47.11|p58.1|CD158A 0.0 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1 protein-coding gene 1 Mesoderm Immune system 0.0135135 0.0 0.0 0.0 +Mm Hs KIR3DL1 NK cells cl-2|NKB1|cl-11|nkat3|NKB1B|AMB11|CD158e1/2|CD158E1|CD158e2 0.0 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 protein-coding gene 1 Mesoderm Immune system 0.0135135 0.0 0.0 6.45536e-05 +Mm KLRA5 NK cells NA 0.0 killer cell lectin-like receptor, subfamily A, member 5 protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs LILRB1 NK cells LIR-1|ILT2|MIR-7|LIR1|CD85j 0.001 leukocyte immunoglobulin like receptor B1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00384862 0.0 +Mm Hs KLRG1 NK cells MAFA|MAFA-L|CLEC15A 0.002 killer cell lectin like receptor G1 protein-coding gene 1 Mesoderm Immune system 0.0810811 0.0531915 0.00160359 0.000839197 +Hs NCR3 NK cells 1C7|NKp30|CD337|LY117 0.0 natural cytotoxicity triggering receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00128287 0.0 +Mm Hs ADAMTS14 NK cells NA 0.0 ADAM metallopeptidase with thrombospondin type 1 motif 14 protein-coding gene 1 Mesoderm Immune system 0.0 0.0106383 0.0 0.000451875 +Mm KLRA10 NK cells NA 0.0 killer cell lectin-like receptor subfamily A, member 10 protein coding gene 1 Mesoderm Immune system 0.0 0.0425532 0.0 0.0 +Mm Hs ITGA2 NK cells CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0106383 0.0461835 0.00303402 +Mm SERPINB9B NK cells NA 0.001 serine (or cysteine) peptidase inhibitor, clade B, member 9b protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs STYK1 NK cells SuRTK106|DKFZp761P1010|NOK 0.002 serine/threonine/tyrosine kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm CAR5B NK cells NA 0.0 carbonic anhydrase 5b, mitochondrial protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000258214 +Mm Hs CLEC2D NK cells LLT1|CLAX|OCIL 0.029 C-type lectin domain family 2 member D protein-coding gene 1 Mesoderm Immune system 0.0675676 0.0 0.0776139 0.019237 +Mm Hs CD247 NK cells CD3H|CD3Q|CD3Z 0.019 CD247 molecule protein-coding gene 1 Mesoderm Immune system 0.216216 0.0425532 0.0516357 0.0123297 +Mm Hs ZBTB16 NK cells PLZF|ZNF145 0.007 zinc finger and BTB domain containing 16 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0121873 0.0 +Mm Hs SPON2 NK cells DIL1 0.017 spondin 2 protein-coding gene 1 Mesoderm Immune system 0.0405405 0.0 0.0490699 0.0 +Hs LAIR2 NK cells CD306 0.001 leukocyte associated immunoglobulin like receptor 2 protein-coding gene 1 Mesoderm Immune system 0.027027 0.0 0.00769724 0.0 +Mm Hs HOPX NK cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Mesoderm Immune system 0.513514 0.0 0.0817832 0.0224001 +Mm Hs CD8A NK cells CD8 0.01 CD8a molecule protein-coding gene 1 Mesoderm Immune system 0.0540541 0.0106383 0.0150738 0.00858563 +Mm Hs TH Noradrenergic neurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs DDC Noradrenergic neurons AADC 0.014 dopa decarboxylase protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00469925 0.0164292 +Mm Hs DBH Noradrenergic neurons DBM 0.001 dopamine beta-hydroxylase protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.000641766 +Mm Hs SLC18A2 Noradrenergic neurons SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs SLC18A3 Noradrenergic neurons VACHT 0.002 solute carrier family 18 member A3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs SLC6A2 Noradrenergic neurons SLC6A5 0.002 solute carrier family 6 member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs SLC39A11 Noradrenergic neurons C17orf26 0.005 solute carrier family 39 member 11 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.0 +Mm Hs SLC9B2 Noradrenergic neurons FLJ23984|NHA2|NHEDC2 0.002 solute carrier family 9 member B2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00720551 0.0 +Mm Hs ICOS Nuocytes AILIM|CD278 0.01 inducible T cell costimulator protein-coding gene 1 Mesoderm Immune system 0.0 0.666667 0.00689223 0.00990035 +Mm Hs IL1RL1 Nuocytes ST2|FIT-1|ST2V|DER4|IL33R 0.007 interleukin 1 receptor like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.866667 0.0147243 0.00379299 +Mm Hs RORA Nuocytes RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0140977 0.0 +Mm Hs IL17RB Nuocytes IL17RH1|EVI27|CRL4|IL17BR 0.001 interleukin 17 receptor B protein-coding gene NA Mesoderm Immune system 0.0 0.0666667 0.000313283 0.00102861 +Mm Hs IL7R Nuocytes CD127|IL7RA 0.031 interleukin 7 receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.933333 0.0711153 0.0214079 +Mm Hs CRLF2 Nuocytes CRL2|TSLPR 0.044 cytokine receptor like factor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0529733 +Mm Hs ARG1 Nuocytes NA 0.007 arginase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.533333 0.00344612 0.00617165 +Mm Hs GATA3 Nuocytes HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0200501 0.027901 +Mm Hs PTGDS Nuocytes L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0582707 0.0552234 +Mm Hs BCL11B Nuocytes CTIP-2|CTIP2|hRIT1-alpha|ZNF856B 0.077 B cell CLL/lymphoma 11B protein-coding gene NA Mesoderm Immune system 0.0 0.1 0.0109649 0.0943105 +Mm Hs IL5 Nuocytes IL-5|EDF 0.002 interleukin 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.3 0.00626566 0.000257152 +Mm Hs IL13 Nuocytes P600|IL-13|ALRH|BHR1|MGC116786|MGC116788|MGC116789 0.004 interleukin 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.2 0.018797 0.0010929 +Mm Hs ANO2 Olfactory epithelial cells C12orf3|TMEM16B 0.001 anoctamin 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.266667 0.00219298 0.000128576 +Mm Hs RARG Olfactory epithelial cells RARC|NR1B3 0.012 retinoic acid receptor gamma protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00657895 0.0 +Mm Hs LRRC45 Olfactory epithelial cells MGC20806 0.005 leucine rich repeat containing 45 protein-coding gene NA Ectoderm Olfactory system 0.0 0.2 0.00125313 0.00527162 +Mm Hs RAB3B Olfactory epithelial cells NA 0.023 RAB3B, member RAS oncogene family protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0191103 0.0 +Mm Hs KCNC4 Olfactory epithelial cells Kv3.4|HKSHIIIC|C1orf30 0.004 potassium voltage-gated channel subfamily C member 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.266667 0.0 0.00411443 +Mm Hs MANEA Olfactory epithelial cells FLJ12838|mandaselin 0.002 mannosidase endo-alpha protein-coding gene NA Ectoderm Olfactory system 0.0 0.2 0.00125313 0.00231437 +Mm Hs PACRG Olfactory epithelial cells PARK2CRG|FLJ32724|Glup|HAK005771 0.014 parkin coregulated protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0184837 0.0127933 +Mm Hs PDE1C Olfactory epithelial cells Hcam3 0.007 phosphodiesterase 1C protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0056391 0.00681453 +Mm Hs GADL1 Olfactory epithelial cells NA 0.0 glutamate decarboxylase like 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.3 0.0 0.0 +Mm Hs TSTD1 Olfactory epithelial cells KAT 0.058 thiosulfate sulfurtransferase like domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.217732 0.0 +Mm Hs TTC21A Olfactory epithelial cells STI2|IFT139A 0.004 tetratricopeptide repeat domain 21A protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0103383 0.0 +Mm Hs KCNA5 Olfactory epithelial cells Kv1.5|HPCN1 0.002 potassium voltage-gated channel subfamily A member 5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.266667 0.000313283 0.00154291 +Mm Hs ACSM4 Olfactory epithelial cells NA 0.001 acyl-CoA synthetase medium chain family member 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.233333 0.0 0.00032144 +Mm Hs CLDN9 Olfactory epithelial cells NA 0.003 claudin 9 protein-coding gene NA Ectoderm Olfactory system 0.0 0.633333 0.0 0.00315011 +Mm Hs DUSP8 Olfactory epithelial cells HVH-5|HB5|FLJ42958|C11orf81 0.027 dual specificity phosphatase 8 protein-coding gene NA Ectoderm Olfactory system 0.0 0.166667 0.000313283 0.0336869 +Mm Hs TTLL3 Olfactory epithelial cells DKFZP434B103|HOTTL 0.004 tubulin tyrosine ligase like 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0 0.0 +Mm Hs ABHD3 Olfactory epithelial cells LABH3 0.01 abhydrolase domain containing 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.3 0.0103383 0.0104147 +Mm Hs KIF9 Olfactory epithelial cells MGC104186 0.014 kinesin family member 9 protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0501253 0.00578592 +Mm CCPG1OS Olfactory epithelial cells NA 0.01 cell cycle progression 1, opposite strand protein coding gene NA Ectoderm Olfactory system 0.0 0.6 0.0 0.011379 +Mm Hs CLSTN2 Olfactory epithelial cells CSTN2|CS2|FLJ39113|CDHR13 0.014 calsyntenin 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.266667 0.00219298 0.0171006 +Mm Hs MEIG1 Olfactory epithelial cells bA2K17.3|SPATA39 0.018 meiosis/spermiogenesis associated 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0140977 0.018965 +Mm Hs ENDOD1 Olfactory epithelial cells KIAA0830 0.038 endonuclease domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0093985 0.0447445 +Mm Hs TTC9 Olfactory epithelial cells KIAA0227|TTC9A 0.013 tetratricopeptide repeat domain 9 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00595238 0.0 +Mm Hs PPP1R14C Olfactory epithelial cells NY-BR-81|KEPI 0.026 protein phosphatase 1 regulatory inhibitor subunit 14C protein-coding gene NA Ectoderm Olfactory system 0.0 0.2 0.00595238 0.0313083 +Mm Hs RETREG1 Olfactory epithelial cells FLJ20152|JK1|FAM134B 0.042 reticulophagy regulator 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0313283 0.0 +Mm Hs WDFY1 Olfactory epithelial cells KIAA1435|FENS-1|WDF1|ZFYVE17 0.026 WD repeat and FYVE domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00595238 0.0 +Mm Hs CASP6 Olfactory epithelial cells NA 0.033 caspase 6 protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.00814536 0.0378014 +Mm Hs FGF12 Olfactory epithelial cells FHF1|FGF12B 0.014 fibroblast growth factor 12 protein-coding gene NA Ectoderm Olfactory system 0.0 0.266667 0.00438596 0.0166506 +Mm Hs TRAF3IP1 Olfactory epithelial cells MIP-T3|DKFZP434F124|MIPT3|IFT54 0.006 TRAF3 interacting protein 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0131579 0.0 +Mm Hs RNF128 Olfactory epithelial cells FLJ23516|GRAIL 0.024 ring finger protein 128, E3 ubiquitin protein ligase protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00156642 0.0 +Mm Hs LMAN2L Olfactory epithelial cells DKFZp564L2423|VIPL 0.008 lectin, mannose binding 2 like protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.000313283 0.00919319 +Mm Hs IFT74 Olfactory epithelial cells CMG1|CMG-1|FLJ22621|CCDC2 0.026 intraflagellar transport 74 protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.0197368 0.0277724 +Mm Hs B9D1 Olfactory epithelial cells EPPB9|MKS9 0.033 B9 domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.0278822 0.0333655 +Mm Hs WDR54 Olfactory epithelial cells FLJ12953 0.016 WD repeat domain 54 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0532581 0.0 +Mm Hs TOLLIP Olfactory epithelial cells IL-1RAcPIP 0.032 toll interacting protein protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0679825 0.0 +Mm Hs ORMDL3 Olfactory epithelial cells NA 0.042 ORMDL sphingolipid biosynthesis regulator 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0159774 0.0490518 +Mm Hs DNAJB14 Olfactory epithelial cells FLJ14281 0.029 DnaJ heat shock protein family (Hsp40) member B14 protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.0181704 0.0315011 +Mm Hs SCN4B Olfactory epithelial cells LQT10 0.003 sodium voltage-gated channel beta subunit 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0 0.0 +Mm Hs NRG1 Olfactory epithelial cells HRG|NDF|GGF|NRG1-IT2 0.012 neuregulin 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0128446 0.0118933 +Mm Hs MAPK8IP2 Olfactory epithelial cells IB2|JIP2|PRKM8IPL 0.025 mitogen-activated protein kinase 8 interacting protein 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.0 0.0306011 +Mm Hs EBF3 Olfactory epithelial cells COE3|DKFZp667B0210 0.012 early B cell factor 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.000626566 0.0139505 +Mm Hs MAPK15 Olfactory epithelial cells ERK8|ERK7 0.006 mitogen-activated protein kinase 15 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0 0.00694311 +Mm Hs CNGA4 Olfactory epithelial cells OCNC2|OCNCb|CNG5|CNCA2|CNGB2 0.001 cyclic nucleotide gated channel alpha 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0 0.0 +Mm Hs KIF1BP Olfactory epithelial cells DKFZP586B0923|TTC20|KBP|KIAA1279 0.023 KIF1 binding protein protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.00657895 0.0271938 +Mm Hs EML2 Olfactory epithelial cells EMAP2|ELP70 0.025 echinoderm microtubule associated protein like 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0109649 0.0280939 +Mm Hs RIIAD1 Olfactory epithelial cells FLJ36032|NCRNA00166|C1orf230 0.019 regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0119048 0.0 +Mm Hs CCDC184 Olfactory epithelial cells LOC387856|C12orf68 0.009 coiled-coil domain containing 184 protein-coding gene NA Ectoderm Olfactory system 0.0 0.333333 0.00689223 0.00977178 +Mm Hs MACROD1 Olfactory epithelial cells LRP16 0.014 MACRO domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.4 0.0172306 0.0100289 +Mm Hs RNF220 Olfactory epithelial cells FLJ10597|C1orf164 0.044 ring finger protein 220 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0175439 0.0 +Mm Hs CERS5 Olfactory epithelial cells Trh4|MGC45411|FLJ25304|LASS5 0.035 ceramide synthase 5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.014411 0.0393443 +Mm Hs RNF121 Olfactory epithelial cells FLJ11099 0.013 ring finger protein 121 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00344612 0.0 +Mm Hs LINGO1 Olfactory epithelial cells FLJ14594|LERN1|LRRN6A 0.019 leucine rich repeat and Ig domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0018797 0.0228222 +Mm Hs BORCS7 Olfactory epithelial cells FLJ40752|C10orf32 0.051 BLOC-1 related complex subunit 7 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0673559 0.047316 +Mm Hs ELMOD3 Olfactory epithelial cells FLJ21977|RBM29|RBED1|DFNB88 0.003 ELMO domain containing 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.633333 0.00250627 0.0016072 +Mm Hs KLHL5 Olfactory epithelial cells NA 0.026 kelch like family member 5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0106516 0.028801 +Mm Hs CWC22 Olfactory epithelial cells KIAA1604|EIF4GL|fSAPb|NCM 0.009 CWC22 spliceosome associated protein homolog protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.00407268 0.0091289 +Mm Hs TRIM66 Olfactory epithelial cells KIAA0298|TIF1D|C11orf29 0.001 tripartite motif containing 66 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00125313 0.0 +Mm Hs CARNS1 Olfactory epithelial cells KIAA1394|ATPGD1 0.003 carnosine synthase 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.00783208 0.00064288 +Mm Hs TMEM107 Olfactory epithelial cells MGC10744 0.032 transmembrane protein 107 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0275689 0.0 +Mm Hs CNPPD1 Olfactory epithelial cells CGI-57|C2orf24 0.02 cyclin Pas1/PHO80 domain containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.4 0.0134712 0.0210865 +Mm Hs NGRN Olfactory epithelial cells DSC92 0.02 neugrin, neurite outgrowth associated protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.0 0.0239794 +Mm Hs EFNA5 Olfactory epithelial cells AF1|LERK7|EPLG7 0.029 ephrin A5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.4 0.0247494 0.029251 +Mm Hs OSCP1 Olfactory epithelial cells C1orf102 0.015 organic solute carrier partner 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.0228697 0.0136291 +Mm Hs PCOLCE2 Olfactory epithelial cells PCPE2 0.017 procollagen C-endopeptidase enhancer 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.0103383 0.0180006 +Mm Hs RIC8B Olfactory epithelial cells FLJ10620|hSyn|RIC8 0.003 RIC8 guanine nucleotide exchange factor B protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.000626566 0.0 +Mm Hs SIAH2 Olfactory epithelial cells NA 0.021 siah E3 ubiquitin protein ligase 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0256892 0.0 +Mm Hs CBX4 Olfactory epithelial cells hPC2|NBP16 0.012 chromobox 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.566667 0.00313283 0.012729 +Mm Hs CYB561 Olfactory epithelial cells FRRS2|CYB561A1 0.027 cytochrome b561 protein-coding gene NA Ectoderm Olfactory system 0.0 0.633333 0.0147243 0.0269367 +Mm Hs SPA17 Olfactory epithelial cells CT22 0.02 sperm autoantigenic protein 17 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0325815 0.0 +Mm Hs NAT14 Olfactory epithelial cells KLP1 0.015 N-acetyltransferase 14 (putative) protein-coding gene NA Ectoderm Olfactory system 0.0 0.566667 0.00657895 0.0152363 +Mm Hs NXNL2 Olfactory epithelial cells RdCVF2|C9orf121 0.001 nucleoredoxin like 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.366667 0.0 0.00122147 +Mm Hs TTC5 Olfactory epithelial cells Strap 0.02 tetratricopeptide repeat domain 5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00313283 0.0 +Mm Hs SLC16A11 Olfactory epithelial cells FLJ90193|MCT11 0.008 solute carrier family 16 member 11 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0 0.0 +Mm Hs LRRIQ1 Olfactory epithelial cells FLJ12303|KIAA1801 0.011 leucine rich repeats and IQ motif containing 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.0307018 0.00675024 +Mm Hs ARL6 Olfactory epithelial cells RP55|BBS3 0.02 ADP ribosylation factor like GTPase 6 protein-coding gene NA Ectoderm Olfactory system 0.0 0.6 0.00783208 0.0221151 +Mm Hs SPEF2 Olfactory epithelial cells KPL2|FLJ23577|CT122 0.009 sperm flagellar 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0128446 0.0 +Mm Hs MAPKAP1 Olfactory epithelial cells MGC2745|SIN1 0.054 mitogen-activated protein kinase associated protein 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.0567043 0.0495661 +Mm Hs FAM131C Olfactory epithelial cells FLJ36766|C1orf117 0.003 family with sequence similarity 131 member C protein-coding gene NA Ectoderm Olfactory system 0.0 0.4 0.000313283 0.00334298 +Mm Hs FAM81A Olfactory epithelial cells MGC26690 0.028 family with sequence similarity 81 member A protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.0 0.0346512 +Mm Hs SH3GLB2 Olfactory epithelial cells KIAA1848 0.048 SH3 domain containing GRB2 like, endophilin B2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0128446 0.0 +Mm Hs MLF1 Olfactory epithelial cells NA 0.042 myeloid leukemia factor 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.633333 0.093985 0.0287367 +Mm Hs FAM92B Olfactory epithelial cells FLJ44299 0.002 family with sequence similarity 92 member B protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.0018797 0.00115718 +Mm Hs PKIB Olfactory epithelial cells PRKACN2 0.036 cAMP-dependent protein kinase inhibitor beta protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.0529449 0.0257795 +Mm Hs PDE4A Olfactory epithelial cells DPDE2 0.013 phosphodiesterase 4A protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.00125313 0.0149791 +Mm Hs FETUB Olfactory epithelial cells NA 0.002 fetuin B protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.000313283 0.00205722 +Mm Hs EBF2 Olfactory epithelial cells FLJ11500|COE2 0.006 early B cell factor 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.9 0.00125313 0.0053359 +Mm Hs CCDC28B Olfactory epithelial cells MGC1203|RP4-622L5.5 0.02 coiled-coil domain containing 28B protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.0191103 0.019415 +Mm Hs NQO1 Olfactory epithelial cells DHQU|QR1|NMOR1|DIA4 0.024 NAD(P)H quinone dehydrogenase 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.3 0.0748747 0.00745741 +Mm Hs DUSP14 Olfactory epithelial cells MKP-L|MKP6 0.025 dual specificity phosphatase 14 protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.0441729 0.0188364 +Mm Hs GRAMD1C Olfactory epithelial cells DKFZp434C0328 0.004 GRAM domain containing 1C protein-coding gene NA Ectoderm Olfactory system 0.0 0.466667 0.0128446 0.00199293 +Mm Hs RTP2 Olfactory epithelial cells MGC78665|Z3CXXC2 0.001 receptor transporter protein 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.000626566 0.0 +Mm Hs SGPL1 Olfactory epithelial cells SPL 0.034 sphingosine-1-phosphate lyase 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0460526 0.0 +Mm Hs GOLGA7B Olfactory epithelial cells bA459F3.4|bA451M19.3|C10orf133|C10orf132 0.018 golgin A7 family member B protein-coding gene NA Ectoderm Olfactory system 0.0 0.766667 0.0 0.0207007 +Mm Hs CFAP126 Olfactory epithelial cells Flattop|Fltp|C1orf192 0.013 cilia and flagella associated protein 126 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0 0.0149791 +Mm Hs CACNB3 Olfactory epithelial cells CACNLB3 0.032 calcium voltage-gated channel auxiliary subunit beta 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0018797 0.0387657 +Mm Hs IFT43 Olfactory epithelial cells FLJ32173|MGC16028|C14orf179 0.053 intraflagellar transport 43 protein-coding gene NA Ectoderm Olfactory system 0.0 0.766667 0.0513784 0.0522019 +Mm Hs ACSL6 Olfactory epithelial cells KIAA0837|LACS5|FACL6 0.022 acyl-CoA synthetase long chain family member 6 protein-coding gene NA Ectoderm Olfactory system 0.0 0.5 0.014411 0.0230794 +Mm Hs SPOCK1 Olfactory epithelial cells testican-1|TIC1|SPOCK 0.025 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0181704 0.0 +Mm Hs CLGN Olfactory epithelial cells NA 0.014 calmegin protein-coding gene NA Ectoderm Olfactory system 0.0 0.766667 0.0238095 0.0108647 +Mm Hs EFCAB10 Olfactory epithelial cells NA 0.012 EF-hand calcium binding domain 10 protein-coding gene NA Ectoderm Olfactory system 0.0 0.433333 0.0150376 0.0109932 +Mm Hs HOMER2 Olfactory epithelial cells CPD|Cupidin|Vesl-2|HOMER-2B|HOMER-2|HOMER-2A|DFNA68 0.022 homer scaffold protein 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.9 0.0100251 0.0230794 +Mm CKMT1 Olfactory epithelial cells NA 0.051 creatine kinase, mitochondrial 1, ubiquitous protein coding gene NA Ectoderm Olfactory system 0.0 0.866667 0.0 0.0610736 +Mm Hs MYCBP Olfactory epithelial cells AMY-1 0.042 MYC binding protein protein-coding gene NA Ectoderm Olfactory system 0.0 0.566667 0.0297619 0.0425587 +Mm Hs RD3 Olfactory epithelial cells LCA12|C1orf36 0.002 retinal degeneration 3, GUCY2D regulator protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0 0.0 +Mm Hs HIST2H2BE Olfactory epithelial cells H2B/q|H2B|H2BFQ 0.004 histone cluster 2 H2B family member e protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.0153509 6.4288e-05 +Mm Hs SCN9A Olfactory epithelial cells Nav1.7|NE-NA|NENA|ETHA 0.011 sodium voltage-gated channel alpha subunit 9 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00407268 0.0 +Mm Hs ABHD16A Olfactory epithelial cells NG26|D6S82E|BAT5 0.039 abhydrolase domain containing 16A protein-coding gene NA Ectoderm Olfactory system 0.0 0.566667 0.0 0.047316 +Mm Hs IMPDH1 Olfactory epithelial cells sWSS2608|LCA11|RP10 0.029 inosine monophosphate dehydrogenase 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.0169173 0.028801 +Mm Hs CMIP Olfactory epithelial cells NA 0.031 c-Maf inducing protein protein-coding gene NA Ectoderm Olfactory system 0.0 0.633333 0.0263158 0.0318869 +Mm Hs TESC Olfactory epithelial cells FLJ20607|CHP3 0.032 tescalcin protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0780075 0.0 +Mm Hs CTXN3 Olfactory epithelial cells NA 0.005 cortexin 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.6 0.0 0.00462874 +Mm Hs S100A5 Olfactory epithelial cells S100D 0.006 S100 calcium binding protein A5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0 0.0 +Mm Hs RSPH1 Olfactory epithelial cells FLJ32753|RSP44|RSPH10A|CILD24|TSGA2 0.021 radial spoke head component 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.0162907 0.0 +Mm Hs FAIM Olfactory epithelial cells FLJ10582|FAIM1 0.051 Fas apoptotic inhibitory molecule protein-coding gene NA Ectoderm Olfactory system 0.0 0.8 0.0125313 0.0581164 +Mm Hs THEM6 Olfactory epithelial cells DSCD75|C8orf55 0.009 thioesterase superfamily member 6 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00313283 0.0 +Mm Hs CNGA2 Olfactory epithelial cells CNG2|OCNC1|OCNCa|OCNCALPHA|OCNCalpha|FLJ46312|CNCA1|CNCA 0.001 cyclic nucleotide gated channel alpha 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.0 0.0 +Mm Hs CNTN4 Olfactory epithelial cells BIG-2 0.005 contactin 4 protein-coding gene NA Ectoderm Olfactory system 0.0 0.8 0.0115915 0.00250723 +Mm Hs EFNA3 Olfactory epithelial cells LERK3|Ehk1-L|EPLG3 0.009 ephrin A3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.8 0.0018797 0.00938605 +Mm Hs RTP1 Olfactory epithelial cells MGC35450|Z3CXXC1 0.001 receptor transporter protein 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.00125313 0.0 +Mm DCDC2A Olfactory epithelial cells NA 0.005 doublecortin domain containing 2a protein coding gene NA Ectoderm Olfactory system 0.0 0.566667 0.0 0.00527162 +Mm Hs AK1 Olfactory epithelial cells NA 0.038 adenylate kinase 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.733333 0.00219298 0.0464159 +Mm Hs FLRT1 Olfactory epithelial cells MGC21624|SPG68 0.015 fibronectin leucine rich transmembrane protein 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.933333 0.0 0.0176792 +Mm Hs JAKMIP1 Olfactory epithelial cells MARLIN1|JAMIP1|Gababrbp|FLJ31564 0.017 janus kinase and microtubule interacting protein 1 protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.000626566 0.0199293 +Mm TMEM74BOS Olfactory epithelial cells NA 0.001 transmembrane 74B, opposite strand antisense lncRNA gene NA Ectoderm Olfactory system NA NA NA NA +Mm Hs CALB2 Olfactory epithelial cells CAL2 0.03 calbindin 2 protein-coding gene NA Ectoderm Olfactory system 0.0 0.533333 0.00281955 0.0365156 +Mm SULT1D1 Olfactory epithelial cells NA 0.011 sulfotransferase family 1D, member 1 protein coding gene NA Ectoderm Olfactory system NA NA NA NA +Mm Hs GNG13 Olfactory epithelial cells h2-35|G(gamma)13 0.006 G protein subunit gamma 13 protein-coding gene NA Ectoderm Olfactory system 0.0 0.666667 0.0 0.0064288 +Mm Hs ACBD7 Olfactory epithelial cells FLJ38219|bA455B2.2 0.002 acyl-CoA binding domain containing 7 protein-coding gene NA Ectoderm Olfactory system 0.0 0.733333 0.0 0.0010929 +Mm Hs FSTL5 Olfactory epithelial cells DKFZp566D234|KIAA1263 0.008 follistatin like 5 protein-coding gene NA Ectoderm Olfactory system 0.0 0.933333 0.00125313 0.00822887 +Mm Hs GNAL Olfactory epithelial cells NA 0.025 G protein subunit alpha L protein-coding gene NA Ectoderm Olfactory system 0.0 0.7 0.00093985 0.0299582 +Mm Hs GFY Olfactory epithelial cells Goofy 0.002 golgi associated olfactory signaling regulator protein-coding gene NA Ectoderm Olfactory system 0.0 0.966667 0.0 0.000128576 +Mm Hs ATF5 Olfactory epithelial cells NA 0.032 activating transcription factor 5 protein-coding gene NA Ectoderm Olfactory system 0.0 1.0 0.0260025 0.0315011 +Mm Hs STOM Olfactory epithelial cells BND7|EPB7|EPB72 0.033 stomatin protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.10307 0.0 +Mm Hs CARTPT Olfactory epithelial cells CART 0.008 CART prepropeptide protein-coding gene NA Ectoderm Olfactory system 0.0 0.6 0.00720551 0.00700739 +Mm Hs STOML3 Olfactory epithelial cells SRO|Epb7.2l 0.004 stomatin like 3 protein-coding gene NA Ectoderm Olfactory system 0.0 0.0 0.000313283 0.0 +Mm Hs OMP Olfactory epithelial cells NA 0.001 olfactory marker protein protein-coding gene 1 Ectoderm Olfactory system 0.0 0.7 0.0 0.00032144 +Mm Hs CSPG4 Oligodendrocyte progenitor cells MCSPG|MEL-CSPG|HMW-MAA 0.015 chondroitin sulfate proteoglycan 4 protein-coding gene 1 Ectoderm Brain 0.0 0.410377 0.000627943 0.0137904 +Mm Hs PDGFRA Oligodendrocyte progenitor cells CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene 1 Ectoderm Brain 1.0 0.849057 0.0455259 0.0329149 +Mm Hs SOX10 Oligodendrocyte progenitor cells DOM|WS4|WS2E 0.04 SRY-box 10 protein-coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs OLIG2 Oligodendrocyte progenitor cells RACK17|OLIGO2|bHLHe19|PRKCBP2|BHLHB1 0.039 oligodendrocyte transcription factor 2 protein-coding gene 1 Ectoderm Brain 0.285714 0.938679 0.000941915 0.037078 +Mm Hs MATN4 Oligodendrocyte progenitor cells NA 0.015 matrilin 4 protein-coding gene 1 Ectoderm Brain 0.0 0.669811 0.0 0.0102127 +Mm Hs C1QL1 Oligodendrocyte progenitor cells C1QRF|C1QTNF14 0.013 complement C1q like 1 protein-coding gene 1 Ectoderm Brain 0.0 0.801887 0.00627944 0.00435829 +Mm Hs GPR37L1 Oligodendrocyte progenitor cells ETBR-LP-2 0.041 G protein-coupled receptor 37 like 1 protein-coding gene 1 Ectoderm Brain 1.0 0.745283 0.0021978 0.041111 +Mm Hs GPR17 Oligodendrocyte progenitor cells NA 0.02 G protein-coupled receptor 17 protein-coding gene 1 Ectoderm Brain 0.0 0.693396 0.0 0.0156768 +Mm Hs KCNIP3 Oligodendrocyte progenitor cells DREAM|KCHIP3|CSEN 0.007 potassium voltage-gated channel interacting protein 3 protein-coding gene 1 Ectoderm Brain 0.0 0.410377 0.0 0.00325246 +Mm Hs TMEM100 Oligodendrocyte progenitor cells FLJ10970|FLJ37856 0.021 transmembrane protein 100 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00376766 0.0 +Mm Hs VCAN Oligodendrocyte progenitor cells PG-M|CSPG2 0.056 versican protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0948195 0.0 +Mm Hs CDO1 Oligodendrocyte progenitor cells NA 0.036 cysteine dioxygenase type 1 protein-coding gene 1 Ectoderm Brain 0.0 0.556604 0.0119309 0.0347362 +Mm Hs EPN2 Oligodendrocyte progenitor cells KIAA1065|EHB21 0.046 epsin 2 protein-coding gene 1 Ectoderm Brain 1.0 0.801887 0.0213501 0.0426072 +Mm Hs LHFPL3 Oligodendrocyte progenitor cells LHFPL4 0.014 LHFPL tetraspan subfamily member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.816038 0.0 0.00630976 +Mm Hs NEU4 Oligodendrocyte progenitor cells NA 0.009 neuraminidase 4 protein-coding gene 1 Ectoderm Brain 0.142857 0.495283 0.000627943 0.00409809 +Mm Hs ASCL1 Oligodendrocyte progenitor cells HASH1|bHLHa46 0.007 achaete-scute family bHLH transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0283019 0.00533752 0.00696026 +Mm Hs LAD1 Oligodendrocyte progenitor cells NA 0.023 ladinin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.00471698 0.0282575 0.0221817 +Mm Hs SLC25A47 Oligodendrocyte progenitor cells C14orf68 0.001 solute carrier family 25 member 47 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313972 0.0 +Mm Hs ETV5 Oligodendrocyte progenitor cells ERM 0.019 ETS variant 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0235849 0.0131868 0.0190594 +Mm Hs NNAT Oligodendrocyte progenitor cells Peg5 0.229 neuronatin protein-coding gene 1 Ectoderm Brain 0.0 0.599057 0.0461538 0.272296 +Mm Hs CSPG5 Oligodendrocyte progenitor cells NGC 0.09 chondroitin sulfate proteoglycan 5 protein-coding gene 1 Ectoderm Brain 0.0 0.867925 0.00156986 0.101607 +Mm Hs OLIG1 Oligodendrocyte progenitor cells BHLHB6|bHLHe21 0.066 oligodendrocyte transcription factor 1 protein-coding gene 1 Ectoderm Brain 1.0 0.995283 0.0021978 0.0696025 +Mm Hs PCDH15 Oligodendrocyte progenitor cells CDHR15|USH1F|DFNB23 0.006 protocadherin related 15 protein-coding gene 1 Ectoderm Brain 0.142857 0.377358 0.00156986 0.00156118 +Mm Hs ALDOC Oligodendrocyte progenitor cells NA 0.078 aldolase, fructose-bisphosphate C protein-coding gene 1 Ectoderm Brain 0.0 0.292453 0.000941915 0.094061 +Mm Hs TNR Oligodendrocyte progenitor cells NA 0.009 tenascin R protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0 0.0 +Mm Hs FYN Oligodendrocyte progenitor cells SLK|MGC45350 0.069 FYN proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Ectoderm Brain 0.0 0.391509 0.0549451 0.0705783 +Mm Hs NKX6-2 Oligodendrocyte progenitor cells NKX6B|GTX|NKX6.1 0.024 NK6 homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000627943 0.0306381 +Mm Hs CNP Oligodendrocyte progenitor cells NA 0.115 2',3'-cyclic nucleotide 3' phosphodiesterase protein-coding gene 1 Ectoderm Brain 0.857143 0.34434 0.066562 0.120926 +Mm Hs GALC Oligodendrocytes NA 0.002 galactosylceramidase protein-coding gene 1 Ectoderm Brain 0.0 0.00134048 0.00410872 0.00128041 +Mm Hs MOG Oligodendrocytes BTN6|BTNL11 0.039 myelin oligodendrocyte glycoprotein protein-coding gene 1 Ectoderm Brain 0.964286 0.906166 0.000316056 0.00323472 +Mm Hs OLIG1 Oligodendrocytes BHLHB6|bHLHe21 0.066 oligodendrocyte transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.142857 0.991957 0.00316056 0.036458 +Mm Hs OLIG2 Oligodendrocytes RACK17|OLIGO2|bHLHe19|PRKCBP2|BHLHB1 0.039 oligodendrocyte transcription factor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.462466 0.00158028 0.0285734 +Hs TF Oligodendrocytes PRO1557|PRO2086 0.004 transferrin protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.00884956 0.0 +Mm Hs OLIG3 Oligodendrocytes Bhlhb7|bHLHe20 0.001 oligodendrocyte transcription factor 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00087607 +Mm Hs SOX10 Oligodendrocytes DOM|WS4|WS2E 0.04 SRY-box 10 protein-coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs GJC2 Oligodendrocytes CX47|CX46.6|SPG44|GJA12 0.021 gap junction protein gamma 2 protein-coding gene 1 Ectoderm Brain 0.0 0.545576 0.0 0.00060651 +Mm Hs GAMT Oligodendrocytes PIG2|TP53I2 0.051 guanidinoacetate N-methyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.520107 0.0666877 0.0220365 +Mm Hs BCAS1 Oligodendrocytes NABC1|AIBC1 0.035 breast carcinoma amplified sequence 1 protein-coding gene 1 Ectoderm Brain 0.214286 0.676944 0.00600506 0.0100411 +Mm Hs ENPP6 Oligodendrocytes MGC33971 0.021 ectonucleotide pyrophosphatase/phosphodiesterase 6 protein-coding gene 1 Ectoderm Brain 0.107143 0.41689 0.0 0.00680639 +Mm Hs TMEM63A Oligodendrocytes KIAA0792 0.016 transmembrane protein 63A protein-coding gene 1 Ectoderm Brain 0.642857 0.0 0.00316056 0.0 +Mm Hs GPR62 Oligodendrocytes NA 0.006 G protein-coupled receptor 62 protein-coding gene 1 Ectoderm Brain 0.0 0.116622 0.0 0.00154997 +Mm Hs BACE1 Oligodendrocytes BACE 0.022 beta-secretase 1 protein-coding gene 1 Ectoderm Brain 0.0357143 0.227882 0.00347661 0.0158366 +Mm Hs CREB5 Oligodendrocytes H_GS165L15.1|CRE-BPA 0.026 cAMP responsive element binding protein 5 protein-coding gene 1 Ectoderm Brain 0.0714286 0.264075 0.0135904 0.0171171 +Mm Hs FGFR2 Oligodendrocytes CEK3|TK14|TK25|ECT1|K-SAM|CD332|KGFR|BEK|JWS 0.034 fibroblast growth factor receptor 2 protein-coding gene 1 Ectoderm Brain 0.321429 0.447721 0.0129583 0.0181953 +Mm Hs SLC25A38 Oligodendrocytes FLJ20551 0.012 solute carrier family 25 member 38 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00790139 0.0 +Mm Hs HDAC11 Oligodendrocytes NA 0.032 histone deacetylase 11 protein-coding gene 1 Ectoderm Brain 0.0357143 0.135389 0.0183312 0.0314037 +Mm Hs TYRO3 Oligodendrocytes Dtk|Brt|Tif|Sky|Etk-2|Rek|RSE 0.019 TYRO3 protein tyrosine kinase protein-coding gene 1 Ectoderm Brain 0.0357143 0.0 0.00916561 0.0 +Mm Hs S1PR5 Oligodendrocytes Edg-8|EDG8 0.011 sphingosine-1-phosphate receptor 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00158028 0.0 +Mm Hs ASPA Oligodendrocytes ACY2 0.027 aspartoacylase protein-coding gene 1 Ectoderm Brain 0.0 0.561662 0.00347661 0.00586293 +Mm Hs EPHB1 Oligodendrocytes Hek6|EPHT2 0.018 EPH receptor B1 protein-coding gene 1 Ectoderm Brain 0.0 0.382038 0.00410872 0.00370645 +Mm Hs HEPACAM Oligodendrocytes FLJ25530|hepaCAM|GLIALCAM 0.033 hepatic and glial cell adhesion molecule protein-coding gene 1 Ectoderm Brain 0.0 0.365952 0.0 0.0250691 +Mm Hs SOX8 Oligodendrocytes NA 0.028 SRY-box 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000632111 0.0 +Mm Hs FASN Oligodendrocytes FAS|SDR27X1 0.048 fatty acid synthase protein-coding gene 1 Ectoderm Brain 0.0 0.256032 0.0322377 0.0368623 +Mm Hs OMG Oligodendrocytes OMGP 0.02 oligodendrocyte myelin glycoprotein protein-coding gene 1 Ectoderm Brain 0.285714 0.340483 0.000948167 0.00822158 +Mm Hs ZDHHC9 Oligodendrocytes ZNF379|CGI-89|ZNF380|ZDHHC10|CXorf11 0.021 zinc finger DHHC-type containing 9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0126422 0.0 +Mm Hs PTGDS Oligodendrocytes L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Ectoderm Brain 1.0 0.469169 0.0499368 0.0343015 +Mm Hs ADAMTS4 Oligodendrocytes KIAA0688|ADAMTS-2|ADMP-1 0.025 ADAM metallopeptidase with thrombospondin type 1 motif 4 protein-coding gene 1 Ectoderm Brain 0.107143 0.441019 0.0116941 0.00754768 +Mm Hs MYRF Oligodendrocytes Ndt80|pqn-47|MRF|C11orf9 0.019 myelin regulatory factor protein-coding gene 1 Ectoderm Brain 0.535714 0.41689 0.000948167 0.00242604 +Mm Hs SEMA4D Oligodendrocytes CD100|coll-4|FLJ39737|SEMAJ|C9orf164 0.036 semaphorin 4D protein-coding gene 1 Ectoderm Brain 0.535714 0.0 0.00252845 0.0 +Mm Hs TMEM125 Oligodendrocytes MGC17299 0.021 transmembrane protein 125 protein-coding gene 1 Ectoderm Brain 0.142857 0.0 0.00695322 0.0 +Mm Hs KLHL2 Oligodendrocytes MAV 0.034 kelch like family member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.613941 0.000632111 0.0138149 +Mm Hs DPY19L1 Oligodendrocytes KIAA0877 0.03 dpy-19 like C-mannosyltransferase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.575067 0.005689 0.00977155 +Mm Hs TSPAN15 Oligodendrocytes NET-7|TM4SF15 0.048 tetraspanin 15 protein-coding gene 1 Ectoderm Brain 0.214286 0.0 0.0249684 0.0 +Mm Hs HAPLN2 Oligodendrocytes BRAL1 0.017 hyaluronan and proteoglycan link protein 2 protein-coding gene 1 Ectoderm Brain 0.25 0.424933 0.0 0.00114563 +Mm Hs NKX6-2 Oligodendrocytes NKX6B|GTX|NKX6.1 0.024 NK6 homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.587131 0.000632111 0.00222387 +Mm Hs GJB1 Oligodendrocytes CX32|CMTX1|CMTX 0.033 gap junction protein beta 1 protein-coding gene 1 Ectoderm Brain 0.535714 0.646113 0.005689 0.00788463 +Mm Hs OPALIN Oligodendrocytes TMP10|HTMP10|TMEM10 0.026 oligodendrocytic myelin paranodal and inner loop protein protein-coding gene 1 Ectoderm Brain 0.214286 0.646113 0.0 0.00074129 +Mm Hs VLDLR Oligodendrocytes CARMQ1|CHRMQ1|VLDLRCH 0.025 very low density lipoprotein receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00379267 0.0 +Mm Hs MCAM Oligodendrocytes MUC18|CD146 0.031 melanoma cell adhesion molecule protein-coding gene 1 Ectoderm Brain 0.0 0.116622 0.0214918 0.0295168 +Mm Hs TMEM163 Oligodendrocytes DKFZP566N034|SV31 0.027 transmembrane protein 163 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000632111 0.0 +Mm Hs ERMN Oligodendrocytes JN|ERMIN|KIAA1189 0.034 ermin protein-coding gene 1 Ectoderm Brain 1.0 0.798928 0.00158028 0.00154997 +Mm Hs FA2H Oligodendrocytes FAAH|FLJ25287|FAXDC1|SPG35 0.039 fatty acid 2-hydroxylase protein-coding gene 1 Ectoderm Brain 0.25 0.903485 0.00347661 0.0040434 +Mm Hs CLDN11 Oligodendrocytes OSP|OTM 0.059 claudin 11 protein-coding gene 1 Ectoderm Brain 0.964286 1.0 0.034134 0.0181953 +Mm Hs ANLN Oligodendrocytes ANILLIN|Scraps|scra 0.023 anillin actin binding protein protein-coding gene 1 Ectoderm Brain 0.857143 0.261394 0.0129583 0.0111193 +Mm Hs ELOVL7 Oligodendrocytes FLJ23563 0.031 ELOVL fatty acid elongase 7 protein-coding gene 1 Ectoderm Brain 0.0 0.576407 0.000632111 0.0103781 +Mm Hs PLLP Oligodendrocytes PMLP|TM4SF11 0.046 plasmolipin protein-coding gene 1 Ectoderm Brain 0.535714 0.797587 0.00979772 0.0173192 +Mm Hs DDC Oligodendrocytes AADC 0.014 dopa decarboxylase protein-coding gene 1 Ectoderm Brain 0.0 0.0321716 0.00474083 0.0158366 +Mm Hs POU3F1 Oligodendrocytes OCT6|SCIP|OTF6 0.013 POU class 3 homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.038874 0.000316056 0.0156345 +Mm Hs NINJ2 Oligodendrocytes NA 0.002 ninjurin 2 protein-coding gene 1 Ectoderm Brain 0.107143 0.0469169 0.000948167 0.0 +Mm Hs SGK2 Oligodendrocytes NA 0.001 SGK2, serine/threonine kinase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000632111 0.0 +Mm Hs GJC3 Oligodendrocytes CX30.2|GJE1 0.044 gap junction protein gamma 3 protein-coding gene 1 Ectoderm Brain 0.0 0.923593 0.0 0.0108498 +Mm Hs GPR37 Oligodendrocytes EDNRBL|hET(B)R-LP|PAELR 0.034 G protein-coupled receptor 37 protein-coding gene 1 Ectoderm Brain 0.5 0.773458 0.000316056 0.00431296 +Mm Hs IL33 Oligodendrocytes DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Ectoderm Brain 0.0 0.148794 0.0107459 0.0141519 +Mm Hs KLK6 Oligodendrocytes Bssp|Klk7|neurosin|PRSS9|PRSS18 0.004 kallikrein related peptidase 6 protein-coding gene 1 Ectoderm Brain 0.5 0.0764075 0.0 0.00026956 +Mm Hs NFE2L3 Oligodendrocytes Nrf3 0.003 nuclear factor, erythroid 2 like 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0134048 0.00726928 0.00148258 +Mm Hs PEX5L Oligodendrocytes PEX5R|PXR2|TRIP8b 0.03 peroxisomal biogenesis factor 5 like protein-coding gene 1 Ectoderm Brain 0.75 0.608579 0.00221239 0.00707595 +Mm Hs CLDN14 Oligodendrocytes DFNB29 0.003 claudin 14 protein-coding gene 1 Ectoderm Brain 0.0 0.0576407 0.0 0.0013478 +Mm Hs ITGB4 Oligodendrocytes CD104 0.013 integrin subunit beta 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0871314 0.0142225 0.00997372 +Mm Hs MYO1D Oligodendrocytes KIAA0727|myr4|PPP1R108 0.01 myosin ID protein-coding gene 1 Ectoderm Brain 0.0 0.0227882 0.0183312 0.00774985 +Mm Hs PDE8A Oligodendrocytes HsT19550 0.015 phosphodiesterase 8A protein-coding gene 1 Ectoderm Brain 0.0 0.0871314 0.00379267 0.014691 +Mm Hs CNTF Oligodendrocytes HCNTF 0.0 ciliary neurotrophic factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs EML1 Oligodendrocytes EMAP|HuEMAP|ELP79|EMAPL 0.002 echinoderm microtubule associated protein like 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0160858 0.00158028 0.0020217 +Mm Hs KIF13B Oligodendrocytes GAKIN|KIAA0639 0.002 kinesin family member 13B protein-coding gene 1 Ectoderm Brain 0.0 0.0160858 0.0 0.00242604 +Mm Hs KIF6 Oligodendrocytes dJ1043E3.1|MGC33317|dJ137F1.4|dJ188D3.1|DKFZp451I2418|C6orf102 0.001 kinesin family member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00252845 0.00101085 +Mm Hs NIPAL4 Oligodendrocytes ICHYN 0.002 NIPA like domain containing 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0469169 0.0 0.00087607 +Mm Hs SEC14L5 Oligodendrocytes KIAA0420|PRELID4B 0.001 SEC14 like lipid binding 5 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SP7 Oligodendrocytes osterix|OSX 0.001 Sp7 transcription factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ST18 Oligodendrocytes KIAA0535|ZC2HC10|NZF3|ZC2H2C3|ZNF387 0.006 ST18, C2H2C-type zinc finger protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.00126422 0.0 +Mm Hs DUSP15 Oligodendrocytes bA243J16.6|VHY|FLJ20645|bA243J16.5|C20orf57 0.02 dual specificity phosphatase 15 protein-coding gene 1 Ectoderm Brain 0.0 0.284182 0.0309735 0.00559337 +Mm Hs PRKCZ Oligodendrocytes PKC2 0.022 protein kinase C zeta protein-coding gene 1 Ectoderm Brain 0.0 0.203753 0.0 0.0192735 +Mm Hs ARSG Oligodendrocytes KIAA1001 0.008 arylsulfatase G protein-coding gene 1 Ectoderm Brain 0.0 0.178284 0.00126422 0.0013478 +Mm Hs NPC1 Oligodendrocytes SLC65A1 0.006 NPC intracellular cholesterol transporter 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0817694 0.0 0.00350428 +Mm Hs MAG Oligodendrocytes SIGLEC4A|SIGLEC-4A|S-MAG|GMA 0.045 myelin associated glycoprotein protein-coding gene 1 Ectoderm Brain 1.0 0.989276 0.00221239 0.00660422 +Mm Hs SLC25A29 Oligodendrocytes FLJ38975|C14orf69 0.0 solute carrier family 25 member 29 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000632111 0.0 +Mm Hs SLC25A19 Oligodendrocytes DNC|MUP1|MCPHA 0.006 solute carrier family 25 member 19 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000316056 0.0 +Mm Hs PLEKHH1 Oligodendrocytes KIAA1200 0.002 pleckstrin homology, MyTH4 and FERM domain containing H1 protein-coding gene 1 Ectoderm Brain 0.321429 0.0321716 0.0 0.00026956 +Mm Hs TMEM88B Oligodendrocytes NA 0.034 transmembrane protein 88B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DBNDD2 Oligodendrocytes HSMNP1|C20orf35 0.014 dysbindin domain containing 2 protein-coding gene 1 Ectoderm Brain 0.0 0.285523 0.0 0.00384123 +Mm Hs EFNB3 Oligodendrocytes LERK-8|EPLG8 0.046 ephrin B3 protein-coding gene 1 Ectoderm Brain 0.0 0.810992 0.00252845 0.0185996 +Mm Hs SGK3 Oligodendrocytes SGK2|SGKL 0.014 serum/glucocorticoid regulated kinase family member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PNPLA2 Oligodendrocytes desnutrin|TTS-2.2|ATGL|FP17548|iPLA2zeta 0.02 patatin like phospholipase domain containing 2 protein-coding gene 1 Ectoderm Brain 0.0 0.00268097 0.0161188 0.0216322 +Mm Hs ARRDC2 Oligodendrocytes CLONE24945|PP2703 0.001 arrestin domain containing 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0187668 0.000948167 0.00020217 +Mm Hs ENPP2 Oligodendrocytes PD-IALPHA|PDNP2 0.08 ectonucleotide pyrophosphatase/phosphodiesterase 2 protein-coding gene 1 Ectoderm Brain 1.0 0.994638 0.0243363 0.045623 +Mm Hs PLP1 Oligodendrocytes GPM6C|SPG2 0.123 proteolipid protein 1 protein-coding gene 1 Ectoderm Brain 1.0 1.0 0.0218078 0.103174 +Mm Hs ITPR2 Oligodendrocytes IP3R2|CFAP48 0.016 inositol 1,4,5-trisphosphate receptor type 2 protein-coding gene 1 Ectoderm Brain 0.0 0.155496 0.005689 0.0109846 +Mm Hs MBP Oligodendrocytes NA 0.12 myelin basic protein protein-coding gene 1 Ectoderm Brain 1.0 1.0 0.0445638 0.0934699 +Mm Hs SLC6A6 Osteoblasts TAUT 0.102 solute carrier family 6 member 6 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000626566 0.0 +Mm Hs VDR Osteoblasts NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00250627 0.0 +Mm Hs LRP4 Osteoblasts MEGF7|CLSS|LRP-4|SOST2 0.046 LDL receptor related protein 4 protein-coding gene 1 Mesoderm Bone 0.0 0.783784 0.0 0.0563417 +Mm Hs EGFL6 Osteoblasts MAEG 0.01 EGF like domain multiple 6 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00814536 0.0106123 +Mm Hs MMP13 Osteoblasts CLG3 0.003 matrix metallopeptidase 13 protein-coding gene 1 Mesoderm Bone 0.0 0.567568 0.0 0.00199383 +Mm Hs GPER1 Osteoblasts FEG-1|GPCR-Br|LERGU|LERGU2|DRY12|LyGPR|CEPR|CMKRL2|GPR30|GPER 0.01 G protein-coupled estrogen receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00156642 0.0127991 +Mm Hs RUNX2 Osteoblasts AML3|PEBP2A1|PEBP2aA1|CCD|CBFA1|CCD1 0.008 runt related transcription factor 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00877193 0.0 +Mm Hs NF2 Osteoblasts merlin|ACN|SCH|BANF 0.016 neurofibromin 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0441729 0.00803962 +Mm Hs LRP5 Osteoblasts LR3|BMND1|HBM|OPS|OPTA1|VBCH2|EVR4|LRP7|OPPG 0.003 LDL receptor related protein 5 protein-coding gene 1 Mesoderm Bone 0.0 0.108108 0.00313283 0.00270131 +Mm Hs PHEX Osteoblasts PEX|HPDR1|HYP1|XLH|HYP|HPDR 0.001 phosphate regulating endopeptidase homolog X-linked protein-coding gene 1 Mesoderm Bone 0.0 0.324324 0.000626566 6.4317e-05 +Mm Hs HIF1A Osteoblasts MOP1|HIF-1alpha|PASD8|HIF1|bHLHe78 0.089 hypoxia inducible factor 1 subunit alpha protein-coding gene 1 Mesoderm Bone 0.0 0.216216 0.101817 0.0853486 +Mm Hs C5AR1 Osteoblasts C5A|C5AR|CD88|C5R1 0.027 complement C5a receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0140977 0.0302933 +Mm Hs CXCL12 Osteoblasts SCYB12|SDF-1a|SDF-1b|PBSF|TLSF-a|TLSF-b|TPAR1|SDF1A|SDF1B|SDF1 0.07 C-X-C motif chemokine ligand 12 protein-coding gene 1 Mesoderm Bone 0.0 0.540541 0.0269424 0.0803319 +Mm Hs COL1A1 Osteoblasts NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0999373 0.0710702 +Mm Hs PLCD4 Osteoblasts NA 0.004 phospholipase C delta 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.00501672 +Mm Hs FOXO1 Osteoblasts FKH1|FKHR|FOXO1A 0.022 forkhead box O1 protein-coding gene 1 Mesoderm Bone 0.0 0.0540541 0.0075188 0.0255981 +Mm Hs SOCS3 Osteoblasts SSI-3|CIS3|SOCS-3|Cish3 0.081 suppressor of cytokine signaling 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0942982 0.0 +Mm Hs IL33 Osteoblasts DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0106516 0.0206457 +Mm Hs MAGED1 Osteoblasts NRAGE|DLXIN-1 0.334 MAGE family member D1 protein-coding gene 1 Mesoderm Bone 0.0 0.72973 0.0845865 0.395935 +Mm Hs PARD6G Osteoblasts PAR-6G|PAR6gamma 0.018 par-6 family cell polarity regulator gamma protein-coding gene 1 Mesoderm Bone 0.0 0.567568 0.000313283 0.0217391 +Mm Hs CD44 Osteoblasts IN|MC56|Pgp1|CD44R|HCELL|CSPG8|MIC4|MDU2|MDU3 0.127 CD44 molecule (Indian blood group) protein-coding gene 1 Mesoderm Bone 0.0 0.189189 0.300439 0.0875354 +Mm Hs NLRP3 Osteoblasts AGTAVPRL|AII|AVP|FCAS|FCU|NALP3|PYPAF1|MWS|CLR1.1|C1orf7|CIAS1 0.004 NLR family pyrin domain containing 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00093985 0.00520967 +Mm Hs ALPL Osteoblasts TNSALP|TNALP|TNAP|HOPS 0.009 alkaline phosphatase, liver/bone/kidney protein-coding gene 1 Mesoderm Bone 0.0 0.72973 0.00407268 0.00881142 +Mm Hs TNFSF11 Osteoblasts TRANCE|RANKL|OPGL|ODF|CD254 0.001 TNF superfamily member 11 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000313283 0.0 +Mm Hs CCL11 Osteoblasts eotaxin|MGC22554|SCYA11 0.008 C-C motif chemokine ligand 11 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00313283 0.00971186 +Mm Hs SPP1 Osteoblasts BSPI|ETA-1|BNSP|OPN 0.057 secreted phosphoprotein 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0532581 0.0 +Mm Hs FAS Osteoblasts CD95|APO-1|FAS1|APT1|TNFRSF6 0.011 Fas cell surface death receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0147243 0.0108052 +Hs TNFRSF10A Osteoblasts DR4|Apo2|TRAILR-1|CD261|TRAILR1 0.001 TNF receptor superfamily member 10a protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00469925 0.0 +Mm Hs WNT5A Osteoblasts hWNT5A 0.015 Wnt family member 5A protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00814536 0.0 +Mm Hs CX3CL1 Osteoblasts C3Xkine|ABCD-3|CXC3C|CXC3|fractalkine|neurotactin|SCYD1 0.033 C-X3-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0056391 0.0403267 +Mm Hs F2R Osteoblasts CF2R 0.036 coagulation factor II thrombin receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0338346 0.03814 +Mm Hs PTH1R Osteoblasts PTHR1 0.019 parathyroid hormone 1 receptor protein-coding gene 1 Mesoderm Bone 0.0 0.864865 0.00501253 0.0214175 +Mm Hs ITGA2 Osteoblasts CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene 1 Mesoderm Bone 0.0 0.027027 0.0451128 0.0030229 +Mm Hs ITGA5 Osteoblasts CD49e|FNRA 0.016 integrin subunit alpha 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0184837 0.0167224 +Mm Hs NOD1 Osteoblasts NLRC1|CLR7.1|CARD4 0.0 nucleotide binding oligomerization domain containing 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.000385902 +Mm Hs NOD2 Osteoblasts BLAU|PSORAS1|CLR16.3|NLRC2|IBD1|CARD15 0.0 nucleotide binding oligomerization domain containing 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.000128634 +Mm Hs THY1 Osteoblasts CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0322682 0.0 +Mm Hs ESR1 Osteoblasts NR3A1|Era|ER-alpha|ESR 0.004 estrogen receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00093985 0.00463082 +Mm Hs CYP27B1 Osteoblasts P450c1|VDD1|PDDR 0.0 cytochrome P450 family 27 subfamily B member 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.0 +Mm Hs P2RX4 Osteoblasts P2X4 0.025 purinergic receptor P2X 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0131579 0.028621 +Mm Hs P2RX5 Osteoblasts P2X5 0.0 purinergic receptor P2X 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0018797 0.0 +Mm Hs INSR Osteoblasts CD220 0.022 insulin receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0632832 0.0133779 +Mm Hs EFNB2 Osteoblasts LERK5|Htk-L|HTKL|MGC126226|MGC126227|MGC126228|EPLG5 0.016 ephrin B2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0291353 0.0140854 +Mm Hs EPHB4 Osteoblasts Tyro11|HTK 0.009 EPH receptor B4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0103383 0.00881142 +Mm Hs VCAM1 Osteoblasts CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00720551 0.0 +Mm Hs FGFR1 Osteoblasts CEK|FLG|BFGFR|N-SAM|CD331|FLT2|KAL2 0.072 fibroblast growth factor receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.648649 0.0588972 0.0719064 +Mm Hs FGFR2 Osteoblasts CEK3|TK14|TK25|ECT1|K-SAM|CD332|KGFR|BEK|JWS 0.034 fibroblast growth factor receptor 2 protein-coding gene 1 Mesoderm Bone 0.0 0.27027 0.0156642 0.0382043 +Mm Hs BGLAP Osteoblasts OCN 0.005 bone gamma-carboxyglutamate protein protein-coding gene 1 Mesoderm Bone 0.0 0.945946 0.0 0.0041806 +Mm Hs TLR5 Osteoblasts TIL3|MGC126430|MGC126431|SLEB1 0.0 toll like receptor 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.0 +Mm Hs CALB1 Osteoblasts CALB 0.019 calbindin 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00125313 0.0236043 +Mm Hs COL11A1 Osteoblasts STL2|CO11A1|COLL6 0.009 collagen type XI alpha 1 chain protein-coding gene 1 Mesoderm Bone 0.0 0.756757 0.00971178 0.00694623 +Mm BGLAP2 Osteoblasts NA 0.005 bone gamma-carboxyglutamate protein 2 protein coding gene 1 Mesoderm Bone 0.0 0.972973 0.0 0.00373038 +Mm Hs COL11A2 Osteoblasts HKE5|DFNA13|DFNB53 0.005 collagen type XI alpha 2 chain protein-coding gene 1 Mesoderm Bone 0.0 0.675676 0.00281955 0.0045665 +Mm Hs IBSP Osteoblasts BSP|SP-II|BSP-II 0.006 integrin binding sialoprotein protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0 0.00475945 +Mm Hs POSTN Osteoblasts OSF-2|PN|periostin 0.033 periostin protein-coding gene 1 Mesoderm Bone 0.0 0.486486 0.023183 0.0336378 +Mm Hs SFRP4 Osteoblasts frpHE|FRP-4|FRPHE|FRZB-2 0.006 secreted frizzled related protein 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00720551 0.0 +Mm Hs BMP1 Osteoblasts PCOLC 0.024 bone morphogenetic protein 1 protein-coding gene NA Mesoderm Bone 0.0 0.864865 0.0100251 0.0262413 +Mm Hs OLFML2B Osteoblasts DKFZP586L151 0.011 olfactomedin like 2B protein-coding gene NA Mesoderm Bone 0.0 0.378378 0.00971178 0.0104193 +Mm Hs COL12A1 Osteoblasts COL12A1L 0.013 collagen type XII alpha 1 chain protein-coding gene 1 Mesoderm Bone 0.0 0.459459 0.0056391 0.0116414 +Mm Hs WISP2 Osteoblasts CTGF-L|CCN5 0.005 WNT1 inducible signaling pathway protein 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00657895 0.0 +Mm Hs SP7 Osteoblasts osterix|OSX 0.001 Sp7 transcription factor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.0 +Mm Hs PENK Osteoblasts NA 0.02 proenkephalin protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0275689 0.019681 +Mm Hs NPNT Osteoblasts EGFL6L|POEM 0.017 nephronectin protein-coding gene 1 Mesoderm Bone 0.0 0.027027 0.00908521 0.0192308 +Mm Hs OLFML1 Osteoblasts UNQ564 0.002 olfactomedin like 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.00225109 +Mm Hs MITF Osteoclast precursor cells MI|bHLHe32|WS2A|WS2 0.004 melanogenesis associated transcription factor protein-coding gene NA Mesoderm Bone 0.0 0.0 0.00595238 0.00340071 +Mm Hs NFKB1 Osteoclast precursor cells KBF1|NFKB-p50|NF-kappaB|NFkappaB|NF-kB1 0.028 nuclear factor kappa B subunit 1 protein-coding gene NA Mesoderm Bone 0.0 0.0 0.0256892 0.0280398 +Mm Hs NFKB2 Osteoclast precursor cells LYT-10|NF-kB2|p49/p100 0.01 nuclear factor kappa B subunit 2 protein-coding gene NA Mesoderm Bone 0.0 0.0 0.00407268 0.0107796 +Mm Hs TNFRSF11A Osteoclast precursor cells RANK|CD265|FEO|PDB2|LOH18CR1 0.001 TNF receptor superfamily member 11a protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000626566 0.0 +Mm Hs TRAF6 Osteoclast precursor cells RNF85 0.001 TNF receptor associated factor 6 protein-coding gene NA Mesoderm Bone 0.0 0.0 0.00093985 0.0 +Mm Hs TREM2 Osteoclast precursor cells TREM-2|Trem2a|Trem2b|Trem2c 0.042 triggering receptor expressed on myeloid cells 2 protein-coding gene NA Mesoderm Bone 0.0 0.0 0.00657895 0.0 +Mm Hs CYSLTR1 Osteoclast precursor cells CysLT1|CysLT(1)|CYSLT1R 0.006 cysteinyl leukotriene receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0206767 0.00295156 +Mm Hs TLR4 Osteoclast precursor cells hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000313283 0.0 +Mm Hs SOST Osteoclasts VBCH|DAND6 0.002 sclerostin protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00689223 0.0 +Mm Hs ZBTB7A Osteoclasts FBI-1|DKFZp547O146|pokemon|ZNF857A|ZBTB7 0.091 zinc finger and BTB domain containing 7A protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0206767 0.0 +Mm Hs SEMA4D Osteoclasts CD100|coll-4|FLJ39737|SEMAJ|C9orf164 0.036 semaphorin 4D protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00720551 0.0 +Mm Hs KCNMA1 Osteoclasts KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0184837 0.0485144 +Mm Hs TNFRSF11B Osteoclasts NA 0.002 TNF receptor superfamily member 11b protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00219298 0.0 +Mm Hs PTPRA Osteoclasts HLPR|HPTPA|RPTPA|PTPRL2|PTPA 0.158 protein tyrosine phosphatase, receptor type A protein-coding gene 1 Mesoderm Bone 0.0 0.5 0.0485589 0.18533 +Mm Hs TNFRSF11A Osteoclasts RANK|CD265|FEO|PDB2|LOH18CR1 0.001 TNF receptor superfamily member 11a protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000626566 0.0 +Mm Hs MMP9 Osteoclasts CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.00971178 0.0168774 +Mm Hs ACP5 Osteoclasts HPAP 0.033 acid phosphatase 5, tartrate resistant protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0181704 0.03645 +Mm Hs RAB3B Osteoclasts NA 0.023 RAB3B, member RAS oncogene family protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0191103 0.0 +Mm Hs ITPR3 Osteoclasts IP3R3 0.007 inositol 1,4,5-trisphosphate receptor type 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0134712 0.00641725 +Mm Hs NRP2 Osteoclasts VEGF165R2 0.04 neuropilin 2 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.035401 0.0412629 +Mm Hs THRA Osteoclasts EAR-7.1/EAR-7.2|THRA3|AR7|ERBA|NR1A1|THRA2|ERBA1 0.28 thyroid hormone receptor alpha protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0303885 0.0 +Mm Hs AGER Osteoclasts SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00125313 0.0135404 +Mm Hs RGS18 Osteoclasts RGS13 0.019 regulator of G protein signaling 18 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00344612 0.0 +Mm Hs PTH1R Osteoclasts PTHR1 0.019 parathyroid hormone 1 receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00501253 0.023423 +Hs LTB4R Osteoclasts BLTR|P2Y7|LTB4R1|P2RY7|GPR16|CMKRL1 0.0 leukotriene B4 receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00156642 0.0 +Mm Hs TRPV5 Osteoclasts CaT2|ECAC1 0.0 transient receptor potential cation channel subfamily V member 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.0 +Mm Hs SNX10 Osteoclasts NA 0.051 sorting nexin 10 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0325815 0.0 +Mm Hs CTSK Osteoclasts PKND|CTSO2|CTSO|PYCD 0.027 cathepsin K protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0175439 0.0285568 +Mm Hs OSCAR Osteoclasts NA 0.0 osteoclast associated, immunoglobulin-like receptor protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.000626566 0.0 +Mm Hs SLC2A1 Osteoclasts DYT18|DYT9|GLUT1|GLUT|HTLVR|CSE 0.062 solute carrier family 2 member 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.056391 0.0 +Mm Hs DCSTAMP Osteoclasts DC-STAMP|FIND|TM7SF4 0.001 dendrocyte expressed seven transmembrane protein protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.00156642 0.000385035 +Mm Hs EGFL7 Osteoclasts ZNEU1 0.092 EGF like domain multiple 7 protein-coding gene 1 Mesoderm Bone 0.0 0.5 0.114975 0.0858628 +Mm Hs SLC39A14 Osteoclasts KIAA0062|NET34|ZIP14 0.006 solute carrier family 39 member 14 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0131579 0.0 +Mm Hs AQP9 Osteoclasts SSC1|HsT17287 0.003 aquaporin 9 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00313283 0.00340114 +Mm Hs ONECUT1 Osteoclasts HNF-6|HNF6|HNF6A 0.001 one cut homeobox 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.000313283 0.00109093 +Mm Hs ITGB3 Osteoclasts CD61|GPIIIa|GP3A 0.001 integrin subunit beta 3 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.000313283 0.00109093 +Mm Hs ITGB5 Osteoclasts NA 0.047 integrin subunit beta 5 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0150376 0.0555092 +Mm Hs IRAK3 Osteoclasts IRAK-M 0.003 interleukin 1 receptor associated kinase 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0037594 0.00288776 +Mm Hs ITGA2 Osteoclasts CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene 1 Mesoderm Bone 0.0 0.5 0.0451128 0.00301611 +Mm Hs TAS1R3 Osteoclasts T1R3 0.0 taste 1 receptor member 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 0.0 +Mm Hs SERPINF1 Osteoclasts EPC-1|PIG35|PEDF 0.057 serpin family F member 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.10589 0.0 +Mm Hs ITGAV Osteoclasts CD51|VNRA|MSK8|VTNR 0.026 integrin subunit alpha V protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0219298 0.0274017 +Mm Hs ITGB1 Osteoclasts CD29|GPIIA|FNRB|MSK12|MDF2 0.276 integrin subunit beta 1 protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.168546 0.301932 +Mm Hs P2RY6 Osteoclasts P2Y6 0.018 pyrimidinergic receptor P2Y6 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00281955 0.021947 +Mm Hs CCL3 Osteoclasts G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00783208 0.0425464 +Mm Hs EPHB1 Osteoclasts Hek6|EPHT2 0.018 EPH receptor B1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00407268 0.0218186 +Hs CA2 Osteoclasts Car2|CA-II|CAII 0.011 carbonic anhydrase 2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0648496 0.0 +Mm Hs HIF1A Osteoclasts MOP1|HIF-1alpha|PASD8|HIF1|bHLHe78 0.089 hypoxia inducible factor 1 subunit alpha protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.101817 0.0856703 +Mm Hs CX3CR1 Osteoclasts CMKDR1|V28|GPR13|CMKBRL1 0.039 C-X3-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00219298 0.0482577 +Mm Hs ESR1 Osteoclasts NR3A1|Era|ER-alpha|ESR 0.004 estrogen receptor 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00093985 0.00462042 +Mm Hs EFNB2 Osteoclasts LERK5|Htk-L|HTKL|MGC126226|MGC126227|MGC126228|EPLG5 0.016 ephrin B2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0291353 0.0140538 +Mm Hs VDR Osteoclasts NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00250627 0.0 +Mm Hs CASR Osteoclasts FHH|NSHPT|GPRC2A|HHC|HHC1 0.001 calcium sensing receptor protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00219298 0.00051338 +Mm Hs CD68 Osteoclasts SCARD1|macrosialin|DKFZp686M18236|LAMP4 0.063 CD68 molecule protein-coding gene 1 Mesoderm Bone 0.0 1.0 0.0 0.0758519 +Mm Hs GRM8 Osteoclasts GLUR8|GPRC1H|mGlu8|MGLUR8 0.002 glutamate metabotropic receptor 8 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00407268 0.00128345 +Mm Hs SMAD4 Osteoclasts DPC4|MADH4 0.018 SMAD family member 4 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00908521 0.0 +Mm Hs SPP1 Osteoclasts BSPI|ETA-1|BNSP|OPN 0.057 secreted phosphoprotein 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0532581 0.0 +Mm Hs SOST Osteocytes VBCH|DAND6 0.002 sclerostin protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.00689223 0.0 +Mm Hs PFN1 Osteocytes NA 0.797 profilin 1 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.789787 0.797048 +Mm Hs EFNB2 Osteocytes LERK5|Htk-L|HTKL|MGC126226|MGC126227|MGC126228|EPLG5 0.016 ephrin B2 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0291353 0.014052 +Mm Hs PDPN Osteocytes T1A-2|Gp38|aggrus|PA2.26 0.062 podoplanin protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0234962 0.071479 +Mm Hs FGF23 Osteocytes NA 0.0 fibroblast growth factor 23 protein-coding gene 1 Mesoderm Bone 0.0 0.0 0.0 6.41643e-05 +Mm Hs SLC2A4 Oxyphil cells GLUT4 0.001 solute carrier family 2 member 4 protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.00250627 0.0 +Mm Hs GCM2 Oxyphil cells hGCMb|GCMB 0.0 glial cells missing homolog 2 protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.0 0.00044915 +Mm Hs ONECUT1 Pancreatic progenitor cells HNF-6|HNF6|HNF6A 0.001 one cut homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000313283 0.00109079 +Mm Hs PDX1 Pancreatic progenitor cells IDX-1|STF-1|PDX-1|MODY4|IPF1 0.005 pancreatic and duodenal homeobox 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00595238 0.00474816 +Mm Hs PTF1A Pancreatic progenitor cells PTF1-p48|bHLHa29 0.001 pancreas associated transcription factor 1a protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.000626566 0.00147578 +Mm Hs CXCR4 Pancreatic progenitor cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.198308 0.0087905 +Mm Hs ISL1 Pancreatic progenitor cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.0134712 0.0313763 +Mm Hs NKX2-2 Pancreatic progenitor cells NKX2.2|NKX2B 0.002 NK2 homeobox 2 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0103383 0.000641643 +Mm Hs EPAS1 Pancreatic progenitor cells MOP2|PASD2|HIF2A|HLF|bHLHe73 0.076 endothelial PAS domain protein 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0567043 0.0830927 +Mm Hs ARX Pancreatic progenitor cells ISSX|CT121|EIEE1|MRXS1|PRTS|MRX76|MRX54|MRX43|MRX36|MRX29|MRX32|MRX33|MRX38|MRX87 0.019 aristaless related homeobox protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00219298 0.0236124 +Mm Hs NEUROG3 Pancreatic progenitor cells Atoh5|Math4B|ngn3|bHLHa7 0.001 neurogenin 3 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.00093985 0.000962464 +Mm Hs SOX9 Pancreatic progenitor cells SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0322682 0.0 +Mm Hs RPL23A Pancreatic progenitor cells L23A 0.174 ribosomal protein L23a protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.818922 0.0 +Mm Hs CTNNB1 Pancreatic progenitor cells beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.212406 0.0114212 +Mm Hs YAP1 Pancreatic progenitor cells YAP65 0.021 Yes associated protein 1 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0197368 0.0 +Mm Hs RGS16 Pancreatic progenitor cells A28-RGS14|RGS-r 0.01 regulator of G protein signaling 16 protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0203634 0.0 +Mm Hs MFNG Pancreatic progenitor cells NA 0.035 MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase protein-coding gene 1 Endoderm Pancreas 0.0 0.0 0.0219298 0.0383061 +Mm Hs TIMP1 Pancreatic stellate cells TIMP|CLGI 0.097 TIMP metallopeptidase inhibitor 1 protein-coding gene NA Endoderm Pancreas 0.956522 0.0 0.405806 0.0 +Mm Hs RGS5 Pancreatic stellate cells NA 0.043 regulator of G protein signaling 5 protein-coding gene 1 Endoderm Pancreas NA NA NA NA +Mm Hs SPON2 Pancreatic stellate cells DIL1 0.017 spondin 2 protein-coding gene NA Endoderm Pancreas 0.869565 0.0 0.0429157 0.0 +Mm Hs GEM Pancreatic stellate cells NA 0.038 GTP binding protein overexpressed in skeletal muscle protein-coding gene NA Endoderm Pancreas 0.956522 0.5 0.0296624 0.0394661 +Mm Hs DYNLT1 Pancreatic stellate cells TCTEL1 0.083 dynein light chain Tctex-type 1 protein-coding gene NA Endoderm Pancreas 0.869565 0.0 0.348375 0.0161715 +Mm Hs PDGFRB Pancreatic stellate cells JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene NA Endoderm Pancreas 0.956522 1.0 0.0296624 0.0333055 +Mm Hs KRT10 Pancreatic stellate cells K10|CK10|KPP 0.099 keratin 10 protein-coding gene NA Endoderm Pancreas 0.782609 0.0 0.384664 0.0288776 +Mm Hs CYGB Pancreatic stellate cells HGB|STAP 0.038 cytoglobin protein-coding gene NA Endoderm Pancreas 0.391304 0.5 0.019249 0.0432523 +Mm Hs CTGF Pancreatic stellate cells IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene NA Endoderm Pancreas 0.217391 0.0 0.0987693 0.0124495 +Mm Hs MMP14 Pancreatic stellate cells MT1-MMP 0.054 matrix metallopeptidase 14 protein-coding gene NA Endoderm Pancreas 0.608696 1.0 0.0312401 0.0567285 +Mm Hs NDUFA4L2 Pancreatic stellate cells NUOMS|FLJ26118 0.031 NDUFA4, mitochondrial complex associated like 2 protein-coding gene NA Endoderm Pancreas 0.913043 0.0 0.0170401 0.0318937 +Mm Hs PDGFRA Pancreatic stellate cells CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene 1 Endoderm Pancreas 0.0 0.5 0.0479647 0.0439582 +Mm Hs INHBA Pancreatic stellate cells NA 0.013 inhibin subunit beta A protein-coding gene 1 Endoderm Pancreas 0.130435 0.5 0.00725781 0.0132837 +Mm Hs TGFB1 Pancreatic stellate cells CED|TGFbeta|TGFB|DPD1 0.11 transforming growth factor beta 1 protein-coding gene 1 Endoderm Pancreas 0.347826 0.0 0.0429157 0.0 +Mm Hs COL6A1 Pancreatic stellate cells NA 0.063 collagen type VI alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.826087 1.0 0.0848848 0.055445 +Mm Hs MMP11 Pancreatic stellate cells STMY3 0.01 matrix metallopeptidase 11 protein-coding gene 1 Endoderm Pancreas 0.434783 0.0 0.00126223 0.00872746 +Mm Hs FN1 Pancreatic stellate cells CIG|LETS|GFND2|FINC 0.091 fibronectin 1 protein-coding gene 1 Endoderm Pancreas 0.652174 0.5 0.0952982 0.0868896 +Mm Hs COL4A1 Pancreatic stellate cells NA 0.105 collagen type IV alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.913043 0.5 0.074787 0.113136 +Mm Hs COL6A2 Pancreatic stellate cells NA 0.056 collagen type VI alpha 2 chain protein-coding gene 1 Endoderm Pancreas 0.913043 0.5 0.0975071 0.0441507 +Mm Hs MGP Pancreatic stellate cells NA 0.082 matrix Gla protein protein-coding gene 1 Endoderm Pancreas 0.782609 0.5 0.111707 0.0731566 +Mm Hs COL3A1 Pancreatic stellate cells EDS4A 0.086 collagen type III alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.869565 1.0 0.0937204 0.081114 +Mm Hs SPARC Pancreatic stellate cells ON 0.307 secreted protein acidic and cysteine rich protein-coding gene 1 Endoderm Pancreas 1.0 0.0 0.225308 0.0 +Mm Hs COL1A1 Pancreatic stellate cells NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Endoderm Pancreas 0.869565 1.0 0.0943515 0.0731566 +Mm Hs TIMP3 Pancreatic stellate cells NA 0.147 TIMP metallopeptidase inhibitor 3 protein-coding gene 1 Endoderm Pancreas 0.695652 0.0 0.157147 0.0 +Mm Hs TNFAIP6 Pancreatic stellate cells TSG6|TSG-6 0.024 TNF alpha induced protein 6 protein-coding gene 1 Endoderm Pancreas 0.608696 0.0 0.022089 0.0 +Mm Hs COL1A2 Pancreatic stellate cells NA 0.097 collagen type I alpha 2 chain protein-coding gene 1 Endoderm Pancreas 0.956522 1.0 0.118334 0.0880447 +Mm Hs SFRP2 Pancreatic stellate cells SARP1|SDF-5|FRP-2 0.009 secreted frizzled related protein 2 protein-coding gene 1 Endoderm Pancreas 0.521739 0.0 0.0201956 0.0 +Mm Hs COL6A3 Pancreatic stellate cells NA 0.032 collagen type VI alpha 3 chain protein-coding gene 1 Endoderm Pancreas 0.652174 1.0 0.0403913 0.0277225 +Mm Hs THY1 Pancreatic stellate cells CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Endoderm Pancreas 0.695652 0.0 0.0274535 0.0 +Mm Hs DEFA5 Paneth cells HD-5|DEF5 0.003 defensin alpha 5 protein-coding gene 1 Endoderm GI tract 0.0 0.45 0.00093985 0.000773944 +Mm Hs MMP7 Paneth cells PUMP-1|MPSL1 0.007 matrix metallopeptidase 7 protein-coding gene 1 Endoderm GI tract 0.0 0.425 0.0250627 0.00148339 +Mm Hs AGR2 Paneth cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene 1 Endoderm GI tract 0.0 0.7875 0.0733083 0.00851338 +Hs DEFA1 Paneth cells HNP-1|DEF1|DEFA2 0.0 defensin alpha 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Hs DEFA6 Paneth cells HD-6|DEF6 0.0 defensin alpha 6 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs CSF2 Paneth cells GM-CSF|GMCSF 0.002 colony stimulating factor 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0093985 0.000773944 +Hs LYZ Paneth cells NA 0.008 lysozyme protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0407268 0.0 +Mm Hs PLA2G2A Paneth cells PLA2B 0.009 phospholipase A2 group IIA protein-coding gene 1 Endoderm GI tract 0.0 0.675 0.0247494 0.00225734 +Mm Hs PRSS1 Paneth cells TRY1 0.002 serine protease 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00971178 0.000128991 +Mm Hs GUCA2B Paneth cells NA 0.019 guanylate cyclase activator 2B protein-coding gene 1 Endoderm GI tract 0.0 0.8625 0.00783208 0.0176717 +Mm LYZ1 Paneth cells NA 0.031 lysozyme 1 protein coding gene 1 Endoderm GI tract 0.0 0.9375 0.0 0.0332796 +Mm REG3B Paneth cells NA 0.013 regenerating islet-derived 3 beta protein coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs MUC2 Paneth cells NA 0.007 mucin 2, oligomeric mucus/gel-forming protein-coding gene 1 Endoderm GI tract 0.0 0.6375 0.00595238 0.0041277 +Mm Hs CLCA1 Paneth cells CaCC|CLCRG1 0.003 chloride channel accessory 1 protein-coding gene NA Endoderm GI tract 0.0 0.1375 0.00219298 0.00264431 +Mm Hs GUCA2A Paneth cells STARA|GUCA2 0.015 guanylate cyclase activator 2A protein-coding gene 1 Endoderm GI tract 0.0 0.725 0.0162907 0.0117381 +Mm Hs REG3G Paneth cells UNQ429|LPPM429|PAP1B 0.017 regenerating family member 3 gamma protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00219298 0.0 +Mm Hs ITLN1 Paneth cells ITLN|FLJ20022|LFR|HL-1|hIntL 0.009 intelectin 1 protein-coding gene 1 Endoderm GI tract 0.0 0.875 0.00595238 0.00580458 +Mm Hs RETNLB Paneth cells HXCP2|FIZZ2|RELMb 0.003 resistin like beta protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00219298 0.0 +Mm ANG4 Paneth cells NA 0.005 angiogenin, ribonuclease A family, member 4 protein coding gene 1 Endoderm GI tract 0.0 0.7125 0.0 0.00238633 +Mm Hs GPX2 Paneth cells GSHPX-GI 0.04 glutathione peroxidase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.7375 0.0479323 0.0343115 +Mm Hs LGALS2 Paneth cells HL14 0.032 galectin 2 protein-coding gene NA Endoderm GI tract 0.0 0.8625 0.0379073 0.0265076 +Mm Hs SPINK4 Paneth cells PEC-60|MGC133107 0.014 serine peptidase inhibitor, Kazal type 4 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00626566 0.0 +Mm Hs FABP4 Paneth cells A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0103383 0.0334086 +Mm Hs CFD Paneth cells ADN|DF|PFD 0.018 complement factor D protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0986842 0.00116092 +Mm Hs ADIPOQ Paneth cells ACRP30|AdipoQ|apM1|GBP28|adiponectin|ACDC 0.004 adiponectin, C1Q and collagen domain containing protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.00457917 +Mm Hs PNLIPRP2 Paneth cells PLRP2 0.003 pancreatic lipase related protein 2 (gene/pseudogene) protein-coding gene 1 Endoderm GI tract 0.0 0.3125 0.00156642 0.00180587 +Mm Hs DMBT1 Paneth cells GP340|muclin|SALSA|Gp-340|hensin|vomeroglandin 0.01 deleted in malignant brain tumors 1 protein-coding gene 1 Endoderm GI tract 0.0 0.2375 0.00281955 0.00986778 +Mm Hs NOD2 Paneth cells BLAU|PSORAS1|CLR16.3|NLRC2|IBD1|CARD15 0.0 nucleotide binding oligomerization domain containing 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.000128991 +Mm Hs LGR4 Paneth cells GPR48 0.017 leucine rich repeat containing G protein-coupled receptor 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0375 0.0128446 0.0168978 +Mm Hs RIPK2 Paneth cells RICK|CARDIAK|CARD3 0.004 receptor interacting serine/threonine kinase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0140977 0.0 +Mm Hs TLR5 Paneth cells TIL3|MGC126430|MGC126431|SLEB1 0.0 toll like receptor 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs WNT3 Paneth cells MGC131950|MGC138321|MGC138323 0.003 Wnt family member 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.0 +Mm Hs KCNN4 Paneth cells KCa3.1|hSK4|hKCa4|hIKCa1|IK 0.027 potassium calcium-activated channel subfamily N member 4 protein-coding gene 1 Endoderm GI tract 0.0 0.125 0.0100251 0.0288939 +Mm Hs RAP1A Paneth cells KREV-1|SMGP21 0.314 RAP1A, member of RAS oncogene family protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.170426 0.0 +Mm Hs ATG16L1 Paneth cells WDR30|FLJ10035|ATG16A|APG16L|ATG16L 0.003 autophagy related 16 like 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00309578 +Mm Hs WNT9B Paneth cells WNT14B|WNT15 0.0 Wnt family member 9B protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs DLL4 Paneth cells NA 0.007 delta like canonical Notch ligand 4 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00281955 0.00780393 +Hs IL4R Paneth cells CD124 0.002 interleukin 4 receptor protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0103383 0.0 +Mm IL4RA Paneth cells NA 0.013 interleukin 4 receptor, alpha protein coding gene 1 Endoderm GI tract 0.0 0.025 0.0 0.0168333 +Mm Hs TLR9 Paneth cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs CTNNB1 Paneth cells beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.212406 0.0114802 +Mm Hs DLL1 Paneth cells NA 0.003 delta like canonical Notch ligand 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00501253 0.00264431 +Mm Hs TM4SF20 Paneth cells FLJ22800|TCCE518 0.019 transmembrane 4 L six family member 20 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00313283 0.0 +Mm DEFA23 Paneth cells NA 0.003 defensin, alpha, 23 protein coding gene 1 Endoderm GI tract 0.0 0.575 0.0 0.0013544 +Mm Hs DEFA3 Paneth cells HNP-3 0.002 defensin alpha 3 protein-coding gene 1 Endoderm GI tract 0.0 0.4 0.0 0.000838439 +Mm DEFA26 Paneth cells NA 0.003 defensin, alpha, 26 protein coding gene NA Endoderm GI tract 0.0 0.55 0.0 0.000773944 +Mm DEFA17 Paneth cells NA 0.007 defensin, alpha, 17 protein coding gene 1 Endoderm GI tract 0.0 0.9 0.0 0.00386972 +Mm MPTX2 Paneth cells NA 0.003 mucosal pentraxin 2 protein coding gene 1 Endoderm GI tract 0.0 0.5125 0.0 0.0014189 +Mm DEFA21 Paneth cells NA 0.007 defensin, alpha, 21 protein coding gene 1 Endoderm GI tract 0.0 0.7125 0.0 0.00561109 +Mm DEFA22 Paneth cells NA 0.007 defensin, alpha, 22 protein coding gene 1 Endoderm GI tract 0.0 0.675 0.0 0.00522412 +Mm DEFA24 Paneth cells NA 0.017 defensin, alpha, 24 protein coding gene 1 Endoderm GI tract 0.0 1.0 0.0 0.0168333 +Mm Hs MPTX1 Paneth cells NA 0.001 mucosal pentraxin 1 (pseudogene) pseudogene 1 Endoderm GI tract 0.0 0.025 0.0 0.00096743 +Mm Hs KLF15 Paneth cells KKLF 0.001 Kruppel like factor 15 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000313283 0.00167688 +Mm DEFA20 Paneth cells NA 0.0 defensin, alpha, 20 protein coding gene 1 Endoderm GI tract 0.0 0.1 0.0 0.0 +Mm Hs KL Parathyroid chief cells NA 0.004 klotho protein-coding gene 1 Endoderm Parathyroid glands 0.0 1.0 0.0 0.00455654 +Mm Hs CASR Parathyroid chief cells FHH|NSHPT|GPRC2A|HHC|HHC1 0.001 calcium sensing receptor protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.333333 0.00219298 0.000449236 +Mm Hs VDR Parathyroid chief cells NR1I1|PPP1R163 0.011 vitamin D receptor protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.00250627 0.0 +Mm Hs FGFR1 Parathyroid chief cells CEK|FLG|BFGFR|N-SAM|CD331|FLT2|KAL2 0.072 fibroblast growth factor receptor 1 protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.0588972 0.0732897 +Mm Hs CYP27B1 Parathyroid chief cells P450c1|VDD1|PDDR 0.0 cytochrome P450 family 27 subfamily B member 1 protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.0 0.0 +Mm Hs LRP2 Parathyroid chief cells gp330 0.01 LDL receptor related protein 2 protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.333333 0.0056391 0.0114234 +Mm Hs PTH Parathyroid chief cells NA 0.0 parathyroid hormone protein-coding gene 1 Endoderm Parathyroid glands 0.0 1.0 0.0 0.000256706 +Mm Hs RAB3A Parathyroid chief cells NA 0.179 RAB3A, member RAS oncogene family protein-coding gene 1 Endoderm Parathyroid glands 0.0 0.0 0.0131579 0.0 +Hs CD24 Parietal cells CD24A 0.039 CD24 molecule protein-coding gene NA Endoderm GI tract 0.0 0.0 0.192043 0.0 +Mm Hs PODXL Parietal cells PCLP|Gp200|PC 0.04 podocalyxin like protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0410401 0.0397818 +Mm Hs KCNQ1 Parietal cells Kv7.1|KCNA8|KVLQT1|JLNS1|LQT1|LQT|KCNA9 0.004 potassium voltage-gated channel subfamily Q member 1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00093985 0.00532563 +Mm Hs PTCH1 Parietal cells BCNS|NBCCS|PTCH 0.012 patched 1 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0191103 0.0110363 +Mm Hs SHH Parietal cells HHG1|SMMCI|TPTPS|MCOPCB5|HPE3 0.001 sonic hedgehog protein-coding gene NA Endoderm GI tract 0.0 0.0 0.000313283 0.0 +Mm Hs HIP1R Parietal cells KIAA0655|HIP3|HIP12|FLJ14000 0.007 huntingtin interacting protein 1 related protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.00814886 +Mm Hs HAMP Parietal cells LEAP-1|HEPC|HFE2B|LEAP1 0.002 hepcidin antimicrobial peptide protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00407268 0.00230991 +Mm Hs KCNE2 Parietal cells MiRP1|LQT6 0.002 potassium voltage-gated channel subfamily E regulatory subunit 2 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00281955 0.00211742 +Mm Hs HDC Parietal cells NA 0.019 histidine decarboxylase protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00156642 0.0228425 +Mm Hs ASAP3 Parietal cells FLJ20199|UPLC1|CENTB6|DDEFL1 0.0 ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.000313283 0.000192493 +Mm Hs SLC12A6 Parietal cells KCC3|ACCPN 0.005 solute carrier family 12 member 6 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00626566 0.0 +Mm Hs AQP4 Parietal cells MIWC 0.024 aquaporin 4 protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00595238 0.0293872 +Mm Hs ATP4B Parietal cells ATP6B 0.0 ATPase H+/K+ transporting subunit beta protein-coding gene NA Endoderm GI tract 0.0 0.0 0.0 6.41643e-05 +Mm Hs BMI1 Parietal cells RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene NA Endoderm GI tract 0.0 0.0 0.00532581 0.00930382 +Mm Hs MPZ Peri-islet Schwann cells HMSNIB|CMT2I|CMT2J|CMT1|CMT1B 0.002 myelin protein zero protein-coding gene NA Endoderm Pancreas 1.0 0.6 0.00188029 0.00141252 +Mm Hs EGFL8 Peri-islet Schwann cells NG3|C6orf8 0.003 EGF like domain multiple 8 protein-coding gene NA Endoderm Pancreas 0.0 1.0 0.0 0.00256822 +Mm Hs GFRA1 Peri-islet Schwann cells RETL1|GDNFR|GFR-ALPHA-1|RET1L|TRNR1|GDNFRA 0.005 GDNF family receptor alpha 1 protein-coding gene NA Endoderm Pancreas 0.0 0.6 0.00282043 0.00372392 +Mm Hs OLFML2A Peri-islet Schwann cells FLJ00237 0.003 olfactomedin like 2A protein-coding gene NA Endoderm Pancreas 1.0 0.5 0.0050141 0.0023114 +Mm Hs GULP1 Peri-islet Schwann cells CED6|CED-6|GULP 0.01 GULP, engulfment adaptor PTB domain containing 1 protein-coding gene NA Endoderm Pancreas 1.0 0.9 0.0294579 0.00404494 +Mm Hs SLITRK6 Peri-islet Schwann cells FLJ22774 0.003 SLIT and NTRK like family member 6 protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.00156691 0.0 +Mm Hs VGLL3 Peri-islet Schwann cells VGL-3 0.009 vestigial like family member 3 protein-coding gene NA Endoderm Pancreas 0.0 0.0 0.0194296 0.0 +Mm Hs GFRA3 Peri-islet Schwann cells GFRa-3 0.005 GDNF family receptor alpha 3 protein-coding gene 1 Endoderm Pancreas 1.0 1.0 0.00219367 0.00494382 +Mm Hs INSC Peri-islet Schwann cells NA 0.005 INSC, spindle orientation adaptor protein protein-coding gene NA Endoderm Pancreas 1.0 0.5 0.00125353 0.00603531 +Mm Hs SLITRK2 Peri-islet Schwann cells KIAA1854|SLITL1|TMEM257|CXorf1 0.006 SLIT and NTRK like family member 2 protein-coding gene NA Endoderm Pancreas 1.0 0.0 0.00125353 0.0 +Mm Hs FIGN Peri-islet Schwann cells NA 0.007 fidgetin, microtubule severing factor protein-coding gene NA Endoderm Pancreas 1.0 1.0 0.00376058 0.0059069 +Mm Hs LRRTM1 Peri-islet Schwann cells FLJ32082 0.005 leucine rich repeat transmembrane neuronal 1 protein-coding gene NA Endoderm Pancreas 0.0 0.3 0.00156691 0.00629213 +Mm Hs SEMA3B Peri-islet Schwann cells SemA|semaV|LUCA-1|sema5|SEMAA 0.009 semaphorin 3B protein-coding gene NA Endoderm Pancreas 1.0 0.0 0.0175494 0.0 +Mm Hs NGFR Peri-islet Schwann cells TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene NA Endoderm Pancreas 1.0 1.0 0.00188029 0.00680578 +Mm Hs PNLIPRP1 Peri-islet Schwann cells PLRP1 0.008 pancreatic lipase related protein 1 protein-coding gene NA Endoderm Pancreas 0.0 0.2 0.00188029 0.00930979 +Mm Hs GFRA2 Peri-islet Schwann cells RETL2|GDNFRB|NTNRA|TRNR2 0.008 GDNF family receptor alpha 2 protein-coding gene NA Endoderm Pancreas 0.0 0.5 0.00438734 0.0094382 +Mm Hs PECAM1 Pericytes CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0289256 0.04427 0.0539008 +Mm Hs PDGFRB Pericytes JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene 1 Mesoderm Vasculature 1.0 0.966942 0.0342229 0.0187056 +Mm Hs CSPG4 Pericytes MCSPG|MEL-CSPG|HMW-MAA 0.015 chondroitin sulfate proteoglycan 4 protein-coding gene 1 Mesoderm Vasculature 0.285714 0.586777 0.0 0.0102327 +Mm Hs ANPEP Pericytes gp150|CD13|PEPN 0.015 alanyl aminopeptidase, membrane protein-coding gene 1 Mesoderm Vasculature 0.0 0.0123967 0.0128728 0.0169458 +Mm Hs ACTA2 Pericytes ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene 1 Mesoderm Vasculature 0.0 0.173554 0.0194662 0.0367594 +Mm Hs DES Pericytes CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Vasculature 0.0 0.214876 0.00941915 0.0202698 +Mm Hs RGS5 Pericytes NA 0.043 regulator of G protein signaling 5 protein-coding gene 1 Mesoderm Vasculature NA NA NA NA +Mm Hs ABCC9 Pericytes SUR2|CMD1O 0.016 ATP binding cassette subfamily C member 9 protein-coding gene 1 Mesoderm Vasculature 0.285714 0.818182 0.000627943 0.00736492 +Mm Hs KCNJ8 Pericytes Kir6.1 0.017 potassium voltage-gated channel subfamily J member 8 protein-coding gene 1 Mesoderm Vasculature 0.428571 0.85124 0.000941915 0.00723457 +Mm Hs CD248 Pericytes TEM1|CD164L1 0.022 CD248 molecule protein-coding gene 1 Mesoderm Vasculature 0.285714 0.652893 0.0138148 0.0141433 +Mm Hs DLK1 Pericytes FA1|pG2|Pref-1|ZOG|Delta1 0.055 delta like non-canonical Notch ligand 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.623967 0.0461538 0.0490778 +Mm Hs TEK Pericytes TIE2|TIE-2|VMCM1|CD202b|VMCM 0.02 TEK receptor tyrosine kinase protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00188383 0.0 +Mm Hs NOTCH3 Pericytes CASIL|CADASIL 0.02 notch 3 protein-coding gene 1 Mesoderm Vasculature 0.857143 0.826446 0.0125589 0.00938539 +Mm Hs GLI1 Pericytes GLI 0.0 GLI family zinc finger 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0 0.000195529 +Mm Hs ICAM1 Pericytes CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.00596546 0.0101675 +Mm Hs ADM Pericytes AM 0.026 adrenomedullin protein-coding gene NA Mesoderm Vasculature 0.0 0.00413223 0.0637363 0.0179235 +Mm ANG2 Pericytes NA 0.0 angiogenin, ribonuclease A family, member 2 protein coding gene NA Mesoderm Vasculature 0.0 0.0 0.0 0.000456234 +Mm Hs ANGPT1 Pericytes KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.00413223 0.00188383 0.0125138 +Mm Hs VEGFA Pericytes VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.0248038 0.0 +Mm Hs ZIC1 Pericytes ZIC|ZNF201 0.046 Zic family member 1 protein-coding gene 1 Mesoderm Vasculature 0.285714 0.0 0.00784929 0.0 +Mm Hs FOXC1 Pericytes FREAC3|IGDA|IHG1|FKHL7|IRID1 0.015 forkhead box C1 protein-coding gene NA Mesoderm Vasculature 0.142857 0.0991736 0.00690738 0.0155771 +Mm Hs POSTN Pericytes OSF-2|PN|periostin 0.033 periostin protein-coding gene NA Mesoderm Vasculature 0.0 0.132231 0.0232339 0.0331747 +Mm Hs COX4I2 Pericytes COXIV-2|COX4B|dJ857M17.2|COX4-2|COX4L2 0.018 cytochrome c oxidase subunit 4I2 protein-coding gene NA Mesoderm Vasculature 0.571429 0.913223 0.00596546 0.00723457 +Mm LHFP Pericytes NA 0.056 lipoma HMGIC fusion partner protein coding gene NA Mesoderm Vasculature 0.0 0.896694 0.0 0.0563123 +Mm Hs HIGD1B Pericytes CLST11240|CLST11240-15 0.021 HIG1 hypoxia inducible domain family member 1B protein-coding gene 1 Mesoderm Vasculature 1.0 0.938017 0.00376766 0.0109496 +Mm Hs PDZD2 Pericytes KIAA0300|PDZK3 0.021 PDZ domain containing 2 protein-coding gene NA Mesoderm Vasculature 0.285714 0.615702 0.0131868 0.0145343 +Mm Hs HSD11B1 Pericytes SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0247934 0.00973312 0.0245063 +Mm Hs MCAM Pericytes MUC18|CD146 0.031 melanoma cell adhesion molecule protein-coding gene 1 Mesoderm Vasculature 0.714286 0.673554 0.0197802 0.0235938 +Mm Hs MXRA8 Pericytes DKFZp586E2023 0.043 matrix remodeling associated 8 protein-coding gene NA Mesoderm Vasculature 0.142857 0.0867769 0.0376766 0.0427557 +Mm Hs PDE5A Pericytes NA 0.011 phosphodiesterase 5A protein-coding gene NA Mesoderm Vasculature 0.142857 0.392562 0.00376766 0.00762563 +Mm Hs NR1H3 Pericytes LXR-a|RLD-1|LXRa 0.008 nuclear receptor subfamily 1 group H member 3 protein-coding gene NA Mesoderm Vasculature 0.0 0.0495868 0.00973312 0.00690869 +Mm Hs SERPING1 Pericytes C1IN|C1-INH|HAE1|HAE2|C1NH 0.066 serpin family G member 1 protein-coding gene NA Mesoderm Vasculature 0.428571 0.0 0.0985871 0.0 +Mm Hs EMID1 Pericytes EMU1|hEmu1|EMI5 0.018 EMI domain containing 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0743802 0.00596546 0.0204002 +Mm Hs ECM1 Pericytes NA 0.034 extracellular matrix protein 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0495868 0.00941915 0.0402138 +Mm Hs COLEC11 Pericytes MGC3279|CL-K1 0.002 collectin subfamily member 11 protein-coding gene 1 Mesoderm Vasculature 0.285714 0.0454545 0.00627944 0.000260705 +Mm Hs RARRES2 Pericytes TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene NA Mesoderm Vasculature 0.142857 0.0 0.0784929 0.0 +Mm Hs REM1 Pericytes GES|REM 0.001 RRAD and GEM like GTPase 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0 0.000313972 0.0 +Mm Hs ASPN Pericytes FLJ20129|SLRR1C|PLAP-1 0.019 asporin protein-coding gene NA Mesoderm Vasculature 0.0 0.268595 0.00722135 0.0179235 +Mm Hs CYGB Pericytes HGB|STAP 0.038 cytoglobin protein-coding gene NA Mesoderm Vasculature 0.142857 0.136364 0.021664 0.0418432 +Mm Hs FABP4 Pericytes A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene NA Mesoderm Vasculature 0.142857 0.0867769 0.0100471 0.0323926 +Mm Hs VTN Pericytes VN 0.029 vitronectin protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00973312 0.0 +Mm Hs STEAP4 Pericytes FLJ23153|TIARP|STAMP2|SchLAH|TNFAIP9 0.007 STEAP4 metalloreductase protein-coding gene 1 Mesoderm Vasculature 0.142857 0.0 0.00565149 0.0 +Mm Hs NDUFA4L2 Pericytes NUOMS|FLJ26118 0.031 NDUFA4, mitochondrial complex associated like 2 protein-coding gene NA Mesoderm Vasculature 1.0 0.942149 0.0213501 0.0175324 +Mm Hs SLC38A11 Pericytes FLJ39822|AVT2 0.003 solute carrier family 38 member 11 protein-coding gene NA Mesoderm Vasculature 0.285714 0.0 0.000627943 0.0 +Mm Hs ATP13A5 Pericytes FLJ16025 0.006 ATPase 13A5 protein-coding gene 1 Mesoderm Vasculature 0.0 0.359504 0.000313972 0.00195529 +Mm Hs AOC3 Pericytes VAP1|HPAO|VAP-1 0.004 amine oxidase, copper containing 3 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0413223 0.00282575 0.0038454 +Mm Hs ANGPT2 Pericytes Ang2 0.004 angiopoietin 2 protein-coding gene 1 Mesoderm Vasculature 0.428571 0.0206612 0.0150706 0.00156423 +Mm Hs INPP4B Pericytes NA 0.01 inositol polyphosphate-4-phosphatase type II B protein-coding gene 1 Mesoderm Vasculature 0.0 0.103306 0.0150706 0.00716939 +Mm Hs GPIHBP1 Pericytes LOC338328|GPI-HBP1 0.017 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 protein-coding gene NA Mesoderm Vasculature 0.0 0.0123967 0.00470958 0.0197484 +Mm Hs VIM Pericytes NA 0.427 vimentin protein-coding gene 1 Mesoderm Vasculature 0.857143 0.0 0.589953 0.0 +Mm Hs PTH1R Pericytes PTHR1 0.019 parathyroid hormone 1 receptor protein-coding gene 1 Mesoderm Vasculature 0.142857 0.152893 0.00470958 0.0213778 +Mm Hs IFITM1 Pericytes 9-27|CD225|DSPA2a|IFI17 0.059 interferon induced transmembrane protein 1 protein-coding gene 1 Mesoderm Vasculature 0.142857 0.884298 0.0320251 0.0519455 +Mm Hs TBX18 Pericytes NA 0.004 T-box 18 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.000313972 0.0 +Mm Hs NT5E Pericytes CD73|eN|eNT|CALJA|NT5 0.005 5'-nucleotidase ecto protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00722135 0.00378023 +Mm Hs MFGE8 Pericytes SED1|EDIL1|BA46|OAcGD3S|HsT19888|MFG-E8|hP47|SPAG10 0.15 milk fat globule-EGF factor 8 protein protein-coding gene 1 Mesoderm Vasculature 1.0 0.979339 0.078179 0.153295 +Mm Hs ALPL Pericytes TNSALP|TNALP|TNAP|HOPS 0.009 alkaline phosphatase, liver/bone/kidney protein-coding gene 1 Mesoderm Vasculature 0.0 0.0 0.00408163 0.0106889 +Mm Hs COL1A1 Pericytes NA 0.081 collagen type I alpha 1 chain protein-coding gene 1 Mesoderm Vasculature 0.142857 0.0826446 0.099843 0.0731278 +Mm Hs MYO1B Pericytes myr1 0.05 myosin IB protein-coding gene 1 Mesoderm Vasculature 0.428571 0.826446 0.0298273 0.0433422 +Mm Hs COG7 Pericytes NA 0.008 component of oligomeric golgi complex 7 protein-coding gene 1 Mesoderm Vasculature 0.0 0.0413223 0.000313972 0.0099068 +Mm Hs P2RY14 Pericytes KIAA0001|GPR105 0.012 purinergic receptor P2Y14 protein-coding gene 1 Mesoderm Vasculature 0.0 0.483471 0.00345369 0.00677834 +Mm Hs HEYL Pericytes bHLHb33|HEY3|HESR3 0.013 hes related family bHLH transcription factor with YRPW motif-like protein-coding gene 1 Mesoderm Vasculature 0.285714 0.661157 0.00313972 0.00488822 +Mm Hs GNB4 Pericytes NA 0.05 G protein subunit beta 4 protein-coding gene 1 Mesoderm Vasculature 0.142857 0.690083 0.0169545 0.0477742 +Mm Hs MSX1 Pericytes HYD1|OFC5|HOX7 0.015 msh homeobox 1 protein-coding gene 1 Mesoderm Vasculature 0.0 0.00413223 0.0248038 0.0133611 +Mm Hs CTGF Pericytes IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Mesoderm Vasculature 0.142857 0.0371901 0.099529 0.0120576 +Mm Hs SAT2 Peritubular myoid cells SSAT2 0.042 spermidine/spermine N1-acetyltransferase family member 2 protein-coding gene NA Mesoderm Reproductive 0.660377 0.0 0.178719 0.0 +Mm Hs LAMC3 Peritubular myoid cells DKFZp434E202 0.002 laminin subunit gamma 3 protein-coding gene NA Mesoderm Reproductive 0.320755 0.0 0.00318573 0.000962464 +Mm Hs APOA1 Peritubular myoid cells NA 0.032 apolipoprotein A1 protein-coding gene NA Mesoderm Reproductive 0.490566 0.0 0.061166 0.0256657 +Mm Hs MYLIP Peritubular myoid cells IDOL 0.02 myosin regulatory light chain interacting protein protein-coding gene NA Mesoderm Reproductive 0.301887 0.0 0.0640331 0.0112287 +Mm Hs TMEM98 Peritubular myoid cells DKFZP564K1964 0.036 transmembrane protein 98 protein-coding gene NA Mesoderm Reproductive 0.301887 0.0 0.121058 0.0 +Mm Hs CYP1B1 Peritubular myoid cells CP1B|GLC3A 0.016 cytochrome P450 family 1 subfamily B member 1 protein-coding gene NA Mesoderm Reproductive 0.169811 0.0 0.0471488 0.008983 +Mm Hs KCNMB1 Peritubular myoid cells hslo-beta 0.004 potassium calcium-activated channel subfamily M regulatory beta subunit 1 protein-coding gene NA Mesoderm Reproductive 0.396226 0.0 0.00382287 0.0026949 +Mm Hs RARRES2 Peritubular myoid cells TIG2|HP10433 0.03 retinoic acid receptor responder 2 protein-coding gene NA Mesoderm Reproductive 0.490566 0.0 0.0716789 0.0 +Mm Hs GSTM3 Peritubular myoid cells GST5 0.024 glutathione S-transferase mu 3 protein-coding gene NA Mesoderm Reproductive 0.792453 0.0 0.0805989 0.0080847 +Mm Hs RNASE1 Peritubular myoid cells RAC1|RNS1 0.022 ribonuclease A family member 1, pancreatic protein-coding gene NA Mesoderm Reproductive 0.509434 0.0 0.0831475 0.0 +Mm Hs CILP Peritubular myoid cells HsT18872 0.003 cartilage intermediate layer protein protein-coding gene NA Mesoderm Reproductive 0.0754717 0.0 0.00254858 0.00263073 +Mm Hs RASD1 Peritubular myoid cells DEXRAS1 0.013 ras related dexamethasone induced 1 protein-coding gene NA Mesoderm Reproductive 0.396226 0.0 0.0264415 0.0 +Mm Hs ALDH1A3 Peritubular myoid cells RALDH3|ALDH6 0.008 aldehyde dehydrogenase 1 family member A3 protein-coding gene NA Mesoderm Reproductive 0.0754717 0.0 0.0340873 0.00327238 +Mm Hs INTS6 Peritubular myoid cells DICE1|HDB|Notchl2|DBI-1|DDX26A|DDX26 0.034 integrator complex subunit 6 protein-coding gene NA Mesoderm Reproductive 0.45283 0.0 0.111819 0.0166827 +Mm Hs EPHX1 Peritubular myoid cells EPHX 0.02 epoxide hydrolase 1 protein-coding gene NA Mesoderm Reproductive 0.301887 0.0 0.035043 0.0161052 +Mm Hs OSR2 Peritubular myoid cells FLJ90037 0.011 odd-skipped related transciption factor 2 protein-coding gene NA Mesoderm Reproductive 0.528302 0.0 0.00892004 0.008983 +Mm Hs C7 Peritubular myoid cells NA 0.003 complement C7 protein-coding gene NA Mesoderm Reproductive 0.188679 0.0 0.0124243 0.00128329 +Mm Hs COL15A1 Peritubular myoid cells NA 0.016 collagen type XV alpha 1 chain protein-coding gene NA Mesoderm Reproductive 0.45283 0.0 0.0210258 0.0141803 +Mm Hs LAMB2 Peritubular myoid cells NPHS5|LAMS 0.019 laminin subunit beta 2 protein-coding gene NA Mesoderm Reproductive 0.0943396 0.0 0.0117872 0.0210459 +Mm Hs MYH11 Peritubular myoid cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene 1 Mesoderm Reproductive 0.339623 0.0 0.0108315 0.0149503 +Mm Hs TPM1 Peritubular myoid cells C15orf13|CMH3 0.253 tropomyosin 1 protein-coding gene 1 Mesoderm Reproductive 0.339623 0.0 0.176489 0.0 +Mm Hs TPM2 Peritubular myoid cells NEM4|AMCD1 0.075 tropomyosin 2 protein-coding gene 1 Mesoderm Reproductive 0.433962 0.0 0.142083 0.0 +Mm Hs TPM4 Peritubular myoid cells NA 0.311 tropomyosin 4 protein-coding gene 1 Mesoderm Reproductive 0.358491 0.0 0.34374 0.0 +Mm Hs MYL9 Peritubular myoid cells MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Reproductive 0.811321 0.0 0.149411 0.0633943 +None WNT Peritubular myoid cells NA 0.0 NA NA 1 Mesoderm Reproductive NA NA NA NA +Mm Hs WNT2B Peritubular myoid cells XWNT2|WNT13 0.001 Wnt family member 2B protein-coding gene 1 Mesoderm Reproductive 0.132075 0.0 0.0035043 0.0 +Mm Hs RCVRN Photoreceptor cells RCV1 0.003 recoverin protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs PDC Photoreceptor cells MEKA 0.004 phosducin protein-coding gene NA Ectoderm Eye 0.0 0.362416 0.0 0.00168437 +Mm Hs NRL Photoreceptor cells D14S46E|RP27|NRL-MAF 0.003 neural retina leucine zipper protein-coding gene NA Ectoderm Eye 0.0 0.248322 0.00281955 0.000518269 +Mm Hs NR2E3 Photoreceptor cells rd7|RP37 0.002 nuclear receptor subfamily 2 group E member 3 protein-coding gene NA Ectoderm Eye 0.0 0.221477 0.0 0.000583053 +Mm Hs SAG Photoreceptor cells ARRESTIN|RP47 0.005 S-antigen visual arrestin protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0018797 0.0 +Mm Hs RHO Photoreceptor cells OPN2|CSNBAD1|RP4 0.006 rhodopsin protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs ROM1 Photoreceptor cells TSPAN23|ROM 0.007 retinal outer segment membrane protein 1 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.000313283 0.0 +Mm Hs CRX Photoreceptor cells LCA7|CORD2 0.002 cone-rod homeobox protein-coding gene 1 Ectoderm Eye 0.0 0.281879 0.0 0.000453485 +Mm Hs PDE6G Photoreceptor cells RP57|PDEG 0.003 phosphodiesterase 6G protein-coding gene NA Ectoderm Eye 0.0 0.342282 0.000313283 0.000971754 +Mm Hs TPBG Photoreceptor cells 5T4-AG|5T4 0.021 trophoblast glycoprotein protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0319549 0.0 +Mm Hs GABRA1 Photoreceptor cells EJM5 0.027 gamma-aminobutyric acid type A receptor alpha1 subunit protein-coding gene NA Ectoderm Eye 0.0 0.597315 0.000313283 0.0267556 +Mm Hs PCBP3 Photoreceptor cells FLJ44028|PCBP3-OT1|PCBP3OT 0.02 poly(rC) binding protein 3 protein-coding gene NA Ectoderm Eye 0.0 0.489933 0.00250627 0.0200181 +Mm Hs FRMD3 Photoreceptor cells EPB41L4O|MGC20553 0.01 FERM domain containing 3 protein-coding gene NA Ectoderm Eye 0.0 0.436242 0.0128446 0.00596009 +Mm Hs ADAMTS5 Photoreceptor cells ADMP-2|ADAMTS11 0.016 ADAM metallopeptidase with thrombospondin type 1 motif 5 protein-coding gene NA Ectoderm Eye 0.0 0.0469799 0.014411 0.0165198 +Mm Hs RD3L Photoreceptor cells TDRD9AS1|TDRD9-AS1 0.003 retinal degeneration 3 like protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs GABRG2 Photoreceptor cells NA 0.024 gamma-aminobutyric acid type A receptor gamma2 subunit protein-coding gene NA Ectoderm Eye 0.0 0.402685 0.00125313 0.0261078 +Mm Hs CNTN4 Photoreceptor cells BIG-2 0.005 contactin 4 protein-coding gene NA Ectoderm Eye 0.0 0.0939597 0.0115915 0.0031744 +Mm Hs RNF152 Photoreceptor cells FLJ39176 0.008 ring finger protein 152 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00438596 0.0 +Mm Hs SYNE1 Photoreceptor cells SYNE-1B|KIAA0796|8B|Nesprin-1|enaptin|MYNE1|CPG2|dJ45H2.2|SCAR8|ARCA1|Nesp1|C6orf98 0.05 spectrin repeat containing nuclear envelope protein 1 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0153509 0.0 +Mm Hs SEBOX Photoreceptor cells OG9|OG9X 0.0 SEBOX homeobox protein-coding gene NA Ectoderm Eye NA NA NA NA +Mm Hs HSPA12A Photoreceptor cells FLJ13874|KIAA0417 0.013 heat shock protein family A (Hsp70) member 12A protein-coding gene NA Ectoderm Eye 0.0 0.127517 0.0 0.0147059 +Mm Hs CNTNAP2 Photoreceptor cells Caspr2|KIAA0868 0.037 contactin associated protein like 2 protein-coding gene NA Ectoderm Eye 0.0 0.0805369 0.0238095 0.0402954 +Mm Hs NLK Photoreceptor cells NA 0.021 nemo like kinase protein-coding gene NA Ectoderm Eye 0.0 0.671141 0.0162907 0.0165198 +Mm Hs NTNG1 Photoreceptor cells KIAA0976|Lmnt1 0.015 netrin G1 protein-coding gene NA Ectoderm Eye 0.0 0.302013 0.00407268 0.0151594 +Mm Hs GLS Photoreceptor cells KIAA0838|GLS1 0.061 glutaminase protein-coding gene NA Ectoderm Eye 0.0 0.52349 0.0197368 0.067958 +Mm Hs STX3 Photoreceptor cells STX3A 0.035 syntaxin 3 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0250627 0.0 +Mm Hs GRM6 Photoreceptor cells GPRC1F|mGlu6|MGLUR6|CSNB1B 0.003 glutamate metabotropic receptor 6 protein-coding gene NA Ectoderm Eye 0.0 0.33557 0.0 6.47836e-05 +Mm Hs STRIP2 Photoreceptor cells KIAA1170|FAR11B|FAM40B 0.005 striatin interacting protein 2 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0075188 0.0 +Mm Hs CHGA Photoreceptor cells NA 0.057 chromogranin A protein-coding gene NA Ectoderm Eye 0.0 0.248322 0.0379073 0.0604431 +Mm Hs RNPC3 Photoreceptor cells KIAA1839|FLJ20008|RBM40 0.02 RNA binding region (RNP1, RRM) containing 3 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00219298 0.0 +Mm Hs VSTM2B Photoreceptor cells NA 0.006 V-set and transmembrane domain containing 2B protein-coding gene NA Ectoderm Eye 0.0 0.0 0.000313283 0.0 +Mm Hs CACNA2D4 Photoreceptor cells NA 0.005 calcium voltage-gated channel auxiliary subunit alpha2delta 4 protein-coding gene NA Ectoderm Eye 0.0 0.66443 0.00219298 6.47836e-05 +Mm Hs VSX2 Photoreceptor cells RET1|HOX10|CHX10 0.004 visual system homeobox 2 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs TRNP1 Photoreceptor cells LOC388610|C1orf225 0.015 TMF1-regulated nuclear protein 1 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00469925 0.0 +Mm Hs NEUROD4 Photoreceptor cells Atoh3|ATH-3|MATH-3|bHLHa4 0.006 neuronal differentiation 4 protein-coding gene NA Ectoderm Eye 0.0 0.718121 0.000313283 0.000842187 +Mm Hs GNB3 Photoreceptor cells NA 0.005 G protein subunit beta 3 protein-coding gene NA Ectoderm Eye 0.0 0.543624 0.00093985 0.00129567 +Mm Hs OTX2 Photoreceptor cells NA 0.013 orthodenticle homeobox 2 protein-coding gene NA Ectoderm Eye 0.0 0.892617 0.00877193 0.00628401 +Mm Hs CACNA2D3 Photoreceptor cells HSA272268 0.008 calcium voltage-gated channel auxiliary subunit alpha2delta 3 protein-coding gene NA Ectoderm Eye 0.0 0.194631 0.00595238 0.00770925 +Mm ZFP365 Photoreceptor cells NA 0.016 zinc finger protein 365 protein coding gene NA Ectoderm Eye NA NA NA NA +Mm Hs LIN7A Photoreceptor cells MALS-1|TIP-33|LIN-7A|VELI1 0.015 lin-7 homolog A, crumbs cell polarity complex component protein-coding gene NA Ectoderm Eye 0.0 0.409396 0.016604 0.0123089 +Mm Hs CCDC136 Photoreceptor cells KIAA1793|NAG6|DKFZP434G156 0.027 coiled-coil domain containing 136 protein-coding gene NA Ectoderm Eye 0.0 0.181208 0.0382206 0.0242939 +Mm Hs NDNF Photoreceptor cells FLJ23191|C4orf31 0.017 neuron derived neurotrophic factor protein-coding gene NA Ectoderm Eye 0.0 0.416107 0.00626566 0.0167142 +Mm Hs GNG13 Photoreceptor cells h2-35|G(gamma)13 0.006 G protein subunit gamma 13 protein-coding gene NA Ectoderm Eye 0.0 0.416107 0.0 0.00375745 +Mm Hs PROX1 Photoreceptor cells NA 0.028 prospero homeobox 1 protein-coding gene NA Ectoderm Eye 0.0 0.530201 0.0109649 0.0276626 +Mm Hs GPR179 Photoreceptor cells CSNB1E|GPR158L1 0.003 G protein-coupled receptor 179 protein-coding gene NA Ectoderm Eye 0.0 0.449664 0.0 6.47836e-05 +Mm Hs CABP5 Photoreceptor cells CaBP3|CABP3 0.004 calcium binding protein 5 protein-coding gene NA Ectoderm Eye 0.0 0.489933 0.0 0.0 +Mm Hs KCNMA1 Photoreceptor cells KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene NA Ectoderm Eye 0.0 0.718121 0.0184837 0.0420446 +Mm CAR8 Photoreceptor cells NA 0.013 carbonic anhydrase 8 protein coding gene NA Ectoderm Eye 0.0 0.147651 0.0 0.0147707 +Mm Hs LRTM1 Photoreceptor cells HT017 0.008 leucine rich repeats and transmembrane domains 1 protein-coding gene NA Ectoderm Eye 0.0 0.731544 0.000626566 0.00246178 +Mm Hs PRKCA Photoreceptor cells PKCA 0.033 protein kinase C alpha protein-coding gene NA Ectoderm Eye 0.0 0.14094 0.0153509 0.0358901 +Mm Hs QPCT Photoreceptor cells QC|GCT 0.026 glutaminyl-peptide cyclotransferase protein-coding gene NA Ectoderm Eye 0.0 0.342282 0.0300752 0.0224799 +Mm Hs CPLX3 Photoreceptor cells CPX-III 0.01 complexin 3 protein-coding gene NA Ectoderm Eye 0.0 0.899329 0.00125313 0.0039518 +Mm Hs B3GALT2 Photoreceptor cells beta3Gal-T2 0.009 beta-1,3-galactosyltransferase 2 protein-coding gene NA Ectoderm Eye 0.0 0.57047 0.00093985 0.00544182 +Mm Hs ISL1 Photoreceptor cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene NA Ectoderm Eye 0.0 0.47651 0.0134712 0.0270796 +Mm Hs PCP2 Photoreceptor cells MGC41903|GPSM4 0.006 Purkinje cell protein 2 protein-coding gene NA Ectoderm Eye 0.0 0.308725 0.018797 0.000842187 +Mm Hs ASMT Pinealocytes HIOMT|ASMTY|HIOMTY 0.0 acetylserotonin O-methyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ADRB1 Pinealocytes ADRB1R 0.002 adrenoceptor beta 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.00237514 +Mm Hs TPH1 Pinealocytes TPRH|TPH 0.002 tryptophan hydroxylase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs SAG Pinealocytes ARRESTIN|RP47 0.005 S-antigen visual arrestin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs GNGT1 Pinealocytes GNG1 0.007 G protein subunit gamma transducin 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00860187 +Mm Hs GNGT2 Pinealocytes GNG9 0.054 G protein subunit gamma transducin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0657337 +Mm Hs ROM1 Pinealocytes TSPAN23|ROM 0.007 retinal outer segment membrane protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs CRX Pinealocytes LCA7|CORD2 0.002 cone-rod homeobox protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00269611 +Mm Hs CNGB1 Pinealocytes RCNC2|RCNCb|GAR1|CNGB1B|RP45|CNCG2|CNCG3L 0.001 cyclic nucleotide gated channel beta 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00147644 +Mm Hs CNGA1 Pinealocytes RCNC1|RCNCa|CNG1|RP49|CNCG1|CNCG 0.002 cyclic nucleotide gated channel alpha 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00205418 +Mm Hs PDE6C Pinealocytes PDEA2|ACHM5|COD4 0.0 phosphodiesterase 6C protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.000577738 +Mm Hs SLC6A6 Pinealocytes TAUT 0.102 solute carrier family 6 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs ADRA1B Pinealocytes NA 0.002 adrenoceptor alpha 1B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00288869 +Mm Hs DRD4 Pinealocytes NA 0.001 dopamine receptor D4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00147644 +Mm Hs CHRNA3 Pinealocytes NA 0.004 cholinergic receptor nicotinic alpha 3 subunit protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.00442932 +Mm Hs CHRNB4 Pinealocytes NA 0.001 cholinergic receptor nicotinic beta 4 subunit protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.000898703 +Mm Hs NEUROD1 Pinealocytes BETA2|BHF-1|NeuroD|bHLHa3|MODY6|NEUROD 0.038 neuronal differentiation 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.023183 0.04256 +Mm Hs PDE6B Pinealocytes CSNB3|rd1|RP40|CSNBAD2|PDEB 0.002 phosphodiesterase 6B protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00125313 0.00231095 +Mm Hs CACNA1F Pinealocytes Cav1.4|JM8|JMC8|CSNBX2|CORDX3|CSNB2A|OA2|CSNB2|AIED 0.0 calcium voltage-gated channel subunit alpha1 F protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 6.41931e-05 +Mm Hs GNG13 Pinealocytes h2-35|G(gamma)13 0.006 G protein subunit gamma 13 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00770317 +Mm Hs AANAT Pinealocytes SNAT 0.0 aralkylamine N-acetyltransferase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CREM Pinealocytes hCREM-2 0.065 cAMP responsive element modulator protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.158208 0.043202 +Mm Hs PDE10A Pinealocytes NA 0.024 phosphodiesterase 10A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00281955 0.0301066 +Mm Hs PMEPA1 Pinealocytes STAG1|TMEPAI 0.048 prostate transmembrane protein, androgen induced 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0250627 0.0539864 +Mm Hs SDC1 Plasma cells CD138|syndecan|SYND1|SDC 0.046 syndecan 1 protein-coding gene 1 Mesoderm Immune system 0.555556 0.0 0.0405577 0.0 +Mm Hs IRF4 Plasma cells LSIRF|MUM1 0.003 interferon regulatory factor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00855513 0.000641684 +Mm Hs CD38 Plasma cells NA 0.016 CD38 molecule protein-coding gene 1 Mesoderm Immune system 0.5 0.0 0.00855513 0.0161063 +Mm Hs PRDM1 Plasma cells PRDI-BF1|BLIMP1 0.005 PR/SET domain 1 protein-coding gene 1 Mesoderm Immune system 0.25 0.0 0.0174271 0.00166838 +Mm Hs CD93 Plasma cells C1qRP|C1qR(P)|dJ737E23.1|CDw93|ECSM3|MXRA4|C1QR1 0.044 CD93 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0193283 0.0489605 +Mm Hs CD27 Plasma cells S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene 1 Mesoderm Immune system 0.722222 0.0 0.0148923 0.0157854 +Mm Hs ENPP1 Plasma cells PC-1|NPPS|M6S1|PDNP1 0.005 ectonucleotide pyrophosphatase/phosphodiesterase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0114068 0.00327259 +Mm Hs KLF4 Plasma cells EZF|GKLF 0.126 Kruppel like factor 4 protein-coding gene 1 Mesoderm Immune system 0.0833333 0.0 0.139417 0.127503 +Mm Hs MS4A4A Plasma cells CD20L1|MS4A7 0.002 membrane spanning 4-domains A4A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00760456 0.000770021 +Mm Hs PIAS1 Plasma cells GU/RH-II|ZMIZ3|DDXBP1 0.018 protein inhibitor of activated STAT 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0307351 0.0155929 +Mm Hs CYCS Plasma cells CYC 0.38 cytochrome c, somatic protein-coding gene 1 Mesoderm Immune system 0.777778 0.0 0.504119 0.34683 +Mm Hs DIABLO Plasma cells SMAC|DIABLO-S|FLJ25049|FLJ10537|DFNA64 0.026 diablo IAP-binding mitochondrial protein protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0329825 +Mm Hs HTRA2 Plasma cells OMI|PARK13|PRSS25 0.001 HtrA serine peptidase 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000316857 0.00102669 +Mm Hs MS4A1 Plasma cells Bp35|MS4A2|CD20 0.014 membrane spanning 4-domains A1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0205957 0.011807 +Mm Hs CD9 Plasma cells BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Mesoderm Immune system 0.277778 1.0 0.270913 0.366145 +Mm Hs CD19 Plasma cells NA 0.007 CD19 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00792142 0.006096 +Hs CD24 Plasma cells CD24A 0.039 CD24 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.194233 0.0 +Mm Hs CD37 Plasma cells TSPAN26 0.116 CD37 molecule protein-coding gene 1 Mesoderm Immune system 0.111111 0.0 0.217047 0.0949692 +Mm Hs CD40 Plasma cells Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.013308 0.0108445 +Mm Hs CD74 Plasma cells DHLAG 0.169 CD74 molecule protein-coding gene 1 Mesoderm Immune system 0.972222 1.0 0.356781 0.125128 +Mm Hs CXCR4 Plasma cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.361111 0.0 0.196451 0.00879107 +Mm Hs GZMB Plasma cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0611534 0.00834189 +Mm Hs TNFRSF17 Plasma cells BCM|CD269|TNFRSF13A|BCMA 0.005 TNF receptor superfamily member 17 protein-coding gene 1 Mesoderm Immune system 0.777778 0.0 0.00126743 0.0 +Mm Hs TNFRSF13B Plasma cells TACI|CD267|IGAD2 0.016 TNF receptor superfamily member 13B protein-coding gene 1 Mesoderm Immune system 0.305556 0.0 0.00190114 0.0 +Mm Hs FCGR2B Plasma cells CD32B 0.031 Fc fragment of IgG receptor IIb protein-coding gene 1 Mesoderm Immune system 0.0277778 0.0 0.004436 0.0360626 +Mm Hs CCR10 Plasma cells GPR2 0.002 C-C motif chemokine receptor 10 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.00095057 0.000705852 +Mm Hs ABCB9 Plasma cells EST122234 0.002 ATP binding cassette subfamily B member 9 protein-coding gene 1 Mesoderm Immune system 0.0277778 0.0 0.000316857 0.00295175 +Mm Hs AMPD1 Plasma cells NA 0.0 adenosine monophosphate deaminase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 6.41684e-05 +Mm Hs ANGPT4 Plasma cells NA 0.001 angiopoietin 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000705852 +Hs ATXN8OS Plasma cells NCRNA00003|SCA8|KLHL1AS 0.0 ATXN8 opposite strand lncRNA non-coding RNA 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs C11ORF80 Plasma cells FLJ22531|TOPOVIBL 0.002 chromosome 11 open reading frame 80 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.01109 0.0 +Mm Hs CD79A Plasma cells MB-1|IGA 0.024 CD79a molecule protein-coding gene 1 Mesoderm Immune system 0.75 0.0 0.0351711 0.0184805 +Mm Hs DENND5B Plasma cells MGC24039 0.013 DENN domain containing 5B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00602028 0.0151437 +Mm Hs EAF2 Plasma cells BM040|TRAITS 0.009 ELL associated factor 2 protein-coding gene 1 Mesoderm Immune system 0.638889 1.0 0.0237643 0.00333676 +Hs FCRL2 Plasma cells FCRH2|IRTA4|CD307b|SPAP1 0.0 Fc receptor like 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs GNG7 Plasma cells FLJ00058 0.009 G protein subunit gamma 7 protein-coding gene 1 Mesoderm Immune system 0.555556 0.0 0.019962 0.00481263 +Mm Hs GPR25 Plasma cells NA 0.0 G protein-coupled receptor 25 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs GUSBP11 Plasma cells NA 0.0 glucuronidase, beta pseudogene 11 pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs HIST1H2AE Plasma cells H2A/a|H2AFA 0.02 histone cluster 1 H2A family member e protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000633714 0.025154 +Mm Hs HIST1H2BG Plasma cells H2B/a|H2B.1A|H2BFA 0.002 histone cluster 1 H2B family member g protein-coding gene 1 Mesoderm Immune system 0.0277778 0.0 0.00792142 0.000449179 +Hs HLA-DOB Plasma cells NA 0.001 major histocompatibility complex, class II, DO beta protein-coding gene 1 Mesoderm Immune system 0.0555556 0.0 0.004436 0.0 +Mm Hs IGHD Plasma cells FLJ00382|FLJ46727|MGC29633 0.008 immunoglobulin heavy constant delta other 1 Mesoderm Immune system 0.0 0.0 0.00887199 0.0075077 +Mm Hs IGHE Plasma cells NA 0.0 immunoglobulin heavy constant epsilon other 1 Mesoderm Immune system 0.0 0.0 0.000316857 0.0 +Mm Hs IGHM Plasma cells NA 0.078 immunoglobulin heavy constant mu other 1 Mesoderm Immune system 0.277778 1.0 0.0525982 0.0825847 +Mm Hs IGKC Plasma cells HCAK1 0.072 immunoglobulin kappa constant other 1 Mesoderm Immune system 1.0 1.0 0.153359 0.0534523 +Hs IGLL3P Plasma cells 16.1|IGLL3 0.0 immunoglobulin lambda like polypeptide 3, pseudogene pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs KCNA3 Plasma cells Kv1.3|MK3|HLK3|HPCN3 0.0 potassium voltage-gated channel subfamily A member 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000449179 +Mm Hs KCNG2 Plasma cells Kv6.2|KCNF2 0.003 potassium voltage-gated channel modifier subfamily G member 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00327259 +Mm Hs LIME1 Plasma cells FLJ20406|dJ583P15.4|LIME 0.0 Lck interacting transmembrane adaptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Hs MAN1A1 Plasma cells NA 0.004 mannosidase alpha class 1A member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0218631 0.0 +Mm Hs MANEA Plasma cells FLJ12838|mandaselin 0.002 mannosidase endo-alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00126743 0.00269507 +Mm Hs MAST1 Plasma cells KIAA0973 0.0 microtubule associated serine/threonine kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs MROH7 Plasma cells FLJ46354|C1orf175|HEATR8 0.002 maestro heat like repeat family member 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0107731 0.000192505 +Mm Hs MZB1 Plasma cells MGC29506|HSPC190|pERp1|MEDA-7 0.025 marginal zone B and B1 cell specific protein protein-coding gene 1 Mesoderm Immune system 0.972222 1.0 0.0275665 0.0208547 +Mm Hs P2RX5 Plasma cells P2X5 0.0 purinergic receptor P2X 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00190114 0.0 +Mm Hs PAX7 Plasma cells Hup1 0.001 paired box 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00095057 0.000898357 +Mm Hs PDK1 Plasma cells NA 0.015 pyruvate dehydrogenase kinase 1 protein-coding gene 1 Mesoderm Immune system 0.333333 0.0 0.0129911 0.0137962 +Mm Hs PNOC Plasma cells PPNOC|N/OFQ|NOP 0.009 prepronociceptin protein-coding gene 1 Mesoderm Immune system 0.0277778 0.0 0.000633714 0.0099461 +Mm Hs RASGRP3 Plasma cells KIAA0846|GRP3|CalDAG-GEFIII 0.025 RAS guanyl releasing protein 3 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.00760456 0.0 +Hs REN Plasma cells NA 0.0 renin protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.002218 0.0 +Mm Hs RGS13 Plasma cells NA 0.003 regulator of G protein signaling 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00475285 0.0 +Hs RPL3P7 Plasma cells NA 0.003 ribosomal protein L3 pseudogene 7 pseudogene 1 Mesoderm Immune system 0.0 0.0 0.0186945 0.0 +Mm Hs SIK1 Plasma cells msk|SNF1LK 0.029 salt inducible kinase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SPAG4 Plasma cells SUN4|CT127 0.005 sperm associated antigen 4 protein-coding gene 1 Mesoderm Immune system 0.305556 0.0 0.01109 0.0 +Mm Hs ST6GALNAC4 Plasma cells ST6GALNACIV|SIAT3C|SIAT7D 0.014 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 protein-coding gene 1 Mesoderm Immune system 0.111111 0.0 0.0190114 0.0 +Mm Hs TGM5 Plasma cells TGX|TGMX 0.001 transglutaminase 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TMEM156 Plasma cells FLJ23235 0.001 transmembrane protein 156 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.00316857 0.0 +Hs UGT2B17 Plasma cells NA 0.0 UDP glucuronosyltransferase family 2 member B17 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs ZBP1 Plasma cells dJ718J7.3|DLM1|DLM-1|DAI|C20orf183 0.015 Z-DNA binding protein 1 protein-coding gene 1 Mesoderm Immune system 0.166667 0.0 0.00538657 0.0 +Hs ZNF165 Plasma cells ZSCAN7|CT53 0.003 zinc finger protein 165 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0171103 0.0 +Mm Hs IGLC2 Plasma cells NA 0.022 immunoglobulin lambda constant 2 other 1 Mesoderm Immune system 0.833333 1.0 0.0361217 0.0146304 +Mm Hs IGHG1 Plasma cells NA 0.006 immunoglobulin heavy constant gamma 1 (G1m marker) other 1 Mesoderm Immune system 0.638889 0.0 0.01109 0.00147587 +Hs IGHG2 Plasma cells NA 0.002 immunoglobulin heavy constant gamma 2 (G2m marker) other 1 Mesoderm Immune system 0.583333 0.0 0.00316857 0.0 +Mm Hs IGHG3 Plasma cells NA 0.005 immunoglobulin heavy constant gamma 3 (G3m marker) other 1 Mesoderm Immune system 0.611111 1.0 0.00823828 0.00205339 +Hs IGHGP Plasma cells IGHGP1 0.003 immunoglobulin heavy constant gamma P (non-functional) other 1 Mesoderm Immune system 0.555556 0.0 0.00887199 0.0 +Mm Hs IGLC3 Plasma cells NA 0.02 immunoglobulin lambda constant 3 (Kern-Oz+ marker) other 1 Mesoderm Immune system 0.722222 1.0 0.0186945 0.0169405 +Mm Hs JCHAIN Plasma cells IGCJ|JCH|IGJ 0.017 joining chain of multimeric IgA and IgM protein-coding gene 1 Mesoderm Immune system 0.833333 1.0 0.0405577 0.00802105 +Hs IGHA1 Plasma cells NA 0.013 immunoglobulin heavy constant alpha 1 other 1 Mesoderm Immune system 0.861111 0.0 0.0605196 0.0 +Hs IGHG4 Plasma cells NA 0.002 immunoglobulin heavy constant gamma 4 (G4m marker) other 1 Mesoderm Immune system 0.555556 0.0 0.00602028 0.0 +Hs IGHA2 Plasma cells NA 0.003 immunoglobulin heavy constant alpha 2 (A2m marker) other 1 Mesoderm Immune system 0.611111 0.0 0.00602028 0.0 +Hs IGLV3-1 Plasma cells NA 0.0 immunoglobulin lambda variable 3-1 other 1 Mesoderm Immune system 0.222222 0.0 0.000316857 0.0 +Hs IGLC7 Plasma cells NA 0.0 immunoglobulin lambda constant 7 other 1 Mesoderm Immune system 0.138889 0.0 0.0 0.0 +Mm Hs SSR4 Plasma cells TRAPD 0.51 signal sequence receptor subunit 4 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.657161 0.0 +Mm Hs IL16 Plasma cells LCF|IL-16|prIL-16|HsT19289|FLJ42735|FLJ16806 0.014 interleukin 16 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0095057 0.0152721 +Mm Hs BHLHA15 Plasma cells MIST1|bHLHa15|BHLHB8 0.0 basic helix-loop-helix family member a15 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000513347 +Mm Hs PPIB Plasma cells CYPB|OI9|B|CYP-S1|SCYLP 0.016 peptidylprolyl isomerase B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00697085 0.0180955 +Mm Hs CD4 Plasmacytoid dendritic cells NA 0.009 CD4 molecule protein-coding gene 1 Mesoderm Immune system 0.272727 0.7 0.0170347 0.00668166 +Mm Hs CD8A Plasmacytoid dendritic cells CD8 0.01 CD8a molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0160883 0.00860906 +Mm Hs CD40 Plasmacytoid dendritic cells Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0132492 0.0108577 +Mm Hs CD80 Plasmacytoid dendritic cells B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00019274 +Mm Hs CD83 Plasmacytoid dendritic cells HB15|BL11 0.045 CD83 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0388013 0.0476068 +Hs LILRA4 Plasmacytoid dendritic cells ILT7|CD85g 0.001 leukocyte immunoglobulin like receptor A4 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.00189274 0.0 +Mm Hs CD86 Plasmacytoid dendritic cells B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0123028 0.0292323 +Mm Hs IL3RA Plasmacytoid dendritic cells CD123 0.008 interleukin 3 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00790234 +Mm Hs CCR7 Plasmacytoid dendritic cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0422713 0.0114359 +Hs CLEC4C Plasmacytoid dendritic cells HECL|DLEC|BDCA2|CD303|CLECSF11|CLECSF7 0.001 C-type lectin domain family 4 member C protein-coding gene 1 Mesoderm Immune system 0.409091 0.0 0.000315457 0.0 +Mm Hs CXCR3 Plasmacytoid dendritic cells CKR-L2|CMKAR3|IP10-R|MigR|CD183|GPR9 0.005 C-X-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0454545 0.0 0.00504732 0.00475426 +Mm Hs TRADD Plasmacytoid dendritic cells Hs.89862 0.015 TNFRSF1A associated via death domain protein-coding gene NA Mesoderm Immune system 0.0454545 0.0 0.0268139 0.0 +Mm Hs ARHGAP9 Plasmacytoid dendritic cells MGC1295|10C 0.023 Rho GTPase activating protein 9 protein-coding gene NA Mesoderm Immune system 0.136364 0.0 0.0236593 0.0222936 +Mm Hs LAMP5 Plasmacytoid dendritic cells dJ1119D9.3|BAD-LAMP|UNC-46|C20orf103 0.005 lysosomal associated membrane protein family member 5 protein-coding gene 1 Mesoderm Immune system 0.0909091 0.0 0.0022082 0.00584645 +Mm Hs GPR183 Plasmacytoid dendritic cells EBI2 0.019 G protein-coupled receptor 183 protein-coding gene 1 Mesoderm Immune system 0.772727 0.0 0.0438486 0.0125924 +Mm Hs MAP3K2 Plasmacytoid dendritic cells MEKK2B|MEKK2 0.009 mitogen-activated protein kinase kinase kinase 2 protein-coding gene NA Mesoderm Immune system 0.227273 0.0 0.0205047 0.00603919 +Mm Hs TNFSF13B Plasmacytoid dendritic cells BAFF|THANK|BLYS|TALL-1|TALL1|CD257|TNFSF20 0.011 TNF superfamily member 13b protein-coding gene NA Mesoderm Immune system 0.0454545 0.0 0.0485804 0.0 +Mm Hs PTCRA Plasmacytoid dendritic cells PTA|PT-ALPHA 0.004 pre T cell antigen receptor alpha protein-coding gene 1 Mesoderm Immune system 0.818182 0.0 0.000630915 0.00327658 +Mm Hs ERN1 Plasmacytoid dendritic cells IRE1|IRE1P 0.002 endoplasmic reticulum to nucleus signaling 1 protein-coding gene 1 Mesoderm Immune system 0.0909091 0.0 0.00536278 0.00122069 +Mm Hs ETV6 Plasmacytoid dendritic cells TEL 0.015 ETS variant 6 protein-coding gene 1 Mesoderm Immune system 0.181818 0.0 0.048265 0.0078381 +Mm Hs MAP3K8 Plasmacytoid dendritic cells Tpl-2|c-COT|MEKK8|ESTF 0.014 mitogen-activated protein kinase kinase kinase 8 protein-coding gene 1 Mesoderm Immune system 0.318182 0.15 0.0454259 0.00745262 +Mm Hs FAM129C Plasmacytoid dendritic cells FLJ39802|BCNP1 0.003 family with sequence similarity 129 member C protein-coding gene 1 Mesoderm Immune system 0.636364 0.0 0.00347003 0.00231288 +Mm Hs SPIB Plasmacytoid dendritic cells SPI-B 0.01 Spi-B transcription factor protein-coding gene 1 Mesoderm Immune system 0.5 0.0 0.00536278 0.0 +Mm Hs GZMB Plasmacytoid dendritic cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0539432 0.00835207 +Mm Hs CXCR4 Plasmacytoid dendritic cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.727273 0.05 0.194637 0.00873755 +Mm Hs PACSIN1 Plasmacytoid dendritic cells SDPI 0.04 protein kinase C and casein kinase substrate in neurons 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.0487632 +Mm Hs TLR7 Plasmacytoid dendritic cells NA 0.001 toll like receptor 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs TLR9 Plasmacytoid dendritic cells CD289 0.0 toll like receptor 9 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs IRF7 Plasmacytoid dendritic cells NA 0.033 interferon regulatory factor 7 protein-coding gene 1 Mesoderm Immune system 1.0 1.0 0.0217666 0.0310312 +Mm Hs IRF8 Plasmacytoid dendritic cells IRF-8|ICSBP|ICSBP1 0.069 interferon regulatory factor 8 protein-coding gene 1 Mesoderm Immune system 1.0 1.0 0.0205047 0.0738195 +Mm Hs IGLL1 Plasmacytoid dendritic cells IGVPB|IGL5|14.1|CD179B|IGLL 0.007 immunoglobulin lambda like polypeptide 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0356467 0.00212014 +Mm Hs CUX2 Plasmacytoid dendritic cells KIAA0293|CDP2|CUTL2 0.024 cut like homeobox 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0302602 +Mm ZFP521 Plasmacytoid dendritic cells NA 0.001 zinc finger protein 521 protein coding gene 1 Mesoderm Immune system NA NA NA NA +Mm Hs MCTP2 Plasmacytoid dendritic cells FLJ11175|FLJ33303 0.001 multiple C2 and transmembrane domain containing 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.05 0.000315457 0.000642467 +Mm Hs KLK1 Plasmacytoid dendritic cells Klk6 0.013 kallikrein 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00820189 0.0129136 +Mm CMAH Plasmacytoid dendritic cells NA 0.003 cytidine monophospho-N-acetylneuraminic acid hydroxylase protein coding gene 1 Mesoderm Immune system 0.0 0.3 0.0 0.0038548 +Mm Hs BLNK Plasmacytoid dendritic cells SLP65|Ly57|SLP-65|BLNK-s|BASH|bca 0.017 B cell linker protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.000630915 0.0184388 +Mm Hs GRM8 Plasmacytoid dendritic cells GLUR8|GPRC1H|mGlu8|MGLUR8 0.002 glutamate metabotropic receptor 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.05 0.00410095 0.00122069 +Mm Hs PRKCA Plasmacytoid dendritic cells PKCA 0.033 protein kinase C alpha protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0154574 0.0356569 +Mm Hs CDH1 Plasmacytoid dendritic cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0419558 0.0573081 +Mm KLRA17 Plasmacytoid dendritic cells NA 0.002 killer cell lectin-like receptor, subfamily A, member 17 protein coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.00141343 +Mm Hs IL17RB Plasmacytoid dendritic cells IL17RH1|EVI27|CRL4|IL17BR 0.001 interleukin 17 receptor B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000315457 0.00115644 +Mm Hs CARD6 Plasmacytoid dendritic cells CINCIN1 0.0 caspase recruitment domain family member 6 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000315457 0.000321234 +Mm Hs CLEC4G Plasmacytoid dendritic cells UNQ431|LSECtin 0.001 C-type lectin domain family 4 member G protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000315457 0.000899454 +Mm Hs S100A8 Plasmacytoid dendritic cells P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene 1 Mesoderm Immune system 0.272727 0.0 0.0785489 0.0 +Mm Hs JCHAIN Plasmacytoid dendritic cells IGCJ|JCH|IGJ 0.017 joining chain of multimeric IgA and IgM protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0429022 0.00809508 +Mm Hs SERPINF1 Plasmacytoid dendritic cells EPC-1|PIG35|PEDF 0.057 serpin family F member 1 protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0996845 0.0 +Mm Hs ITM2C Plasmacytoid dendritic cells BRI3|E25|hRPC.1050_D_4|ITM3|BRICD2C 0.354 integral membrane protein 2C protein-coding gene 1 Mesoderm Immune system 1.0 1.0 0.22429 0.381497 +Mm Hs TCF4 Plasmacytoid dendritic cells SEF2-1B|ITF2|bHLHb19|E2-2 0.394 transcription factor 4 protein-coding gene 1 Mesoderm Immune system 0.909091 0.0 0.164353 0.0 +Mm Hs BCL11A Plasmacytoid dendritic cells BCL11A-XL|BCL11A-L|BCL11A-S|CTIP1|HBFQTL5|ZNF856|EVI9 0.134 B cell CLL/lymphoma 11A protein-coding gene 1 Mesoderm Immune system 0.909091 1.0 0.107886 0.141535 +Mm Hs MZB1 Plasmacytoid dendritic cells MGC29506|HSPC190|pERp1|MEDA-7 0.025 marginal zone B and B1 cell specific protein protein-coding gene 1 Mesoderm Immune system 0.954545 0.4 0.0318612 0.0204305 +Mm Hs DERL3 Plasmacytoid dendritic cells FLJ43842|MGC71803|derlin-3|IZP6|C22orf14 0.01 derlin 3 protein-coding gene 1 Mesoderm Immune system 0.772727 0.0 0.0287066 0.00443302 +Mm Hs ZFAT Plasmacytoid dendritic cells KIAA1485|ZNF406|ZFAT1 0.001 zinc finger and AT-hook domain containing protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000630915 0.0 +Mm Hs NRP1 Plasmacytoid dendritic cells VEGF165R|CD304 0.099 neuropilin 1 protein-coding gene 1 Mesoderm Immune system 0.5 0.05 0.0621451 0.107356 +Mm Hs SLC15A4 Plasmacytoid dendritic cells PHT1|PTR4 0.006 solute carrier family 15 member 4 protein-coding gene 1 Mesoderm Immune system 0.454545 0.0 0.0164038 0.0 +Mm Hs CCR9 Plasmacytoid dendritic cells GPR-9-6|CDw199|GPR28 0.005 C-C motif chemokine receptor 9 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0 0.00443302 +Mm Hs IRF5 Plasmacytoid dendritic cells NA 0.028 interferon regulatory factor 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.8 0.000315457 0.0332798 +Mm Hs BST2 Plasmacytoid dendritic cells CD317|tetherin 0.177 bone marrow stromal cell antigen 2 protein-coding gene 1 Mesoderm Immune system 0.454545 1.0 0.202839 0.166078 +Mm Hs CCL5 Platelets RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Blood 1.0 0.0 0.0846926 0.0327301 +Mm Hs VEGFA Platelets VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0247804 0.0 +Mm Hs PECAM1 Platelets CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0442284 0.0534591 +Hs FCGR2A Platelets CD32A|IGFR2|CDw32|FCGR2A1 0.002 Fc fragment of IgG receptor IIa protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00972397 0.0 +Mm Hs CD36 Platelets SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0345044 0.0441535 +Mm Hs ITGA2B Platelets CD41B|CD41|PPP1R93|GP2B 0.003 integrin subunit alpha 2b protein-coding gene 1 Mesoderm Blood 0.5 1.0 0.00345044 0.00295212 +Mm Hs GP1BA Platelets CD42b|GPIbalpha|GP1B 0.0 glycoprotein Ib platelet subunit alpha protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.000313676 0.0 +Mm Hs SPN Platelets LSN|CD43|GPL115 0.029 sialophorin protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0508156 0.0 +Mm Hs CD46 Platelets TRA2.10|MGC26544|MIC10 0.014 CD46 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0787328 0.000898473 +Mm Hs ITGA2 Platelets CD49b|CD49B 0.01 integrin subunit alpha 2 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0451694 0.0030163 +Mm Hs ITGB3 Platelets CD61|GPIIIa|GP3A 0.001 integrin subunit beta 3 protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.0 0.00102683 +Mm Hs SELP Platelets CD62|PSEL|PADGEM|GMP140|CD62P|GRMP 0.003 selectin P protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00125471 0.0 +Mm Hs CD69 Platelets CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.111355 0.00738031 +Mm Hs CD84 Platelets SLAMF5|hCD84|mCD84 0.023 CD84 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.00941029 0.0271467 +Mm Hs CD109 Platelets FLJ38569|DKFZp762L1111|CPAMD7 0.006 CD109 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00219573 0.00635348 +Mm Hs CCR3 Platelets CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.00147606 +Mm Hs CD226 Platelets DNAM-1|DNAM1|PTA1|TLiSA1 0.001 CD226 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.000627353 0.000641766 +Mm Hs TNFSF14 Platelets LIGHT|LTg|HVEM-L|CD258 0.001 TNF superfamily member 14 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00313676 0.0 +Mm Hs LRRC32 Platelets D11S833E 0.007 leucine rich repeat containing 32 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.011606 0.0068669 +Mm Hs LTBR Platelets TNFCR|TNFR-RP|TNFR2-RP|TNF-R-III|TNFRSF3|D12S370 0.024 lymphotoxin beta receptor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0181932 0.0250931 +Mm Hs PF4 Platelets SCYB4|CXCL4 0.029 platelet factor 4 protein-coding gene 1 Mesoderm Blood 1.0 1.0 0.00219573 0.0349763 +Mm Hs GP5 Platelets CD42d 0.001 glycoprotein V platelet protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.0 0.001091 +Mm Hs F13A1 Platelets F13A 0.021 coagulation factor XIII A chain protein-coding gene 1 Mesoderm Blood 0.5 0.666667 0.00376412 0.0231036 +Mm Hs THBS1 Platelets TSP1|THBS|TSP|THBS-1|TSP-1 0.04 thrombospondin 1 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0517566 0.0 +Mm Hs ABCC4 Platelets MRP4|EST170205|MOAT-B|MOATB 0.004 ATP binding cassette subfamily C member 4 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00156838 0.00455654 +Mm Hs BIN2 Platelets BRAP-1 0.06 bridging integrator 2 protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.0461104 0.0620588 +Mm Hs FERMT3 Platelets URP2|KIND3|MIG2B|MGC10966|MIG-2|UNC112C 0.045 fermitin family member 3 protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.020389 0.0480683 +Mm Hs PTCRA Platelets PTA|PT-ALPHA 0.004 pre T cell antigen receptor alpha protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.00595985 0.00327301 +Mm Hs TUBB1 Platelets dJ543J19.4 0.0 tubulin beta 1 class VI protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.000627353 0.0 +Mm Hs GP9 Platelets CD42a|GPIX 0.001 glycoprotein IX platelet protein-coding gene 1 Mesoderm Blood 0.5 1.0 0.0 0.000770119 +Mm Hs NCOA4 Platelets ARA70|RFG|ELE1|PTC3|DKFZp762E1112 0.02 nuclear receptor coactivator 4 protein-coding gene 1 Mesoderm Blood 1.0 0.0 0.0934755 0.00346554 +Mm Hs RGS18 Platelets RGS13 0.019 regulator of G protein signaling 18 protein-coding gene 1 Mesoderm Blood 0.75 0.0 0.00250941 0.0 +Mm Hs PPBP Platelets SCYB7|TGB|NAP-2-L1|LA-PF4|MDGF|LDGF|Beta-TG|CTAP3|CXCL7|b-TG1|TGB1|CTAPIII|NAP-2|THBGB1 0.001 pro-platelet basic protein protein-coding gene 1 Mesoderm Blood 1.0 1.0 0.00219573 0.000641766 +Mm Hs DAB2 Platelets DOC-2 0.068 DAB2, clathrin adaptor protein protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0476788 0.0738673 +Mm Hs HFE Platelets HLA-H 0.017 homeostatic iron regulator protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000313676 0.0213708 +Mm Hs CXCR4 Platelets LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.198243 0.0087922 +Mm Hs CLEC1B Platelets CLEC2 0.003 C-type lectin domain family 1 member B protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.000627353 0.00308048 +Mm Hs MPL Platelets CD110|TPOR 0.001 MPL proto-oncogene, thrombopoietin receptor protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0 0.00102683 +Mm Hs F5 Platelets NA 0.003 coagulation factor V protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.00250941 0.00269542 +Mm Hs TREML1 Platelets TLT1|dJ238O23.3 0.0 triggering receptor expressed on myeloid cells like 1 protein-coding gene 1 Mesoderm Blood 0.5 0.0 0.0 0.0 +Mm Hs P2RY12 Platelets P2Y12|SP1999|HORK3 0.025 purinergic receptor P2Y12 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0 0.0317674 +Mm Hs PRKAR2B Platelets NA 0.028 protein kinase cAMP-dependent type II regulatory subunit beta protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0138018 0.03196 +Mm Hs STX11 Platelets NA 0.009 syntaxin 11 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0141154 0.0 +Mm Hs MFSD2B Platelets NA 0.003 major facilitator superfamily domain containing 2B protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.000313676 0.00308048 +Mm Hs ALOX12 Platelets 12S-LOX 0.001 arachidonate 12-lipoxygenase, 12S type protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0 0.000770119 +Mm Hs PLEK Platelets NA 0.051 pleckstrin protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.0448557 0.052689 +Mm Hs SELPLG Platelets PSGL-1|CD162 0.09 selectin P ligand protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00784191 0.0 +Mm Hs ADGRE5 Platelets TM7LN1|CD97 0.04 adhesion G protein-coupled receptor E5 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0388959 0.0408163 +Mm Hs CD40 Platelets Bp50|TNFRSF5 0.012 CD40 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0131744 0.0108458 +Hs ERO1A Platelets ERO1-alpha|Ero1alpha|ERO1L 0.009 endoplasmic reticulum oxidoreductase 1 alpha protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0367001 0.0 +Mm Hs CD9 Platelets BA2|P24|TSPAN29|MRP-1|MIC3 0.344 CD9 molecule protein-coding gene 1 Mesoderm Blood 0.5 1.0 0.270703 0.366063 +Mm Hs F11R Platelets PAM-1|JCAM|JAM-1|JAM-A|JAMA|CD321|JAM1 0.071 F11 receptor protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0266625 0.0824028 +Mm Hs TLR4 Platelets hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000313676 0.0 +Mm Hs CRLF2 Platelets CRL2|TSLPR 0.044 cytokine receptor like factor 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0528815 +Mm Hs IL1A Platelets IL1F1|IL-1A|IL1-ALPHA|IL1 0.006 interleukin 1 alpha protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00564617 0.00648184 +Mm Hs SCARB1 Platelets SRB1|CLA-1|SR-BI|CD36L1 0.027 scavenger receptor class B member 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00627353 0.0 +Mm Hs ADAM10 Platelets kuz|HsT18717|CD156c 0.064 ADAM metallopeptidase domain 10 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0279172 0.0729688 +Mm Hs CCR1 Platelets MIP1aR|CD191|SCYAR1|CMKBR1 0.014 C-C motif chemokine receptor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0053325 0.0140547 +Mm Hs CCR4 Platelets CC-CKR-4|CMKBR4|CKR4|k5-5|ChemR13|CD194 0.0 C-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000627353 0.0 +Mm Hs F2R Platelets CF2R 0.036 coagulation factor II thrombin receptor protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.033877 0.0379926 +Mm Hs NRGN Platelets NA 0.031 neurogranin protein-coding gene 1 Mesoderm Blood 0.75 1.0 0.0100376 0.0343345 +Mm Hs OST4 Platelets NA 0.172 oligosaccharyltransferase complex subunit 4, non-catalytic protein-coding gene 1 Mesoderm Blood 0.75 0.666667 0.607591 0.0689899 +Mm Hs SPARC Platelets ON 0.307 secreted protein acidic and cysteine rich protein-coding gene 1 Mesoderm Blood 0.75 0.0 0.230238 0.0 +Mm Hs GP1BB Platelets CD42c|GPIbbeta 0.002 glycoprotein Ib platelet subunit beta protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0 0.00282377 +Mm Hs GPX1 Platelets NA 0.477 glutathione peroxidase 1 protein-coding gene 1 Mesoderm Blood 1.0 1.0 0.491844 0.4708 +Hs CAVIN2 Platelets SDR|PS-p68|cavin-2|SDPR 0.006 caveolae associated protein 2 protein-coding gene 1 Mesoderm Blood 1.0 0.0 0.0363864 0.0 +Mm Hs PPDPF Platelets dJ697K14.9|exdpf|C20orf149 0.466 pancreatic progenitor cell differentiation and proliferation factor protein-coding gene 1 Mesoderm Blood 0.75 0.333333 0.692597 0.417276 +Mm Hs MYL9 Platelets MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Blood 0.5 1.0 0.159975 0.063214 +Mm Hs MAP3K7CL Platelets TAKL|TAK1L|TAKL-1|TAKL-2|TAKL-4|C21orf7 0.006 MAP3K7 C-terminal like protein-coding gene 1 Mesoderm Blood 0.75 0.0 0.0065872 0.00526248 +Mm Hs PTGS1 Platelets PGHS-1|PTGHS 0.029 prostaglandin-endoperoxide synthase 1 protein-coding gene 1 Mesoderm Blood 0.25 0.666667 0.00345044 0.0358747 +Mm Hs GNG11 Platelets GNGT11 0.138 G protein subunit gamma 11 protein-coding gene 1 Mesoderm Blood 1.0 1.0 0.115433 0.145167 +Mm Hs GRAP2 Platelets Grf40|GrbX|GRBLG|GADS|Mona 0.005 GRB2 related adaptor protein 2 protein-coding gene 1 Mesoderm Blood 0.5 0.333333 0.00282309 0.00564754 +Mm Hs CTSA Platelets GSL|PPGB 0.104 cathepsin A protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0238394 0.121679 +Hs MPIG6B Platelets G6b|NG31|G6b-B|C6orf25 0.0 megakaryocyte and platelet inhibitory receptor G6b protein-coding gene 1 Mesoderm Blood 0.5 0.0 0.0 0.0 +Mm Hs HIST1H3H Platelets H3/k|H3F1K|H3FK 0.0 histone cluster 1 H3 family member h protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0 0.0 +Mm Hs WIPF1 Platelets WIP|WASPIP 0.02 WAS/WASL interacting protein family member 1 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0457967 0.0 +Hs C2ORF88 Platelets MGC13057|smAKAP 0.006 chromosome 2 open reading frame 88 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.031054 0.0 +Mm Hs ARHGDIB Platelets Ly-GDI|RhoGDI2|RAP1GN1|GDIA2|GDID4 0.201 Rho GDP dissociation inhibitor beta protein-coding gene 1 Mesoderm Blood 1.0 1.0 0.35665 0.167822 +Mm Hs CDKN2D Platelets INK4D 0.086 cyclin dependent kinase inhibitor 2D protein-coding gene 1 Mesoderm Blood 0.5 0.333333 0.0495609 0.0954948 +Hs CA2 Platelets Car2|CA-II|CAII 0.011 carbonic anhydrase 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.064931 0.0 +Hs HLA-A Platelets NA 0.126 major histocompatibility complex, class I, A protein-coding gene 1 Mesoderm Blood 1.0 0.0 0.693538 0.0 +Mm Hs PDLIM1 Platelets CLP-36|hCLIM1|CLP36 0.109 PDZ and LIM domain 1 protein-coding gene 1 Mesoderm Blood 0.5 1.0 0.196989 0.0865742 +Mm Hs PDZK1IP1 Platelets DD96|MAP17|SPAP 0.025 PDZK1 interacting protein 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0432873 0.0232319 +Mm Hs AGPAT1 Platelets LPAAT-alpha 0.005 1-acylglycerol-3-phosphate O-acyltransferase 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0060326 +Mm Hs SMOX Platelets FLJ20746|dJ779E11.1|PAOh1|MGC1010|SMO|C20orf16 0.025 spermine oxidase protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.00752823 0.0 +Mm Hs SRGN Platelets PPG 0.236 serglycin protein-coding gene 1 Mesoderm Blood 1.0 0.0 0.329674 0.0 +Mm Hs HIST1H2BK Platelets H2BFAiii|H2BFT 0.0 histone cluster 1 H2B family member k protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000313676 0.00019253 +Mm Hs SH3BGRL2 Platelets NA 0.008 SH3 domain binding glutamate rich protein like 2 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.00595985 0.0 +Mm Hs ATP2A3 Platelets SERCA3 0.01 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.0109787 0.0100116 +Mm Hs ALDH2 Platelets NA 0.185 aldehyde dehydrogenase 2 family member protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0937892 0.206199 +Mm LYZ2 Platelets NA 0.124 lysozyme 2 protein coding gene 1 Mesoderm Blood 0.0 1.0 0.0 0.148505 +Mm Hs ALOX5AP Platelets FLAP 0.09 arachidonate 5-lipoxygenase activating protein protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.0690088 0.0931203 +Mm Hs RAP1B Platelets RAL1B|DKFZp586H0723 0.33 RAP1B, member of RAS oncogene family protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.129548 0.0 +Mm Hs FHL1 Platelets SLIM1|KYO-T|bA535K18.1|FHL1B|XMPMA|FLH1A|MGC111107 0.063 four and a half LIM domains 1 protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.0884567 0.0573097 +Mm Hs VWF Platelets F8VWF 0.016 von Willebrand factor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0266625 0.0 +Mm Hs LAPTM5 Platelets NA 0.199 lysosomal protein transmembrane 5 protein-coding gene 1 Mesoderm Blood 0.25 1.0 0.275408 0.18316 +Mm Hs RASGRP2 Platelets CALDAG-GEFI 0.066 RAS guanyl releasing protein 2 protein-coding gene 1 Mesoderm Blood 0.25 0.0 0.0235257 0.0 +Mm Hs HIST1H2BC Platelets H2B/l|H2BFL 0.192 histone cluster 1 H2B family member c protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.0131744 0.237068 +Mm Hs SLC2A3 Platelets GLUT3 0.04 solute carrier family 2 member 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0759097 0.0 +Mm Hs ARHGAP10 Platelets FLJ20896|FLJ41791|GRAF2 0.008 Rho GTPase activating protein 10 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0147428 0.0060326 +Hs RTL8B Platelets MAR8B|CXX1c|SIRH4|FAM127C 0.001 retrotransposon Gag like 8B protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00564617 0.0 +Mm Hs TREML2 Platelets FLJ13693|TLT2|dJ238O23.1|C6orf76 0.002 triggering receptor expressed on myeloid cells like 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs MMRN1 Platelets ECM|EMILIN4|GPIa*|MMRN 0.005 multimerin 1 protein-coding gene 1 Mesoderm Blood 0.0 0.666667 0.00909661 0.00378642 +Mm Hs ILK Platelets NA 0.026 integrin linked kinase protein-coding gene 1 Mesoderm Blood 0.25 0.333333 0.0906524 0.00744449 +Mm Hs NOD2 Platelets BLAU|PSORAS1|CLR16.3|NLRC2|IBD1|CARD15 0.0 nucleotide binding oligomerization domain containing 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.000128353 +Hs NOX5 Platelets NOX5A|NOX5B 0.0 NADPH oxidase 5 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000313676 0.0 +Mm Hs SERPINE1 Platelets PAI|PLANH1|PAI1 0.014 serpin family E member 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0388959 0.0 +Mm Hs MAPK14 Platelets PRKM14|Mxi2|PRKM15|CSPB1|CSBP1|CSBP2 0.024 mitogen-activated protein kinase 14 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00909661 0.0259274 +Mm Hs ABCA3 Platelets ABC-C|EST111653|LBM180|ABC3 0.001 ATP binding cassette subfamily A member 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00376412 0.00057759 +Mm Hs CXCL14 Platelets BRAK|NJAC|bolekine|Kec|MIP-2g|BMAC|SCYB14 0.049 C-X-C motif chemokine ligand 14 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.04266 0.048325 +Mm Hs ESAM Platelets W117m 0.064 endothelial cell adhesion molecule protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.0429737 0.0706585 +Mm Hs PREX1 Platelets KIAA1415|P-REX1 0.01 phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00250941 0.0106533 +Mm Hs S100A9 Platelets MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.103513 0.0 +Mm Hs ATP8A1 Platelets ATPIA 0.049 ATPase phospholipid transporting 8A1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0053325 0.0603902 +Mm Hs PRKCD Platelets NA 0.042 protein kinase C delta protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00784191 0.0484533 +Mm Hs PTGS2 Platelets NA 0.009 prostaglandin-endoperoxide synthase 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0138018 0.00840714 +Mm Hs F7 Platelets NA 0.003 coagulation factor VII protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000313676 0.00327301 +Mm Hs SLC26A4 Platelets PDS|DFNB4 0.001 solute carrier family 26 member 4 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.000941029 0.0 +Mm Hs PALLD Platelets KIAA0992|SIH002|CGI-151 0.053 palladin, cytoskeletal associated protein protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.102258 0.0424849 +Mm Hs SLC17A9 Platelets FLJ23412|VNUT|C20orf59 0.001 solute carrier family 17 member 9 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs IL33 Platelets DVS27|DKFZp586H0523|NF-HEV|IL1F11|C9orf26 0.018 interleukin 33 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.010665 0.0206007 +Mm Hs SIRT3 Platelets SIR2L3 0.002 sirtuin 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00627353 0.0 +Mm Hs CYP2U1 Platelets SPG49 0.001 cytochrome P450 family 2 subfamily U member 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.00147606 +Mm Hs TLR1 Platelets rsc786|KIAA0012|CD281 0.0 toll like receptor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs TLR6 Platelets CD286 0.0 toll like receptor 6 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs BGLAP Platelets OCN 0.005 bone gamma-carboxyglutamate protein protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.00641766 +Mm Hs LGALS8 Platelets PCTA-1 0.015 galectin 8 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0254078 0.013798 +Mm Hs ITGB2 Platelets CD18|MFI7 0.07 integrin subunit beta 2 protein-coding gene 1 Mesoderm Blood 0.0 1.0 0.111355 0.060326 +Mm Hs CD40LG Platelets CD40L|gp39|hCD40L|CD154|HIGM1|IMD3|TNFSF5 0.003 CD40 ligand protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0100376 0.00121936 +Mm Hs ANGPT1 Platelets KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene 1 Mesoderm Blood 0.0 0.333333 0.00188206 0.0123219 +Mm Hs ACKR3 Platelets GPR159|CMKOR1|CXCR7 0.01 atypical chemokine receptor 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0065872 0.0114234 +Mm Hs PRMT8 Pluripotent stem cells HRMT1L4 0.005 protein arginine methyltransferase 8 protein-coding gene 1 NA NA 0.0 0.0 0.00156642 0.00564646 +Mm Hs NCOA5 Pluripotent stem cells bA465L10.6 0.003 nuclear receptor coactivator 5 protein-coding gene 1 NA NA 0.0 0.0 0.00156642 0.00340071 +Mm Hs TRIM32 Pluripotent stem cells HT2A|TATIP|BBS11|LGMD2H 0.035 tripartite motif containing 32 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs PRDM14 Pluripotent stem cells NA 0.0 PR/SET domain 14 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.000128329 +Mm Hs FGF4 Pluripotent stem cells K-FGF|HBGF-4|HST|HST-1|KFGF 0.002 fibroblast growth factor 4 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00263073 +Mm Hs NANOG Pluripotent stem cells FLJ12581|FLJ40451 0.002 Nanog homeobox protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00218158 +Mm Hs POU5F1 Pluripotent stem cells Oct4|MGC22487|OTF3 0.003 POU class 5 homeobox 1 protein-coding gene 1 NA NA 0.0 0.0 0.000626566 0.00256657 +Mm Hs MSH2 Pluripotent stem cells HNPCC1|COCA1 0.019 mutS homolog 2 protein-coding gene NA NA NA 0.0 0.0 0.0153509 0.0190568 +Mm ZFP819 Pluripotent stem cells NA 0.0 zinc finger protein 819 protein coding gene 1 NA NA NA NA NA NA +Mm Hs GATA2 Pluripotent stem cells NFE1B 0.02 GATA binding protein 2 protein-coding gene NA NA NA 0.0 0.0 0.0134712 0.0218158 +Mm Hs ZFX Pluripotent stem cells ZNF926 0.006 zinc finger protein X-linked protein-coding gene 1 NA NA 0.0 0.0 0.0140977 0.0 +Mm Hs TERF1 Pluripotent stem cells PIN2|TRF1|TRBF1 0.034 telomeric repeat binding factor 1 protein-coding gene 1 NA NA 0.0 0.0 0.0811404 0.0 +Hs TEX19 Pluripotent stem cells FLJ35767 0.001 testis expressed 19 protein-coding gene 1 NA NA 0.0 0.0 0.00469925 0.0 +Mm Hs TERT Pluripotent stem cells TRT|TCS1|hEST2|EST2 0.0 telomerase reverse transcriptase protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Hs ZNF296 Pluripotent stem cells ZNF342 0.0 zinc finger protein 296 protein-coding gene 1 NA NA 0.0 0.0 0.000626566 0.0 +Mm Hs NAP1L1 Pluripotent stem cells MGC8688|MGC23410 0.532 nucleosome assembly protein 1 like 1 protein-coding gene 1 NA NA 0.0 0.0 0.71084 0.485916 +Mm Hs SOX2 Pluripotent stem cells NA 0.082 SRY-box 2 protein-coding gene 1 NA NA 0.0 0.0 0.0288221 0.0 +Mm Hs ALPL Pluripotent stem cells TNSALP|TNALP|TNAP|HOPS 0.009 alkaline phosphatase, liver/bone/kidney protein-coding gene 1 NA NA 0.0 0.0 0.00407268 0.0105229 +Mm Hs HK2 Pluripotent stem cells NA 0.024 hexokinase 2 protein-coding gene 1 NA NA 0.0 0.0 0.0137845 0.0275265 +Mm Hs SPN Pluripotent stem cells LSN|CD43|GPL115 0.029 sialophorin protein-coding gene 1 NA NA 0.0 0.0 0.0507519 0.0 +Mm Hs ESRP1 Pluripotent stem cells FLJ20171|RBM35A 0.013 epithelial splicing regulatory protein 1 protein-coding gene 1 NA NA 0.0 0.0 0.0137845 0.0119987 +Mm Hs PODXL Podocytes PCLP|Gp200|PC 0.04 podocalyxin like protein-coding gene 1 Mesoderm Kidney 1.0 0.944444 0.0343849 0.0387358 +Mm Hs ADAMTS13 Podocytes VWFCP|vWF-CP|FLJ42993|MGC118899|MGC118900|DKFZp434C2322|C9orf8 0.0 ADAM metallopeptidase with thrombospondin type 1 motif 13 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 6.42385e-05 +Mm Hs LCN2 Podocytes NGAL|24p3 0.043 lipocalin 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0570978 0.0418192 +Mm Hs VEGFA Podocytes VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Mesoderm Kidney 0.727273 0.0 0.0198738 0.0 +Mm Hs SLC2A4 Podocytes GLUT4 0.001 solute carrier family 2 member 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00252366 0.0 +Mm Hs NLRP3 Podocytes AGTAVPRL|AII|AVP|FCAS|FCU|NALP3|PYPAF1|MWS|CLR1.1|C1orf7|CIAS1 0.004 NLR family pyrin domain containing 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000946372 0.00520331 +Mm Hs SYNPO Podocytes KIAA1029 0.009 synaptopodin protein-coding gene 1 Mesoderm Kidney 0.545455 0.0 0.00567823 0.0 +Mm Hs NPHS1 Podocytes CNF|NPHN 0.002 NPHS1, nephrin protein-coding gene 1 Mesoderm Kidney 0.954545 0.888889 0.000315457 0.0 +Mm Hs NPHS2 Podocytes SRN1|PDCN 0.002 NPHS2, podocin protein-coding gene 1 Mesoderm Kidney 1.0 0.888889 0.000315457 0.000192715 +Mm Hs LAMA3 Podocytes nicein-150kDa|kalinin-165kDa|BM600-150kDa|epiligrin|LAMNA 0.005 laminin subunit alpha 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0113565 0.00379007 +Mm Hs FOXC2 Podocytes MFH-1|FKHL14 0.003 forkhead box C2 protein-coding gene 1 Mesoderm Kidney 0.409091 0.0555556 0.00536278 0.00237682 +Mm Hs WT1 Podocytes WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0157729 0.0 +Mm Hs CD80 Podocytes B7.1|B7-1|CD28LG|CD28LG1 0.0 CD80 molecule protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.000192715 +Mm Hs DES Podocytes CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00946372 0.0233186 +Mm Hs PTPRO Podocytes PTPU2|GLEPP1|PTP-U2|PTP-oc|NPHS6 0.011 protein tyrosine phosphatase, receptor type O protein-coding gene 1 Mesoderm Kidney 1.0 0.5 0.000630915 0.0116272 +Mm Hs LMX1B Podocytes NPS1 0.001 LIM homeobox transcription factor 1 beta protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0 0.0008351 +Mm Hs MYOC Podocytes TIGR|JOAG1|GLC1A 0.003 myocilin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00157729 0.00398278 +Mm Hs CDH13 Podocytes CDHH 0.026 cadherin 13 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0246057 0.0272371 +Mm Hs SEMA3G Podocytes FLJ00014|sem2 0.003 semaphorin 3G protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00189274 0.0 +Mm Hs THSD7A Podocytes KIAA0960 0.016 thrombospondin type 1 domain containing 7A protein-coding gene 1 Mesoderm Kidney 0.909091 0.0 0.0135647 0.0 +Mm Hs MAFB Podocytes KRML 0.053 MAF bZIP transcription factor B protein-coding gene 1 Mesoderm Kidney 1.0 0.833333 0.0526814 0.0519689 +Mm Hs ENPEP Podocytes gp160|CD249 0.011 glutamyl aminopeptidase protein-coding gene NA Mesoderm Kidney 0.681818 0.944444 0.00189274 0.0114344 +Mm Hs CLIC5 Podocytes DFNB102 0.016 chloride intracellular channel 5 protein-coding gene 1 Mesoderm Kidney 1.0 0.944444 0.00662461 0.0159311 +Mm Hs RAB3B Podocytes NA 0.023 RAB3B, member RAS oncogene family protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0192429 0.0 +Mm Hs DPP4 Podocytes CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.888889 0.0132492 0.0202994 +Mm Hs ANGPTL2 Podocytes NA 0.013 angiopoietin like 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.00599369 0.0148391 +Mm Hs ITGB5 Podocytes NA 0.047 integrin subunit beta 5 protein-coding gene 1 Mesoderm Kidney 0.0 0.333333 0.015142 0.0551808 +Mm Hs RHPN1 Podocytes KIAA1929|RHPN|ODF5 0.002 rhophilin Rho GTPase binding protein 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000946372 0.0 +Mm Hs BCAM Podocytes CD239|LU 0.049 basal cell adhesion molecule (Lutheran blood group) protein-coding gene 1 Mesoderm Kidney 0.954545 0.111111 0.0460568 0.0493994 +Mm Hs MAGI2 Podocytes ACVRIP1|MAGI-2 0.006 membrane associated guanylate kinase, WW and PDZ domain containing 2 protein-coding gene 1 Mesoderm Kidney 0.909091 0.0555556 0.015142 0.00321192 +Mm Hs COL4A3 Podocytes NA 0.006 collagen type IV alpha 3 chain protein-coding gene 1 Mesoderm Kidney 0.0454545 0.944444 0.000315457 0.0058457 +Mm Hs EFNB1 Podocytes LERK2|Elk-L|EPLG2|CFNS 0.031 ephrin B1 protein-coding gene 1 Mesoderm Kidney 0.863636 0.222222 0.0154574 0.0348815 +Mm Hs NPR1 Podocytes GUCY2A|ANPa|ANPRA|NPRA 0.009 natriuretic peptide receptor 1 protein-coding gene 1 Mesoderm Kidney 0.181818 0.0 0.000630915 0.0112417 +Mm Hs PLOD2 Podocytes LH2 0.019 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 protein-coding gene 1 Mesoderm Kidney 0.545455 0.277778 0.0347003 0.0132331 +Mm Hs SRGAP1 Podocytes KIAA1304|ARHGAP13 0.025 SLIT-ROBO Rho GTPase activating protein 1 protein-coding gene 1 Mesoderm Kidney 0.954545 0.0 0.0741325 0.0 +Mm Hs LAMB2 Podocytes NPHS5|LAMS 0.019 laminin subunit beta 2 protein-coding gene 1 Mesoderm Kidney 0.0454545 0.0555556 0.0129338 0.021006 +Mm Hs NPR3 Podocytes FLJ14054|NPRC|ANPRC|C5orf23 0.005 natriuretic peptide receptor 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.722222 0.00662461 0.00398278 +Mm Hs ITGA3 Podocytes CD49c|VLA3a|VCA-2|GAP-B3|MSK18 0.012 integrin subunit alpha 3 protein-coding gene 1 Mesoderm Kidney 0.181818 0.111111 0.018612 0.00892914 +Mm Hs PLCE1 Podocytes KIAA1516|NPHS3 0.005 phospholipase C epsilon 1 protein-coding gene 1 Mesoderm Kidney 0.363636 0.111111 0.00599369 0.00443245 +Mm Hs PROS1 Podocytes PROS 0.024 protein S protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.00378549 0.0286504 +Mm Hs MERTK Podocytes mer|RP38|c-Eyk|Tyro12 0.016 MER proto-oncogene, tyrosine kinase protein-coding gene 1 Mesoderm Kidney 0.0 0.722222 0.000946372 0.0190146 +Mm Hs MYO1D Podocytes KIAA0727|myr4|PPP1R108 0.01 myosin ID protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0182965 0.00841524 +Mm Hs TCF21 Podocytes POD1|bHLHa23 0.014 transcription factor 21 protein-coding gene 1 Mesoderm Kidney 0.863636 0.0 0.0 0.0 +Mm Hs TNS2 Podocytes KIAA1075|C1-TEN|TENC1 0.007 tensin 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00315457 0.0 +Mm Hs ADM Podocytes AM 0.026 adrenomedullin protein-coding gene 1 Mesoderm Kidney 0.272727 0.444444 0.0621451 0.0172159 +Mm Hs OPTN Podocytes FIP2|HYPL|FIP-2|TFIIIA-INTP|HIP7|GLC1E 0.025 optineurin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0943218 0.00957153 +Mm Hs PARD3B Podocytes Par3L|PAR3beta|ALS2CR19 0.002 par-3 family cell polarity regulator beta protein-coding gene 1 Mesoderm Kidney 0.318182 0.5 0.00283912 0.00109205 +Mm Hs SEMA3E Podocytes M-SemaK|KIAA0331|coll-5|SEMAH 0.005 semaphorin 3E protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs MYO1E Podocytes MYO1C|HuncM-IC|MGC104638 0.015 myosin IE protein-coding gene 1 Mesoderm Kidney 0.0 0.111111 0.0107256 0.0163808 +Mm Hs NEBL Podocytes LASP2|LNEBL 0.035 nebulette protein-coding gene 1 Mesoderm Kidney 0.409091 0.111111 0.0129338 0.0396351 +Mm Hs SH2D4A Podocytes FLJ20967|SH2A|PPP1R38 0.007 SH2 domain containing 4A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00946372 0.0 +Mm Hs TDRD5 Podocytes FLJ34823|TUDOR3 0.002 tudor domain containing 5 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0022082 0.0 +Mm Hs PTH1R Podocytes PTHR1 0.019 parathyroid hormone 1 receptor protein-coding gene 1 Mesoderm Kidney 0.681818 0.833333 0.000315457 0.0224835 +Mm Hs IQGAP2 Podocytes NA 0.037 IQ motif containing GTPase activating protein 2 protein-coding gene 1 Mesoderm Kidney 0.409091 0.444444 0.0567823 0.0324404 +Mm Hs CTGF Podocytes IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Mesoderm Kidney 0.863636 0.277778 0.0943218 0.0121411 +Mm Hs FAT1 Podocytes CDHF7|CDHR8 0.028 FAT atypical cadherin 1 protein-coding gene 1 Mesoderm Kidney 0.227273 0.111111 0.0246057 0.0291 +Mm Hs ILDR2 Podocytes C1orf32 0.018 immunoglobulin like domain containing receptor 2 protein-coding gene NA Mesoderm Kidney 0.0 0.611111 0.000630915 0.0224192 +Mm Hs FOXD1 Podocytes FREAC4|FKHL8 0.002 forkhead box D1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0 0.00211987 +Mm Hs TRIB2 Podocytes GS3955 0.03 tribbles pseudokinase 2 protein-coding gene 1 Mesoderm Kidney 0.636364 0.0 0.00977918 0.0 +Mm Hs LOXL2 Podocytes WS9-14|LOR 0.021 lysyl oxidase like 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.166667 0.0167192 0.0208133 +Mm Hs COL4A5 Podocytes ASLN|ATS 0.009 collagen type IV alpha 5 chain protein-coding gene 1 Mesoderm Kidney 0.0909091 0.0555556 0.0160883 0.00693775 +Mm Hs FOXC1 Podocytes FREAC3|IGDA|IHG1|FKHL7|IRID1 0.015 forkhead box C1 protein-coding gene 1 Mesoderm Kidney 0.0909091 0.111111 0.00662461 0.0167662 +Mm Hs PLEKHH2 Podocytes KIAA2028|PLEKHH1L 0.003 pleckstrin homology, MyTH4 and FERM domain containing H2 protein-coding gene 1 Mesoderm Kidney 0.0 0.111111 0.00567823 0.00237682 +Mm Hs CTNNAL1 Podocytes CLLP|alpha-CATU 0.028 catenin alpha like 1 protein-coding gene 1 Mesoderm Kidney 0.227273 0.166667 0.0914826 0.00892914 +Mm Hs DACH1 Podocytes DACH 0.013 dachshund family transcription factor 1 protein-coding gene 1 Mesoderm Kidney 0.909091 0.222222 0.0214511 0.0109205 +Mm Hs SULF1 Podocytes KIAA1077|SULF-1|hSulf-1 0.013 sulfatase 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0176656 0.0 +Mm Hs HSPB8 Podocytes H11|E2IG1|HSP22|HspB8|CMT2L 0.024 heat shock protein family B (small) member 8 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00599369 0.0278795 +Mm Hs KANK1 Podocytes KANK|ANKRD15 0.027 KN motif and ankyrin repeat domains 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.166667 0.00757098 0.0316696 +Mm Hs ADCY1 Podocytes AC1|DFNB44 0.017 adenylate cyclase 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.00126183 0.0202351 +Mm Hs DOCK5 Podocytes FLJ21034 0.009 dedicator of cytokinesis 5 protein-coding gene 1 Mesoderm Kidney 0.0454545 0.0 0.0369085 0.00211987 +Mm Hs CRB2 Podocytes FLJ38464|FLJ16786 0.001 crumbs 2, cell polarity complex component protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0 0.000899338 +Mm Hs LRRC49 Podocytes FLJ20156 0.012 leucine rich repeat containing 49 protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0157729 0.0119484 +Mm Hs CORO2B Podocytes ClipinC|KIAA0925 0.018 coronin 2B protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0 0.0225477 +Mm Hs ARHGAP24 Podocytes DKFZP564B1162|FLJ33877|FilGAP 0.005 Rho GTPase activating protein 24 protein-coding gene 1 Mesoderm Kidney 0.0 0.944444 0.000630915 0.00565298 +Mm Hs GPRC5A Podocytes RAIG1|PEIG-1|RAI3 0.024 G protein-coupled receptor class C group 5 member A protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0839117 0.00970001 +Mm Hs COL4A4 Podocytes CA44 0.007 collagen type IV alpha 4 chain protein-coding gene 1 Mesoderm Kidney 0.181818 0.833333 0.00126183 0.00713047 +Mm Hs AIF1L Podocytes IBA2|FLJ12783|C9orf58 0.01 allograft inflammatory factor 1 like protein-coding gene 1 Mesoderm Kidney 0.863636 0.277778 0.0164038 0.00648808 +Mm Hs MET Podocytes HGFR|RCCP2|DFNB97 0.006 MET proto-oncogene, receptor tyrosine kinase protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.0164038 0.00462517 +Mm Hs EPB41L5 Podocytes KIAA1548|FLJ12957|BE37|YMO1|YRT 0.011 erythrocyte membrane protein band 4.1 like 5 protein-coding gene 1 Mesoderm Kidney 0.0454545 0.111111 0.0179811 0.00989272 +Mm Hs DOCK1 Podocytes DOCK180|ced5 0.01 dedicator of cytokinesis 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0555556 0.00189274 0.0127835 +Mm Hs AJUBA Podocytes MGC15563|JUB 0.008 ajuba LIM protein protein-coding gene 1 Mesoderm Kidney 0.0909091 0.0555556 0.00820189 0.00783709 +Mm Hs CD2AP Podocytes CMS 0.068 CD2 associated protein protein-coding gene 1 Mesoderm Kidney 0.454545 0.944444 0.0277603 0.0771504 +Mm Hs GOLIM4 Podocytes GPP130|GIMPC|P138|GOLPH4 0.056 golgi integral membrane protein 4 protein-coding gene 1 Mesoderm Kidney 1.0 0.944444 0.0750789 0.0468941 +Mm Hs ZBTB8A Podocytes BOZF1|FLJ90065|ZNF916A|ZBTB8 0.001 zinc finger and BTB domain containing 8A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm QK Podocytes NA 0.268 quaking protein coding gene 1 Mesoderm Kidney 0.0 0.777778 0.0 0.333976 +Mm Hs TOB1 Podocytes TOB|TROB|TROB1 0.128 transducer of ERBB2, 1 protein-coding gene 1 Mesoderm Kidney 0.5 0.0 0.341325 0.0 +Mm Hs WSB2 Podocytes SBA2|MGC10210 0.005 WD repeat and SOCS box containing 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00662461 0.0 +Mm Hs EMC2 Podocytes KIAA0103|TTC35 0.065 ER membrane protein complex subunit 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.166667 0.0511041 0.0680285 +Mm Hs EHD4 Podocytes PAST4 0.066 EH domain containing 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.166667 0.0268139 0.0753517 +Mm Hs ZFP91 Podocytes PZF|ZNF757 0.083 ZFP91 zinc finger protein protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0205047 0.0 +Mm Hs ETF1 Podocytes eRF1|TB3-1|SUP45L1|ERF 0.137 eukaryotic translation termination factor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.277778 0.112618 0.137278 +Mm Hs EMC7 Podocytes C15orf24 0.224 ER membrane protein complex subunit 7 protein-coding gene 1 Mesoderm Kidney 0.363636 0.111111 0.153312 0.237554 +Mm Hs LUC7L2 Podocytes CGI-74|CGI-59|H_NH0792N18.3|FLJ10657|LUC7B2|hLuc7B2 0.367 LUC7 like 2, pre-mRNA splicing factor protein-coding gene 1 Mesoderm Kidney 0.0909091 0.277778 0.0640379 0.441318 +Mm Hs MAPT Podocytes MTBT1|tau|PPND|FTDP-17|TAU|MSTD|MTBT2|FLJ31424|MGC138549|PPP1R103|DDPAC|MAPTL 0.198 microtubule associated protein tau protein-coding gene 1 Mesoderm Kidney 0.0 0.5 0.0176656 0.243978 +Mm Hs CDKN1C Podocytes P57|BWCR|BWS 0.097 cyclin dependent kinase inhibitor 1C protein-coding gene 1 Mesoderm Kidney 0.318182 0.888889 0.0451104 0.107664 +Mm Hs AQP2 Principal cells NA 0.001 aquaporin 2 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.000626566 0.000320965 +Mm Hs SCNN1A Principal cells ENaCalpha|SCNN1 0.008 sodium channel epithelial 1 alpha subunit protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0106516 0.0 +Mm Hs AQP3 Principal cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0711153 0.0154705 +Mm Hs KCNJ1 Principal cells Kir1.1|ROMK1 0.002 potassium voltage-gated channel subfamily J member 1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.000626566 0.00218257 +Mm Hs AVPR2 Principal cells V2R|DIR3|DIR 0.0 arginine vasopressin receptor 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SCNN1G Principal cells ENaCgamma|SCNEG 0.002 sodium channel epithelial 1 gamma subunit protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs HSD11B2 Principal cells SDR9C3 0.004 hydroxysteroid 11-beta dehydrogenase 2 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0109649 0.00224676 +Mm Hs FXYD4 Principal cells CHIF 0.003 FXYD domain containing ion transport regulator 4 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0 0.00269611 +Mm Hs APELA Principal cells Ende|ELA|tdl 0.004 apelin receptor early endogenous ligand protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.00219298 0.00423674 +Mm Hs NPNT Principal cells EGFL6L|POEM 0.017 nephronectin protein-coding gene NA Mesoderm Kidney 0.0 0.857143 0.00908521 0.0188728 +Mm Hs SCNN1B Principal cells ENaCbeta 0.003 sodium channel epithelial 1 beta subunit protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00313283 0.0 +Mm Hs KCNE1 Principal cells minK|ISK|JLNS2|LQT5 0.001 potassium voltage-gated channel subfamily E regulatory subunit 1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.0 0.000641931 +Mm Hs CDH16 Principal cells NA 0.004 cadherin 16 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.00093985 0.00449352 +Mm Hs ADGRG1 Principal cells TM7LN4|TM7XN1|GPR56 0.045 adhesion G protein-coupled receptor G1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.0213033 0.0499422 +Mm Hs TSPAN8 Principal cells CO-029|TM4SF3 0.047 tetraspanin 8 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0479323 0.0 +Mm Hs CDO1 Principal cells NA 0.036 cysteine dioxygenase type 1 protein-coding gene NA Mesoderm Kidney 0.0 0.857143 0.0119048 0.0414687 +Mm Hs TMEM45B Principal cells BC016153|FLJ40787 0.02 transmembrane protein 45B protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0162907 0.0 +Mm Hs TACSTD2 Principal cells TROP2|GA733-1|EGP-1|M1S1 0.033 tumor associated calcium signal transducer 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0983709 0.0 +Mm Hs PDZK1IP1 Principal cells DD96|MAP17|SPAP 0.025 PDZK1 interacting protein 1 protein-coding gene NA Mesoderm Kidney 0.0 1.0 0.0432331 0.0227885 +Mm Hs L1CAM Principal cells CD171|HSAS1|SPG1|HSAS|MIC5 0.018 L1 cell adhesion molecule protein-coding gene NA Mesoderm Kidney 0.0 0.428571 0.00156642 0.0211837 +Mm Hs CLDN4 Principal cells CPE-R|WBSCR8|hCPE-R|CPETR|CPETR1 0.047 claudin 4 protein-coding gene NA Mesoderm Kidney 0.0 0.285714 0.128446 0.0285659 +Mm Hs TBCK Principal cells MGC16169|HSPC302 0.006 TBC1 domain containing kinase protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00156642 0.0 +Mm Hs TMEM229A Principal cells NA 0.017 transmembrane protein 229A protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm GSTT1 Principal cells NA 0.022 glutathione S-transferase theta 1 protein-coding gene NA Mesoderm Kidney 0.0 0.857143 0.0 0.027603 +Mm Hs GPRC5B Principal cells RAIG-2 0.02 G protein-coupled receptor class C group 5 member B protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0100251 0.0229169 +Mm TMEM178 Principal cells NA 0.009 transmembrane protein 178 protein coding gene NA Mesoderm Kidney NA NA NA NA +Mm Hs PHACTR1 Principal cells KIAA1733|dJ257A7.2|RPEL1 0.039 phosphatase and actin regulator 1 protein-coding gene NA Mesoderm Kidney 0.0 0.285714 0.0335213 0.0401849 +Mm Hs CELSR2 Principal cells KIAA0279|MEGF3|Flamingo1|CDHF10|ADGRC2|EGFL2 0.019 cadherin EGF LAG seven-pass G-type receptor 2 protein-coding gene NA Mesoderm Kidney 0.0 0.285714 0.0 0.0230453 +Mm Hs FZD7 Principal cells FzE3 0.003 frizzled class receptor 7 protein-coding gene NA Mesoderm Kidney 0.0 0.142857 0.00093985 0.00192579 +Mm Hs SLC2A9 Principal cells Glut9|GLUTX|URATv1 0.0 solute carrier family 2 member 9 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs RNF186 Principal cells FLJ20225 0.013 ring finger protein 186 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00250627 0.0 +Mm Hs TRPV5 Principal cells CaT2|ECAC1 0.0 transient receptor potential cation channel subfamily V member 5 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs STC1 Principal cells STC 0.005 stanniocalcin 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0178571 0.0 +Mm Hs PELI2 Principal cells NA 0.005 pellino E3 ubiquitin protein ligase family member 2 protein-coding gene NA Mesoderm Kidney 0.0 0.428571 0.00219298 0.00552061 +Mm Hs KLK1 Principal cells Klk6 0.013 kallikrein 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.285714 0.00814536 0.0140583 +Mm Hs ACER2 Principal cells FLJ41587|ALKCDase2|ASAH3L 0.012 alkaline ceramidase 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0144434 +Mm Hs AQP4 Principal cells MIWC 0.024 aquaporin 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00595238 0.0294004 +Mm Hs FZD1 Principal cells DKFZp564G072 0.01 frizzled class receptor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00281955 0.0122609 +Mm Hs GATA3 Principal cells HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.0200501 0.0293362 +Mm Hs LGALS3 Principal cells MAC-2|GALIG|LGALS2 0.164 galectin 3 protein-coding gene 1 Mesoderm Kidney 0.0 1.0 0.308897 0.127937 +Mm Hs PTGES Principal cells MGST-IV|PIG12|MGST1-L1|TP53I12|MGST1L1 0.013 prostaglandin E synthase protein-coding gene 1 Mesoderm Kidney 0.0 0.428571 0.00438596 0.013288 +Mm Hs TSPAN1 Principal cells TSPAN-1|NET-1 0.028 tetraspanin 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0654762 0.0 +Mm Hs NR3C2 Principal cells MR|MLR 0.003 nuclear receptor subfamily 3 group C member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.285714 0.00657895 0.00243934 +Mm Hs HES1 Principal cells FLJ20408|HES-1|Hes1|bHLHb39|HRY 0.129 hes family bHLH transcription factor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.714286 0.145677 0.127359 +Mm Hs AQP1 Proximal tubule cells CHIP28|CO 0.037 aquaporin 1 (Colton blood group) protein-coding gene 1 Mesoderm Kidney 0.0 0.357143 0.0178627 0.041057 +Mm Hs CLDN2 Proximal tubule cells NA 0.009 claudin 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.157143 0.00282043 0.00979697 +Mm Hs DPP4 Proximal tubule cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene 1 Mesoderm Kidney 1.0 0.0142857 0.0128486 0.0213342 +Mm Hs ENPEP Proximal tubule cells gp160|CD249 0.011 glutamyl aminopeptidase protein-coding gene 1 Mesoderm Kidney 1.0 0.0142857 0.00626763 0.012504 +Mm Hs SLC36A2 Proximal tubule cells PAT2|tramdorin|TRAMD1 0.003 solute carrier family 36 member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC5A1 Proximal tubule cells D22S675|NAGT|SGLT1 0.011 solute carrier family 5 member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00219367 0.0 +Mm Hs SLC6A18 Proximal tubule cells FLJ31236|Xtrp2 0.001 solute carrier family 6 member 18 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC6A19 Proximal tubule cells NA 0.006 solute carrier family 6 member 19 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm SLC6A20B Proximal tubule cells NA 0.0 solute carrier family 6 (neurotransmitter transporter), member 20B protein coding gene 1 Mesoderm Kidney NA NA NA NA +Mm Hs SLC5A2 Proximal tubule cells SGLT2 0.001 solute carrier family 5 member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00658101 0.0 +Mm Hs LRP2 Proximal tubule cells gp330 0.01 LDL receptor related protein 2 protein-coding gene 1 Mesoderm Kidney 1.0 0.785714 0.00532748 0.00799227 +Mm Hs PDZK1 Proximal tubule cells PDZD1|NHERF3 0.002 PDZ domain containing 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0285714 0.0034472 0.00116017 +Mm Hs MIOX Proximal tubule cells ALDRL6 0.005 myo-inositol oxygenase protein-coding gene 1 Mesoderm Kidney 0.0 0.985714 0.0 0.00135353 +Mm Hs SLC34A1 Proximal tubule cells NAPI-3|NPTIIa|SLC11|NPT2|SLC17A2 0.004 solute carrier family 34 member 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0 0.0 +Mm Hs TTC36 Proximal tubule cells HBP21 0.002 tetratricopeptide repeat domain 36 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000940144 0.0 +Mm Hs ASS1 Proximal tubule cells CTLN1|ASS 0.048 argininosuccinate synthase 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.928571 0.0404262 0.044602 +Mm Hs PCK1 Proximal tubule cells PEPCK-C 0.008 phosphoenolpyruvate carboxykinase 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.9 0.0153557 0.0034805 +Mm Hs FUT9 Proximal tubule cells Fuc-TIX 0.039 fucosyltransferase 9 protein-coding gene 1 Mesoderm Kidney 0.0 0.814286 0.00188029 0.044602 +Mm Hs KHK Proximal tubule cells NA 0.037 ketohexokinase protein-coding gene 1 Mesoderm Kidney 0.0 0.871429 0.000313381 0.0413149 +Mm Hs SLC4A4 Proximal tubule cells NBC1|HNBC1|NBC2|pNBC|hhNMC|SLC4A5 0.033 solute carrier family 4 member 4 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.0119085 0.0 +Mm Hs GLYAT Proximal tubule cells GAT|ACGNAT 0.004 glycine-N-acyltransferase protein-coding gene 1 Mesoderm Kidney 1.0 0.757143 0.00188029 0.00116017 +Mm Hs FBP1 Proximal tubule cells NA 0.016 fructose-bisphosphatase 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.785714 0.0147289 0.0136642 +Mm Hs SLC22A6 Proximal tubule cells ROAT1|PAHT|OAT1 0.003 solute carrier family 22 member 6 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313381 0.0 +Mm Hs SLC22A12 Proximal tubule cells OAT4L|RST|URAT1 0.002 solute carrier family 22 member 12 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC47A1 Proximal tubule cells FLJ10847|MATE1 0.002 solute carrier family 47 member 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.000313381 0.0 +Mm Hs NOX4 Proximal tubule cells KOX-1|KOX 0.003 NADPH oxidase 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.314286 0.0 0.00186916 +Mm Hs SLC17A1 Proximal tubule cells NAPI-1|NPT1 0.002 solute carrier family 17 member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC13A3 Proximal tubule cells NADC3|SDCT2 0.002 solute carrier family 13 member 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00219367 0.0 +Mm Hs CYP2E1 Proximal tubule cells CYP2E 0.003 cytochrome P450 family 2 subfamily E member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.328571 0.00438734 0.00193361 +Mm Hs SLC22A8 Proximal tubule cells OAT3 0.021 solute carrier family 22 member 8 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs FOLR1 Proximal tubule cells FOLR 0.017 folate receptor 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.371429 0.00908806 0.018176 +Mm Hs SLC7A13 Proximal tubule cells AGT-1|XAT2 0.001 solute carrier family 7 member 13 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs AK4 Proximal tubule cells AK3 0.008 adenylate kinase 4 protein-coding gene 1 Mesoderm Kidney 1.0 0.157143 0.0153557 0.00438286 +Mm Hs SLC5A8 Proximal tubule cells AIT 0.003 solute carrier family 5 member 8 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.00156691 0.0 +Mm Hs SLC22A1 Proximal tubule cells NA 0.003 solute carrier family 22 member 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00219367 0.0 +Mm Hs GHR Proximal tubule cells GHBP 0.019 growth hormone receptor protein-coding gene 1 Mesoderm Kidney 0.0 0.414286 0.000626763 0.0212053 +Mm Hs UPB1 Proximal tubule cells BUP1 0.001 beta-ureidopropionase 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC17A3 Proximal tubule cells NPT4 0.001 solute carrier family 17 member 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs GCDH Proximal tubule cells ACAD5 0.007 glutaryl-CoA dehydrogenase protein-coding gene 1 Mesoderm Kidney 0.0 0.328571 0.00219367 0.00657428 +Mm Hs GSTZ1 Proximal tubule cells GSTZ1-1|MAAI|MAI 0.024 glutathione S-transferase zeta 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.271429 0.0448135 0.0164357 +Mm Hs ASL Proximal tubule cells NA 0.017 argininosuccinate lyase protein-coding gene 1 Mesoderm Kidney 0.0 0.157143 0.0147289 0.0166291 +Mm Hs FAH Proximal tubule cells NA 0.009 fumarylacetoacetate hydrolase protein-coding gene 1 Mesoderm Kidney 1.0 0.271429 0.0122219 0.00605865 +Mm SLCO1A6 Proximal tubule cells NA 0.001 solute carrier organic anion transporter family, member 1a6 protein coding gene 1 Mesoderm Kidney NA NA NA NA +Mm ECI3 Proximal tubule cells NA 0.001 enoyl-Coenzyme A delta isomerase 3 protein coding gene 1 Mesoderm Kidney 0.0 0.228571 0.0 0.000386723 +Mm Hs TMEM106A Proximal tubule cells MGC20235 0.014 transmembrane protein 106A protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000626763 0.0 +Mm Hs GSTA2 Proximal tubule cells GST2 0.007 glutathione S-transferase alpha 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.385714 0.00971482 0.00483403 +Mm Hs CRYL1 Proximal tubule cells lambda-CRY|MGC149525|MGC149526 0.018 crystallin lambda 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.328571 0.0213099 0.0159845 +Mm Hs SLC5A12 Proximal tubule cells MGC52019|SMCT2 0.001 solute carrier family 5 member 12 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm KAP Proximal tubule cells NA 0.007 kidney androgen regulated protein protein coding gene 1 Mesoderm Kidney 0.0 0.7 0.0 0.00605865 +Mm Hs AOAH Proximal tubule cells NA 0.004 acyloxyacyl hydrolase protein-coding gene 1 Mesoderm Kidney 0.0 0.0142857 0.00564086 0.00380277 +Mm Hs SLC13A1 Proximal tubule cells NaSi-1|NAS1 0.002 solute carrier family 13 member 1 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.000313381 0.0 +Mm Hs ABCC2 Proximal tubule cells DJS|cMRP|CMOAT 0.004 ATP binding cassette subfamily C member 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.114286 0.000940144 0.00380277 +Mm Hs PKHD1 Proximal tubule cells ARPKD|FCYT|FPC|TIGM1 0.005 PKHD1, fibrocystin/polyductin protein-coding gene NA Mesoderm Kidney 0.0 0.0571429 0.0144155 0.00270706 +Mm Hs SLC9A8 Proximal tubule cells KIAA0939|NHE8 0.001 solute carrier family 9 member A8 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm SLC22A19 Proximal tubule cells NA 0.0 solute carrier family 22 (organic anion transporter), member 19 protein coding gene 1 Mesoderm Kidney NA NA NA NA +None TMEM27 Proximal tubule cells NA 0.011 NA NA 1 Mesoderm Kidney 1.0 0.0 0.0034472 0.0 +Mm Hs SCIN Proximal tubule cells KIAA1905 0.006 scinderin protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0103416 0.0 +Mm Hs ALPL Proximal tubule cells TNSALP|TNALP|TNAP|HOPS 0.009 alkaline phosphatase, liver/bone/kidney protein-coding gene 1 Mesoderm Kidney 0.0 0.128571 0.00407396 0.00999033 +Mm Hs G6PC Proximal tubule cells GSD1a|G6PT 0.002 glucose-6-phosphatase catalytic subunit protein-coding gene 1 Mesoderm Kidney 0.0 0.242857 0.000313381 0.00135353 +Mm KEG1 Proximal tubule cells NA 0.004 kidney expressed gene 1 protein coding gene 1 Mesoderm Kidney 0.0 0.814286 0.0 0.00103126 +Mm Hs SLC22A13 Proximal tubule cells OCTL1|OCTL3|OAT10|ORCTL3 0.0 solute carrier family 22 member 13 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs SLC22A7 Proximal tubule cells NLT|OAT2 0.001 solute carrier family 22 member 7 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313381 0.0 +Mm Hs SLC16A9 Proximal tubule cells FLJ43803|MCT9|C10orf36 0.001 solute carrier family 16 member 9 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00282043 0.0 +Mm Hs AGXT2 Proximal tubule cells AGT2 0.001 alanine--glyoxylate aminotransferase 2 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.000313381 0.000708991 +Mm Hs SORD Proximal tubule cells NA 0.033 sorbitol dehydrogenase protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0103416 0.0 +Mm Hs SOD3 Proximal tubule cells EC-SOD 0.027 superoxide dismutase 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0614228 0.0 +Mm Hs HNF4A Proximal tubule cells NR2A1|HNF4|TCF14|MODY|MODY1 0.019 hepatocyte nuclear factor 4 alpha protein-coding gene 1 Mesoderm Kidney 0.0 0.342857 0.00783454 0.0203029 +Mm Hs NME4 Proximal tubule cells nm23-H4|NM23H4|NDPKD 0.077 NME/NM23 nucleoside diphosphate kinase 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.204951 0.0398969 +Mm Hs APOE Proximal tubule cells AD2 0.343 apolipoprotein E protein-coding gene 1 Mesoderm Kidney 1.0 0.2 0.132247 0.390267 +Mm Hs HGD Proximal tubule cells HGO|AKU 0.003 homogentisate 1,2-dioxygenase protein-coding gene 1 Mesoderm Kidney 1.0 0.228571 0.00438734 0.00116017 +Mm Hs OSGIN1 Proximal tubule cells BDGI|OKL38 0.006 oxidative stress induced growth inhibitor 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0428571 0.00313381 0.00625201 +Mm Hs HSD11B1 Proximal tubule cells SDR26C1|HSD11B|HSD11 0.022 hydroxysteroid 11-beta dehydrogenase 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00971482 0.0246213 +Mm Hs SERPINF2 Proximal tubule cells API|ALPHA-2-PI|A2AP|AAP|PLI 0.005 serpin family F member 2 protein-coding gene 1 Mesoderm Kidney 1.0 0.0 0.00877468 0.0 +Mm Hs HAAO Proximal tubule cells NA 0.002 3-hydroxyanthranilate 3,4-dioxygenase protein-coding gene 1 Mesoderm Kidney 0.0 0.1 0.000626763 0.00148244 +Mm Hs PPIC Proximal tubule cells CYPC 0.114 peptidylprolyl isomerase C protein-coding gene 1 Mesoderm Kidney 0.0 0.0428571 0.0861799 0.119562 +Mm Hs TFF3 Proximal tubule cells HITF|ITF 0.022 trefoil factor 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0451269 0.0 +Mm Hs GNG13 Proximal tubule cells h2-35|G(gamma)13 0.006 G protein subunit gamma 13 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00773445 +Mm Hs SLC23A3 Proximal tubule cells SVCT3|FLJ31168|Yspl1 0.0 solute carrier family 23 member 3 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs GC Proximal tubule cells VDBP|hDBP 0.009 GC, vitamin D binding protein protein-coding gene 1 Mesoderm Kidney 0.0 0.0285714 0.0141022 0.0077989 +Mm Hs CACNG5 Proximal tubule cells NA 0.003 calcium voltage-gated channel auxiliary subunit gamma 5 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0 0.00328714 +Mm Hs TGFBI Proximal tubule cells BIGH3|CDB1|CDGG1|CSD3|LCD1|CSD1|CSD2 0.065 transforming growth factor beta induced protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0654967 0.0 +Mm Hs RBP4 Proximal tubule cells NA 0.032 retinol binding protein 4 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.0376058 0.0 +Mm Hs NAPSA Proximal tubule cells NAPA|Kdap 0.054 napsin A aspartic peptidase protein-coding gene 1 Mesoderm Kidney 0.0 0.385714 0.0084613 0.0612955 +Mm Hs MMP11 Pulmonary alveolar type I cells STMY3 0.01 matrix metallopeptidase 11 protein-coding gene 1 Endoderm Lungs 0.0 0.323529 0.00438596 0.00803807 +Mm Hs ICAM1 Pulmonary alveolar type I cells CD54 0.009 intercellular adhesion molecule 1 protein-coding gene 1 Endoderm Lungs 0.0 0.294118 0.00595238 0.00938846 +Mm Hs CTGF Pulmonary alveolar type I cells IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Endoderm Lungs 0.0 0.617647 0.0996241 0.0111247 +Mm Hs SEMA3B Pulmonary alveolar type I cells SemA|semaV|LUCA-1|sema5|SEMAA 0.009 semaphorin 3B protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0178571 0.0 +Mm GRAMD2 Pulmonary alveolar type I cells NA 0.002 GRAM domain containing 2 protein coding gene 1 Endoderm Lungs 0.0 0.676471 0.0 0.000643045 +Mm Hs SCNN1B Pulmonary alveolar type I cells ENaCbeta 0.003 sodium channel epithelial 1 beta subunit protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00313283 0.0 +Mm Hs SEMA3E Pulmonary alveolar type I cells M-SemaK|KIAA0331|coll-5|SEMAH 0.005 semaphorin 3E protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs SCNN1G Pulmonary alveolar type I cells ENaCgamma|SCNEG 0.002 sodium channel epithelial 1 gamma subunit protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs SCNN1A Pulmonary alveolar type I cells ENaCalpha|SCNN1 0.008 sodium channel epithelial 1 alpha subunit protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0106516 0.0 +Mm Hs COL4A4 Pulmonary alveolar type I cells CA44 0.007 collagen type IV alpha 4 chain protein-coding gene 1 Endoderm Lungs 0.0 0.882353 0.00250627 0.00617324 +Mm Hs CYP4B1 Pulmonary alveolar type I cells NA 0.018 cytochrome P450 family 4 subfamily B member 1 protein-coding gene 1 Endoderm Lungs 0.0 0.588235 0.0128446 0.0178767 +Mm Hs RTKN2 Pulmonary alveolar type I cells Em:AC024597.2|bA531F24.1|FLJ39352|PLEKHK1 0.007 rhotekin 2 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0275689 0.0 +Mm Hs CLIC5 Pulmonary alveolar type I cells DFNB102 0.016 chloride intracellular channel 5 protein-coding gene 1 Endoderm Lungs 0.0 0.970588 0.0134712 0.0149187 +Mm CYP2B10 Pulmonary alveolar type I cells NA 0.004 cytochrome P450, family 2, subfamily b, polypeptide 10 protein coding gene 1 Endoderm Lungs 0.0 0.617647 0.0 0.00327953 +Mm Hs AKAP5 Pulmonary alveolar type I cells AKAP75|AKAP79 0.006 A-kinase anchoring protein 5 protein-coding gene 1 Endoderm Lungs 0.0 0.970588 0.0 0.00553019 +Mm Hs GPRC5A Pulmonary alveolar type I cells RAIG1|PEIG-1|RAI3 0.024 G protein-coupled receptor class C group 5 member A protein-coding gene 1 Endoderm Lungs 0.0 0.970588 0.0833333 0.00765224 +Mm Hs SEC14L3 Pulmonary alveolar type I cells TAP2 0.006 SEC14 like lipid binding 3 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm Hs COL4A3 Pulmonary alveolar type I cells NA 0.006 collagen type IV alpha 3 chain protein-coding gene 1 Endoderm Lungs 0.0 0.970588 0.000626566 0.00482284 +Mm Hs CLDN18 Pulmonary alveolar type I cells SFTPJ 0.01 claudin 18 protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.00407268 0.00970999 +Mm Hs AGER Pulmonary alveolar type I cells SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.00125313 0.0113819 +Mm Hs HOPX Pulmonary alveolar type I cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.091792 0.0201273 +Mm Hs AQP5 Pulmonary alveolar type I cells NA 0.018 aquaporin 5 protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.0419799 0.011832 +Mm Hs EMP2 Pulmonary alveolar type I cells XMP 0.065 epithelial membrane protein 2 protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.0902256 0.0549161 +Mm Hs VEGFA Pulmonary alveolar type I cells VEGF-A|VPF|VEGF 0.021 vascular endothelial growth factor A protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0247494 0.0 +Mm Hs KRT7 Pulmonary alveolar type I cells CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Endoderm Lungs 0.0 1.0 0.10119 0.0453347 +Mm Hs IGFBP6 Pulmonary alveolar type I cells NA 0.039 insulin like growth factor binding protein 6 protein-coding gene 1 Endoderm Lungs 0.0 0.676471 0.0839599 0.0280368 +Mm Hs PXDC1 Pulmonary alveolar type I cells C6orf145 0.028 PX domain containing 1 protein-coding gene 1 Endoderm Lungs 0.0 0.823529 0.0018797 0.0326667 +Mm Hs AQP3 Pulmonary alveolar type I cells GIL 0.025 aquaporin 3 (Gill blood group) protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0711153 0.0159475 +Mm Hs CRLF1 Pulmonary alveolar type I cells CLF-1|CISS|CISS1 0.015 cytokine receptor like factor 1 protein-coding gene 1 Endoderm Lungs 0.0 0.617647 0.00532581 0.0160118 +Mm Hs EGFL6 Pulmonary alveolar type I cells MAEG 0.01 EGF like domain multiple 6 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00814536 0.0106102 +Mm Hs FSTL3 Pulmonary alveolar type I cells FLRG|FSRP 0.004 follistatin like 3 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0147243 0.000450132 +Mm Hs MEX3B Pulmonary alveolar type I cells DKFZp434J0617|RNF195|RKHD3 0.004 mex-3 RNA binding family member B protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0112782 0.0028937 +Mm Hs RADIL Pulmonary alveolar type I cells FLJ10324|KIAA1849|RASIP2 0.0 Rap associating with DIL domain protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.000313283 0.0 +Mm Hs SMARCA1 Pulmonary alveolar type I cells NURF140|SWI|hSNF2L|SNF2L1|SNF2L 0.015 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0413534 0.0 +Mm Hs P2RX7 Pulmonary alveolar type I cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00877193 0.00347245 +Mm Hs PDPN Pulmonary alveolar type I cells T1A-2|Gp38|aggrus|PA2.26 0.062 podoplanin protein-coding gene 1 Endoderm Lungs 0.0 0.970588 0.0234962 0.0695132 +Mm Hs IRX1 Pulmonary alveolar type II cells IRX-5 0.009 iroquois homeobox 1 protein-coding gene 1 Endoderm Lungs 0.0 0.431818 0.0 0.00724778 +Mm Hs EGFL6 Pulmonary alveolar type II cells MAEG 0.01 EGF like domain multiple 6 protein-coding gene 1 Endoderm Lungs 0.0 0.666667 0.00817867 0.00498285 +Mm Hs CEBPA Pulmonary alveolar type II cells C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene 1 Endoderm Lungs 0.0 0.265152 0.0 0.0279557 +Mm Hs NKX2-1 Pulmonary alveolar type II cells TTF-1|TTF1|NKX2A|BCH|TITF1 0.01 NK2 homeobox 1 protein-coding gene 1 Endoderm Lungs 0.615385 0.651515 0.00283108 0.00595354 +Mm Hs MUC1 Pulmonary alveolar type II cells CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Endoderm Lungs 1.0 0.765152 0.0289399 0.00608296 +Mm Hs CLDN18 Pulmonary alveolar type II cells SFTPJ 0.01 claudin 18 protein-coding gene 1 Endoderm Lungs 0.769231 0.893939 0.000943693 0.00433573 +Mm Hs AGER Pulmonary alveolar type II cells SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene 1 Endoderm Lungs 0.307692 0.969697 0.0 0.00537113 +Mm Hs LAMP3 Pulmonary alveolar type II cells TSC403|DC-LAMP|DCLAMP|CD208 0.008 lysosomal associated membrane protein 3 protein-coding gene 1 Endoderm Lungs 0.538462 0.80303 0.0113243 6.47124e-05 +Mm Hs SFTA2 Pulmonary alveolar type II cells SFTPG 0.01 surfactant associated 2 protein-coding gene 1 Endoderm Lungs 0.923077 0.0 0.00220195 0.0 +Mm Hs SFTPD Pulmonary alveolar type II cells SP-D|COLEC7|SFTP4 0.01 surfactant protein D protein-coding gene 1 Endoderm Lungs 0.923077 0.0 0.000629129 0.0 +Mm Hs SLC34A2 Pulmonary alveolar type II cells NAPI-3B 0.01 solute carrier family 34 member 2 protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.00346021 0.0 +Mm CXCL15 Pulmonary alveolar type II cells NA 0.01 chemokine (C-X-C motif) ligand 15 protein coding gene 1 Endoderm Lungs 0.0 0.931818 0.0 0.004724 +Mm Hs SFTPB Pulmonary alveolar type II cells SP-B|SFTP3 0.015 surfactant protein B protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.0188739 0.0 +Mm Hs SFTPA1 Pulmonary alveolar type II cells SP-A|SP-A1|COLEC4|SFTP1 0.015 surfactant protein A1 protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.0138408 0.0 +Mm Hs SFTPC Pulmonary alveolar type II cells SP-C|PSP-C|SMDP2|BRICD6|SFTP2 0.029 surfactant protein C protein-coding gene 1 Endoderm Lungs 1.0 0.0 0.0191884 0.0 +Mm Hs SDC1 Pulmonary alveolar type II cells CD138|syndecan|SYND1|SDC 0.046 syndecan 1 protein-coding gene NA Endoderm Lungs 0.0 0.0 0.0465555 0.0 +Mm Hs ADGRF5 Pulmonary alveolar type II cells DKFZp564O1923|KIAA0758|GPR116 0.047 adhesion G protein-coupled receptor F5 protein-coding gene 1 Endoderm Lungs 0.538462 0.590909 0.0157282 0.0500227 +Mm Hs ABCD3 Pulmonary alveolar type II cells PMP70|ZWS2 0.041 ATP binding cassette subfamily D member 3 protein-coding gene 1 Endoderm Lungs 0.0 0.340909 0.00943693 0.0467223 +Mm Hs SOAT1 Pulmonary alveolar type II cells STAT 0.042 sterol O-acyltransferase 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0113243 0.0 +Mm Hs ETV5 Pulmonary alveolar type II cells ERM 0.019 ETS variant 5 protein-coding gene 1 Endoderm Lungs 0.0769231 0.44697 0.0128971 0.0154663 +Mm Hs CD36 Pulmonary alveolar type II cells SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Endoderm Lungs 0.230769 0.840909 0.0336584 0.037339 +Mm Hs LPCAT1 Pulmonary alveolar type II cells FLJ12443|AYTL2 0.025 lysophosphatidylcholine acyltransferase 1 protein-coding gene 1 Endoderm Lungs 0.692308 0.856061 0.00786411 0.0217434 +Mm Hs NAPSA Pulmonary alveolar type II cells NAPA|Kdap 0.054 napsin A aspartic peptidase protein-coding gene 1 Endoderm Lungs 1.0 0.871212 0.0044039 0.0558468 +Mm CBR2 Pulmonary alveolar type II cells NA 0.027 carbonyl reductase 2 protein coding gene 1 Endoderm Lungs 0.0 0.969697 0.0 0.0253672 +Mm Hs ABCA3 Pulmonary alveolar type II cells ABC-C|EST111653|LBM180|ABC3 0.001 ATP binding cassette subfamily A member 3 protein-coding gene 1 Endoderm Lungs 0.692308 0.00757576 0.000943693 0.000517699 +Mm SCD1 Pulmonary alveolar type II cells NA 0.036 stearoyl-Coenzyme A desaturase 1 protein coding gene 1 Endoderm Lungs NA NA NA NA +Mm Hs S100G Pulmonary alveolar type II cells CABP9K|CABP1|CALB3 0.024 S100 calcium binding protein G protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0 +Mm LYZ1 Pulmonary alveolar type II cells NA 0.031 lysozyme 1 protein coding gene 1 Endoderm Lungs 0.0 0.795455 0.0 0.0314502 +Mm Hs PGC Pulmonary alveolar type II cells NA 0.005 progastricsin protein-coding gene 1 Endoderm Lungs 0.769231 0.0 0.00251651 0.00478871 +Mm Hs CXCR2 Pulmonary alveolar type II cells CMKAR2|CD182|IL8RB 0.003 C-X-C motif chemokine receptor 2 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.00355918 +Mm Hs CXCL2 Pulmonary alveolar type II cells SCYB2|GROb|MIP-2a|MGSA-b|CINC-2a|GRO2 0.041 C-X-C motif chemokine ligand 2 protein-coding gene 1 Endoderm Lungs 0.846154 0.0606061 0.0534759 0.0379214 +Hs GRK2 Pulmonary alveolar type II cells BARK1|ADRBK1 0.001 G protein-coupled receptor kinase 2 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00786411 0.0 +Mm Hs RUNX3 Pulmonary alveolar type II cells AML2|PEBP2A3|CBFA3 0.018 runt related transcription factor 3 protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.0207612 0.0 +Mm Hs CTNND1 Pulmonary alveolar type II cells KIAA0384|p120cas|p120ctn|CTNND 0.04 catenin delta 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0454545 0.0443536 0.0390215 +Mm CD59A Pulmonary alveolar type II cells NA 0.033 CD59a antigen protein coding gene 1 Endoderm Lungs 0.0 0.0 0.0 0.0417395 +Mm Hs PPP1R14C Pulmonary alveolar type II cells NY-BR-81|KEPI 0.026 protein phosphatase 1 regulatory inhibitor subunit 14C protein-coding gene 1 Endoderm Lungs 0.0 0.598485 0.00597672 0.0267909 +Mm Hs DDX3Y Pulmonary alveolar type II cells DBY 0.029 DEAD-box helicase 3 Y-linked protein-coding gene 1 Endoderm Lungs 0.0769231 0.0227273 0.0500157 0.0253025 +Mm Hs PIGR Pulmonary alveolar type II cells NA 0.031 polymeric immunoglobulin receptor protein-coding gene 1 Endoderm Lungs 0.692308 0.00757576 0.0415225 0.0293147 +Mm H2-Q6 Pulmonary alveolar type II cells NA 0.023 histocompatibility 2, Q region locus 6 protein coding gene 1 Endoderm Lungs 0.0 0.0681818 0.0 0.0275028 +Mm LY6I Pulmonary alveolar type II cells NA 0.004 lymphocyte antigen 6 complex, locus I protein coding gene 1 Endoderm Lungs 0.0 0.227273 0.0 0.00213551 +Mm WFDC17 Pulmonary alveolar type II cells NA 0.037 WAP four-disulfide core domain 17 protein coding gene 1 Endoderm Lungs NA NA NA NA +Mm Hs LRG1 Pulmonary alveolar type II cells LRG 0.026 leucine rich alpha-2-glycoprotein 1 protein-coding gene 1 Endoderm Lungs 0.0 0.477273 0.00346021 0.0277616 +Mm Hs NRN1 Pulmonary alveolar type II cells NRN 0.021 neuritin 1 protein-coding gene 1 Endoderm Lungs 0.0 0.0151515 0.0100661 0.0231023 +Mm Hs PPBP Pulmonary alveolar type II cells SCYB7|TGB|NAP-2-L1|LA-PF4|MDGF|LDGF|Beta-TG|CTAP3|CXCL7|b-TG1|TGB1|CTAPIII|NAP-2|THBGB1 0.001 pro-platelet basic protein protein-coding gene 1 Endoderm Lungs 0.0 0.0 0.00346021 0.000841261 +Mm Hs IL1B Pulmonary alveolar type II cells IL1F2|IL-1B|IL1-BETA 0.027 interleukin 1 beta protein-coding gene 1 Endoderm Lungs 0.0 0.0378788 0.0254797 0.0276322 +Mm Hs INMT Pulmonary alveolar type II cells NA 0.016 indolethylamine N-methyltransferase protein-coding gene 1 Endoderm Lungs 0.0 0.0681818 0.00975149 0.0162428 +Mm Hs CRLF1 Pulmonary alveolar type II cells CLF-1|CISS|CISS1 0.015 cytokine receptor like factor 1 protein-coding gene 1 Endoderm Lungs 0.0 0.159091 0.00534759 0.0161134 +Mm Hs ANGPT1 Pulmonary vascular smooth muscle cells KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0018797 0.0123837 +Mm Hs PDGFRB Pulmonary vascular smooth muscle cells JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0363409 0.0334296 +Mm Hs GJA5 Purkinje fiber cells CX40 0.002 gap junction protein alpha 5 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00156642 0.00166827 +Mm Hs B3GAT1 Purkinje fiber cells GlcAT-P|HNK-1|NK-1|CD57|LEU7 0.014 beta-1,3-glucuronyltransferase 1 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00281955 0.016811 +Mm Hs GJC1 Purkinje fiber cells CX45|GJA7 0.026 gap junction protein gamma 1 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0112782 0.0297722 +Mm Hs KCNK3 Purkinje fiber cells K2p3.1|TASK|TASK-1 0.005 potassium two pore domain channel subfamily K member 3 protein-coding gene NA Mesoderm Heart 0.0 0.0 0.00156642 0.00641643 +Mm Hs NEFM Purkinje fiber cells NFM|NF-M|NEF3 0.028 neurofilament medium protein-coding gene NA Mesoderm Heart 0.0 0.0 0.0200501 0.0283606 +Mm Hs CALB1 Purkinje neurons CALB 0.019 calbindin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.097561 0.00125313 0.0233531 +Mm Hs ABAT Purkinje neurons GABAT 0.032 4-aminobutyrate aminotransferase protein-coding gene NA Ectoderm Brain 0.0 0.146341 0.00344612 0.0383428 +Mm Hs GRIN1 Purkinje neurons GluN1|NMDAR1 0.016 glutamate ionotropic receptor NMDA type subunit 1 protein-coding gene NA Ectoderm Brain 0.0 0.219512 0.00125313 0.0198147 +Mm Hs GAD1 Purkinje neurons GAD 0.03 glutamate decarboxylase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.829268 0.00344612 0.0351904 +Mm Hs HDAC6 Purkinje neurons KIAA0901|JM21|HD6|FLJ16239|PPP1R90 0.006 histone deacetylase 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00344612 0.00694802 +Mm Hs PRKG1 Purkinje neurons PGK|PKG|PKG1|PRKGR1B|PRKG1B 0.002 protein kinase cGMP-dependent 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.00205867 +Mm Hs ATP2B2 Purkinje neurons PMCA2 0.048 ATPase plasma membrane Ca2+ transporting 2 protein-coding gene NA Ectoderm Brain 0.0 0.658537 0.00125313 0.0574498 +Mm Hs PDE5A Purkinje neurons NA 0.011 phosphodiesterase 5A protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00407268 0.0136387 +Mm Hs ITPR3 Purkinje neurons IP3R3 0.007 inositol 1,4,5-trisphosphate receptor type 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0134712 0.00643335 +Mm Hs PDE1B Purkinje neurons PDES1B 0.006 phosphodiesterase 1B protein-coding gene NA Ectoderm Brain 0.0 0.0243902 0.0 0.00752702 +Mm Hs PDE1A Purkinje neurons NA 0.018 phosphodiesterase 1A protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0216165 0.0176917 +Mm CAR8 Purkinje neurons NA 0.013 carbonic anhydrase 8 protein coding gene 1 Ectoderm Brain 0.0 0.0487805 0.0 0.0159547 +Mm Hs OMP Purkinje neurons NA 0.001 olfactory marker protein protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.00167267 +Mm Hs PDE9A Purkinje neurons NA 0.003 phosphodiesterase 9A protein-coding gene NA Ectoderm Brain 0.0 0.0243902 0.0037594 0.00250901 +Mm Hs CBLN1 Purkinje neurons NA 0.005 cerebellin 1 precursor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0150376 0.00373134 +Mm Hs MRPS35 Purkinje neurons MRPS28|MDS023 0.048 mitochondrial ribosomal protein S35 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0695489 0.0376994 +Mm Hs PVALB Purkinje neurons D22S749 0.005 parvalbumin protein-coding gene NA Ectoderm Brain 0.0 0.170732 0.00344612 0.00540401 +Mm Hs SHANK2 Purkinje neurons CTTNBP1|ProSAP1|SHANK|SPANK-3|CORTBP1 0.002 SH3 and multiple ankyrin repeat domains 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs CACNA2D2 Purkinje neurons KIAA0558 0.027 calcium voltage-gated channel auxiliary subunit alpha2delta 2 protein-coding gene NA Ectoderm Brain 0.0 0.0487805 0.00125313 0.0342898 +Mm Hs NKAIN4 Purkinje neurons bA261N11.2|FAM77A|C20orf58 0.036 sodium/potassium transporting ATPase interacting 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00908521 0.0422028 +Mm Hs CNTNAP2 Purkinje neurons Caspr2|KIAA0868 0.037 contactin associated protein like 2 protein-coding gene NA Ectoderm Brain 0.0 0.121951 0.0238095 0.0404658 +Mm Hs TH Purkinje neurons DYT5b 0.002 tyrosine hydroxylase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0018797 0.0 +Mm Hs CERK Purkinje neurons hCERK|FLJ23239|dA59H18.3|DKFZp434E0211|FLJ21430|KIAA1646|LK4|dA59H18.2 0.011 ceramide kinase protein-coding gene NA Ectoderm Brain 0.0 0.097561 0.0093985 0.0109367 +Mm Hs CD3G Purkinje neurons NA 0.048 CD3g molecule protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0845865 0.0408518 +Mm Hs KCNA2 Purkinje neurons Kv1.2 0.019 potassium voltage-gated channel subfamily A member 2 protein-coding gene NA Ectoderm Brain 0.0 0.146341 0.0 0.0240607 +Mm Hs SLC22A15 Purkinje neurons FLIPT1 0.017 solute carrier family 22 member 15 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CACNG2 Purkinje neurons stargazin|MGC138502|MGC138504 0.014 calcium voltage-gated channel auxiliary subunit gamma 2 protein-coding gene NA Ectoderm Brain 0.0 0.243902 0.0 0.0170484 +Mm Hs SYT2 Purkinje neurons NA 0.002 synaptotagmin 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CPLX1 Purkinje neurons CPX-I 0.026 complexin 1 protein-coding gene NA Ectoderm Brain 0.0 0.243902 0.0 0.0319738 +Mm Hs PKP4 Purkinje neurons p0071 0.03 plakophilin 4 protein-coding gene NA Ectoderm Brain 0.0 0.146341 0.00720551 0.0355764 +Mm Hs KCNMA1 Purkinje neurons KCa1.1|mSLO1|SLO 0.043 potassium calcium-activated channel subfamily M alpha 1 protein-coding gene NA Ectoderm Brain 0.0 0.195122 0.0184837 0.0481215 +Mm Hs ADGRB1 Purkinje neurons BAI1 0.019 adhesion G protein-coupled receptor B1 protein-coding gene NA Ectoderm Brain 0.0 0.292683 0.000313283 0.0228384 +Mm Hs HCN1 Purkinje neurons BCNG-1|HAC-2|BCNG1 0.005 hyperpolarization activated cyclic nucleotide gated potassium channel 1 protein-coding gene NA Ectoderm Brain 0.0 0.146341 0.0 0.00585435 +Mm Hs SLC24A2 Purkinje neurons NCKX2 0.026 solute carrier family 24 member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00783208 0.0 +Mm Hs GABRA1 Purkinje neurons EJM5 0.027 gamma-aminobutyric acid type A receptor alpha1 subunit protein-coding gene NA Ectoderm Brain 0.0 0.121951 0.000313283 0.0319738 +Mm Hs CLSTN3 Purkinje neurons CSTN3|KIAA0726|CDHR14 0.033 calsyntenin 3 protein-coding gene NA Ectoderm Brain 0.0 0.121951 0.00250627 0.0404658 +Mm Hs SLC24A3 Purkinje neurons NA 0.013 solute carrier family 24 member 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs DLG4 Purkinje neurons PSD-95|PSD95|SAP90|SAP-90 0.022 discs large MAGUK scaffold protein 4 protein-coding gene NA Ectoderm Brain 0.0 0.097561 0.000313283 0.0278564 +Mm Hs CNPY1 Purkinje neurons NA 0.001 canopy FGF signaling regulator 1 protein-coding gene NA Ectoderm Brain 0.0 0.0243902 0.0 0.000707669 +Mm Hs SLC12A5 Purkinje neurons KIAA1176|KCC2 0.048 solute carrier family 12 member 5 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0037594 0.0 +Mm Hs SLC32A1 Purkinje neurons VGAT|bA122O1.1|VIAAT 0.026 solute carrier family 32 member 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs GRIA3 Purkinje neurons GluA3|GLURC|MRX94|GLUR3 0.02 glutamate ionotropic receptor AMPA type subunit 3 protein-coding gene NA Ectoderm Brain 0.0 0.170732 0.00219298 0.0227097 +Mm Hs CAMK2A Purkinje neurons KIAA0968|CAMKA 0.026 calcium/calmodulin dependent protein kinase II alpha protein-coding gene NA Ectoderm Brain 0.0 0.341463 0.0 0.0309444 +Mm Hs PENK Purkinje neurons NA 0.02 proenkephalin protein-coding gene NA Ectoderm Brain 0.0 0.097561 0.0275689 0.0194287 +Mm Hs HIVEP2 Purkinje neurons MBP-2|HIV-EP2|MIBP1|ZAS2|Schnurri-2|ZNF40B 0.055 human immunodeficiency virus type I enhancer binding protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.439024 0.00250627 0.0674858 +Mm Hs NRIP3 Purkinje neurons C11orf14 0.021 nuclear receptor interacting protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.390244 0.0322682 0.0180134 +Mm Hs TSHZ1 Purkinje neurons NY-CO-33|SDCCAG33 0.015 teashirt zinc finger homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00469925 0.0 +Mm Hs PCBP3 Purkinje neurons FLJ44028|PCBP3-OT1|PCBP3OT 0.02 poly(rC) binding protein 3 protein-coding gene NA Ectoderm Brain 0.0 0.317073 0.00250627 0.0237391 +Mm Hs GPSM1 Purkinje neurons DKFZP727I051 0.004 G protein signaling modulator 1 protein-coding gene NA Ectoderm Brain 0.0 0.268293 0.00093985 0.00450335 +Mm Hs PPM1E Purkinje neurons POPX1|KIAA1072|PP2CH|CaMKP-N 0.014 protein phosphatase, Mg2+/Mn2+ dependent 1E protein-coding gene NA Ectoderm Brain 0.0 0.317073 0.00344612 0.0163407 +Mm Hs DLGAP1 Purkinje neurons GKAP|SAPAP1|DAP-1 0.036 DLG associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.707317 0.00219298 0.0429104 +Mm Hs GNG4 Purkinje neurons NA 0.013 G protein subunit gamma 4 protein-coding gene NA Ectoderm Brain 0.0 0.243902 0.0175439 0.011194 +Mm Hs SHISA8 Purkinje neurons Orf26|C22orf17 0.004 shisa family member 8 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SYNPR Purkinje neurons MGC26651 0.022 synaptoporin protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs PRKCA Purkinje neurons PKCA 0.033 protein kinase C alpha protein-coding gene NA Ectoderm Brain 0.0 0.463415 0.0153509 0.0357694 +Mm Hs PCP4L1 Purkinje neurons IQM1 0.044 Purkinje cell protein 4 like 1 protein-coding gene NA Ectoderm Brain 0.0 0.487805 0.0 0.0541688 +Mm Hs PCP4 Purkinje neurons PEP-19 0.083 Purkinje cell protein 4 protein-coding gene 1 Ectoderm Brain 0.0 0.731707 0.0194236 0.0953423 +Mm Hs SLC1A6 Purkinje neurons EAAT4 0.003 solute carrier family 1 member 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313283 0.0 +Mm Hs GRID2 Purkinje neurons GluD2|GluR-delta-2 0.005 glutamate ionotropic receptor delta type subunit 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0487805 0.0162907 0.00257334 +Mm Hs GAD2 Purkinje neurons GAD65 0.073 glutamate decarboxylase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.463415 0.0244361 0.0856922 +Mm Hs CD3E Pyramidal cells NA 0.041 CD3e molecule protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0996241 0.0298383 +Mm Hs DLG4 Pyramidal cells PSD-95|PSD95|SAP90|SAP-90 0.022 discs large MAGUK scaffold protein 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0280416 +Mm Hs CAMK2A Pyramidal cells KIAA0968|CAMKA 0.026 calcium/calmodulin dependent protein kinase II alpha protein-coding gene NA Ectoderm Brain 0.0 1.0 0.0 0.0316992 +Mm Hs GRM1 Pyramidal cells GPRC1A|mGlu1|MGLUR1|PPP1R85 0.004 glutamate metabotropic receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00500513 +Mm Hs GRM5 Pyramidal cells MGLUR5|GPRC1E|mGlu5|PPP1R86 0.033 glutamate metabotropic receptor 5 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.0419661 +Mm Hs TBR1 Pyramidal cells NA 0.018 T-box, brain 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs POU3F1 Pyramidal cells OCT6|SCIP|OTF6 0.013 POU class 3 homeobox 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0167479 +Mm Hs EMX1 Pyramidal cells NA 0.023 empty spiracles homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0291324 +Mm Hs FEZF2 Pyramidal cells FLJ10142|FKSG36|TOF|FEZL|Zfp312|ZNF312 0.008 FEZ family zinc finger 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.00975359 +Mm Hs NRGN Pyramidal cells NA 0.031 neurogranin protein-coding gene NA Ectoderm Brain 0.0 1.0 0.0109649 0.0344584 +Mm Hs GRIA3 Pyramidal cells GluA3|GLURC|MRX94|GLUR3 0.02 glutamate ionotropic receptor AMPA type subunit 3 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00219298 0.0231006 +Mm Hs SPINK8 Pyramidal cells NA 0.002 serine peptidase inhibitor, Kazal type 8 (putative) protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs PCP4 Pyramidal cells PEP-19 0.083 Purkinje cell protein 4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0194236 0.0969584 +Mm Hs SYNPR Pyramidal cells MGC26651 0.022 synaptoporin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs NR4A2 Pyramidal cells TINUR|NOT|RNR1|HZF-3|NURR1 0.033 nuclear receptor subfamily 4 group A member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0780075 0.025539 +Mm Hs AGER Pyramidal cells SCARJ1 0.011 advanced glycosylation end-product specific receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0135395 +Mm Hs GRIN2D Pyramidal cells GluN2D|EB11|NR2D|NMDAR2D 0.002 glutamate ionotropic receptor NMDA type subunit 2D protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00198922 +Mm Hs YWHAZ Pyramidal cells KCIP-1|14-3-3-zeta|YWHAD 0.497 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.518797 0.0 +Mm Hs KCNN4 Pyramidal cells KCa3.1|hSK4|hKCa4|hIKCa1|IK 0.027 potassium calcium-activated channel subfamily N member 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0100251 0.0293891 +Mm Hs DAB1 Pyramidal cells NA 0.045 DAB1, reelin adaptor protein protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0018797 0.0567248 +Mm Hs CCM2 Pyramidal cells MGC4607|OSM|C7orf22 0.052 CCM2 scaffold protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0435464 0.0505647 +Mm Hs MAP2 Pyramidal cells MAP2A|MAP2B|MAP2C 0.179 microtubule associated protein 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0266291 0.216376 +Mm Hs CALB1 Pyramidal cells CALB 0.019 calbindin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0235498 +Mm Hs ADRB2 Pyramidal cells ADRBR|B2AR|ADRB2R 0.016 adrenoceptor beta 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0100251 0.0181597 +Mm Hs RTN4 Pyramidal cells NSP-CL|KIAA0886|NOGO|ASY 0.553 reticulon 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.504699 0.0 +Mm Hs PDE2A Pyramidal cells NA 0.0 phosphodiesterase 2A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 6.41684e-05 +Mm Hs KCNB1 Pyramidal cells Kv2.1 0.015 potassium voltage-gated channel subfamily B member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0192505 +Mm Hs KCNB2 Pyramidal cells Kv2.2 0.007 potassium voltage-gated channel subfamily B member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.00834189 +Mm Hs KCNQ2 Pyramidal cells Kv7.2|ENB1|KCNA11|HNSPC 0.014 potassium voltage-gated channel subfamily Q member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0228697 0.0130262 +Mm Hs KCNQ3 Pyramidal cells Kv7.3|EBN2 0.017 potassium voltage-gated channel subfamily Q member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0205981 +Mm Hs SATB2 Pyramidal cells KIAA1034|FLJ21474 0.015 SATB homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00407268 0.0 +Mm Hs OXTR Pyramidal cells NA 0.001 oxytocin receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.00166838 +Mm Hs CCK Pyramidal cells NA 0.033 cholecystokinin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.038501 +Mm Hs KCND2 Pyramidal cells Kv4.2|RK5|KIAA1044 0.009 potassium voltage-gated channel subfamily D member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.010652 +Mm Hs KCND3 Pyramidal cells Kv4.3|KSHIVB|SCA22|SCA19 0.004 potassium voltage-gated channel subfamily D member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.00532598 +Mm Hs PAX6 Radial glia cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Ectoderm Brain 0.0 0.75 0.014411 0.0587896 +Mm Hs SLC1A3 Radial glia cells EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109649 0.0 +Mm Hs PDGFD Radial glia cells SCDGF-B|MSTP036|IEGF 0.003 platelet derived growth factor D protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0037594 0.00269559 +Mm Hs GLI3 Radial glia cells PAP-A|PAPA1|PAPB|ACLS|PPDIV|GCPS|PHS 0.003 GLI family zinc finger 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.00218214 +Mm Hs NOTCH3 Radial glia cells CASIL|CADASIL 0.02 notch 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.014411 0.0220782 +Mm Hs VCAM1 Radial glia cells CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00720551 0.0 +Mm Hs HES5 Radial glia cells bHLHb38 0.036 hes family bHLH transcription factor 5 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.00125313 0.0420384 +Mm Hs OLIG2 Radial glia cells RACK17|OLIGO2|bHLHe19|PRKCBP2|BHLHB1 0.039 oligodendrocyte transcription factor 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.049355 +Mm Hs GFAP Radial glia cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0056391 0.0146974 +Mm Hs EMX2 Radial glia cells NA 0.027 empty spiracles homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.25 0.0112782 0.0315769 +Mm Hs CDH4 Radial glia cells NA 0.017 cadherin 4 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.000313283 0.0201527 +Mm Hs SPRY1 Radial glia cells hSPRY1 0.019 sprouty RTK signaling antagonist 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0303885 0.0 +Mm Hs AXIN2 Radial glia cells MGC126582|DKFZp781B0869 0.006 axin 2 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.000626566 0.00776587 +Mm Hs RIIAD1 Radial glia cells FLJ36032|NCRNA00166|C1orf230 0.019 regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0119048 0.0 +Mm Hs HMOX1 Red pulp macrophages bK286B10|HO-1 0.046 heme oxygenase 1 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.0363409 0.0466701 +Mm Hs TREML4 Red pulp macrophages TLT4 0.003 triggering receptor expressed on myeloid cells like 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs CD86 Red pulp macrophages B7.2|B7-2|CD28LG2 0.026 CD86 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.310345 0.012218 0.0286706 +Mm Hs NR1H3 Red pulp macrophages LXR-a|RLD-1|LXRa 0.008 nuclear receptor subfamily 1 group H member 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.551724 0.00971178 0.00655696 +Mm Hs SLC11A1 Red pulp macrophages NRAMP|NRAMP1 0.017 solute carrier family 11 member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00657895 0.0 +Mm Hs ADGRE1 Red pulp macrophages TM7LN3|EMR1 0.033 adhesion G protein-coupled receptor E1 protein-coding gene 1 Mesoderm Immune system 0.0 0.862069 0.000626566 0.0397917 +Mm Hs MERTK Red pulp macrophages mer|RP38|c-Eyk|Tyro12 0.016 MER proto-oncogene, tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.551724 0.00093985 0.0188352 +Mm Hs CCR3 Red pulp macrophages CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.62069 0.0 0.000321419 +Mm Hs SPIC Red pulp macrophages MGC40611|SPI-C 0.002 Spi-C transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs SLC40A1 Red pulp macrophages MTP1|IREG1|FPN1|HFE4|SLC11A3 0.033 solute carrier family 40 member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.035401 0.0 +Mm Hs VCAM1 Red pulp macrophages CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00720551 0.0 +Mm Hs SIGLEC1 Red pulp macrophages SIGLEC-1|CD169|FLJ00051|FLJ00055|FLJ00073|FLJ32150|dJ1009E24.1|sialoadhesin 0.0 sialic acid binding Ig like lectin 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs RUVBL1 Reticulocytes TIP49|NMP238|RVB1|TIP49a|Pontin52|ECP54|Rvb1|INO80H 0.059 RuvB like AAA ATPase 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.091792 0.0 +Mm Hs TFRC Reticulocytes CD71|TFR1|p90 0.042 transferrin receptor protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0614035 0.0 +Mm Hs UCP3 Reticulocytes SLC25A9 0.0 uncoupling protein 3 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs FOLR1 Reticulocytes FOLR 0.017 folate receptor 1 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0093985 0.0197626 +Mm Hs UBE2O Reticulocytes E2-230K 0.0 ubiquitin conjugating enzyme E2 O protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0 0.0 +Mm Hs CD36 Reticulocytes SCARB3|GPIV|GP4|GP3B 0.042 CD36 molecule protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0344612 0.044145 +Mm Hs ITGA4 Reticulocytes CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.0112782 0.0412576 +Mm Hs SLC11A2 Reticulocytes DCT1|NRAMP2 0.007 solute carrier family 11 member 2 protein-coding gene 1 Mesoderm Blood 0.0 0.0 0.00657895 0.0 +Mm Hs PRKCA Retinal ganglion cells PKCA 0.033 protein kinase C alpha protein-coding gene NA Ectoderm Brain 0.0 0.456522 0.0153557 0.0356522 +Mm Hs NGF Retinal ganglion cells NGFB 0.003 nerve growth factor protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626763 0.00347513 +Mm Hs POU4F2 Retinal ganglion cells Brn-3b|BRN3B 0.002 POU class 4 homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.543478 0.0 0.000386125 +Mm Hs NHLH2 Retinal ganglion cells bHLHa34|HEN2 0.021 nescient helix-loop-helix 2 protein-coding gene NA Ectoderm Brain 1.0 0.0652174 0.00125353 0.0259347 +Hs RNU1-1 Retinal ganglion cells Rnu1a1|U1|HU1-1|U1A1|HSD1|RNU1|RNU1G4|RNU1A3|RNU1A 0.0 RNA, U1 small nuclear 1 non-coding RNA NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ATF6B Retinal ganglion cells CREBL1 0.022 activating transcription factor 6 beta protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.00877468 0.0221378 +Mm Hs SNX16 Retinal ganglion cells NA 0.007 sorting nexin 16 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0109683 0.0 +Mm Hs IRX5 Retinal ganglion cells IRX-2a 0.009 iroquois homeobox 5 protein-coding gene NA Ectoderm Brain 0.0 0.413043 0.000940144 0.0104897 +Mm Hs YDJC Retinal ganglion cells NA 0.02 YdjC chitooligosaccharide deacetylase homolog protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0510812 0.0 +Mm Hs DPP10 Retinal ganglion cells DPRP3|DPL2|DPPY 0.01 dipeptidyl peptidase like 10 protein-coding gene NA Ectoderm Brain 0.0 0.630435 0.000940144 0.0108115 +Mm Hs SHD Retinal ganglion cells NA 0.005 Src homology 2 domain containing transforming protein D protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00564086 0.0 +Mm Hs SMIM18 Retinal ganglion cells NA 0.004 small integral membrane protein 18 protein-coding gene NA Ectoderm Brain 1.0 0.0 0.0 0.0 +Mm Hs GALNT14 Retinal ganglion cells GalNac-T10|FLJ12691|GalNac-T14 0.003 polypeptide N-acetylgalactosaminyltransferase 14 protein-coding gene NA Ectoderm Brain 0.0 0.565217 0.000626763 0.00250981 +Mm Hs CHRNB3 Retinal ganglion cells NA 0.002 cholinergic receptor nicotinic beta 3 subunit protein-coding gene NA Ectoderm Brain 0.0 0.73913 0.0 0.000900959 +Mm Hs THEM4 Retinal ganglion cells CTMP 0.01 thioesterase superfamily member 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0128486 0.0 +Mm Hs SCAPER Retinal ganglion cells Zfp291|ZNF291 0.016 S-phase cyclin A associated protein in the ER protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0332184 0.0 +Mm Hs GALNTL6 Retinal ganglion cells GALNT17|GalNAc-T6L 0.01 polypeptide N-acetylgalactosaminyltransferase like 6 protein-coding gene NA Ectoderm Brain 0.0 0.73913 0.0 0.0106828 +Mm Hs CCDC184 Retinal ganglion cells LOC387856|C12orf68 0.009 coiled-coil domain containing 184 protein-coding gene NA Ectoderm Brain 1.0 0.826087 0.00658101 0.00797992 +Mm Hs NKAIN3 Retinal ganglion cells FLJ39630|FAM77D 0.009 sodium/potassium transporting ATPase interacting 3 protein-coding gene NA Ectoderm Brain 1.0 0.586957 0.00971482 0.00746509 +Mm Hs LHFPL5 Retinal ganglion cells MGC33835|dJ510O8.8|Tmhs|DFNB67 0.004 LHFPL tetraspan subfamily member 5 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.0 0.00244546 +Mm Hs SRRM3 Retinal ganglion cells FLJ37078 0.007 serine/arginine repetitive matrix 3 protein-coding gene NA Ectoderm Brain 1.0 0.0 0.000940144 0.0 +Mm Hs GALNT9 Retinal ganglion cells GALNAC-T9 0.004 polypeptide N-acetylgalactosaminyltransferase 9 protein-coding gene NA Ectoderm Brain 0.0 0.804348 0.000313381 0.00302465 +Mm Hs MTUS2 Retinal ganglion cells TIP150|CAZIP|KIAA0774 0.006 microtubule associated scaffold protein 2 protein-coding gene NA Ectoderm Brain 0.0 0.847826 0.0 0.00495527 +Mm Hs IGLON5 Retinal ganglion cells LOC402665 0.004 IgLON family member 5 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.00219367 0.00205933 +Mm Hs DCTN1 Retinal ganglion cells NA 0.021 dynactin subunit 1 protein-coding gene NA Ectoderm Brain 0.0 0.847826 0.00752115 0.02143 +Mm Hs GGT7 Retinal ganglion cells D20S101|dJ18C9.2|GGTL5|GGTL3 0.007 gamma-glutamyltransferase 7 protein-coding gene NA Ectoderm Brain 0.0 0.847826 0.000313381 0.00598494 +Mm Hs BTBD10 Retinal ganglion cells GMRP1|GMRP-1|MGC13007 0.018 BTB domain containing 10 protein-coding gene NA Ectoderm Brain 0.0 0.847826 0.0319649 0.0127421 +Mm Hs EFNA3 Retinal ganglion cells LERK3|Ehk1-L|EPLG3 0.009 ephrin A3 protein-coding gene NA Ectoderm Brain 0.0 0.847826 0.00188029 0.0084304 +Mm Hs SLC29A4 Retinal ganglion cells FLJ34923|ENT4 0.006 solute carrier family 29 member 4 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00940144 0.0 +Mm Hs STOML1 Retinal ganglion cells hUNC-24|SLP-1|STORP|FLJ36370 0.008 stomatin like 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000940144 0.0 +Mm Hs FBXO44 Retinal ganglion cells FBG3|MGC14140|Fbxo6a|Fbx44 0.01 F-box protein 44 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.00282043 0.00939571 +Mm Hs NELL1 Retinal ganglion cells IDH3GL|FLJ45906 0.005 neural EGFL like 1 protein-coding gene NA Ectoderm Brain 0.0 0.521739 0.000940144 0.00450479 +Mm Hs RTN2 Retinal ganglion cells NSPL1|SPG12 0.011 reticulon 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00219367 0.0 +Mm Hs BBC3 Retinal ganglion cells JFY1|PUMA 0.009 BCL2 binding component 3 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.0150423 0.00611365 +Mm Hs EVC2 Retinal ganglion cells LBN 0.001 EvC ciliary complex subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.347826 0.000313381 0.000579188 +Mm Hs SYT16 Retinal ganglion cells yt14r|CHR14SYT|Strep14 0.007 synaptotagmin 16 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00250705 0.0 +Mm Hs CPNE5 Retinal ganglion cells CPN5|COPN5|KIAA1599 0.008 copine 5 protein-coding gene NA Ectoderm Brain 0.0 0.717391 0.000940144 0.00804428 +Mm Hs TTLL1 Retinal ganglion cells C22orf7 0.01 tubulin tyrosine ligase like 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313381 0.0 +Mm Hs GPHN Retinal ganglion cells KIAA1385 0.008 gephyrin protein-coding gene NA Ectoderm Brain 0.0 0.891304 0.00125353 0.00740073 +Mm Hs SIX6 Retinal ganglion cells Six9|OPTX2 0.004 SIX homeobox 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ABLIM3 Retinal ganglion cells KIAA0843 0.005 actin binding LIM protein family member 3 protein-coding gene NA Ectoderm Brain 0.0 0.869565 0.00156691 0.00386125 +Mm Hs POU6F2 Retinal ganglion cells RPF-1 0.002 POU class 6 homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.586957 0.0 0.00102967 +Mm Hs GRIP1 Retinal ganglion cells NA 0.006 glutamate receptor interacting protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.000313381 0.00547011 +Mm ZFP580 Retinal ganglion cells NA 0.01 zinc finger protein 580 protein coding gene NA Ectoderm Brain NA NA NA NA +Mm Hs TOX2 Retinal ganglion cells dJ1108D11.2|GCX-1|C20orf100 0.008 TOX high mobility group box family member 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00564086 0.0 +Mm Hs NARF Retinal ganglion cells FLJ10067|DKFZp434G0420|IOP2 0.031 nuclear prelamin A recognition factor protein-coding gene NA Ectoderm Brain 1.0 0.891304 0.115011 0.00669284 +Mm Hs BARHL2 Retinal ganglion cells NA 0.004 BarH like homeobox 2 protein-coding gene NA Ectoderm Brain 0.0 0.521739 0.0 0.00366819 +Mm Hs DTX1 Retinal ganglion cells hDx-1|RNF140 0.007 deltex E3 ubiquitin ligase 1 protein-coding gene NA Ectoderm Brain 0.0 0.869565 0.000313381 0.00662848 +Mm Hs MAB21L2 Retinal ganglion cells NA 0.006 mab-21 like 2 protein-coding gene NA Ectoderm Brain 0.0 0.826087 0.00438734 0.00405431 +Mm Hs KCTD8 Retinal ganglion cells NA 0.005 potassium channel tetramerization domain containing 8 protein-coding gene NA Ectoderm Brain 0.0 0.869565 0.0 0.00398996 +Mm Hs CPNE4 Retinal ganglion cells COPN4|CPN4 0.006 copine 4 protein-coding gene NA Ectoderm Brain 1.0 0.673913 0.000626763 0.0060493 +Mm Hs KLHDC8A Retinal ganglion cells FLJ10748 0.005 kelch domain containing 8A protein-coding gene NA Ectoderm Brain 0.0 0.891304 0.000940144 0.00366819 +Mm Hs IRX6 Retinal ganglion cells IRX-3|IRX7 0.001 iroquois homeobox 6 protein-coding gene NA Ectoderm Brain 0.0 0.413043 0.0 0.000193063 +Mm Hs CHRNA6 Retinal ganglion cells NA 0.003 cholinergic receptor nicotinic alpha 6 subunit protein-coding gene NA Ectoderm Brain 0.0 0.804348 0.0 0.00160886 +Mm Hs CACNB3 Retinal ganglion cells CACNLB3 0.032 calcium voltage-gated channel auxiliary subunit beta 3 protein-coding gene NA Ectoderm Brain 1.0 0.913043 0.00156691 0.0369393 +Mm Hs CSDC2 Retinal ganglion cells PIPPin 0.013 cold shock domain containing C2 protein-coding gene NA Ectoderm Brain 0.0 0.913043 0.00156691 0.0128065 +Mm Hs AKAP7 Retinal ganglion cells AKAP18|AKAP15 0.02 A-kinase anchoring protein 7 protein-coding gene NA Ectoderm Brain 0.0 0.913043 0.00564086 0.0209151 +Mm Hs HPCA Retinal ganglion cells NA 0.015 hippocalcin protein-coding gene NA Ectoderm Brain 0.0 0.934783 0.0034472 0.0150589 +Mm Hs ISL1 Retinal ganglion cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.630435 0.0134754 0.0296029 +Mm Hs SLC17A6 Retinal ganglion cells DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene 1 Ectoderm Brain 1.0 0.0 0.0 0.0 +Mm Hs FGF12 Retinal ganglion cells FHF1|FGF12B 0.014 fibroblast growth factor 12 protein-coding gene NA Ectoderm Brain 0.0 0.891304 0.00438734 0.0145441 +Mm Hs DNER Retinal ganglion cells UNQ26|bet 0.046 delta/notch like EGF repeat containing protein-coding gene NA Ectoderm Brain 1.0 0.978261 0.0178627 0.0516764 +Mm Hs TMEM163 Retinal ganglion cells DKFZP566N034|SV31 0.027 transmembrane protein 163 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000626763 0.0 +Mm Hs RBPMS Retinal ganglion cells HERMES 0.076 RNA binding protein, mRNA processing factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0858665 0.0 +Mm Hs POU4F1 Retinal ganglion cells RDC-1|BRN3A 0.006 POU class 4 homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0 0.00514834 +Mm Hs RBPMS2 Retinal ganglion cells NA 0.017 RNA binding protein, mRNA processing factor 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00720777 0.0 +Mm Hs CDK14 Retinal ganglion cells PFTAIRE1|PFTK1 0.024 cyclin dependent kinase 14 protein-coding gene NA Ectoderm Brain 0.0 1.0 0.00407396 0.0260635 +Mm Hs FXYD7 Retinal ganglion cells NA 0.024 FXYD domain containing ion transport regulator 7 protein-coding gene NA Ectoderm Brain 1.0 0.978261 0.000626763 0.0272862 +Mm Hs NEFM Retinal ganglion cells NFM|NF-M|NEF3 0.028 neurofilament medium protein-coding gene NA Ectoderm Brain 1.0 1.0 0.019743 0.0254843 +Mm Hs SNCG Retinal ganglion cells BCSG1|SR|persyn 0.03 synuclein gamma protein-coding gene NA Ectoderm Brain 1.0 0.0 0.0379191 0.0 +Mm Hs PAX6 Retinal progenitor cells D11S812E|AN2 0.049 paired box 6 protein-coding gene 1 Ectoderm Eye 0.0 0.888889 0.014411 0.0584874 +Mm Hs CALB2 Retinal progenitor cells CAL2 0.03 calbindin 2 protein-coding gene NA Ectoderm Eye 0.0 0.777778 0.00281955 0.0370442 +Mm Hs SIX6 Retinal progenitor cells Six9|OPTX2 0.004 SIX homeobox 6 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs RHO Retinal progenitor cells OPN2|CSNBAD1|RP4 0.006 rhodopsin protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs SIX3 Retinal progenitor cells HPE2 0.014 SIX homeobox 3 protein-coding gene NA Ectoderm Eye 0.0 0.0 0.00313283 0.0 +Mm Hs NEFH Retinal progenitor cells NA 0.009 neurofilament heavy protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0037594 0.0106574 +Mm Hs LGR5 Retinal progenitor cells HG38|FEX|GPR67|GPR49 0.002 leucine rich repeat containing G protein-coupled receptor 5 protein-coding gene 1 Ectoderm Eye 0.0 0.666667 0.000313283 0.00160503 +Mm Hs SAG Retinal progenitor cells ARRESTIN|RP47 0.005 S-antigen visual arrestin protein-coding gene NA Ectoderm Eye 0.0 0.0 0.0018797 0.0 +Mm Hs RAX Retinal progenitor cells RX 0.006 retina and anterior neural fold homeobox protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0 0.0 +Mm Hs NOTCH1 Retinal progenitor cells TAN1 0.007 notch 1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.00469925 0.00763996 +Mm Hs HES1 Retinal progenitor cells FLJ20408|HES-1|Hes1|bHLHb39|HRY 0.129 hes family bHLH transcription factor 1 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.145677 0.127696 +Mm Hs MSI1 Retinal progenitor cells NA 0.022 musashi RNA binding protein 1 protein-coding gene 1 Ectoderm Eye 0.0 0.111111 0.0253759 0.0215716 +Mm Hs SOX9 Retinal progenitor cells SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Ectoderm Eye 0.0 0.0 0.0322682 0.0 +Mm SMGC Salivary mucous cells NA 0.001 submandibular gland protein C protein coding gene NA Ectoderm Oral cavity NA NA NA NA +Mm SCGB2B27 Salivary mucous cells NA 0.001 secretoglobin, family 2B, member 27 protein coding gene NA Ectoderm Oral cavity NA NA NA NA +Mm SCGB1B27 Salivary mucous cells NA 0.001 secretoglobin, family 1B, member 27 protein coding gene NA Ectoderm Oral cavity NA NA NA NA +Mm SCGB2B26 Salivary mucous cells NA 0.001 secretoglobin, family 2B, member 26 protein coding gene NA Ectoderm Oral cavity NA NA NA NA +Mm MUCL2 Salivary mucous cells NA 0.001 mucin-like 2 protein coding gene NA Ectoderm Oral cavity 0.0 0.814815 0.0 0.0 +Mm Hs KRT14 Salivary mucous cells EBS3|EBS4 0.019 keratin 14 protein-coding gene NA Ectoderm Oral cavity 0.666667 0.296296 0.0191283 0.0187042 +Mm PROL1 Salivary mucous cells NA 0.001 proline rich, lacrimal 1 protein coding gene NA Ectoderm Oral cavity 0.0 0.814815 0.0 0.0 +Mm Hs PIP Salivary mucous cells GCDFP-15|GCDFP15|GPIP4 0.001 prolactin induced protein protein-coding gene NA Ectoderm Oral cavity 0.0 0.814815 0.00188147 6.42756e-05 +Mm Hs MUCL1 Salivary mucous cells SBEM 0.001 mucin like 1 protein-coding gene NA Ectoderm Oral cavity 0.0 0.814815 0.0 0.0 +Mm Hs CNN1 Salivary mucous cells Sm-Calp 0.012 calponin 1 protein-coding gene NA Ectoderm Oral cavity 0.333333 0.037037 0.028222 0.00893431 +Mm Hs THBS1 Salivary mucous cells TSP1|THBS|TSP|THBS-1|TSP-1 0.04 thrombospondin 1 protein-coding gene NA Ectoderm Oral cavity 0.666667 0.0 0.0514268 0.0 +Mm CAR6 Salivary mucous cells NA 0.001 carbonic anhydrase 6 protein coding gene NA Ectoderm Oral cavity 0.0 0.814815 0.0 0.000128551 +Mm Hs MYH11 Salivary mucous cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene NA Ectoderm Oral cavity 0.0 0.037037 0.0163061 0.0149119 +Mm Hs KRT17 Salivary mucous cells PCHC1 0.025 keratin 17 protein-coding gene NA Ectoderm Oral cavity 1.0 0.259259 0.0736908 0.0152976 +Mm Hs PAX7 Satellite cells Hup1 0.001 paired box 7 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.00093985 0.00083451 +Mm Hs DMD Satellite cells DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85 0.012 dystrophin protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00469925 0.0143151 +Mm Hs CDH1 Satellite cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0416667 0.0572602 +Mm Hs ERBB2 Satellite cells HER-2|CD340|HER2|NGL 0.004 erb-b2 receptor tyrosine kinase 2 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00689223 0.00410836 +Mm Hs PAX3 Satellite cells HUP2|WS1 0.004 paired box 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00407268 0.00385159 +Mm Hs MYF5 Satellite cells bHLHc2 0.001 myogenic factor 5 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.428571 0.0 0.00173321 +Mm Hs CDH15 Satellite cells CDH3 0.003 cadherin 15 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.00156642 0.00301708 +Mm Hs CXCR4 Satellite cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.198308 0.00879445 +Mm Hs FOXK1 Satellite cells IMAGE:5164497 0.004 forkhead box K1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0147243 0.00147644 +Mm Hs ITGA7 Satellite cells NA 0.003 integrin subunit alpha 7 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00156642 0.0037232 +Mm Hs TCF21 Satellite cells POD1|bHLHa23 0.014 transcription factor 21 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00595238 0.0 +Mm Hs ISL1 Satellite cells Isl-1|ISLET1 0.028 ISL LIM homeobox 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.0134712 0.0313904 +Mm Hs MESP1 Satellite cells MGC10676|bHLHc5 0.005 mesoderm posterior bHLH transcription factor 1 protein-coding gene NA Mesoderm Skeletal muscle 0.0 0.0 0.00689223 0.00494287 +Mm Hs MET Satellite cells HGFR|RCCP2|DFNB97 0.006 MET proto-oncogene, receptor tyrosine kinase protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0162907 0.0046861 +Mm Hs CALCR Satellite cells CTR 0.0 calcitonin receptor protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.000385159 +Mm Hs ASB5 Satellite cells NA 0.002 ankyrin repeat and SOCS box containing 5 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 1.0 0.00156642 0.00166902 +Mm Hs SRXN1 Satellite cells Npn3|SRX1|YKL086W|dJ850E9.2|C20orf139 0.022 sulfiredoxin 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs BDKRB1 Satellite cells BKR1|B1BKR|bradyb1 0.0 bradykinin receptor B1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0018797 0.000256772 +Mm Hs CDCP1 Satellite cells CD318|SIMA135 0.01 CUB domain containing protein 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0250627 0.00751059 +Mm Hs VCAM1 Satellite cells CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00720551 0.0 +Mm Hs MYOD1 Satellite cells MYOD|bHLHc1|MYF3 0.004 myogenic differentiation 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.857143 0.000626566 0.00295288 +Mm Hs SOX8 Satellite cells NA 0.028 SRY-box 8 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.000626566 0.0 +Mm Hs SPRY1 Satellite cells hSPRY1 0.019 sprouty RTK signaling antagonist 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0303885 0.0 +Mm Hs CXCL1 Satellite cells SCYB1|GROa|MGSA-a|NAP-3|MGSA|GRO1|FSP 0.032 C-X-C motif chemokine ligand 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 1.0 0.0457393 0.0301066 +Mm Hs HMOX1 Satellite cells bK286B10|HO-1 0.046 heme oxygenase 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.857143 0.0363409 0.0480806 +Mm Hs TNFRSF12A Satellite cells FN14|TweakR|CD266 0.084 TNF receptor superfamily member 12A protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.150689 0.0 +Mm Hs RUNX1 Satellite cells PEBP2A2|AMLCR1|AML1|CBFA2 0.054 runt related transcription factor 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0313283 0.0 +Mm Hs BARX2 Satellite cells NA 0.006 BARX homeobox 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.000313283 0.00706124 +Mm Hs TRIM32 Satellite cells HT2A|TATIP|BBS11|LGMD2H 0.035 tripartite motif containing 32 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0 0.0 +Mm Hs VAMP2 Satellite cells VAMP-2|SYB2 0.186 vesicle associated membrane protein 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.367794 0.0 +Mm Hs PEG3 Satellite cells ZKSCAN22|KIAA0287|ZNF904|ZSCAN24 0.113 paternally expressed 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.0263158 0.133457 +Mm Hs MSTN Satellite cells GDF8 0.002 myostatin protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0 0.00237514 +Mm ZFP423 Satellite cells NA 0.041 zinc finger protein 423 protein coding gene 1 Mesoderm Skeletal muscle NA NA NA NA +Mm Hs SCRIB Satellite cells KIAA0147|SCRB1|Vartul 0.005 scribbled planar cell polarity protein protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00219298 0.0 +Mm Hs NFATC2 Satellite cells NF-ATP|NFATp|NFAT1 0.001 nuclear factor of activated T cells 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0 0.000706124 +Mm Hs IRF2 Satellite cells NA 0.03 interferon regulatory factor 2 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0125313 0.0340865 +Mm Hs BMI1 Satellite cells RNF51|PCGF4 0.009 BMI1 proto-oncogene, polycomb ring finger protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.00532581 0.009308 +Mm Hs SIX1 Satellite cells DFNA23 0.014 SIX homeobox 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.0 0.0269424 0.0 +Mm Hs HOXC10 Satellite cells HOX3I 0.003 homeobox C10 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.00344612 0.00346643 +Mm Hs NOTCH3 Satellite cells CASIL|CADASIL 0.02 notch 3 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.014411 0.0220182 +Mm Hs HEYL Satellite cells bHLHb33|HEY3|HESR3 0.013 hes related family bHLH transcription factor with YRPW motif-like protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.0037594 0.0150212 +Mm Hs GAL Satellite cells GMAP|GAL-GMAP|GLNN|GALN 0.014 galanin and GMAP prepropeptide protein-coding gene 1 Mesoderm Skeletal muscle 0.0 1.0 0.0184837 0.0107844 +Mm Hs NCAM1 Satellite cells NCAM|CD56 0.351 neural cell adhesion molecule 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.0297619 0.431249 +Mm Hs CAV1 Satellite cells NA 0.077 caveolin 1 protein-coding gene 1 Mesoderm Skeletal muscle 0.0 0.142857 0.121241 0.0677879 +Mm Hs GLUL Satellite glial cells GLNS 0.298 glutamate-ammonia ligase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.300439 0.305294 +Mm Hs GFAP Satellite glial cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0056391 0.0149503 +Mm Hs EDNRB Satellite glial cells ETB|HSCR2|HSCR 0.057 endothelin receptor type B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0213033 0.0674366 +Mm Hs BDKRB2 Satellite glial cells BK-2 0.001 bradykinin receptor B2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.00044915 +Mm Hs TGFA Satellite glial cells NA 0.007 transforming growth factor alpha protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00845865 0.0 +Mm Hs EPOR Satellite glial cells NA 0.004 erythropoietin receptor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0147243 0.00250241 +Mm Hs TNF Satellite glial cells TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125313 0.0 +Mm Hs IL6 Satellite glial cells IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0134712 0.00648059 +Mm Hs MAPK1 Satellite glial cells ERK2|p41mapk|MAPK2|PRKM2|PRKM1 0.171 mitogen-activated protein kinase 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.058584 0.197177 +Mm Hs JAK2 Satellite glial cells JTK10 0.006 Janus kinase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.00673725 +Mm Hs SSTR1 Satellite glial cells NA 0.0 somatostatin receptor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SLC6A1 Satellite glial cells GAT1|GABATR|GABATHG 0.043 solute carrier family 6 member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00313283 0.0 +Mm Hs PTGDS Satellite glial cells L-PGDS 0.054 prostaglandin D2 synthase protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0582707 0.0551171 +Mm Hs SOX2 Satellite glial cells NA 0.082 SRY-box 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0288221 0.0 +Mm Hs CDH1 Satellite glial cells uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0416667 0.0572345 +Hs CXCL8 Satellite glial cells SCYB8|LUCT|LECT|MDNCF|TSG-1|IL-8|NAP-1|3-10C|MONAP|AMCF-I|LYNAP|NAF|b-ENAP|GCP-1|K60|GCP1|IL8 0.02 C-X-C motif chemokine ligand 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.118734 0.0 +Mm Hs KCNJ10 Satellite glial cells Kir4.1|Kir1.2 0.046 potassium voltage-gated channel subfamily J member 10 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00219298 0.056657 +Mm Hs AQP4 Satellite glial cells MIWC 0.024 aquaporin 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00595238 0.0293872 +Mm Hs CNGA3 Satellite glial cells CCNC1|CCNCa|CNG3|CNCG3|ACHM2 0.0 cyclic nucleotide gated channel alpha 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs TLR4 Satellite glial cells hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs P2RY12 Satellite glial cells P2Y12|SP1999|HORK3 0.025 purinergic receptor P2Y12 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0318255 +Mm Hs P2RX7 Satellite glial cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00877193 0.00346487 +Mm Hs SLC1A3 Satellite glial cells EAAT1|GLAST|EA6 0.074 solute carrier family 1 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0109649 0.0 +Mm Hs IL17A Satellite glial cells IL-17A|IL-17|CTLA8|IL17 0.0 interleukin 17A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.000256657 +Mm Hs MPZ Schwann cells HMSNIB|CMT2I|CMT2J|CMT1|CMT1B 0.002 myelin protein zero protein-coding gene 1 Ectoderm Brain 0.0 0.218391 0.00219298 0.00058072 +Mm Hs ITGB4 Schwann cells CD104 0.013 integrin subunit beta 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0114943 0.0140977 0.0136792 +Mm Hs LAMC1 Schwann cells LAMB2 0.058 laminin subunit gamma 1 protein-coding gene NA Ectoderm Brain 0.0 0.126437 0.0507519 0.0596206 +Mm Hs S100B Schwann cells S100beta 0.066 S100 calcium binding protein B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.033208 0.0 +Mm Hs POU3F1 Schwann cells OCT6|SCIP|OTF6 0.013 POU class 3 homeobox 1 protein-coding gene 1 Ectoderm Brain 0.0 0.149425 0.000313283 0.0160021 +Mm Hs GFAP Schwann cells FLJ45472 0.013 glial fibrillary acidic protein protein-coding gene 1 Ectoderm Brain 0.0 0.091954 0.0056391 0.014518 +Mm Hs MAG Schwann cells SIGLEC4A|SIGLEC-4A|S-MAG|GMA 0.045 myelin associated glycoprotein protein-coding gene 1 Ectoderm Brain 0.0 0.045977 0.0109649 0.0536843 +Mm Hs OLIG1 Schwann cells BHLHB6|bHLHe21 0.066 oligodendrocyte transcription factor 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00438596 0.0826558 +Mm Hs TST Schwann cells NA 0.047 thiosulfate sulfurtransferase protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0194236 0.0 +Mm Hs NDRG1 Schwann cells DRG1|RTP|TDD5|CAP43 0.084 N-myc downstream regulated 1 protein-coding gene 1 Ectoderm Brain 0.0 0.402299 0.0620301 0.0902052 +Mm Hs CTHRC1 Schwann cells NA 0.031 collagen triple helix repeat containing 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0229885 0.0319549 0.0319396 +Mm Hs NF2 Schwann cells merlin|ACN|SCH|BANF 0.016 neurofibromin 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0441729 0.00806556 +Mm Hs SEPT9 Schwann cells MSF1|KIAA0991|PNUTL4|AF17q25|SeptD1 0.081 septin 9 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.142231 0.0 +Mm Hs AGR2 Schwann cells XAG-2|HAG-2|PDIA17 0.024 anterior gradient 2, protein disulphide isomerase family member protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0733083 0.0125823 +Mm Hs NGFR Schwann cells TNFRSF16|CD271|p75NTR 0.007 nerve growth factor receptor protein-coding gene 1 Ectoderm Brain 0.0 0.091954 0.00219298 0.00696864 +Mm Hs CLDN19 Schwann cells NA 0.001 claudin 19 protein-coding gene 1 Ectoderm Brain 0.0 0.0689655 0.000626566 0.000516196 +Mm Hs PRX Schwann cells KIAA1620 0.002 periaxin protein-coding gene 1 Ectoderm Brain 0.0 0.0804598 0.000313283 0.00174216 +Mm Hs NTRK1 Schwann cells TRKA|MTC 0.004 neurotrophic receptor tyrosine kinase 1 protein-coding gene NA Ectoderm Brain 0.0 0.0229885 0.0 0.00464576 +Mm Hs ART3 Schwann cells NA 0.021 ADP-ribosyltransferase 3 protein-coding gene NA Ectoderm Brain 0.0 0.758621 0.016604 0.0189702 +Mm Hs BCAS1 Schwann cells NABC1|AIBC1 0.035 breast carcinoma amplified sequence 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0804598 0.00783208 0.0417473 +Mm Hs NPY Schwann cells PYY4 0.015 neuropeptide Y protein-coding gene NA Ectoderm Brain 0.0 0.229885 0.0056391 0.015873 +Mm Hs ASPA Schwann cells ACY2 0.027 aspartoacylase protein-coding gene 1 Ectoderm Brain 0.0 0.310345 0.00344612 0.0309072 +Mm Hs LGI4 Schwann cells NA 0.002 leucine rich repeat LGI family member 4 protein-coding gene NA Ectoderm Brain 0.0 0.183908 0.00438596 0.000258098 +Mm Hs BAG3 Schwann cells NA 0.036 BCL2 associated athanogene 3 protein-coding gene NA Ectoderm Brain 0.0 0.0344828 0.0642231 0.0314234 +Mm Hs RXRG Schwann cells NR2B3 0.004 retinoid X receptor gamma protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs SOX10 Schwann cells DOM|WS4|WS2E 0.04 SRY-box 10 protein-coding gene 1 Ectoderm Brain NA NA NA NA +Mm Hs CMTM5 Schwann cells FLJ37521|CKLFSF5 0.044 CKLF like MARVEL transmembrane domain containing 5 protein-coding gene 1 Ectoderm Brain 0.0 0.574713 0.00783208 0.0498774 +Mm Hs BCHE Schwann cells CHE2 0.003 butyrylcholinesterase protein-coding gene NA Ectoderm Brain 0.0 0.0229885 0.00532581 0.00232288 +Mm Hs EGFL8 Schwann cells NG3|C6orf8 0.003 EGF like domain multiple 8 protein-coding gene 1 Ectoderm Brain 0.0 0.241379 0.0 0.00187121 +Mm Hs GFRA3 Schwann cells GFRa-3 0.005 GDNF family receptor alpha 3 protein-coding gene 1 Ectoderm Brain 0.0 0.16092 0.00250627 0.00471028 +Mm Hs SEMA3B Schwann cells SemA|semaV|LUCA-1|sema5|SEMAA 0.009 semaphorin 3B protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0178571 0.0 +Mm Hs MATN2 Schwann cells NA 0.017 matrilin 2 protein-coding gene 1 Ectoderm Brain 0.0 0.655172 0.0178571 0.0141954 +Mm Hs SCN7A Schwann cells Nav2.1|Nav2.2|NaG|SCN6A 0.017 sodium voltage-gated channel alpha subunit 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00814536 0.0 +Mm Hs CD82 Schwann cells R2|IA4|TSPAN27|ST6|KAI1 0.097 CD82 molecule protein-coding gene 1 Ectoderm Brain 0.0 0.045977 0.0632832 0.105239 +Mm Hs TAGLN Schwann cells SM22|WS3-10|TAGLN1|DKFZp686P11128 0.01 transgelin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.000626566 0.0 +Mm Hs NOV Schwann cells IGFBP9|CCN3 0.004 nephroblastoma overexpressed protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00469925 0.00471028 +Mm Hs ALDOC Schwann cells NA 0.078 aldolase, fructose-bisphosphate C protein-coding gene 1 Ectoderm Brain 0.0 0.229885 0.00093985 0.0960124 +Mm Hs APOD Schwann cells NA 0.062 apolipoprotein D protein-coding gene 1 Ectoderm Brain 0.0 0.298851 0.0689223 0.0611692 +Mm Hs CRYAB Schwann cells HSPB5|CRYA2 0.136 crystallin alpha B protein-coding gene 1 Ectoderm Brain 0.0 0.977012 0.10683 0.142405 +Mm Hs PLP1 Schwann cells GPM6C|SPG2 0.123 proteolipid protein 1 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0303885 0.141309 +Mm Hs PMP22 Schwann cells HNPP|GAS3|Sp110 0.102 peripheral myelin protein 22 protein-coding gene 1 Ectoderm Brain 0.0 0.850575 0.0958647 0.0987869 +Mm Hs CADM4 Schwann cells TSLL2|Necl-4|SynCAM4|IGSF4C 0.082 cell adhesion molecule 4 protein-coding gene 1 Ectoderm Brain 0.0 0.310345 0.00971178 0.0993677 +Mm Hs KCNA1 Schwann cells Kv1.1|RBK1|HUK1|MBK1|AEMK 0.031 potassium voltage-gated channel subfamily A member 1 protein-coding gene 1 Ectoderm Brain 0.0 0.643678 0.0 0.0349077 +Mm Hs CNP Schwann cells NA 0.115 2',3'-cyclic nucleotide 3' phosphodiesterase protein-coding gene 1 Ectoderm Brain 0.0 0.770115 0.0682957 0.120338 +Mm Hs GPR37L1 Schwann cells ETBR-LP-2 0.041 G protein-coupled receptor 37 like 1 protein-coding gene 1 Ectoderm Brain 0.0 0.816092 0.00438596 0.0463931 +Mm Hs NRN1 Schwann cells NRN 0.021 neuritin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0344828 0.0100251 0.0229707 +Mm CD59A Schwann cells NA 0.033 CD59a antigen protein coding gene 1 Ectoderm Brain 0.0 0.896552 0.0 0.0365854 +Mm Hs STMN1 Schwann cells OP18|PR22|PP19|Lag|FLJ32206|LAP18|C1orf215 0.43 stathmin 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.419486 0.0 +Mm Hs CAMP Sebocytes CAP18|FALL39|FALL-39|LL37 0.022 cathelicidin antimicrobial peptide protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000313283 0.0259865 +Mm Hs IHH Sebocytes HHG2|BDA1 0.002 indian hedgehog protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00205326 +Mm Hs CRHR1 Sebocytes CRF-R|CRF1|CRHR 0.002 corticotropin releasing hormone receptor 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.00205326 +Mm Hs CALCA Sebocytes CALC1 0.004 calcitonin related polypeptide alpha protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00125313 0.00513314 +Mm Hs F2RL1 Sebocytes GPR11 0.005 F2R like trypsin receptor 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00657895 0.00519731 +Mm Hs KLF5 Sebocytes IKLF|CKLF|BTEB2 0.062 Kruppel like factor 5 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0911654 0.057042 +Mm Hs EXO1 Sebocytes HEX1|hExoI 0.005 exonuclease 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00125313 0.00590311 +Mm Hs CRH Sebocytes CRH1 0.001 corticotropin releasing hormone protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000626566 0.00128329 +Mm Hs CEBPB Sebocytes NFIL6|IL6DBP|C/EBP-beta|TCF5 0.138 CCAAT enhancer binding protein beta protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.158521 0.13051 +Mm Hs CDH1 Sebocytes uvomorulin|CD324|UVO 0.056 cadherin 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0416667 0.0572345 +Mm Hs LTA4H Sebocytes NA 0.053 leukotriene A4 hydrolase protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0742481 0.0431184 +Mm Hs RDH12 Sebocytes FLJ30273|SDR7C2|LCA13|RP53 0.003 retinol dehydrogenase 12 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000313283 0.0 +Mm Hs CEBPA Sebocytes C/EBP-alpha|CEBP 0.025 CCAAT enhancer binding protein alpha protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0299647 +Mm Hs ADIPOR1 Sebocytes PAQR1|ACDCR1 0.206 adiponectin receptor 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.113722 0.222457 +Hs S100A7 Sebocytes S100A7c|PSOR1 0.0 S100 calcium binding protein A7 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs ANGPTL4 Sebocytes pp1158|PGAR|ARP4|HFARP|FIAF 0.031 angiopoietin like 4 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0300752 0.0327879 +Mm Hs CYP24A1 Sebocytes CP24|P450-CC24|CYP24 0.0 cytochrome P450 family 24 subfamily A member 1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00250627 6.41643e-05 +Mm Hs PTGER2 Sebocytes NA 0.001 prostaglandin E receptor 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00501253 0.0 +Mm Hs CNR2 Sebocytes CB2 0.0 cannabinoid receptor 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 6.41643e-05 +Mm Hs KRT7 Sebocytes CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.10119 0.0474174 +Mm Hs SRD5A2 Sebocytes NA 0.001 steroid 5 alpha-reductase 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00344612 0.0 +Mm Hs FFAR2 Sebocytes FFA2R|GPR43 0.01 free fatty acid receptor 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0122554 +Mm Hs FFAR3 Sebocytes FFA3R|GPR41 0.0 free fatty acid receptor 3 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.000641643 +Mm Hs MUC1 Sebocytes CD227|PEM|ADMCKD|ADMCKD1|MCKD|MCKD1 0.016 mucin 1, cell surface associated protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0328947 0.012512 +Mm Hs HRH1 Sebocytes NA 0.0 histamine receptor H1 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.000313283 0.0 +Mm Hs TPH1 Serotonergic neurons TPRH|TPH 0.002 tryptophan hydroxylase 1 protein-coding gene NA Ectoderm Brain 1.0 0.0 0.000940144 0.0 +Mm Hs SLC6A4 Serotonergic neurons 5-HTT|SERT1|HTT|OCD1 0.002 solute carrier family 6 member 4 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125353 0.0 +Mm Hs FEV Serotonergic neurons Pet-1 0.003 FEV, ETS transcription factor protein-coding gene 1 Ectoderm Brain 1.0 1.0 0.00313381 0.00340092 +Mm Hs TPH2 Serotonergic neurons NTPH|FLJ37295 0.001 tryptophan hydroxylase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs DDC Serotonergic neurons AADC 0.014 dopa decarboxylase protein-coding gene 1 Ectoderm Brain 1.0 1.0 0.00438734 0.0165554 +Mm Hs SLC18A2 Serotonergic neurons SVMT|SVAT|VMAT2 0.006 solute carrier family 18 member A2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00125353 0.0 +Mm Hs ESM1 Serotonergic neurons NA 0.006 endothelial cell specific molecule 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0122219 0.0048768 +Mm Hs SLC22A3 Serotonergic neurons NA 0.004 solute carrier family 22 member 3 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Hs KITLG Sertoli cells SCF|Kitl|KL-1|FPH2|SLF|DFNA69 0.001 KIT ligand protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00626566 0.0 +Mm Hs AMH Sertoli cells MIS 0.004 anti-Mullerian hormone protein-coding gene 1 Mesoderm Reproductive 0.0 0.947368 0.0150376 0.000128642 +Mm Hs INHBB Sertoli cells NA 0.005 inhibin subunit beta B protein-coding gene 1 Mesoderm Reproductive 0.0 0.710526 0.00344612 0.00347334 +Mm Hs SHBG Sertoli cells ABP|TEBG|MGC126834|MGC138391 0.001 sex hormone binding globulin protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00281955 0.0 +Mm Hs GATA1 Sertoli cells ERYF1|NFE1|GATA-1 0.008 GATA binding protein 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0178571 0.00591754 +Mm Hs GATA4 Sertoli cells NA 0.008 GATA binding protein 4 protein-coding gene 1 Mesoderm Reproductive 0.0 0.710526 0.00469925 0.00623915 +Mm Hs DHH Sertoli cells HHG-3|MGC35145 0.002 desert hedgehog protein-coding gene 1 Mesoderm Reproductive 0.0 0.710526 0.0 0.00141506 +Mm Hs AR Sertoli cells AIS|NR3C4|SMAX1|HUMARA|DHTR|SBMA 0.013 androgen receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0018797 0.016016 +Mm Hs GDNF Sertoli cells ATF1|ATF2|HFB1-GDNF 0.0 glial cell derived neurotrophic factor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000313283 0.000192963 +Mm Hs MAFB Sertoli cells KRML 0.053 MAF bZIP transcription factor B protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0592105 0.0530006 +Mm Hs GAMT Sertoli cells PIG2|TP53I2 0.051 guanidinoacetate N-methyltransferase protein-coding gene 1 Mesoderm Reproductive 0.0 0.815789 0.0661028 0.0439956 +Mm Hs MEIG1 Sertoli cells bA2K17.3|SPATA39 0.018 meiosis/spermiogenesis associated 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0263158 0.0140977 0.0195536 +Mm KITL Sertoli cells NA 0.041 kit ligand protein coding gene 1 Mesoderm Reproductive 0.0 0.552632 0.0 0.0497202 +Mm Hs HES5 Sertoli cells bHLHb38 0.036 hes family bHLH transcription factor 5 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00125313 0.0423876 +Mm CCL9 Sertoli cells NA 0.037 chemokine (C-C motif) ligand 9 protein coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0442529 +Mm Hs NF2 Sertoli cells merlin|ACN|SCH|BANF 0.016 neurofibromin 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0441729 0.00804014 +Mm Hs INHA Sertoli cells NA 0.006 inhibin subunit alpha protein-coding gene 1 Mesoderm Reproductive 0.0 1.0 0.0134712 0.00257284 +Mm Hs DES Sertoli cells CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0093985 0.0233486 +Mm Hs FAS Sertoli cells CD95|APO-1|FAS1|APT1|TNFRSF6 0.011 Fas cell surface death receptor protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0147243 0.0108059 +Hs FASLG Sertoli cells FasL|CD178|APT1LG1|TNFSF6 0.0 Fas ligand protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000626566 0.0 +Hs TF Sertoli cells PRO1557|PRO2086 0.004 transferrin protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0175439 0.0 +Mm Hs WT1 Sertoli cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0225564 0.0 +Mm Hs AARD Sertoli cells LOC441376|C8orf85 0.012 alanine and arginine rich domain containing protein protein-coding gene 1 Mesoderm Reproductive 0.0 1.0 0.0137845 0.0103557 +Mm CST12 Sertoli cells NA 0.003 cystatin 12 protein coding gene 1 Mesoderm Reproductive 0.0 1.0 0.0 0.00102914 +Mm DEFB19 Sertoli cells NA 0.003 defensin beta 19 protein coding gene 1 Mesoderm Reproductive 0.0 1.0 0.0 0.00167235 +Mm Hs CST9 Sertoli cells CTES7A 0.002 cystatin 9 protein-coding gene 1 Mesoderm Reproductive 0.0 0.921053 0.0 0.000771853 +Mm RHOX8 Sertoli cells NA 0.002 reproductive homeobox 8 protein coding gene 1 Mesoderm Reproductive NA NA NA NA +Mm GSTM6 Sertoli cells NA 0.006 glutathione S-transferase, mu 6 protein coding gene 1 Mesoderm Reproductive 0.0 0.947368 0.0 0.00540297 +Mm ETD Sertoli cells NA 0.001 embryonic testis differentiation protein coding gene 1 Mesoderm Reproductive 0.0 0.736842 0.0 0.000128642 +Mm Hs TMEM184A Sertoli cells MGC9712|SDMG1 0.006 transmembrane protein 184A protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs WNT6 Sertoli cells NA 0.007 Wnt family member 6 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00532581 0.0 +Mm Hs MRO Sertoli cells FLJ30140|C18orf3 0.004 maestro protein-coding gene 1 Mesoderm Reproductive 0.0 0.789474 0.000313283 0.00315173 +Mm Hs HSD17B3 Sertoli cells SDR12C2 0.002 hydroxysteroid 17-beta dehydrogenase 3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.736842 0.00281955 0.000321605 +Mm Hs AMHR2 Sertoli cells MISR2|MISRII 0.002 anti-Mullerian hormone receptor type 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.473684 0.0 0.000900495 +Mm Hs SEMA5B Sertoli cells SemG|KIAA1445|FLJ10372|SEMAG 0.003 semaphorin 5B protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs SCX Sertoli cells bHLHa48|bHLHa41|SCXA|SCXB 0.003 scleraxis bHLH transcription factor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00219298 0.0 +Mm Hs HSD17B1 Sertoli cells MGC138140|SDR28C1|EDH17B2 0.002 hydroxysteroid 17-beta dehydrogenase 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.657895 0.00469925 0.000128642 +Mm TSX Sertoli cells NA 0.0 testis specific X-linked gene protein coding gene 1 Mesoderm Reproductive NA NA NA NA +Mm Hs STIM1 Sertoli cells GOK|D11S4896E 0.01 stromal interaction molecule 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00093985 0.0 +Mm Hs ANKRD7 Sertoli cells TSA806 0.01 ankyrin repeat domain 7 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0491855 0.00295877 +Mm Hs PHF7 Sertoli cells NYD-SP6|HSPC226 0.018 PHD finger protein 7 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0617168 0.00939088 +Mm Hs CXCL12 Sertoli cells SCYB12|SDF-1a|SDF-1b|PBSF|TLSF-a|TLSF-b|TPAR1|SDF1A|SDF1B|SDF1 0.07 C-X-C motif chemokine ligand 12 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0269424 0.0816235 +Mm Hs STAR Sertoli cells StAR|STARD1 0.001 steroidogenic acute regulatory protein protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000313283 0.0 +Mm Hs WFDC2 Sertoli cells HE4|WAP5|dJ461P17.6|EDDM4 0.056 WAP four-disulfide core domain 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0942982 0.0 +Mm Hs PRND Sertoli cells DPL|dJ1068H6.4|DOPPEL|PrPLP 0.0 prion like protein doppel protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0018797 0.0 +Mm Hs HSPBAP1 Sertoli cells FLJ22623|PASS1 0.005 HSPB1 associated protein 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0103383 0.00405223 +Mm Hs NXF3 Sertoli cells NA 0.0 nuclear RNA export factor 3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00093985 0.000128642 +Mm Hs GBA2 Sertoli cells KIAA1605|AD035|DKFZp762K054|SPG46 0.001 glucosylceramidase beta 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00125313 0.000900495 +Mm Hs PADI2 Sertoli cells KIAA0994|PDI2 0.007 peptidyl arginine deiminase 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0075188 0.00720396 +Mm Hs ABCG8 Sertoli cells GBD4 0.002 ATP binding cassette subfamily G member 8 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.00257284 +Mm Hs DIAPH2 Sertoli cells POF2|DIA2 0.005 diaphanous related formin 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00783208 0.00398791 +Mm Hs CTSA Sertoli cells GSL|PPGB 0.104 cathepsin A protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0241228 0.121953 +Mm Hs PFKFB3 Sertoli cells NA 0.006 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00689223 0.00566026 +Mm Hs MSI1 Sertoli cells NA 0.022 musashi RNA binding protein 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.184211 0.0253759 0.021226 +Mm Hs NOTCH2 Sertoli cells NA 0.096 notch 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.605263 0.0200501 0.113398 +Mm Hs GATA6 Sertoli cells NA 0.019 GATA binding protein 6 protein-coding gene 1 Mesoderm Reproductive 0.0 0.605263 0.00469925 0.0196823 +Mm Hs CLDN11 Sertoli cells OSP|OTM 0.059 claudin 11 protein-coding gene 1 Mesoderm Reproductive 0.0 0.473684 0.0422932 0.0641925 +Mm Hs OCLN Sertoli cells PPP1R115 0.013 occludin protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.000313283 0.0160803 +Mm SERPINA3N Sertoli cells NA 0.009 serine (or cysteine) peptidase inhibitor, clade A, member 3N protein coding gene 1 Mesoderm Reproductive NA NA NA NA +Mm Hs SERPINB9 Sertoli cells CAP3|PI9 0.018 serpin family B member 9 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0328947 0.0 +Mm Hs SERPING1 Sertoli cells C1IN|C1-INH|HAE1|HAE2|C1NH 0.066 serpin family G member 1 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0993108 0.0 +Mm Hs CD55 Sertoli cells TC|CROM|DAF 0.037 CD55 molecule (Cromer blood group) protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.12594 0.0197466 +Mm Hs CD46 Sertoli cells TRA2.10|MGC26544|MIC10 0.014 CD46 molecule protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0786341 0.000900495 +Mm Hs CLU Sertoli cells SGP-2|SP-40|TRPM-2|KUB1|CLU2|CLI|APOJ 0.168 clusterin protein-coding gene 1 Mesoderm Reproductive 0.0 1.0 0.216165 0.160803 +Mm Hs FSHR Sertoli cells FSHRO|LGR1|ODG1 0.0 follicle stimulating hormone receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0 0.0 +Mm Hs RXRB Sertoli cells NR2B2|H-2RIIBP|RCoR-1 0.009 retinoid X receptor beta protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00125313 0.0 +Mm Hs PRLR Sertoli cells NA 0.013 prolactin receptor protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0106516 0.0138934 +Mm Hs SLC16A3 Sertoli cells NA 0.033 solute carrier family 16 member 3 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0614035 0.0 +Mm Hs EPS8 Sertoli cells NA 0.02 epidermal growth factor receptor pathway substrate 8 protein-coding gene 1 Mesoderm Reproductive 0.0 0.105263 0.0413534 0.0149868 +Mm Hs NR1H2 Sertoli cells NER|NER-I|RIP15|LXR-b|LXRb 0.039 nuclear receptor subfamily 1 group H member 2 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0548246 0.033061 +Mm Hs BCAR3 Sertoli cells SH2D3B|AND-34 0.007 BCAR3, NSP family adaptor protein protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.00595238 0.00688236 +Mm Hs SOX9 Sertoli cells SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Mesoderm Reproductive 0.0 0.0 0.0322682 0.0 +Mm Hs ACTA2 Smooth muscle cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene 1 Mesoderm Smooth muscle 0.904762 1.0 0.0135604 0.0313632 +Mm Hs CNN1 Smooth muscle cells Sm-Calp 0.012 calponin 1 protein-coding gene 1 Mesoderm Smooth muscle 0.571429 0.421488 0.0249133 0.0057553 +Mm Hs HEXIM1 Smooth muscle cells CLP-1|MAQ1 0.019 hexamethylene bisacetamide inducible 1 protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.0330578 0.0296436 0.0175892 +Mm Hs TAGLN Smooth muscle cells SM22|WS3-10|TAGLN1|DKFZp686P11128 0.01 transgelin protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.000630716 0.0 +Mm Hs RGS5 Smooth muscle cells NA 0.043 regulator of G protein signaling 5 protein-coding gene 1 Mesoderm Smooth muscle NA NA NA NA +Mm Hs WFDC1 Smooth muscle cells PS20 0.024 WAP four-disulfide core domain 1 protein-coding gene 1 Mesoderm Smooth muscle 0.285714 0.0 0.0129297 0.0 +Mm Hs NOTCH3 Smooth muscle cells CASIL|CADASIL 0.02 notch 3 protein-coding gene 1 Mesoderm Smooth muscle 0.571429 0.495868 0.0107222 0.0183652 +Mm Hs RPRM Smooth muscle cells FLJ90327|REPRIMO 0.039 reprimo, TP53 dependent G2 arrest mediator homolog protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.00283822 0.0 +Mm Hs DES Smooth muscle cells CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene 1 Mesoderm Smooth muscle 0.238095 0.735537 0.00788395 0.0177186 +Mm Hs FHL2 Smooth muscle cells SLIM3|DRAL 0.043 four and a half LIM domains 2 protein-coding gene 1 Mesoderm Smooth muscle 0.238095 0.0826446 0.103122 0.0281945 +Mm Hs FBLN5 Smooth muscle cells EVEC|UP50|DANCE|ARMD3 0.027 fibulin 5 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.115702 0.0277515 0.0270305 +Mm Hs LOX Smooth muscle cells NA 0.017 lysyl oxidase protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0743802 0.0151372 0.0164252 +Mm Hs NF2 Smooth muscle cells merlin|ACN|SCH|BANF 0.016 neurofibromin 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.00826446 0.0444655 0.00801862 +Mm Hs ANGPT1 Smooth muscle cells KIAA0003|Ang1 0.01 angiopoietin 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0165289 0.00189215 0.0123513 +Mm Hs CRABP1 Smooth muscle cells CRABP|CRABPI|RBP5 0.025 cellular retinoic acid binding protein 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.00826446 0.0302744 0.0234739 +Mm Hs MYH11 Smooth muscle cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene 1 Mesoderm Smooth muscle 1.0 0.958678 0.0097761 0.00756596 +Mm Hs FABP4 Smooth muscle cells A-FABP|aP2 0.028 fatty acid binding protein 4 protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.206612 0.00946074 0.0318805 +Mm Hs ACTC1 Smooth muscle cells CMD1R|ACTC 0.011 actin, alpha, cardiac muscle 1 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.0826446 0.013245 0.00788929 +Mm Hs ANKRD1 Smooth muscle cells C-193|ALRP|CVARP|MCARP 0.007 ankyrin repeat domain 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.00788395 0.00666063 +Mm Hs OBSCN Smooth muscle cells KIAA1556|UNC89|KIAA1639|ARHGEF30 0.002 obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.000315358 0.00271599 +Mm Hs PDE4DIP Smooth muscle cells KIAA0477|KIAA0454|MMGL|CMYA2 0.012 phosphodiesterase 4D interacting protein protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0247934 0.00189215 0.0140326 +Mm Hs LMO7 Smooth muscle cells FBX20|KIAA0858|FBXO20 0.028 LIM domain 7 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0384737 0.0272892 +Mm Hs MYH6 Smooth muscle cells NA 0.003 myosin heavy chain 6 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0 0.00349198 +Mm Hs NEXN Smooth muscle cells nexilin|NELIN 0.014 nexilin F-actin binding protein protein-coding gene 1 Mesoderm Smooth muscle 0.428571 0.46281 0.0141911 0.00931195 +Mm Hs ACTG2 Smooth muscle cells ACTSG|ACTL3|ACTA3 0.011 actin, gamma 2, smooth muscle, enteric protein-coding gene 1 Mesoderm Smooth muscle 0.52381 0.31405 0.0173447 0.00717796 +Mm Hs MUSTN1 Smooth muscle cells Mustang 0.013 musculoskeletal, embryonic nuclear protein 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.876033 0.0 0.00995861 +Mm Hs SOD3 Smooth muscle cells EC-SOD 0.027 superoxide dismutase 3 protein-coding gene 1 Mesoderm Smooth muscle 0.857143 0.0 0.0561337 0.0 +Mm Hs HSPB6 Smooth muscle cells FLJ32389|Hsp20|PPP1R91 0.005 heat shock protein family B (small) member 6 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.157025 0.00189215 0.00497931 +Mm Hs RRAD Smooth muscle cells REM3|RAD 0.007 RRAD, Ras related glycolysis inhibitor and calcium channel regulator protein-coding gene 1 Mesoderm Smooth muscle 0.285714 0.0 0.00346894 0.0 +Mm Hs LMOD1 Smooth muscle cells 64kD|D1|1D 0.01 leiomodin 1 protein-coding gene 1 Mesoderm Smooth muscle 0.761905 0.652893 0.0116682 0.00387998 +Mm Hs ITGA1 Smooth muscle cells VLA1|CD49a 0.043 integrin subunit alpha 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0952381 0.46281 0.0223904 0.0456544 +Mm Hs SPEG Smooth muscle cells MGC12676|KIAA1297|SPEGalpha|SPEGbeta|BPEG|APEG1 0.005 SPEG complex locus protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.000315358 0.0 +Mm Hs EHD2 Smooth muscle cells PAST2 0.034 EH domain containing 2 protein-coding gene 1 Mesoderm Smooth muscle 0.333333 0.38843 0.0192368 0.0353725 +Mm Hs RBPMS2 Smooth muscle cells NA 0.017 RNA binding protein, mRNA processing factor 2 protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.0 0.00630716 0.0 +Mm Hs MAP3K7CL Smooth muscle cells TAKL|TAK1L|TAKL-1|TAKL-2|TAKL-4|C21orf7 0.006 MAP3K7 C-terminal like protein-coding gene 1 Mesoderm Smooth muscle 0.238095 0.61157 0.0059918 0.000517331 +Mm Hs SLC38A11 Smooth muscle cells FLJ39822|AVT2 0.003 solute carrier family 38 member 11 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.0 0.000946074 0.0 +Mm Hs GJA4 Smooth muscle cells CX37 0.02 gap junction protein alpha 4 protein-coding gene 1 Mesoderm Smooth muscle 0.285714 0.578512 0.0116682 0.0174599 +Mm Hs KAT2B Smooth muscle cells P/CAF|GCN5L|PCAF 0.005 lysine acetyltransferase 2B protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.000946074 0.0059493 +Mm Hs LGR6 Smooth muscle cells FLJ14471 0.002 leucine rich repeat containing G protein-coupled receptor 6 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0330578 0.0 0.00193999 +Mm Hs MSRB3 Smooth muscle cells FLJ36866|DKFZp686C1178|DFNB74 0.007 methionine sulfoxide reductase B3 protein-coding gene 1 Mesoderm Smooth muscle 0.52381 0.132231 0.0148218 0.00316865 +Mm Hs AKT2 Smooth muscle cells NA 0.014 AKT serine/threonine kinase 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0165289 0.00788395 0.0140326 +Mm Hs RASL12 Smooth muscle cells RIS 0.004 RAS like family 12 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.000946074 0.0 +Mm Hs ZBTB44 Smooth muscle cells HSPC063|ZNF851|BTBD15 0.013 zinc finger and BTB domain containing 44 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0362662 0.0 +Mm Hs WWP2 Smooth muscle cells AIP2 0.007 WW domain containing E3 ubiquitin protein ligase 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.00315358 0.0 +Mm Hs SSPN Smooth muscle cells SPN1|SPN2|KRAG 0.004 sarcospan protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.00220751 0.0 +Mm Hs OTUD1 Smooth muscle cells DUBA7|OTDC1 0.003 OTU deubiquitinase 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0330578 0.00283822 0.00265132 +Mm Hs FAS Smooth muscle cells CD95|APO-1|FAS1|APT1|TNFRSF6 0.011 Fas cell surface death receptor protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0495868 0.0148218 0.0104759 +Mm Hs VASN Smooth muscle cells SLITL2 0.012 vasorin protein-coding gene 1 Mesoderm Smooth muscle 0.0952381 0.0 0.0264901 0.0 +Mm Hs PDGFD Smooth muscle cells SCDGF-B|MSTP036|IEGF 0.003 platelet derived growth factor D protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0330578 0.0037843 0.00245732 +Mm Hs SMOC1 Smooth muscle cells NA 0.006 SPARC related modular calcium binding 1 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.0 0.00567644 0.0 +Mm Hs AAED1 Smooth muscle cells C9orf21 0.018 AhpC/TSA antioxidant enzyme domain containing 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0991736 0.0201829 0.0152613 +Mm Hs AOC3 Smooth muscle cells VAP1|HPAO|VAP-1 0.004 amine oxidase, copper containing 3 protein-coding gene 1 Mesoderm Smooth muscle 0.285714 0.322314 0.000946074 0.00193999 +Mm Hs SEC24D Smooth muscle cells KIAA0755 0.013 SEC24 homolog D, COPII coat complex component protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0252286 0.0 +Mm Hs KCNAB1 Smooth muscle cells AKR6A3|KCNA1B|hKvBeta3|Kvb1.3|hKvb3 0.006 potassium voltage-gated channel subfamily A member regulatory beta subunit 1 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.214876 0.0 0.00562597 +Mm Hs MYLK4 Smooth muscle cells SgK085 0.0 myosin light chain kinase family member 4 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0330578 0.0 0.000258665 +Mm Hs KIF1C Smooth muscle cells SPAX2|SPG58 0.014 kinesin family member 1C protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0661157 0.0321665 0.00937662 +Mm Hs MRVI1 Smooth muscle cells JAW1L|IRAG 0.003 murine retrovirus integration site 1 homolog protein-coding gene 1 Mesoderm Smooth muscle 0.0952381 0.264463 0.0037843 0.000581997 +Mm Hs JPH2 Smooth muscle cells JP-2 0.002 junctophilin 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.14876 0.0 0.00200466 +Mm Hs ITGA9 Smooth muscle cells RLC|ITGA4L|ALPHA-RLC 0.004 integrin subunit alpha 9 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0578512 0.0 0.00446198 +Mm Hs KCNMB1 Smooth muscle cells hslo-beta 0.004 potassium calcium-activated channel subfamily M regulatory beta subunit 1 protein-coding gene 1 Mesoderm Smooth muscle 0.238095 0.115702 0.00883002 0.00181066 +Mm Hs NOX4 Smooth muscle cells KOX-1|KOX 0.003 NADPH oxidase 4 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0413223 0.0 0.00297465 +Mm Hs NOV Smooth muscle cells IGFBP9|CCN3 0.004 nephroblastoma overexpressed protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0661157 0.00473037 0.00420331 +Mm Hs DMPK Smooth muscle cells DMK|DM1PK|MDPK|MT-PK|DM 0.006 DM1 protein kinase protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.206612 0.0 0.00569064 +Mm Hs SH3BGR Smooth muscle cells 21-GARP 0.007 SH3 domain binding glutamate rich protein protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.00946074 0.0 +Mm Hs ITGA8 Smooth muscle cells NA 0.005 integrin subunit alpha 8 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.165289 0.00819931 0.00303932 +Mm Hs TCF21 Smooth muscle cells POD1|bHLHa23 0.014 transcription factor 21 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0059918 0.0 +Mm Hs ADAMDEC1 Smooth muscle cells M12.219 0.003 ADAM like decysin 1 protein-coding gene 1 Mesoderm Smooth muscle 0.190476 0.0165289 0.0126143 0.000905328 +Mm Hs HHIP Smooth muscle cells FLJ20992 0.008 hedgehog interacting protein protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.0661157 0.0116682 0.0069193 +Mm Hs MFAP5 Smooth muscle cells MAGP2|MP25 0.021 microfibril associated protein 5 protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.107438 0.0097761 0.0234092 +Mm Hs SPON2 Smooth muscle cells DIL1 0.017 spondin 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0 0.0491958 0.0 +Mm Hs LAMB2 Smooth muscle cells NPHS5|LAMS 0.019 laminin subunit beta 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.46281 0.013245 0.0175892 +Mm Hs GJC1 Smooth muscle cells CX45|GJA7 0.026 gap junction protein gamma 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0952381 0.297521 0.0107222 0.0276772 +Mm Hs ACKR3 Smooth muscle cells GPR159|CMKOR1|CXCR7 0.01 atypical chemokine receptor 3 protein-coding gene 1 Mesoderm Smooth muscle 0.047619 0.107438 0.00630716 0.0106699 +Mm Hs OGN Smooth muscle cells mimecan|OIF|SLRR3A 0.031 osteoglycin protein-coding gene 1 Mesoderm Smooth muscle 0.142857 0.181818 0.0258594 0.0312985 +Mm Hs SMTN Smooth muscle cells NA 0.017 smoothelin protein-coding gene 1 Mesoderm Smooth muscle 0.428571 0.0 0.0189215 0.0 +Mm Hs BGN Smooth muscle cells DSPG1|SLRR1A 0.097 biglycan protein-coding gene 1 Mesoderm Smooth muscle 0.714286 0.719008 0.0611794 0.102173 +Mm Hs MYL9 Smooth muscle cells MYRL2|MLC2|LC20|MRLC1 0.081 myosin light chain 9 protein-coding gene 1 Mesoderm Smooth muscle 1.0 1.0 0.154841 0.0560657 +Mm Hs MYLK Smooth muscle cells smMLCK|MYLK1|MLCK1 0.047 myosin light chain kinase protein-coding gene 1 Mesoderm Smooth muscle 1.0 0.958678 0.0491958 0.0396405 +Mm Hs PCP4L1 Smooth muscle cells IQM1 0.044 Purkinje cell protein 4 like 1 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.735537 0.0 0.0499871 +Mm Hs SNCG Smooth muscle cells BCSG1|SR|persyn 0.03 synuclein gamma protein-coding gene 1 Mesoderm Smooth muscle 0.52381 0.0 0.0350047 0.0 +Mm Hs PLN Smooth muscle cells CMD1P 0.006 phospholamban protein-coding gene 1 Mesoderm Smooth muscle 0.666667 0.198347 0.00914538 0.00323332 +Mm Hs NRP2 Smooth muscle cells VEGF165R2 0.04 neuropilin 2 protein-coding gene 1 Mesoderm Smooth muscle 0.0 0.0578512 0.0356354 0.0412571 +Mm Hs CAPN1 Spermatocytes muCANP|muCL|CANPL1 0.018 calpain 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0484177 0.0107154 +Mm Hs JAKMIP1 Spermatocytes MARLIN1|JAMIP1|Gababrbp|FLJ31564 0.017 janus kinase and microtubule interacting protein 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.000632911 0.0209175 +Mm Hs SMCP Spermatocytes NA 0.013 sperm mitochondria associated cysteine rich protein protein-coding gene NA Mesoderm Reproductive 0.125 0.0 0.0379747 0.0 +Mm Hs GKAP1 Spermatocytes GKAP42|FKSG21 0.037 G kinase anchoring protein 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0537975 0.0358037 +Mm Hs SPATA33 Spermatocytes FLJ31606|C16orf55 0.023 spermatogenesis associated 33 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0708861 0.0 +Mm Hs NOTCH3 Spermatocytes CASIL|CADASIL 0.02 notch 3 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.014557 0.0220725 +Hs GCNA Spermatocytes NAAR1|ACRC 0.0 germ cell nuclear acidic peptidase protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00189873 0.0 +Hs TP73 Spermatocytes P73 0.0 tumor protein p73 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.000632911 0.0 +Mm Hs PGK2 Spermatocytes PGKPS|PGK-2 0.012 phosphoglycerate kinase 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0335443 0.00827719 +Mm Hs ACR Spermatocytes NA 0.003 acrosin protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00759494 0.00243824 +Mm Hs SYCP1 Spermatocytes HOM-TES-14|CT8 0.008 synaptonemal complex protein 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0253165 0.0 +Mm Hs SYCP2 Spermatocytes NA 0.006 synaptonemal complex protein 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0256329 0.0 +Mm Hs SYCP3 Spermatocytes NA 0.003 synaptonemal complex protein 3 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0117089 0.0 +Mm Hs TXNDC8 Spermatocytes bA427L11.2|TRX6|SPTRX-3 0.005 thioredoxin domain containing 8 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0129747 0.0 +Mm Hs TEX101 Spermatocytes MGC4766|SGRG|CT131|SPATA44 0.005 testis expressed 101 protein-coding gene NA Mesoderm Reproductive 0.03125 0.0 0.0101266 0.0 +Mm Hs CD46 Spermatocytes TRA2.10|MGC26544|MIC10 0.014 CD46 molecule protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0794304 0.0008983 +Mm Hs INHBB Spermatocytes NA 0.005 inhibin subunit beta B protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.00348101 0.00519731 +Mm Hs PRM1 Spermatocytes CT94.1 0.022 protamine 1 protein-coding gene NA Mesoderm Reproductive 1.0 0.0 0.0844937 0.00904716 +Mm Hs PRM2 Spermatocytes CT94.2 0.022 protamine 2 protein-coding gene NA Mesoderm Reproductive 1.0 0.0 0.0797468 0.00930382 +Mm Hs IGF2 Spermatocytes FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene NA Mesoderm Reproductive 0.15625 0.0 0.0452532 0.0008983 +Mm Hs TNP1 Spermatocytes NA 0.018 transition protein 1 protein-coding gene NA Mesoderm Reproductive 0.8125 0.0 0.0623418 0.0 +Mm Hs OSR2 Spermatocytes FLJ90037 0.011 odd-skipped related transciption factor 2 protein-coding gene NA Mesoderm Reproductive 0.21875 0.0 0.0155063 0.008983 +Mm Hs ABHD2 Spermatozoa LABH2 0.06 abhydrolase domain containing 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0416667 0.0655759 +Mm Hs HVCN1 Spermatozoa MGC15619|Hv1|VSOP 0.014 hydrogen voltage gated channel 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0125313 0.0138595 +Mm Hs GPR55 Spermatozoa NA 0.0 G protein-coupled receptor 55 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0 0.000128329 +Mm Hs ABCA1 Spermatozoa TGD|HDLDT1 0.032 ATP binding cassette subfamily A member 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0169173 0.0365095 +Mm Hs SLC31A1 Spermatozoa hCTR1|CTR1|COPT1 0.052 solute carrier family 31 member 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0112782 0.0 +Mm Hs LDHC Spermatozoa CT32 0.014 lactate dehydrogenase C protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0382206 0.010138 +Mm Hs PRKAA2 Spermatozoa AMPK|AMPKa2|PRKAA 0.008 protein kinase AMP-activated catalytic subunit alpha 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0037594 0.00956048 +Mm Hs HSPA2 Spermatozoa NA 0.03 heat shock protein family A (Hsp70) member 2 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0429198 0.0289381 +Mm Hs ODF1 Spermatozoa ODFPG|ODF27|RT7|HSPB10|CT133 0.004 outer dense fiber of sperm tails 1 protein-coding gene NA Mesoderm Reproductive 0.0 0.0 0.0112782 0.00230991 +Hs MMP1 Stromal cells NA 0.003 matrix metallopeptidase 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0156642 0.0 +Mm Hs MMP2 Stromal cells TBE-1|CLG4|CLG4A 0.045 matrix metallopeptidase 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0676692 0.0385751 +Mm Hs MMP9 Stromal cells CLG4B 0.015 matrix metallopeptidase 9 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00971178 0.017009 +Mm Hs TLR3 Stromal cells CD283 0.003 toll like receptor 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00720551 0.0 +Mm Hs MME Stromal cells CALLA|CD10 0.017 membrane metalloendopeptidase protein-coding gene NA Mesoderm Connective tissue 0.0 0.2 0.0269424 0.0149551 +Mm Hs PECAM1 Stromal cells CD31 0.051 platelet and endothelial cell adhesion molecule 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0441729 0.0535302 +Mm Hs ITGA4 Stromal cells CD49d|CD49D 0.036 integrin subunit alpha 4 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0112782 0.0412709 +Hs ICAM3 Stromal cells CDW50|ICAM-R|CD50 0.0 intercellular adhesion molecule 3 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs ITGAV Stromal cells CD51|VNRA|MSK8|VTNR 0.026 integrin subunit alpha V protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0219298 0.0275353 +Mm Hs ICAM1 Stromal cells CD54 0.009 intercellular adhesion molecule 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00595238 0.0100128 +Mm Hs VCAM1 Stromal cells CD106 0.041 vascular cell adhesion molecule 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00720551 0.0 +Mm Hs KIT Stromal cells CD117|SCFR|C-Kit|PBT 0.015 KIT proto-oncogene receptor tyrosine kinase protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00250627 0.0185494 +Mm Hs PDGFRA Stromal cells CD140a|PDGFR2|GAS9 0.044 platelet derived growth factor receptor alpha protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.047619 0.0440308 +Mm Hs PDGFRB Stromal cells JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene NA Mesoderm Connective tissue 0.0 0.8 0.0363409 0.0331836 +Mm Hs MADCAM1 Stromal cells MACAM1 0.001 mucosal vascular addressin cell adhesion molecule 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00219298 0.00147625 +Mm Hs B4GALNT1 Stromal cells beta1-4GalNAc-T|GALGT|SPG26 0.003 beta-1,4-N-acetyl-galactosaminyltransferase 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0042362 +Mm Hs TLR1 Stromal cells rsc786|KIAA0012|CD281 0.0 toll like receptor 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs TLR2 Stromal cells TIL4|CD282 0.014 toll like receptor 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00093985 0.0 +Mm Hs TLR4 Stromal cells hToll|CD284|TLR-4|ARMD10 0.0 toll like receptor 4 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.000313283 0.0 +Mm Hs CDH11 Stromal cells CAD11 0.039 cadherin 11 protein-coding gene NA Mesoderm Connective tissue 0.0 1.0 0.0516917 0.0360077 +Mm Hs CALB2 Stromal cells CAL2 0.03 calbindin 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00281955 0.037484 +Mm Hs DES Stromal cells CMD1I|CSM1|CSM2 0.021 desmin protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0093985 0.0232991 +Mm Hs MMRN2 Stromal cells EndoGlyx-1|FLJ13465|EMILIN3 0.022 multimerin 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00845865 0.0262516 +Mm Hs CD248 Stromal cells TEM1|CD164L1 0.022 CD248 molecule protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.014411 0.0240693 +Mm Hs FAP Stromal cells NA 0.006 fibroblast activation protein alpha protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.00250627 0.00654685 +Mm Hs LAMC2 Stromal cells nicein-100kDa|kalinin-105kDa|BM600-100kDa|EBR2|LAMB2T|LAMNB2|EBR2A 0.012 laminin subunit gamma 2 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0225564 0.010077 +Mm Hs SNED1 Stromal cells FLJ00133|SST3|Snep 0.001 sushi, nidogen and EGF like domains 1 protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0 0.0 +Mm Hs TNC Stromal cells MGC167029|HXB|DFNA56 0.033 tenascin C protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0128446 0.0 +Mm Hs LUM Stromal cells SLRR2D|LDC 0.051 lumican protein-coding gene NA Mesoderm Connective tissue 0.0 0.0 0.0870927 0.0427471 +Mm Hs COL15A1 Stromal cells NA 0.016 collagen type XV alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0281955 0.0141849 +Mm Hs GDF10 Stromal cells BMP-3b 0.005 growth differentiation factor 10 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.000313283 0.00654685 +Mm Hs COL4A1 Stromal cells NA 0.105 collagen type IV alpha 1 chain protein-coding gene 1 Mesoderm Connective tissue 0.0 0.2 0.0808271 0.113158 +Mm Hs BMP4 Stromal cells BMP2B 0.019 bone morphogenetic protein 4 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.4 0.0241228 0.0164955 +Mm Hs WNT2 Stromal cells IRP|INT1L1 0.004 Wnt family member 2 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.0075188 0.0 +Mm Hs BMP5 Stromal cells NA 0.002 bone morphogenetic protein 5 protein-coding gene 1 Mesoderm Connective tissue 0.0 0.0 0.00657895 0.000770218 +Mm Hs CD3D T cells T3D 0.053 CD3d molecule protein-coding gene 1 Mesoderm Immune system 0.964427 0.864486 0.0571623 0.0262833 +Mm Hs CD3G T cells NA 0.048 CD3g molecule protein-coding gene 1 Mesoderm Immune system 0.687747 0.906542 0.0326642 0.0286904 +Mm Hs CD3E T cells NA 0.041 CD3e molecule protein-coding gene 1 Mesoderm Immune system 0.810277 0.766355 0.0384485 0.0195823 +Mm Hs HOPX T cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene NA Mesoderm Immune system 0.134387 0.0233645 0.0881252 0.0222497 +Mm Hs CCL3 T cells G0S19-1|LD78ALPHA|MIP-1-alpha|SCYA3 0.036 C-C motif chemokine ligand 3 protein-coding gene NA Mesoderm Immune system 0.0316206 0.0794393 0.00578428 0.0420272 +Mm Hs CCL4 T cells MIP-1-beta|Act-2|AT744.1|SCYA4 0.049 C-C motif chemokine ligand 4 protein-coding gene NA Mesoderm Immune system 0.16996 0.154206 0.045934 0.047492 +Hs GIMAP2 T cells DKFZp586D0824|HIMAP2|IMAP2|IAN12 0.003 GTPase, IMAP family member 2 protein-coding gene NA Mesoderm Immune system 0.142292 0.0 0.00476352 0.0 +Mm Hs SYT3 T cells NA 0.004 synaptotagmin 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs NOTCH3 T cells CASIL|CADASIL 0.02 notch 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0156516 0.0223798 +Mm Hs SEMA6D T cells KIAA1479|FLJ11598 0.026 semaphorin 6D protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00170126 0.0 +Mm Hs DKK3 T cells REIC 0.034 dickkopf WNT signaling pathway inhibitor 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0408302 0.0359118 +Mm Hs IFIT3 T cells ISG60|RIG-G|CIG-49|IFI60|GARG-49|IRG2|IFIT4 0.014 interferon induced protein with tetratricopeptide repeats 3 protein-coding gene NA Mesoderm Immune system 0.0158103 0.0327103 0.0224566 0.0111248 +Mm Hs CERK T cells hCERK|FLJ23239|dA59H18.3|DKFZp434E0211|FLJ21430|KIAA1646|LK4|dA59H18.2 0.011 ceramide kinase protein-coding gene NA Mesoderm Immune system 0.0 0.0046729 0.0102076 0.011255 +Mm CCL6 T cells NA 0.043 chemokine (C-C motif) ligand 6 protein coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.0535424 +Mm Hs PMCH T cells MCH 0.0 pro-melanin concentrating hormone protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 6.50576e-05 +Mm Hs CD4 T cells NA 0.009 CD4 molecule protein-coding gene 1 Mesoderm Immune system 0.0355731 0.0654206 0.0173528 0.00676599 +Mm Hs LTB T cells TNFSF3|TNFC 0.065 lymphotoxin beta protein-coding gene 1 Mesoderm Immune system 0.83004 0.518692 0.105818 0.0388394 +Mm GIMAP3 T cells NA 0.019 GTPase, IMAP family member 3 protein coding gene NA Mesoderm Immune system 0.0 0.303738 0.0 0.0194522 +Mm Hs CXCR6 T cells TYMSTR|STRL33|BONZO|CD186 0.014 C-X-C motif chemokine receptor 6 protein-coding gene 1 Mesoderm Immune system 0.00395257 0.495327 0.000340252 0.0106694 +Mm Hs IL7R T cells CD127|IL7RA 0.031 interleukin 7 receptor protein-coding gene 1 Mesoderm Immune system 0.545455 0.383178 0.0302824 0.0181511 +Mm Hs SATB1 T cells NA 0.03 SATB homeobox 1 protein-coding gene NA Mesoderm Immune system 0.0750988 0.0 0.00238176 0.0 +Mm Hs LEF1 T cells TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene 1 Mesoderm Immune system 0.00790514 0.205607 0.00952705 0.0253074 +Mm Hs ITK T cells PSCTK2|LYK 0.004 IL2 inducible T cell kinase protein-coding gene 1 Mesoderm Immune system 0.0118577 0.186916 0.0 0.00253725 +Mm Hs TRBC2 T cells TCRBC2 0.066 T cell receptor beta constant 2 other 1 Mesoderm Immune system 0.940711 0.0 0.0833617 0.0 +Mm Hs PTPRCAP T cells CD45-AP 0.072 protein tyrosine phosphatase, receptor type C associated protein protein-coding gene NA Mesoderm Immune system 0.0 0.920561 0.0 0.0749463 +Mm Hs GEM T cells NA 0.038 GTP binding protein overexpressed in skeletal muscle protein-coding gene NA Mesoderm Immune system 0.00395257 0.135514 0.039129 0.0381888 +Mm Hs CD7 T cells LEU-9|TP41|Tp40 0.03 CD7 molecule protein-coding gene 1 Mesoderm Immune system 0.664032 0.196262 0.055461 0.013597 +Mm Hs MAFF T cells hMafF 0.054 MAF bZIP transcription factor F protein-coding gene NA Mesoderm Immune system 0.0 0.0233645 0.104457 0.0479474 +Mm Hs TGIF1 T cells HPE4 0.065 TGFB induced factor homeobox 1 protein-coding gene NA Mesoderm Immune system 0.00790514 0.0 0.116706 0.0 +Mm Hs RORA T cells RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene NA Mesoderm Immune system 0.0316206 0.0 0.0125893 0.0 +Mm Hs TNFAIP3 T cells OTUD7C 0.035 TNF alpha induced protein 3 protein-coding gene NA Mesoderm Immune system 0.343874 0.0 0.0537598 0.0 +Mm Hs CREM T cells hCREM-2 0.065 cAMP responsive element modulator protein-coding gene NA Mesoderm Immune system 0.3083 0.383178 0.145288 0.038449 +Mm Hs PXDC1 T cells C6orf145 0.028 PX domain containing 1 protein-coding gene NA Mesoderm Immune system 0.0 0.154206 0.00204151 0.032724 +Mm Hs NABP1 T cells FLJ22833|DKFZp667M1322|FLJ13624|MGC111163|SSB2|hSSB2|SOSS-B2|OBFC2A 0.022 nucleic acid binding protein 1 protein-coding gene NA Mesoderm Immune system 0.0118577 0.149533 0.0517183 0.0154837 +Mm Hs FAM110A T cells bA371L19.3|C20orf55 0.014 family with sequence similarity 110 member A protein-coding gene NA Mesoderm Immune system 0.0 0.116822 0.00884655 0.0133368 +Hs EEF1B2P3 T cells EEF1B4 0.039 eukaryotic translation elongation factor 1 beta 2 pseudogene 3 pseudogene NA Mesoderm Immune system 0.490119 0.0 0.179993 0.0 +Mm Hs TRAC T cells NA 0.042 T cell receptor alpha constant other 1 Mesoderm Immune system 0.972332 0.0 0.0595441 0.0 +Mm Hs CD69 T cells CLEC2C 0.024 CD69 molecule protein-coding gene 1 Mesoderm Immune system 0.434783 0.0654206 0.0833617 0.00657082 +Hs PFN1P1 T cells NA 0.044 profilin 1 pseudogene 1 pseudogene NA Mesoderm Immune system 0.371542 0.0 0.218442 0.0 +Hs IL32 T cells NK4|TAIF|TAIFb|TAIFd 0.036 interleukin 32 protein-coding gene 1 Mesoderm Immune system 0.976285 0.0 0.138482 0.0 +Mm Hs CXCR4 T cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.6917 0.0233645 0.155835 0.0085876 +Mm H2-Q7 T cells NA 0.06 histocompatibility 2, Q region locus 7 protein coding gene NA Mesoderm Immune system 0.0 0.462617 0.0 0.066684 +Mm TRBC1 T cells TCRBC1|BV05S1J2.2 0.036 T cell receptor beta constant 1 other 1 Mesoderm Immune system NA NA NA NA +Mm Hs SEPT1 T cells PNUTL3 0.055 septin 1 protein-coding gene NA Mesoderm Immune system 0.027668 0.0 0.00136101 0.0 +Mm Hs BCL2 T cells Bcl-2|PPP1R50 0.043 BCL2, apoptosis regulator protein-coding gene NA Mesoderm Immune system 0.0118577 0.200935 0.000680504 0.0495739 +Mm Hs CYTL1 T cells C17|C4orf4 0.012 cytokine like 1 protein-coding gene NA Mesoderm Immune system 0.0 0.00934579 0.0302824 0.00800208 +Mm Hs CD2 T cells NA 0.04 CD2 molecule protein-coding gene 1 Mesoderm Immune system 0.715415 0.327103 0.04049 0.0255026 +Mm Hs CTSW T cells NA 0.026 cathepsin W protein-coding gene 1 Mesoderm Immune system 0.181818 0.261682 0.051378 0.0160692 +Mm Hs PTPN22 T cells Lyp|Lyp1|Lyp2|PTPN8 0.009 protein tyrosine phosphatase, non-receptor type 22 protein-coding gene NA Mesoderm Immune system 0.0434783 0.271028 0.00374277 0.00618047 +Mm Hs TXK T cells TKL|PSCTK5|BTKL|RLK|PTK4 0.003 TXK tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00238176 0.0 +Mm Hs GDPD3 T cells MGC4171 0.006 glycerophosphodiester phosphodiesterase domain containing 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0046729 0.00646478 0.0038384 +Mm Hs TRAF1 T cells EBI6 0.01 TNF receptor associated factor 1 protein-coding gene 1 Mesoderm Immune system 0.0513834 0.0 0.00204151 0.0 +Mm Hs IL2RA T cells IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene NA Mesoderm Immune system 0.193676 0.196262 0.00510378 0.00409863 +Hs CD8B T cells CD8B1 0.003 CD8b molecule protein-coding gene NA Mesoderm Immune system 0.177866 0.0 0.00170126 0.0 +Mm Hs BATF3 T cells JUNDM1|SNFT 0.008 basic leucine zipper ATF-like transcription factor 3 protein-coding gene 1 Mesoderm Immune system 0.0750988 0.0046729 0.00340252 0.00715633 +Hs GZMH T cells CGL-2|CCP-X|CSP-C|CTSGL2 0.005 granzyme H protein-coding gene NA Mesoderm Immune system 0.0750988 0.0 0.0275604 0.0 +Mm Hs LAG3 T cells CD223 0.011 lymphocyte activating 3 protein-coding gene NA Mesoderm Immune system 0.110672 0.121495 0.00204151 0.0100189 +Mm CD8B1 T cells NA 0.008 CD8 antigen, beta chain 1 protein coding gene NA Mesoderm Immune system 0.0 0.345794 0.0 0.00507449 +Mm Hs GZMK T cells TRYP2|PRSS 0.001 granzyme K protein-coding gene 1 Mesoderm Immune system 0.00395257 0.0934579 0.0 0.00026023 +Mm Hs GZMB T cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene NA Mesoderm Immune system 0.173913 0.168224 0.0506975 0.00611541 +Mm Hs SH2D1A T cells XLP|DSHP|XLPD|EBVS|IMD5|LYP 0.011 SH2 domain containing 1A protein-coding gene NA Mesoderm Immune system 0.158103 0.0 0.00544403 0.0 +Mm Hs MYO1G T cells HA-2 0.022 myosin IG protein-coding gene NA Mesoderm Immune system 0.110672 0.126168 0.0163321 0.0182161 +Mm Hs FMNL1 T cells C17orf1B|FMNL 0.022 formin like 1 protein-coding gene NA Mesoderm Immune system 0.0197628 0.182243 0.00544403 0.0241364 +Mm Hs S1PR4 T cells EDG6 0.015 sphingosine-1-phosphate receptor 4 protein-coding gene NA Mesoderm Immune system 0.0632411 0.0 0.0166723 0.0 +Mm Hs CD247 T cells CD3H|CD3Q|CD3Z 0.019 CD247 molecule protein-coding gene 1 Mesoderm Immune system 0.3083 0.275701 0.0336849 0.00884783 +Mm MS4A4C T cells NA 0.011 membrane-spanning 4-domains, subfamily A, member 4C protein coding gene NA Mesoderm Immune system 0.0 0.0140187 0.0 0.0121007 +Mm Hs GIMAP5 T cells HIMAP3|IAN5|IAN4L1 0.016 GTPase, IMAP family member 5 protein-coding gene NA Mesoderm Immune system 0.0 0.154206 0.0 0.0178908 +Mm Hs CD28 T cells NA 0.011 CD28 molecule protein-coding gene NA Mesoderm Immune system 0.0158103 0.242991 0.00170126 0.00969358 +Mm Hs CD160 T cells BY55|NK1|NK28 0.002 CD160 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.046729 0.0 0.00240713 +None TCRG-C2 T cells NA 0.007 NA NA NA Mesoderm Immune system NA NA NA NA +Mm TCRG-C1 T cells Cgamma1|Gm17004 0.01 T cell receptor gamma, constant 1 NA NA Mesoderm Immune system NA NA NA NA +None TCRG-C4 T cells NA 0.003 NA NA NA Mesoderm Immune system NA NA NA NA +Mm Hs TRDC T cells NA 0.011 T cell receptor delta constant other 1 Mesoderm Immune system 0.0118577 0.0 0.0268799 0.0 +Mm H2-T3 T cells NA 0.002 histocompatibility 2, T region locus 3 protein coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00247219 +None H2-T10 T cells NA 0.002 NA NA NA Mesoderm Immune system 0.0 0.0233645 0.0 0.00149632 +Mm Hs RHOH T cells RhoH|TTF|ARHH 0.023 ras homolog family member H protein-coding gene NA Mesoderm Immune system 0.29249 0.0 0.0238176 0.0 +Mm Hs KLRB1 T cells CD161|NKR-P1|NKR-P1A|hNKR-P1A|CLEC5B 0.008 killer cell lectin like receptor B1 protein-coding gene NA Mesoderm Immune system 0.16996 0.0 0.0370874 0.000715633 +Mm Hs CCR2 T cells CC-CKR-2|CKR2|MCP-1-R|CD192|FLJ78302|CMKBR2 0.022 C-C motif chemokine receptor 2 protein-coding gene NA Mesoderm Immune system 0.0 0.205607 0.0 0.0238111 +Mm Hs IL2RB T cells CD122|IL15RB 0.02 interleukin 2 receptor subunit beta protein-coding gene NA Mesoderm Immune system 0.0790514 0.453271 0.0136101 0.0134669 +Mm Hs CD163L1 T cells M160|CD163B|SCARI2|WC1 0.003 CD163 molecule like 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.158879 0.00238176 0.00104092 +Mm TRDV4 T cells NA 0.001 T cell receptor delta variable 4 NA 1 Mesoderm Immune system NA NA NA NA +Mm Hs MBD2 T cells NA 0.018 methyl-CpG binding domain protein 2 protein-coding gene NA Mesoderm Immune system 0.027668 0.0420561 0.0268799 0.0156138 +Mm Hs ICOS T cells AILIM|CD278 0.01 inducible T cell costimulator protein-coding gene 1 Mesoderm Immune system 0.0632411 0.369159 0.00204151 0.00618047 +Mm Hs IL18R1 T cells IL1RRP|IL-1Rrp|CD218a 0.013 interleukin 18 receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.331776 0.000680504 0.0123609 +Mm Hs TNFRSF4 T cells ACT35|OX40|CD134|TXGP1L 0.006 TNF receptor superfamily member 4 protein-coding gene 1 Mesoderm Immune system 0.0909091 0.0 0.00816604 0.0 +Mm Hs CCL20 T cells LARC|MIP-3a|exodus-1|ST38|CKb4|SCYA20 0.005 C-C motif chemokine ligand 20 protein-coding gene 1 Mesoderm Immune system 0.0395257 0.0 0.0248384 0.000910806 +Mm Hs CLEC2D T cells LLT1|CLAX|OCIL 0.029 C-type lectin domain family 2 member D protein-coding gene 1 Mesoderm Immune system 0.604743 0.0046729 0.0319837 0.0193221 +Mm Hs CD8A T cells CD8 0.01 CD8a molecule protein-coding gene 1 Mesoderm Immune system 0.166008 0.350467 0.00306227 0.0038384 +Mm Hs CD6 T cells Tp120 0.007 CD6 molecule protein-coding gene 1 Mesoderm Immune system 0.126482 0.149533 0.00544403 0.00409863 +Mm Hs S100A4 T cells P9KA|18A2|PEL98|42A|CAPL 0.098 S100 calcium binding protein A4 protein-coding gene 1 Mesoderm Immune system 0.849802 0.0 0.330044 0.0 +Mm Hs CCL5 T cells RANTES|SISd|TCP228|MGC17164|D17S136E|SCYA5 0.042 C-C motif chemokine ligand 5 protein-coding gene 1 Mesoderm Immune system 0.347826 0.28972 0.0632868 0.0291458 +Mm Hs LCK T cells NA 0.048 LCK proto-oncogene, Src family tyrosine kinase protein-coding gene 1 Mesoderm Immune system 0.648221 0.705607 0.0330044 0.0309023 +Mm Hs CD81 T cells TAPA-1|TSPAN28|TAPA1 0.598 CD81 molecule protein-coding gene 1 Mesoderm Immune system 0.0474308 0.0607477 0.208574 0.709973 +Mm Hs THY1 T cells CD90 0.095 Thy-1 cell surface antigen protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0350459 0.0 +Mm Hs LAT T cells NA 0.034 linker for activation of T cells protein-coding gene 1 Mesoderm Immune system 0.12253 0.869159 0.00476352 0.026023 +Mm Hs SKAP1 T cells SKAP55|SCAP1 0.028 src kinase associated phosphoprotein 1 protein-coding gene 1 Mesoderm Immune system 0.0909091 0.0 0.0119088 0.0 +Mm Hs TCF7 T cells TCF-1 0.03 transcription factor 7 protein-coding gene 1 Mesoderm Immune system 0.205534 0.0 0.0217761 0.0 +Mm Hs CCR7 T cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.339921 0.0514019 0.0163321 0.0108646 +Mm Hs MYB T cells c-myb 0.027 MYB proto-oncogene, transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.242991 0.0146308 0.0253074 +Hs CCL4L2 T cells NA 0.002 C-C motif chemokine ligand 4 like 2 protein-coding gene 1 Mesoderm Immune system 0.0118577 0.0 0.0139503 0.0 +Hs PYHIN1 T cells IFIX|MGC23885 0.002 pyrin and HIN domain family member 1 protein-coding gene 1 Mesoderm Immune system 0.027668 0.0 0.00884655 0.0 +Mm Hs GZMA T cells HFSP|CTLA3 0.026 granzyme A protein-coding gene 1 Mesoderm Immune system 0.280632 0.336449 0.047295 0.0139223 +Mm Hs JUNB T cells NA 0.387 JunB proto-oncogene, AP-1 transcription factor subunit protein-coding gene 1 Mesoderm Immune system 0.675889 0.691589 0.515822 0.35645 +Mm Hs DUSP2 T cells PAC-1 0.042 dual specificity phosphatase 2 protein-coding gene 1 Mesoderm Immune system 0.29249 0.17757 0.0398095 0.0370178 +Mm Hs IFNG T cells NA 0.003 interferon gamma protein-coding gene 1 Mesoderm Immune system 0.0790514 0.11215 0.00680504 0.000195173 +Mm Hs CD52 T cells HE5|EDDM5|CDW52 0.181 CD52 molecule protein-coding gene 1 Mesoderm Immune system 0.916996 0.700935 0.222865 0.1523 +Mm Hs BRAF T cells BRAF1 0.025 B-Raf proto-oncogene, serine/threonine kinase protein-coding gene 1 Mesoderm Immune system 0.0 0.0046729 0.0173528 0.0281049 +Mm Hs CD3D T cells naive T3D 0.053 CD3d molecule protein-coding gene NA NA NA 1.0 0.0 0.1288 0.0377927 +Mm Hs CD4 T cells naive NA 0.009 CD4 molecule protein-coding gene NA NA NA 0.0 0.0 0.0188029 0.00757138 +Mm Hs SELL T cells naive LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene NA NA NA 1.0 0.0 0.0598558 0.0 +Mm Hs CCR7 T cells naive BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene NA NA NA 1.0 0.0 0.0416797 0.0114212 +Mm Hs CD2 T cytotoxic cells NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Immune system 1.0 0.0 0.0934169 0.0296439 +Mm Hs CD27 T cytotoxic cells S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.022884 0.0157844 +Mm Hs CD28 T cytotoxic cells NA 0.011 CD28 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00282132 0.012897 +Mm Hs CD5 T cytotoxic cells NA 0.004 CD5 molecule protein-coding gene NA Mesoderm Immune system 0.5 0.0 0.00376176 0.00442733 +Mm Hs CD69 T cytotoxic cells CLEC2C 0.024 CD69 molecule protein-coding gene NA Mesoderm Immune system 0.5 0.0 0.110972 0.00737889 +Mm Hs CD8A T cytotoxic cells CD8 0.01 CD8a molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0159875 0.00859801 +Mm Hs GZMB T cytotoxic cells CCPI|CGL-1|CSP-B|CGL1|CTSGL1|SECT|CSPB 0.017 granzyme B protein-coding gene 1 Mesoderm Immune system 1.0 0.0 0.0598746 0.00834135 +Mm Hs TRAC T cytotoxic cells NA 0.042 T cell receptor alpha constant other 1 Mesoderm Immune system 1.0 0.0 0.131348 0.0 +Mm Hs BCL6 T follicular helper cells ZBTB27|LAZ3|BCL5|BCL6A|ZNF51 0.004 B cell CLL/lymphoma 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0037594 0.00481232 +Mm Hs CD3D T follicular helper cells T3D 0.053 CD3d molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.129073 0.0377927 +Mm Hs CD4 T follicular helper cells NA 0.009 CD4 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.018797 0.00757138 +Mm Hs CD84 T follicular helper cells SLAMF5|hCD84|mCD84 0.023 CD84 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0093985 0.0272698 +Hs IL6R T follicular helper cells CD126 0.001 interleukin 6 receptor protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00595238 0.0 +Mm Hs SLAMF1 T follicular helper cells CD150|SLAM 0.001 signaling lymphocytic activation molecule family member 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00156642 0.0 +Mm Hs CD40LG T follicular helper cells CD40L|gp39|hCD40L|CD154|HIGM1|IMD3|TNFSF5 0.003 CD40 ligand protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0100251 0.00121912 +Mm Hs CXCR5 T follicular helper cells MDR15|CD185|BLR1 0.001 C-X-C motif chemokine receptor 5 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00102663 +Mm Hs TNFSF4 T follicular helper cells OX-40L|gp34|CD252|TXGP1 0.0 TNF superfamily member 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00093985 0.0 +Mm Hs ICOS T follicular helper cells AILIM|CD278 0.01 inducible T cell costimulator protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00689223 0.0111646 +Mm Hs PDCD1 T follicular helper cells CD279|hSLE1|PD-1|SLEB2 0.003 programmed cell death 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00469925 0.00250241 +Mm Hs CD200 T follicular helper cells MRC|OX-2 0.111 CD200 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0228697 0.134681 +Mm Hs P2RX7 T follicular helper cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00877193 0.00346487 +Mm Hs IFNG T helper cells NA 0.003 interferon gamma protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0125313 0.00173244 +Mm Hs IL2 T helper cells IL-2|TCGF 0.001 interleukin 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00134745 +Mm Hs TBX21 T helper cells TBLYM|T-bet 0.0 T-box 21 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs DPP4 T helper cells CD26|ADCP2 0.02 dipeptidyl peptidase 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0131579 0.0213025 +Mm Hs KLRD1 T helper cells CD94 0.02 killer cell lectin like receptor D1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0388471 0.0166185 +Mm Hs CXCR3 T helper cells CKR-L2|CMKAR3|IP10-R|MigR|CD183|GPR9 0.005 C-X-C motif chemokine receptor 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00532581 0.00474816 +Mm Hs CCR1 T helper cells MIP1aR|CD191|SCYAR1|CMKBR1 0.014 C-C motif chemokine receptor 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00532581 0.014052 +Mm Hs CCR5 T helper cells CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.018351 +Mm Hs TNFSF11 T helper cells TRANCE|RANKL|OPGL|ODF|CD254 0.001 TNF superfamily member 11 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000313283 0.0 +Mm Hs HAVCR2 T helper cells Tim-3|TIM3|FLJ14428|TIMD3|CD366 0.003 hepatitis A virus cellular receptor 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00532581 0.00295156 +Mm Hs IL18R1 T helper cells IL1RRP|IL-1Rrp|CD218a 0.013 interleukin 18 receptor 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000626566 0.0167469 +Mm Hs LTBR T helper cells TNFCR|TNFR-RP|TNFR2-RP|TNF-R-III|TNFRSF3|D12S370 0.024 lymphotoxin beta receptor protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0181704 0.0250882 +Mm Hs TNF T helper cells TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00125313 0.0 +Mm Hs LTA T helper cells TNFSF1|LT|TNFB 0.001 lymphotoxin alpha protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00438596 0.000256657 +Mm Hs GATA3 T helper cells HDR 0.03 GATA binding protein 3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0200501 0.0297722 +Mm Hs CSF2 T helper cells GM-CSF|GMCSF 0.002 colony stimulating factor 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0093985 0.000769971 +Mm Hs IL4 T helper cells BSF1|IL-4|BCGF1|BCGF-1|MGC79402 0.002 interleukin 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0026949 +Mm Hs IL5 T helper cells IL-5|EDF 0.002 interleukin 5 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00626566 0.000834135 +Mm Hs IL6 T helper cells IL-6|BSF2|HSF|IFNB2 0.007 interleukin 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0134712 0.00648059 +Mm Hs IL10 T helper cells CSIF|IL10A|IL-10 0.001 interleukin 10 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00128329 +Mm Hs IL13 T helper cells P600|IL-13|ALRH|BHR1|MGC116786|MGC116788|MGC116789 0.004 interleukin 13 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.018797 0.00147578 +Mm Hs CCR8 T helper cells CY6|TER1|CKR-L1|GPR-CY6|CDw198|CMKBRL2|CMKBR8 0.002 C-C motif chemokine receptor 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00198909 +Mm Hs CXCR4 T helper cells LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.198308 0.0087905 +Mm Hs CCR3 T helper cells CC-CKR-3|CKR3|CD193|CMKBR3 0.001 C-C motif chemokine receptor 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00147578 +Mm Hs CCR7 T helper cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0419799 0.0114212 +Mm Hs ICOS T helper cells AILIM|CD278 0.01 inducible T cell costimulator protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00689223 0.0111646 +Mm Hs PTGDR2 T helper cells CRTH2|CD294|GPR44 0.0 prostaglandin D2 receptor 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs HAVCR1 T helper cells HAVCR-1|TIM-1|HAVCR|TIMD1|CD365|KIM1 0.001 hepatitis A virus cellular receptor 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00134745 +Mm Hs IL1R2 T helper cells CD121b|IL1RB 0.007 interleukin 1 receptor type 2 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00720551 0.00660892 +Mm Hs IRF4 T helper cells LSIRF|MUM1 0.003 interferon regulatory factor 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00845865 0.000641643 +Mm Hs STAT6 T helper cells D12S1644|IL-4-STAT 0.01 signal transducer and activator of transcription 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00814536 0.0 +Mm Hs IL17A T helper cells IL-17A|IL-17|CTLA8|IL17 0.0 interleukin 17A protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000256657 +Mm Hs IL17F T helper cells IL-17F|ML1 0.0 interleukin 17F protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.000513314 +Mm Hs IL21 T helper cells Za11 0.0 interleukin 21 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000313283 0.0 +Mm Hs IL22 T helper cells ILTIF|zcyto18|IL-TIF|IL-D110|TIFa|TIFIL-23|MGC79382|MGC79384 0.0 interleukin 22 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000256657 +Mm Hs RORA T helper cells RZRA|ROR1|ROR2|ROR3|NR1F1 0.045 RAR related orphan receptor A protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0140977 0.0 +Mm Hs RORC T helper cells RZRG|RORG|NR1F3|TOR 0.004 RAR related orphan receptor C protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000313283 0.0 +None CD3 T helper cells NA 0.0 NA NA NA Mesoderm Immune system NA NA NA NA +Mm Hs CD38 T helper cells NA 0.016 CD38 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0140977 0.0161052 +Mm Hs KLRB1 T helper cells CD161|NKR-P1|NKR-P1A|hNKR-P1A|CLEC5B 0.008 killer cell lectin like receptor B1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.047619 0.000705807 +Mm Hs AHR T helper cells bHLHe76 0.007 aryl hydrocarbon receptor protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0112782 0.00692974 +Mm Hs CCR10 T helper cells GPR2 0.002 C-C motif chemokine receptor 10 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00281955 0.000705807 +Mm Hs CD3D T helper cells T3D 0.053 CD3d molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.129073 0.0377927 +Mm Hs CD4 T helper cells NA 0.009 CD4 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.018797 0.00757138 +Mm Hs CCR4 T helper cells CC-CKR-4|CMKBR4|CKR4|k5-5|ChemR13|CD194 0.0 C-C motif chemokine receptor 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000626566 0.0 +Mm Hs CCR6 T helper cells CKR-L3|GPR-CY4|CMKBR6|GPR29|DRY-6|DCR2|BN-1|CD196|STRL22 0.001 C-C motif chemokine receptor 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00186076 +Mm Hs IL9 T helper cells IL-9|HP40 0.0 interleukin 9 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs CD2 T helper cells NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.093985 0.0296439 +Mm Hs CD28 T helper cells NA 0.011 CD28 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00281955 0.012897 +Mm Hs CD5 T helper cells NA 0.004 CD5 molecule protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00407268 0.00442733 +Mm Hs IL1RL1 T helper cells ST2|FIT-1|ST2V|DER4|IL33R 0.007 interleukin 1 receptor like 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0147243 0.00545396 +Mm Hs FOXP3 T helper cells JM2|XPID|AIID|PIDX|DIETER|SCURFIN|IPEX 0.0 forkhead box P3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000320821 +Mm Hs CD3G T helper cells NA 0.048 CD3g molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0845865 0.0407443 +Mm Hs TNFRSF4 T helper cells ACT35|OX40|CD134|TXGP1L 0.006 TNF receptor superfamily member 4 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0147243 0.0 +Mm IL4RA T helper cells NA 0.013 interleukin 4 receptor, alpha protein coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.0168752 +Mm Hs CD40LG T helper cells CD40L|gp39|hCD40L|CD154|HIGM1|IMD3|TNFSF5 0.003 CD40 ligand protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0100251 0.00121912 +Mm Hs IL17RB T helper cells IL17RH1|EVI27|CRL4|IL17BR 0.001 interleukin 17 receptor B protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.000313283 0.00115496 +Mm Hs HPGDS T helper cells GSTS|H-PGDS|PGD2|GSTS1-1|GSTS1 0.033 hematopoietic prostaglandin D synthase protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0184837 0.0371511 +Mm Hs NFATC2 T helper cells NF-ATP|NFATp|NFAT1 0.001 nuclear factor of activated T cells 2 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000705807 +Mm Hs NFKB1 T helper cells KBF1|NFKB-p50|NF-kappaB|NFkappaB|NF-kB1 0.028 nuclear factor kappa B subunit 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0256892 0.0280398 +Mm Hs NR3C1 T helper cells GR|GRL 0.069 nuclear receptor subfamily 3 group C member 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0548246 0.0739814 +Mm Hs PPARG T helper cells PPARG1|PPARG2|NR1C3|PPARgamma 0.006 peroxisome proliferator activated receptor gamma protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0109649 0.00461983 +Mm Hs SELL T memory cells LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene NA Mesoderm Immune system 0.634146 0.0 0.0526817 0.0 +Mm Hs CCR7 T memory cells BLR2|CDw197|CD197|CMKBR7|EBI1 0.016 C-C motif chemokine receptor 7 protein-coding gene 1 Mesoderm Immune system 0.390244 0.178125 0.0374484 0.00792663 +Mm Hs CD4 T memory cells NA 0.009 CD4 molecule protein-coding gene NA Mesoderm Immune system 0.097561 0.225 0.0177721 0.00301343 +Mm Hs CCR5 T memory cells CKR-5|CC-CKR-5|CKR5|CD195|IDDM22|CMKBR5 0.015 C-C motif chemokine receptor 5 (gene/pseudogene) protein-coding gene NA Mesoderm Immune system 0.0 0.015625 0.0 0.0184081 +Mm Hs CD69 T memory cells CLEC2C 0.024 CD69 molecule protein-coding gene NA Mesoderm Immune system 0.609756 0.053125 0.104729 0.00641991 +Mm Hs ITGB5 T memory cells NA 0.047 integrin subunit beta 5 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0152333 0.0566656 +Mm Hs BCL2 T memory cells Bcl-2|PPP1R50 0.043 BCL2, apoptosis regulator protein-coding gene NA Mesoderm Immune system 0.0 0.378125 0.0015868 0.0448084 +Mm Hs GRAP2 T memory cells Grf40|GrbX|GRBLG|GADS|Mona 0.005 GRB2 related adaptor protein 2 protein-coding gene NA Mesoderm Immune system 0.0 0.13125 0.00349096 0.00307894 +Mm Hs TBC1D10C T memory cells FLJ00332|Carabin|EPI64C 0.026 TBC1 domain family member 10C protein-coding gene NA Mesoderm Immune system 0.317073 0.0 0.0218978 0.0 +Mm Hs CYTIP T memory cells B3-1|HE|CYBR|CYTHIP|PSCDBP 0.062 cytohesin 1 interacting protein protein-coding gene NA Mesoderm Immune system 0.487805 0.56875 0.0663282 0.0493285 +Mm Hs KPNA4 T memory cells QIP1|SRP3|IPOA3|MGC12217|MGC26703 0.069 karyopherin subunit alpha 4 protein-coding gene NA Mesoderm Immune system 0.0 0.096875 0.0418915 0.0759253 +Mm Hs CD247 T memory cells CD3H|CD3Q|CD3Z 0.019 CD247 molecule protein-coding gene NA Mesoderm Immune system 0.560976 0.3875 0.0488734 0.00465116 +Mm Hs EPSTI1 T memory cells BRESI1|MGC29634 0.041 epithelial stromal interaction 1 protein-coding gene NA Mesoderm Immune system 0.146341 0.33125 0.0276103 0.0370783 +Mm Hs APBB1IP T memory cells INAG1|RIAM 0.052 amyloid beta precursor protein binding family B member 1 interacting protein protein-coding gene NA Mesoderm Immune system 0.243902 0.271875 0.0180895 0.0543072 +Mm Hs CD27 T memory cells S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene NA Mesoderm Immune system 0.365854 0.259375 0.0184069 0.010678 +Mm Hs RHOH T memory cells RhoH|TTF|ARHH 0.023 ras homolog family member H protein-coding gene NA Mesoderm Immune system 0.463415 0.0 0.0396699 0.0 +Mm Hs GIMAP1 T memory cells HIMAP1|IMAP38|IMAP1|IAN2 0.05 GTPase, IMAP family member 1 protein-coding gene NA Mesoderm Immune system 0.390244 0.6375 0.0234846 0.0427121 +Mm Hs ACP5 T memory cells HPAP 0.033 acid phosphatase 5, tartrate resistant protein-coding gene NA Mesoderm Immune system 0.0 0.15625 0.0184069 0.0340649 +Mm Hs IKZF1 T memory cells hIk-1|LyF-1|Hs.54452|IKAROS|PPP1R92|ZNFN1A1 0.037 IKAROS family zinc finger 1 protein-coding gene NA Mesoderm Immune system 0.317073 0.353125 0.0364963 0.0289551 +Mm Hs SP100 T memory cells NA 0.058 SP100 nuclear antigen protein-coding gene NA Mesoderm Immune system 0.146341 0.0 0.0641066 0.0 +Mm Hs DGKA T memory cells DGK-alpha|DAGK1 0.01 diacylglycerol kinase alpha protein-coding gene NA Mesoderm Immune system 0.195122 0.21875 0.0015868 0.00753357 +Mm Hs IL7R T memory cells CD127|IL7RA 0.031 interleukin 7 receptor protein-coding gene NA Mesoderm Immune system 0.756098 0.40625 0.0622025 0.0151327 +Mm Hs ITGB7 T memory cells NA 0.031 integrin subunit beta 7 protein-coding gene NA Mesoderm Immune system 0.0 0.609375 0.0 0.0261382 +Mm Hs NKG7 T memory cells GMP-17 0.056 natural killer cell granule protein 7 protein-coding gene NA Mesoderm Immune system 0.0243902 0.359375 0.108854 0.0393711 +Mm Hs CD28 T memory cells NA 0.011 CD28 molecule protein-coding gene NA Mesoderm Immune system 0.097561 0.4125 0.0015868 0.00452014 +Mm H2-T23 T memory cells NA 0.056 histocompatibility 2, T region locus 23 protein coding gene NA Mesoderm Immune system 0.0 0.221875 0.0 0.0653128 +Mm GIMAP3 T memory cells NA 0.019 GTPase, IMAP family member 3 protein coding gene NA Mesoderm Immune system 0.0 0.65 0.0 0.0102195 +Mm H2-Q7 T memory cells NA 0.06 histocompatibility 2, Q region locus 7 protein coding gene NA Mesoderm Immune system 0.0 0.7125 0.0 0.0586964 +Mm Hs BIN2 T memory cells BRAP-1 0.06 bridging integrator 2 protein-coding gene NA Mesoderm Immune system 0.170732 0.51875 0.0447477 0.0526695 +Mm Hs RAPGEF6 T memory cells RA-GEF-2|PDZ-GEF2|PDZGEF2 0.032 Rap guanine nucleotide exchange factor 6 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.0 +Mm Hs ARHGEF1 T memory cells P115-RHOGEF|SUB1.5|LBCL2 0.054 Rho guanine nucleotide exchange factor 1 protein-coding gene NA Mesoderm Immune system 0.195122 0.703125 0.0126944 0.0494595 +Mm MIR142HG T memory cells NA 0.018 Mir142 host gene (non-protein coding) lincRNA gene NA Mesoderm Immune system 0.0 0.1125 0.0 0.0204389 +Mm Hs S100A9 T memory cells MIF|NIF|LIAG|MRP14|MAC387|CGLB|CAGB 0.061 S100 calcium binding protein A9 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.104729 0.0 +Mm SLFN2 T memory cells NA 0.065 schlafen 2 protein coding gene NA Mesoderm Immune system NA NA NA NA +Mm Hs ARHGAP15 T memory cells BM046 0.035 Rho GTPase activating protein 15 protein-coding gene NA Mesoderm Immune system 0.170732 0.409375 0.0311012 0.0256797 +Mm Hs CD3E T memory cells NA 0.041 CD3e molecule protein-coding gene NA Mesoderm Immune system 0.926829 0.78125 0.0888607 0.0140845 +Mm Hs SKAP1 T memory cells SKAP55|SCAP1 0.028 src kinase associated phosphoprotein 1 protein-coding gene NA Mesoderm Immune system 0.146341 0.0 0.0165027 0.0 +Mm Hs GIMAP4 T memory cells HIMAP4|FLJ11110|IMAP4|IAN1 0.043 GTPase, IMAP family member 4 protein-coding gene NA Mesoderm Immune system 0.634146 0.68125 0.0498255 0.0268588 +Mm Hs CD2 T memory cells NA 0.04 CD2 molecule protein-coding gene NA Mesoderm Immune system 0.804878 0.684375 0.084735 0.0159188 +Mm Hs PTPRC T memory cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Mesoderm Immune system 1.0 0.8625 0.205966 0.0903374 +Mm Hs LAT T memory cells NA 0.034 linker for activation of T cells protein-coding gene NA Mesoderm Immune system 0.170732 0.8875 0.0120597 0.0197838 +Mm MS4A6B T memory cells NA 0.043 membrane-spanning 4-domains, subfamily A, member 6B protein coding gene NA Mesoderm Immune system 0.0 0.74375 0.0 0.0366852 +Mm Hs TCF7 T memory cells TCF-1 0.03 transcription factor 7 protein-coding gene NA Mesoderm Immune system 0.634146 0.0 0.0285624 0.0 +Mm Hs LEF1 T memory cells TCF1ALPHA|TCF10|TCF7L3 0.025 lymphoid enhancer binding factor 1 protein-coding gene NA Mesoderm Immune system 0.0731707 0.325 0.00856871 0.0215526 +Mm Hs SEPT1 T memory cells PNUTL3 0.055 septin 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00349096 0.0 +Mm Hs ARHGAP45 T memory cells KIAA0223|HA-1|HMHA1 0.088 Rho GTPase activating protein 45 protein-coding gene NA Mesoderm Immune system 0.317073 0.884375 0.0104729 0.0856207 +Mm Hs SATB1 T memory cells NA 0.03 SATB homeobox 1 protein-coding gene NA Mesoderm Immune system 0.0243902 0.0 0.00793399 0.0 +Mm Hs PTPRCAP T memory cells CD45-AP 0.072 protein tyrosine phosphatase, receptor type C associated protein protein-coding gene NA Mesoderm Immune system 0.0 0.94375 0.0 0.0685883 +Mm Hs S100A8 T memory cells P8|CGLA|CAGA 0.064 S100 calcium binding protein A8 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0809267 0.0 +Mm Hs LTB T memory cells TNFSF3|TNFC 0.065 lymphotoxin beta protein-coding gene NA Mesoderm Immune system 1.0 0.81875 0.152333 0.0292172 +Mm Hs LCK T memory cells NA 0.048 LCK proto-oncogene, Src family tyrosine kinase protein-coding gene NA Mesoderm Immune system 0.97561 0.915625 0.0701365 0.0218146 +Mm TRBC1 T memory cells TCRBC1|BV05S1J2.2 0.036 T cell receptor beta constant 1 other NA Mesoderm Immune system NA NA NA NA +Mm Hs TRAC T memory cells NA 0.042 T cell receptor alpha constant other NA Mesoderm Immune system 0.97561 0.0 0.120914 0.0 +Mm Hs CD3G T memory cells NA 0.048 CD3g molecule protein-coding gene NA Mesoderm Immune system 0.951219 0.940625 0.0733101 0.0218801 +Mm Hs CD3D T memory cells T3D 0.053 CD3d molecule protein-coding gene NA Mesoderm Immune system 1.0 0.921875 0.11774 0.0192597 +Mm MS4A4B T memory cells NA 0.023 membrane-spanning 4-domains, subfamily A, member 4B protein coding gene NA Mesoderm Immune system 0.0 0.7375 0.0 0.0127088 +Mm Hs TRBC2 T memory cells TCRBC2 0.066 T cell receptor beta constant 2 other NA Mesoderm Immune system 1.0 0.0 0.140273 0.0 +Mm Hs CD7 T memory cells LEU-9|TP41|Tp40 0.03 CD7 molecule protein-coding gene NA Mesoderm Immune system 0.853659 0.10625 0.0939384 0.0142155 +Mm Hs CXCR6 T memory cells TYMSTR|STRL33|BONZO|CD186 0.014 C-X-C motif chemokine receptor 6 protein-coding gene NA Mesoderm Immune system 0.0 0.325 0.000634719 0.0108745 +Mm Hs ICOS T memory cells AILIM|CD278 0.01 inducible T cell costimulator protein-coding gene NA Mesoderm Immune system 0.146341 0.21875 0.00507775 0.00681297 +Mm Hs CCR6 T memory cells CKR-L3|GPR-CY4|CMKBR6|GPR29|DRY-6|DCR2|BN-1|CD196|STRL22 0.001 C-C motif chemokine receptor 6 protein-coding gene NA Mesoderm Immune system 0.0 0.065625 0.0 0.000524075 +Mm Hs ITGAE T memory cells CD103|HUMINAE 0.033 integrin subunit alpha E protein-coding gene NA Mesoderm Immune system 0.0 0.025 0.130435 0.00537177 +Mm Hs ENPP1 T memory cells PC-1|NPPS|M6S1|PDNP1 0.005 ectonucleotide pyrophosphatase/phosphodiesterase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0114249 0.00334098 +Mm Hs FOXP3 T regulatory cells JM2|XPID|AIID|PIDX|DIETER|SCURFIN|IPEX 0.0 forkhead box P3 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.000320862 +Mm Hs IKZF2 T regulatory cells Helios|ZNFN1A2 0.011 IKAROS family zinc finger 2 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.000626566 0.0125136 +Mm Hs CD4 T regulatory cells NA 0.009 CD4 molecule protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.018797 0.00757235 +Mm Hs IL2RA T regulatory cells IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0200501 0.00673811 +Mm Hs ENTPD1 T regulatory cells NTPDase-1|ATPDase|SPG64|CD39 0.014 ectonucleoside triphosphate diphosphohydrolase 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.00657895 0.0152089 +Mm Hs SELL T regulatory cells LSEL|LAM1|LAM-1|hLHRc|Leu-8|Lyam-1|PLNHR|CD62L|LYAM1|LNHR 0.035 selectin L protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0601504 0.0 +Mm Hs NT5E T regulatory cells CD73|eN|eNT|CALJA|NT5 0.005 5'-nucleotidase ecto protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.00720551 0.003722 +Mm Hs ITGAE T regulatory cells CD103|HUMINAE 0.033 integrin subunit alpha E protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.128759 0.00577552 +Mm Hs TNFRSF4 T regulatory cells ACT35|OX40|CD134|TXGP1L 0.006 TNF receptor superfamily member 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0147243 0.0 +Mm Hs CTLA4 T regulatory cells CD152|CELIAC3|IDDM12 0.004 cytotoxic T-lymphocyte associated protein 4 protein-coding gene 1 Mesoderm Immune system 0.0 1.0 0.00814536 0.00275942 +Mm Hs CCR4 T regulatory cells CC-CKR-4|CMKBR4|CKR4|k5-5|ChemR13|CD194 0.0 C-C motif chemokine receptor 4 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.000626566 0.0 +Mm Hs LAG3 T regulatory cells CD223 0.011 lymphocyte activating 3 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0106516 0.011551 +Mm Hs IZUMO1R T regulatory cells Folbp3|JUNO|FOLR4 0.002 IZUMO1 receptor, JUNO protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00250273 +Mm Hs CNGB1 T regulatory cells RCNC2|RCNCb|GAR1|CNGB1B|RP45|CNCG2|CNCG3L 0.001 cyclic nucleotide gated channel beta 1 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0 0.00192517 +Mm Hs TNFRSF18 T regulatory cells AITR|GITR|CD357 0.013 TNF receptor superfamily member 18 protein-coding gene NA Mesoderm Immune system 0.0 0.0 0.0137845 0.0 +Mm Hs MAF T regulatory cells c-MAF 0.072 MAF bZIP transcription factor protein-coding gene 1 Mesoderm Immune system 0.0 0.5 0.0366541 0.0822691 +Mm Hs IL10 T regulatory cells CSIF|IL10A|IL-10 0.001 interleukin 10 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0 0.00128345 +Mm Hs IL1R1 T regulatory cells D2S1473|CD121A|IL1R 0.008 interleukin 1 receptor type 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0191103 0.00635308 +Mm Hs ITGB8 T regulatory cells NA 0.031 integrin subunit beta 8 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.116855 0.0136046 +Mm Hs LRRC32 T regulatory cells D11S833E 0.007 leucine rich repeat containing 32 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0115915 0.00686646 +Mm Hs FOLR1 T regulatory cells FOLR 0.017 folate receptor 1 protein-coding gene 1 Mesoderm Immune system 0.0 0.0 0.0093985 0.0197651 +Mm Hs GPR50 Tanycytes H9|Mel1c 0.001 G protein-coupled receptor 50 protein-coding gene 1 Ectoderm Brain 0.0 0.619048 0.0 0.000578258 +Mm Hs DRD2 Tanycytes NA 0.0 dopamine receptor D2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.000578258 +Mm Hs DIO2 Tanycytes TXDI2|SelY 0.003 iodothyronine deiodinase 2 protein-coding gene 1 Ectoderm Brain 0.0 0.428571 0.0056391 0.00173477 +Mm Hs COL23A1 Tanycytes DKFZp434K0621 0.005 collagen type XXIII alpha 1 chain protein-coding gene 1 Ectoderm Brain 0.0 0.952381 0.0 0.00475456 +Mm Hs SLC16A2 Tanycytes XPCT|MCT8|DXS128|AHDS|MRX22 0.023 solute carrier family 16 member 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00344612 0.0 +Mm Hs LHX2 Tanycytes LH-2|hLhx2 0.092 LIM homeobox 2 protein-coding gene 1 Ectoderm Brain 0.0 0.047619 0.00532581 0.114045 +Mm Hs PTN Tanycytes HBNF|HBGF8|NEGF1 0.313 pleiotrophin protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.0905388 0.369121 +Mm Hs SLC17A8 Tanycytes VGLUT3|DFNA25 0.001 solute carrier family 17 member 8 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs COL25A1 Tanycytes NA 0.008 collagen type XXV alpha 1 chain protein-coding gene 1 Ectoderm Brain 0.0 0.380952 0.0103383 0.00700334 +Mm Hs RAX Tanycytes RX 0.006 retina and anterior neural fold homeobox protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs PRDX6 Tanycytes AOP2|KIAA0106|1-Cys|NSGPx|PRX|aiPLA2|MGC46173 0.396 peroxiredoxin 6 protein-coding gene 1 Ectoderm Brain 0.0 1.0 0.473684 0.369378 +Mm CD59A Tanycytes NA 0.033 CD59a antigen protein coding gene 1 Ectoderm Brain 0.0 0.0952381 0.0 0.0413133 +Mm Hs CRYM Tanycytes DFNA40 0.015 crystallin mu protein-coding gene 1 Ectoderm Brain 0.0 0.285714 0.00156642 0.0186327 +Mm Hs VCAN Tanycytes PG-M|CSPG2 0.056 versican protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0968045 0.0 +Mm Hs FRZB Tanycytes FRZB-PEN|FRZB1|SRFP3|FRP-3|SFRP3|FRE|FRITZ|FRZB-1|FZRB|hFIZ 0.012 frizzled related protein protein-coding gene 1 Ectoderm Brain 0.0 0.285714 0.0303885 0.0075816 +Mm Hs PENK Tanycytes NA 0.02 proenkephalin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0275689 0.0196608 +Mm Hs CACNA2D2 Tanycytes KIAA0558 0.027 calcium voltage-gated channel auxiliary subunit alpha2delta 2 protein-coding gene 1 Ectoderm Brain 0.0 0.047619 0.00125313 0.0343099 +Mm Hs ADM Tanycytes AM 0.026 adrenomedullin protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0635965 0.0177332 +Mm Hs SPRR1A Tanycytes NA 0.004 small proline rich protein 1A protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs SCN7A Tanycytes Nav2.1|Nav2.2|NaG|SCN6A 0.017 sodium voltage-gated channel alpha subunit 7 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00814536 0.0 +Mm FNDC3C1 Tanycytes NA 0.001 fibronectin type III domain containing 3C1 protein coding gene 1 Ectoderm Brain 0.0 0.380952 0.0 0.000578258 +Mm Hs MEST Tanycytes PEG1 0.039 mesoderm specific transcript protein-coding gene 1 Ectoderm Brain 0.0 0.047619 0.103697 0.0206888 +Mm Hs IGFBP5 Tanycytes NA 0.075 insulin like growth factor binding protein 5 protein-coding gene 1 Ectoderm Brain 0.0 0.380952 0.0927318 0.0696479 +Mm Hs RGCC Tanycytes bA157L14.2|RGC-32|RGC32|C13orf15 0.14 regulator of cell cycle protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.128446 0.0 +Mm Hs RGS7BP Tanycytes R7BP 0.034 regulator of G protein signaling 7 binding protein protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CTGF Tanycytes IGFBP8|CCN2 0.028 connective tissue growth factor protein-coding gene 1 Ectoderm Brain 0.0 0.0952381 0.0996241 0.0123362 +Mm Hs TGFB2 Tanycytes NA 0.041 transforming growth factor beta 2 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.00156642 0.0 +Mm Hs TAS1R1 Taste receptor cells T1R1|GPR70 0.0 taste 1 receptor member 1 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs TAS1R2 Taste receptor cells T1R2|GPR71 0.0 taste 1 receptor member 2 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs TAS1R3 Taste receptor cells T1R3 0.0 taste 1 receptor member 3 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs P2RX7 Taste receptor cells P2X7|MGC20089 0.004 purinergic receptor P2X 7 protein-coding gene NA NA NA 0.0 0.0 0.00877193 0.00346487 +Mm Hs CCK Taste receptor cells NA 0.033 cholecystokinin protein-coding gene 1 NA NA 0.0 0.0 0.00344612 0.0384986 +Mm Hs KCNQ1 Taste receptor cells Kv7.1|KCNA8|KVLQT1|JLNS1|LQT1|LQT|KCNA9 0.004 potassium voltage-gated channel subfamily Q member 1 protein-coding gene 1 NA NA 0.0 0.0 0.00093985 0.00532563 +Mm Hs KCNH2 Taste receptor cells Kv11.1|HERG|erg1|LQT2 0.002 potassium voltage-gated channel subfamily H member 2 protein-coding gene 1 NA NA 0.0 0.0 0.00501253 0.00198909 +Mm Hs GNAT3 Taste receptor cells gustducin|GDCA 0.0 G protein subunit alpha transducin 3 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.000192493 +Mm Hs TRPM5 Taste receptor cells LTRPC5|MTR1 0.002 transient receptor potential cation channel subfamily M member 5 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Hs TAS2R20 Taste receptor cells T2R20|T2R56|TAS2R49 0.0 taste 2 receptor member 20 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs NR3C1 Taste receptor cells GR|GRL 0.069 nuclear receptor subfamily 3 group C member 1 protein-coding gene 1 NA NA 0.0 0.0 0.0548246 0.0739814 +Mm Hs SYP Taste receptor cells MRX96 0.049 synaptophysin protein-coding gene 1 NA NA 0.0 0.0 0.00720551 0.0 +Mm Hs SV2B Taste receptor cells KIAA0735|HsT19680 0.009 synaptic vesicle glycoprotein 2B protein-coding gene 1 NA NA 0.0 0.0 0.000626566 0.0 +Hs CA4 Taste receptor cells CAIV|Car4|RP17 0.002 carbonic anhydrase 4 protein-coding gene 1 NA NA 0.0 0.0 0.0147243 0.0 +Mm Hs PKD2L1 Taste receptor cells TRPP3|PKD2L|PKDL 0.0 polycystin 2 like 1, transient receptor potential cation channel protein-coding gene 1 NA NA 0.0 0.0 0.0 6.41643e-05 +Mm Hs MCOLN3 Taste receptor cells TRPML3|FLJ11006|TRP-ML3 0.002 mucolipin 3 protein-coding gene 1 NA NA 0.0 0.0 0.00156642 0.00230991 +Mm Hs TRPM8 Taste receptor cells NA 0.0 transient receptor potential cation channel subfamily M member 8 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Hs TAS2R4 Taste receptor cells T2R4 0.0 taste 2 receptor member 4 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.0 +Mm Hs PROX1 Taste receptor cells NA 0.028 prospero homeobox 1 protein-coding gene 1 NA NA 0.0 0.0 0.0109649 0.0324671 +Mm Hs GRM4 Taste receptor cells GPRC1D|mGlu4|MGLUR4 0.001 glutamate metabotropic receptor 4 protein-coding gene 1 NA NA 0.0 0.0 0.0 0.00109079 +Mm Hs NOTCH1 Thymocytes TAN1 0.007 notch 1 protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00469925 0.00763555 +Mm Hs CD38 Thymocytes NA 0.016 CD38 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0140977 0.0161052 +Mm Hs CXCR4 Thymocytes LESTR|NPY3R|HM89|NPYY3R|D2S201E|fusin|HSY3RR|CD184 0.04 C-X-C motif chemokine receptor 4 protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.198308 0.0087905 +Mm Hs TNF Thymocytes TNFSF2|DIF|TNF-alpha|TNFA 0.008 tumor necrosis factor protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00125313 0.0 +Hs CD1D Thymocytes NA 0.0 CD1d molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00093985 0.0 +Mm Hs CD2 Thymocytes NA 0.04 CD2 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.093985 0.0296439 +Hs CD1A Thymocytes NA 0.0 CD1a molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0 0.0 +Mm Hs CD4 Thymocytes NA 0.009 CD4 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.018797 0.00757138 +Mm Hs CD5 Thymocytes NA 0.004 CD5 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00407268 0.00442733 +Mm Hs CD8A Thymocytes CD8 0.01 CD8a molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0159774 0.00859801 +Mm Hs IL2RA Thymocytes IL2R|IDDM10 0.009 interleukin 2 receptor subunit alpha protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0200501 0.00673725 +Mm Hs CD69 Thymocytes CLEC2C 0.024 CD69 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.111216 0.00737889 +Mm Hs SLAMF1 Thymocytes CD150|SLAM 0.001 signaling lymphocytic activation molecule family member 1 protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00156642 0.0 +Hs CD99 Thymocytes MIC2 0.007 CD99 molecule (Xg blood group) protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00156642 0.0 +Mm Hs TAGAP Thymocytes FLJ32631|IDDM21|ARHGAP47 0.004 T cell activation RhoGTPase activating protein protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00344612 0.0 +Mm MS4A4B Thymocytes NA 0.023 membrane-spanning 4-domains, subfamily A, member 4B protein coding gene 1 Endoderm Thymus 0.0 0.0 0.0 0.0275906 +Mm Hs UCP2 Thymocytes SLC25A8|BMIQ4 0.013 uncoupling protein 2 protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00501253 0.0 +Mm Hs TSHR Thymocytes LGR3 0.0 thyroid stimulating hormone receptor protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0 0.0 +Mm Hs CD27 Thymocytes S152|Tp55|TNFRSF7 0.018 CD27 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0228697 0.0157844 +Mm Hs CD28 Thymocytes NA 0.011 CD28 molecule protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.00281955 0.012897 +Mm Hs BCL6 Thymocytes ZBTB27|LAZ3|BCL5|BCL6A|ZNF51 0.004 B cell CLL/lymphoma 6 protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0037594 0.00481232 +Mm Hs CIDEA Thymocytes CIDE-A 0.004 cell death-inducing DFFA-like effector a protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.0 0.00494065 +Mm Hs EZR Thymocytes VIL2 0.219 ezrin protein-coding gene 1 Endoderm Thymus 0.0 0.0 0.26817 0.206481 +Mm Hs SLC26A4 Transient cells PDS|DFNB4 0.001 solute carrier family 26 member 4 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00093985 0.0 +Mm CAR12 Transient cells NA 0.004 carbonic anhydrase 12 protein coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.00519731 +Mm Hs RHBG Transient cells SLC42A2 0.002 Rh family B glycoprotein (gene/pseudogene) protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.0 +Mm Hs HEPACAM2 Transient cells FLJ38683 0.012 HEPACAM family member 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0112782 0.012512 +Mm Hs INSRR Transient cells IRR 0.001 insulin receptor related receptor protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.000769971 +Mm Hs CLCNKB Transient cells hClC-Kb 0.002 chloride voltage-gated channel Kb protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0 0.00288739 +Mm Hs COL18A1 Transient cells KNO1|KNO 0.032 collagen type XVIII alpha 1 chain protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0153509 0.036317 +Mm Hs SLC43A2 Transient cells MGC34680 0.016 solute carrier family 43 member 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0056391 0.0 +Mm Hs TMEM117 Transient cells DKFZp434K2435 0.002 transmembrane protein 117 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.000626566 0.0 +Mm Hs PARM1 Transient cells DKFZP564O0823|Cipar1|WSC4 0.02 prostate androgen-regulated mucin-like protein 1 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.018797 0.0207892 +Mm Hs ST14 Transient cells SNC19|MT-SP1|TMPRSS14|PRSS14 0.02 suppression of tumorigenicity 14 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.039787 0.0 +Mm Hs ENPP5 Transient cells NA 0.028 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative) protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.000626566 0.0349695 +Mm Hs GCLC Transient cells GLCLC|GLCL 0.021 glutamate-cysteine ligase catalytic subunit protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0093985 0.0238049 +Mm Hs SYT7 Transient cells IPCA-7|SYT-VII|MGC150517|PCANAP7 0.024 synaptotagmin 7 protein-coding gene 1 Mesoderm Kidney 0.0 0.0 0.00626566 0.0 +Mm Hs ITGAV Transient cells CD51|VNRA|MSK8|VTNR 0.026 integrin subunit alpha V protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0219298 0.0275265 +Mm Hs TMEM50B Transient cells C21orf4 0.029 transmembrane protein 50B protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0598371 0.0 +Mm Hs CTNNB1 Transient cells beta-catenin|armadillo|CTNNB 0.052 catenin beta 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.212406 0.0114212 +Mm Hs ACO2 Transient cells ACONM 0.012 aconitase 2 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00093985 0.0147578 +Mm Hs SMPD1 Transient cells NA 0.023 sphingomyelin phosphodiesterase 1 protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0203634 0.0 +Mm Hs OGDH Transient cells E1k 0.067 oxoglutarate dehydrogenase protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00720551 0.0814886 +Mm Hs SEC23B Transient cells CDA-II|CDAII|HEMPAS|CDAN2 0.02 Sec23 homolog B, coat complex II component protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0238095 0.0 +Mm Hs CDC42BPB Transient cells MRCKB|KIAA1124 0.003 CDC42 binding protein kinase beta protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.0119048 0.0008983 +Mm Hs PIP4K2C Transient cells FLJ22055|PIP5K2C 0.005 phosphatidylinositol-5-phosphate 4-kinase type 2 gamma protein-coding gene NA Mesoderm Kidney 0.0 0.0 0.00469925 0.00551813 +Mm Hs KRT86 Trichocytes MNX|Hb6|KRTHB6 0.001 keratin 86 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.00344612 0.0 +Mm Hs DSG2 Trichocytes CDHF5 0.019 desmoglein 2 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0451128 0.012127 +Mm Hs KRT81 Trichocytes Hb-1|KRTHB1 0.002 keratin 81 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0119048 0.0 +Mm Hs DSG4 Trichocytes CDHF13|LAH 0.0 desmoglein 4 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 6.41643e-05 +Hs KRT37 Trichocytes KRTHA7 0.0 keratin 37 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.0 +Mm Hs HOXC13 Trichocytes HOX3G 0.001 homeobox C13 protein-coding gene 1 Mesoderm Skin 0.0 0.0 0.0 0.000641643 +Mm Hs CREBRF Trigeminal neurons C5orf41 0.009 CREB3 regulatory factor protein-coding gene NA Ectoderm Brain 0.0 0.125 0.0137845 0.00735626 +Mm Hs PRKX Trigeminal neurons PKX1 0.009 protein kinase X-linked protein-coding gene NA Ectoderm Brain 0.0 0.329545 0.00877193 0.00754985 +Mm Hs PRDM12 Trigeminal neurons PFM9 0.002 PR/SET domain 12 protein-coding gene NA Ectoderm Brain 0.0 0.443182 0.0 0.0 +Mm Hs DHCR24 Trigeminal neurons KIAA0018|seladin-1|DCE 0.018 24-dehydrocholesterol reductase protein-coding gene NA Ectoderm Brain 0.0 0.261364 0.0604637 0.00387172 +Mm Hs CALCA Trigeminal neurons CALC1 0.004 calcitonin related polypeptide alpha protein-coding gene NA Ectoderm Brain 0.0 0.534091 0.00125313 0.00212944 +Mm Hs CALCB Trigeminal neurons FLJ30166|CGRP-II|CALC2 0.003 calcitonin related polypeptide beta protein-coding gene NA Ectoderm Brain 0.0 0.522727 0.0 0.000967929 +Mm Hs VWA5A Trigeminal neurons BCSC-1|LOH11CR2A 0.011 von Willebrand factor A domain containing 5A protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00908521 0.0 +Mm PRRXL1 Trigeminal neurons NA 0.004 paired related homeobox protein-like 1 protein coding gene NA Ectoderm Brain 0.0 0.75 0.0 0.000387172 +Mm Hs PPP1R1C Trigeminal neurons Inhibitor-1-like 0.008 protein phosphatase 1 regulatory inhibitor subunit 1C protein-coding gene NA Ectoderm Brain 0.0 0.818182 0.0191103 0.0018068 +Mm Hs AVIL Trigeminal neurons p92|FLJ12386|ADVIL|DOC6 0.005 advillin protein-coding gene NA Ectoderm Brain 0.0 0.806818 0.000313283 0.00219397 +Mm Hs PIRT Trigeminal neurons NA 0.005 phosphoinositide interacting regulator of transient receptor potential channels protein-coding gene NA Ectoderm Brain 0.0 0.886364 0.0 0.00193586 +Mm Hs TAC1 Trigeminal neurons NPK|TAC2|NKNA 0.01 tachykinin precursor 1 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00532581 0.0 +Mm Hs PRPH Trigeminal neurons PRPH1|NEF4 0.011 peripherin protein-coding gene NA Ectoderm Brain 0.0 1.0 0.0241228 0.00329096 +Mm Hs SCN9A Trigeminal neurons Nav1.7|NE-NA|NENA|ETHA 0.011 sodium voltage-gated channel alpha subunit 9 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00407268 0.0 +Mm Hs RUFY2 Trigeminal neurons RABIP4R|FLJ10063|KIAA1537|ZFYVE13 0.013 RUN and FYVE domain containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00971178 0.0 +Mm Hs FAM189B Trigeminal neurons cote1|C1orf2 0.013 family with sequence similarity 189 member B protein-coding gene NA Ectoderm Brain 0.0 0.909091 0.00877193 0.00806608 +Mm Hs CLGN Trigeminal neurons NA 0.014 calmegin protein-coding gene NA Ectoderm Brain 0.0 0.704545 0.0238095 0.00838872 +Mm Hs SCN7A Trigeminal neurons Nav2.1|Nav2.2|NaG|SCN6A 0.017 sodium voltage-gated channel alpha subunit 7 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00814536 0.0 +Mm Hs NEFH Trigeminal neurons NA 0.009 neurofilament heavy protein-coding gene NA Ectoderm Brain 0.0 0.670455 0.0037594 0.00690456 +Mm Hs GCNT2 Trigeminal neurons IGNT|NAGCT1|bA421M1.1|bA360O19.2|ULG3|NACGT1|II|GCNT5|CCAT 0.015 glucosaminyl (N-acetyl) transferase 2 (I blood group) protein-coding gene NA Ectoderm Brain 0.0 0.693182 0.0109649 0.0121959 +Mm Hs ZDHHC2 Trigeminal neurons ZNF372|DHHC2 0.015 zinc finger DHHC-type containing 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0056391 0.0 +Mm Hs PARM1 Trigeminal neurons DKFZP564O0823|Cipar1|WSC4 0.02 prostate androgen-regulated mucin-like protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.704545 0.018797 0.0169065 +Mm Hs AHNAK2 Trigeminal neurons C14orf78 0.019 AHNAK nucleoprotein 2 protein-coding gene NA Ectoderm Brain 0.0 0.715909 0.00783208 0.0180035 +Mm Hs PHF24 Trigeminal neurons KIAA1045 0.011 PHD finger protein 24 protein-coding gene NA Ectoderm Brain 0.0 0.715909 0.000313283 0.00955024 +Mm Hs KCNAB2 Trigeminal neurons AKR6A5|KCNA2B|HKvbeta2.1|HKvbeta2.2 0.018 potassium voltage-gated channel subfamily A regulatory beta subunit 2 protein-coding gene NA Ectoderm Brain 0.0 0.659091 0.0106516 0.0147771 +Mm Hs ATL1 Trigeminal neurons AD-FSP|SPG3|SPG3A 0.017 atlastin GTPase 1 protein-coding gene NA Ectoderm Brain 0.0 0.647727 0.00313283 0.0174873 +Mm Hs HSPB8 Trigeminal neurons H11|E2IG1|HSP22|HspB8|CMT2L 0.024 heat shock protein family B (small) member 8 protein-coding gene NA Ectoderm Brain 0.0 0.727273 0.00595238 0.0238756 +Mm Hs FKBP1B Trigeminal neurons OTK4|FKBP12.6|FKBP9|FKBP1L 0.02 FK506 binding protein 1B protein-coding gene NA Ectoderm Brain 0.0 0.715909 0.0200501 0.0138091 +Mm Hs TLN2 Trigeminal neurons KIAA0320 0.024 talin 2 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00689223 0.0 +Mm Hs SYNM Trigeminal neurons KIAA0353|DMN 0.017 synemin protein-coding gene NA Ectoderm Brain 0.0 0.0 0.00093985 0.0 +Mm Hs GDAP1 Trigeminal neurons CMT4|CMT2K|CMT4A 0.021 ganglioside induced differentiation associated protein 1 protein-coding gene NA Ectoderm Brain 0.0 0.522727 0.0075188 0.021359 +Mm Hs DGKZ Trigeminal neurons DAGK5|hDGKzeta|DGK-ZETA 0.025 diacylglycerol kinase zeta protein-coding gene NA Ectoderm Brain 0.0 0.681818 0.00281955 0.0263277 +Mm Hs PRUNE2 Trigeminal neurons BMCC1|BNIPXL|A214N16.3|bA214N16.3|C9orf65|KIAA0367 0.033 prune homolog 2 protein-coding gene NA Ectoderm Brain 0.0 0.988636 0.00720551 0.03491 +Mm Hs SLC17A6 Trigeminal neurons DNPI|VGLUT2 0.016 solute carrier family 17 member 6 protein-coding gene NA Ectoderm Brain 0.0 0.0 0.000313283 0.0 +Mm Hs FGF13 Trigeminal neurons FHF2|FGF2 0.022 fibroblast growth factor 13 protein-coding gene NA Ectoderm Brain 0.0 0.840909 0.00093985 0.0231012 +Mm Hs DGKH Trigeminal neurons DGKeta 0.022 diacylglycerol kinase eta protein-coding gene NA Ectoderm Brain 0.0 0.943182 0.00720551 0.0205201 +Mm Hs CPNE3 Trigeminal neurons NA 0.061 copine 3 protein-coding gene NA Ectoderm Brain 0.0 0.670455 0.0667293 0.0530425 +Mm Hs CCDC92 Trigeminal neurons FLJ22471 0.026 coiled-coil domain containing 92 protein-coding gene NA Ectoderm Brain 0.0 0.625 0.0159774 0.0256824 +Mm Hs SNCG Trigeminal neurons BCSG1|SR|persyn 0.03 synuclein gamma protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0382206 0.0 +Mm Hs NICN1 Trigeminal neurons MGC12936 0.022 nicolin 1 protein-coding gene NA Ectoderm Brain 0.0 0.670455 0.0 0.0240046 +Mm Hs NEFM Trigeminal neurons NFM|NF-M|NEF3 0.028 neurofilament medium protein-coding gene NA Ectoderm Brain 0.0 0.852273 0.0200501 0.023682 +Mm Hs RGS7BP Trigeminal neurons R7BP 0.034 regulator of G protein signaling 7 binding protein protein-coding gene NA Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs ADD2 Trigeminal neurons ADDB 0.029 adducin 2 protein-coding gene NA Ectoderm Brain 0.0 0.659091 0.0137845 0.0301349 +Mm Hs PIEZO2 Trigeminal neurons FLJ23403|FLJ23144|HsT748|HsT771|FLJ34907|FAM38B2|C18orf30|C18orf58|FAM38B 0.006 piezo type mechanosensitive ion channel component 2 protein-coding gene 1 Ectoderm Brain 0.0 0.613636 0.000626566 0.00432342 +Mm Hs VAMP1 Trigeminal neurons VAMP-1|SYB1 0.003 vesicle associated membrane protein 1 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs SCN10A Trigeminal neurons Nav1.8|hPN3|SNS|PN3 0.003 sodium voltage-gated channel alpha subunit 10 protein-coding gene 1 Ectoderm Brain 0.0 0.0 0.0 0.0 +Mm Hs CD4 Trophoblast cells NA 0.009 CD4 molecule protein-coding gene NA Zygote Embryo 0.0 0.0 0.018797 0.00757138 +Mm Hs TTPA Trophoblast cells AVED 0.001 alpha tocopherol transfer protein protein-coding gene NA Zygote Embryo 0.0 0.0 0.0 0.0 +Mm Hs TNFRSF9 Trophoblast cells CD137|4-1BB|ILA 0.003 TNF receptor superfamily member 9 protein-coding gene NA Zygote Embryo 0.0 0.0 0.00344612 0.0 +Mm Hs STAR Trophoblast cells StAR|STARD1 0.001 steroidogenic acute regulatory protein protein-coding gene NA Zygote Embryo 0.0 0.0 0.000313283 0.0 +Mm Hs HOPX Trophoblast cells LAGY|OB1|NECC1|SMAP31 0.033 HOP homeobox protein-coding gene NA Zygote Embryo 0.0 0.0 0.091792 0.022265 +Hs S100P Trophoblast cells NA 0.009 S100 calcium binding protein P protein-coding gene NA Zygote Embryo 0.0 0.0 0.0510652 0.0 +Mm Hs ADAM19 Trophoblast cells MLTNB 0.013 ADAM metallopeptidase domain 19 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0238095 0.0113571 +Mm Hs CYP24A1 Trophoblast cells CP24|P450-CC24|CYP24 0.0 cytochrome P450 family 24 subfamily A member 1 protein-coding gene NA Zygote Embryo 0.0 0.0 0.00250627 6.41643e-05 +Mm Hs LIF Trophoblast cells CDF|HILDA 0.002 LIF, interleukin 6 family cytokine protein-coding gene NA Zygote Embryo 0.0 0.0 0.00532581 0.00109079 +Mm Hs HAND1 Trophoblast cells eHand|Thing1|Hxt|bHLHa27 0.005 heart and neural crest derivatives expressed 1 protein-coding gene NA Zygote Embryo 0.0 0.0 0.014411 0.00192493 +Mm Hs ELF5 Trophoblast cells NA 0.004 E74 like ETS transcription factor 5 protein-coding gene NA Zygote Embryo 0.0 0.0 0.00438596 0.00384986 +Mm Hs SIRT1 Trophoblast cells SIR2L1 0.003 sirtuin 1 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0106516 0.0 +Mm Hs PTHLH Trophoblast cells PTHRP 0.002 parathyroid hormone like hormone protein-coding gene NA Zygote Embryo 0.0 0.0 0.00250627 0.00243824 +Mm Hs ACKR2 Trophoblast cells CCR10|D6|CCR9|CMKBR9 0.001 atypical chemokine receptor 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.000313283 0.00141161 +Mm Hs IGF2 Trophoblast cells FLJ44734|IGF-II|C11orf43 0.013 insulin like growth factor 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0463659 0.0008983 +Hs SIGLEC6 Trophoblast cells OB-BP1|SIGLEC-6|CD327|CD33L|CD33L1 0.0 sialic acid binding Ig like lectin 6 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0 0.0 +Mm Hs CDX2 Trophoblast cells CDX3 0.015 caudal type homeobox 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.00814536 0.0170035 +Mm Hs KRT7 Trophoblast cells CK7|K2C7 0.056 keratin 7 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.10119 0.0474174 +Mm Hs DLX3 Trophoblast cells NA 0.001 distal-less homeobox 3 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0 0.000769971 +Mm Hs GCM1 Trophoblast cells hGCMa|GCMA 0.0 glial cells missing homolog 1 protein-coding gene NA Zygote Embryo 0.0 0.0 0.00125313 0.0 +Mm Hs ASCL2 Trophoblast cells HASH2|bHLHa45 0.005 achaete-scute family bHLH transcription factor 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0075188 0.00481232 +Hs CGB3 Trophoblast cells CGB 0.0 chorionic gonadotropin subunit beta 3 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0 0.0 +Mm Hs INHBA Trophoblast cells NA 0.013 inhibin subunit beta A protein-coding gene NA Zygote Embryo 0.0 0.0 0.00814536 0.0133462 +Mm Hs MLANA Trophoblast cells NA 0.002 melan-A protein-coding gene NA Zygote Embryo 0.0 0.0 0.0 0.00166827 +Mm Hs SERPINE1 Trophoblast cells PAI|PLANH1|PAI1 0.014 serpin family E member 1 protein-coding gene NA Zygote Embryo 0.0 0.0 0.0388471 0.0 +Mm Hs PHLDA2 Trophoblast cells IPL|BWR1C|HLDA2|TSSC3 0.033 pleckstrin homology like domain family A member 2 protein-coding gene NA Zygote Embryo 0.0 0.0 0.140038 0.00654475 +Mm Hs TFEB Trophoblast cells TCFEB|bHLHe35 0.003 transcription factor EB protein-coding gene NA Zygote Embryo 0.0 0.0 0.00156642 0.0 +Mm Hs PERP Trophoblast cells PIGPC1|dJ496H19.1|KCP1|THW|KRTCAP1 0.077 PERP, TP53 apoptosis effector protein-coding gene 1 Zygote Embryo 0.0 0.0 0.167607 0.0519731 +Mm Hs PARP1 Trophoblast cells PARP|PPOL|ADPRT 0.113 poly(ADP-ribose) polymerase 1 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.219925 0.080462 +Hs ERVFRD-1 Trophoblast cells HERV-W/FRD|HERV-FRD|envFRD|ERVFRDE1|syncytin-2 0.0 endogenous retrovirus group FRD member 1, envelope protein-coding gene 1 Zygote Embryo 0.0 0.0 0.000626566 0.0 +Hs HLA-G Trophoblast cells NA 0.001 major histocompatibility complex, class I, G protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00595238 0.0 +Mm Hs ISG20 Trophoblast progenitor cells HEM45 0.043 interferon stimulated exonuclease gene 20 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.140664 0.0210459 +Mm Hs FOXO4 Trophoblast progenitor cells AFX1|MLLT7 0.004 forkhead box O4 protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00125313 0.00442733 +Mm Hs TFAP2C Trophoblast progenitor cells AP2-GAMMA|TFAP2G|hAP-2g 0.012 transcription factor AP-2 gamma protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00657895 0.0 +Mm Hs TFAP2C Trophoblast stem cells AP2-GAMMA|TFAP2G|hAP-2g 0.012 transcription factor AP-2 gamma protein-coding gene 1 Zygote Embryo 0.0 0.0 0.00657895 0.0 +Mm Hs SUCNR1 Tuft cells GPR91 0.0 succinate receptor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.000626566 0.0 +Mm Hs FABP1 Tuft cells L-FABP 0.03 fatty acid binding protein 1 protein-coding gene 1 Endoderm GI tract 0.0 0.692308 0.0413534 0.0273568 +Mm Hs POU2F3 Tuft cells OCT11|PLA-1|Skn-1a|Epoc-1 0.001 POU class 2 homeobox 3 protein-coding gene 1 Endoderm GI tract 0.0 0.384615 0.000313283 0.000706396 +Mm SIGLECF Tuft cells NA 0.002 sialic acid binding Ig-like lectin F protein coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs CDHR2 Tuft cells PC-LKC|FLJ20124|FLJ20383|PCLKC|PCDH24 0.013 cadherin related family member 2 protein-coding gene 1 Endoderm GI tract 0.0 0.769231 0.016604 0.0121372 +Mm Hs AVIL Tuft cells p92|FLJ12386|ADVIL|DOC6 0.005 advillin protein-coding gene 1 Endoderm GI tract 0.0 1.0 0.000313283 0.00590804 +Mm Hs ESPN Tuft cells DFNB36 0.017 espin protein-coding gene 1 Endoderm GI tract 0.0 1.0 0.0150376 0.0179168 +Mm Hs LRMP Tuft cells JAW1 0.015 lymphoid restricted membrane protein protein-coding gene 1 Endoderm GI tract 0.0 1.0 0.00250627 0.0152196 +Mm Hs TRPM5 Tuft cells LTRPC5|MTR1 0.002 transient receptor potential cation channel subfamily M member 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs DCLK1 Tuft cells KIAA0369|DCLK|DCDC3A|DCAMKL1 0.159 doublecortin like kinase 1 protein-coding gene 1 Endoderm GI tract 0.0 0.923077 0.0075188 0.195993 +Mm Hs TAS1R3 Tuft cells T1R3 0.0 taste 1 receptor member 3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs SOX9 Tuft cells SRA1|CMD1|CMPD1 0.086 SRY-box 9 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0322682 0.0 +Mm TUBB5 Tuft cells NA 0.606 tubulin, beta 5 class I protein coding gene 1 Endoderm GI tract NA NA NA NA +Mm Hs CAMK2B Tuft cells CAM2|CAMK2|CAMKB 0.08 calcium/calmodulin dependent protein kinase II beta protein-coding gene 1 Endoderm GI tract 0.0 0.230769 0.0106516 0.0968405 +Mm Hs GNAT3 Tuft cells gustducin|GDCA 0.0 G protein subunit alpha transducin 3 protein-coding gene 1 Endoderm GI tract 0.0 0.230769 0.0 0.0 +Mm Hs IL25 Tuft cells IL-17E|IL17E 0.0 interleukin 25 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm Hs PLCB2 Tuft cells FLJ38135 0.001 phospholipase C beta 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0769231 0.000313283 0.0010917 +Mm Hs GFI1B Tuft cells ZNF163B 0.005 growth factor independent 1B transcriptional repressor protein-coding gene 1 Endoderm GI tract 0.0 0.153846 0.0191103 0.0017981 +Mm Hs ATOH1 Tuft cells HATH1|MATH-1|Math1|bHLHa14 0.003 atonal bHLH transcription factor 1 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00093985 0.00282558 +Mm CD24A Tuft cells NA 0.322 CD24a antigen protein coding gene 1 Endoderm GI tract 0.0 1.0 0.0 0.399371 +Mm Hs ASIC5 Tuft cells INAC|HINAC|ACCN5 0.0 acid sensing ion channel subunit family member 5 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 6.42178e-05 +Mm Hs KLF3 Tuft cells BKLF 0.066 Kruppel like factor 3 protein-coding gene 1 Endoderm GI tract 0.0 0.230769 0.0651629 0.067814 +Mm Hs KLF6 Tuft cells CPBP|GBF|Zf9|ST12|COPEB 0.3 Kruppel like factor 6 protein-coding gene 1 Endoderm GI tract 0.0 0.230769 0.431078 0.276201 +Mm Hs DRD3 Tuft cells NA 0.0 dopamine receptor D3 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0 +Mm NRADD Tuft cells NA 0.011 neurotrophin receptor associated death domain protein coding gene 1 Endoderm GI tract 0.0 0.0769231 0.0 0.0133573 +Mm Hs GNG13 Tuft cells h2-35|G(gamma)13 0.006 G protein subunit gamma 13 protein-coding gene 1 Endoderm GI tract 0.0 0.230769 0.0 0.00751349 +Mm Hs NREP Tuft cells P311|D4S114|PRO1873|PTZ17|SEZ17|C5orf13 0.216 neuronal regeneration related protein protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.0892857 0.248973 +Mm Hs RGS2 Tuft cells G0S8 0.128 regulator of G protein signaling 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.10589 0.0 +Mm Hs RAC2 Tuft cells EN-7 0.172 Rac family small GTPase 2 protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.18515 0.0 +Mm Hs PTGS1 Tuft cells PGHS-1|PTGHS 0.029 prostaglandin-endoperoxide synthase 1 protein-coding gene 1 Endoderm GI tract 0.0 1.0 0.0037594 0.0351914 +Mm Hs IRF7 Tuft cells NA 0.033 interferon regulatory factor 7 protein-coding gene 1 Endoderm GI tract 0.0 0.538462 0.0285088 0.031852 +Mm Hs FFAR3 Tuft cells FFA3R|GPR41 0.0 free fatty acid receptor 3 protein-coding gene 1 Endoderm GI tract 0.0 0.615385 0.0 0.000128436 +Mm Hs ALOX5 Tuft cells 5-LOX 0.006 arachidonate 5-lipoxygenase protein-coding gene 1 Endoderm GI tract 0.0 1.0 0.00313283 0.00558695 +Mm Hs TSLP Tuft cells NA 0.003 thymic stromal lymphopoietin protein-coding gene 1 Endoderm GI tract 0.0 0.0 0.00250627 0.0 +Mm IL4RA Tuft cells NA 0.013 interleukin 4 receptor, alpha protein coding gene 1 Endoderm GI tract 0.0 0.0 0.0 0.0168893 +Mm Hs IL13RA1 Tuft cells IL-13Ra|NR4|CD213a1 0.016 interleukin 13 receptor subunit alpha 1 protein-coding gene 1 Endoderm GI tract 0.0 0.923077 0.0291353 0.0126509 +Mm Hs IL17RB Tuft cells IL17RH1|EVI27|CRL4|IL17BR 0.001 interleukin 17 receptor B protein-coding gene 1 Endoderm GI tract 0.0 0.538462 0.000313283 0.000706396 +Mm Hs PTPRC Tuft cells T200|CD45 0.125 protein tyrosine phosphatase, receptor type C protein-coding gene 1 Endoderm GI tract 0.0 0.0769231 0.216165 0.106216 +Mm Hs BATF3 Undefined placental cells JUNDM1|SNFT 0.008 basic leucine zipper ATF-like transcription factor 3 protein-coding gene NA Trophoblast Placenta 0.0 0.208333 0.00909661 0.0068119 +Mm Hs DIO3 Undefined placental cells TXDI3 0.0 iodothyronine deiodinase 3 protein-coding gene NA Trophoblast Placenta 0.0 0.0416667 0.000313676 0.000257053 +Mm Hs DKKL1 Undefined placental cells SGY-1|CT34 0.019 dickkopf like acrosomal protein 1 protein-coding gene NA Trophoblast Placenta 0.0 0.5 0.0354454 0.015616 +Mm Hs DUSP9 Undefined placental cells MKP-4|MKP4 0.014 dual specificity phosphatase 9 protein-coding gene NA Trophoblast Placenta 1.0 0.75 0.0065872 0.0142022 +Mm FTHL17A Undefined placental cells NA 0.001 ferritin, heavy polypeptide-like 17, member A protein coding gene NA Trophoblast Placenta 0.0 0.375 0.0 0.000514106 +Mm Hs H19 Undefined placental cells D11S813E|ASM1|NCRNA00008|LINC00008 0.061 H19, imprinted maternally expressed transcript non-coding RNA NA Trophoblast Placenta 0.0 0.833333 0.0294856 0.0686331 +Mm Hs LAS1L Undefined placental cells FLJ12525 0.025 LAS1 like, ribosome biogenesis factor protein-coding gene NA Trophoblast Placenta 0.0 0.375 0.00972397 0.0273119 +Mm Hs LDOC1 Undefined placental cells Mar7|Mart7|SIRH7|RTL7|BCUR1 0.005 LDOC1, regulator of NFKB signaling protein-coding gene NA Trophoblast Placenta 0.0 0.458333 0.0175659 0.000257053 +Mm Hs MBNL3 Undefined placental cells CHCR|FLJ11316|MBLX39|MBXL 0.006 muscleblind like splicing regulator 3 protein-coding gene NA Trophoblast Placenta 0.75 0.375 0.00595985 0.00552664 +Mm Hs PHLDA2 Undefined placental cells IPL|BWR1C|HLDA2|TSSC3 0.033 pleckstrin homology like domain family A member 2 protein-coding gene NA Trophoblast Placenta 1.0 0.416667 0.138959 0.00591222 +Mm PRL3B1 Undefined placental cells NA 0.001 prolactin family 3, subfamily b, member 1 protein coding gene NA Trophoblast Placenta 0.0 0.333333 0.0 0.000706895 +Mm Hs PRSS8 Undefined placental cells NA 0.009 serine protease 8 protein-coding gene NA Trophoblast Placenta 0.0 0.333333 0.000313676 0.0113103 +Mm RHOX5 Undefined placental cells NA 0.013 reproductive homeobox 5 protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm RHOX6 Undefined placental cells NA 0.004 reproductive homeobox 6 protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm RHOX9 Undefined placental cells NA 0.002 reproductive homeobox 9 protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm Hs SCT Undefined placental cells NA 0.011 secretin protein-coding gene NA Trophoblast Placenta 0.0 0.0 0.0122334 0.0 +Mm SERPINB9E Undefined placental cells NA 0.0 serine (or cysteine) peptidase inhibitor, clade B, member 9e protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm SERPINB9G Undefined placental cells NA 0.0 serine (or cysteine) peptidase inhibitor, clade B, member 9g protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm TEX19.1 Undefined placental cells NA 0.007 testis expressed gene 19.1 protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm Hs TFRC Undefined placental cells CD71|TFR1|p90 0.042 transferrin receptor protein-coding gene NA Trophoblast Placenta 0.5 0.0 0.0608532 0.0 +Mm TPBPA Undefined placental cells NA 0.001 trophoblast specific protein alpha protein coding gene NA Trophoblast Placenta NA NA NA NA +Mm Hs KRT23 Undefined placental cells K23|DKFZP434G032|HAIK1|CK23|MGC26158 0.014 keratin 23 protein-coding gene NA Trophoblast Placenta 1.0 0.0 0.0564617 0.00552664 +Mm Hs TRPV1 Urothelial cells NA 0.001 transient receptor potential cation channel subfamily V member 1 protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs NAT1 Urothelial cells AAC1 0.0 N-acetyltransferase 1 protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs UPK1B Urothelial cells TSPAN20|UPK1 0.001 uroplakin 1B protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs PIEZO1 Urothelial cells KIAA0233|FAM38A 0.01 piezo type mechanosensitive ion channel component 1 protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.25 0.0162907 0.00821513 +Mm Hs UMODL1 Urothelial cells NA 0.0 uromodulin like 1 protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs IVL Urothelial cells NA 0.001 involucrin protein-coding gene 1 Mesoderm Urinary bladder 0.0 1.0 0.000313283 0.00141198 +Mm Hs SLC14A1 Urothelial cells HsT1341|RACH1|RACH2|JK 0.008 solute carrier family 14 member 1 (Kidd blood group) protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0181704 0.0 +Mm Hs UPK3A Urothelial cells UPK3 0.0 uroplakin 3A protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs UPK1A Urothelial cells TSPAN21 0.0 uroplakin 1A protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs UPK2 Urothelial cells UPII|MGC138598 0.0 uroplakin 2 protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs UPK3B Urothelial cells MGC10902|UPIIIb|FLJ32198 0.0 uroplakin 3B protein-coding gene 1 Mesoderm Urinary bladder 0.0 0.0 0.0 0.0 +Mm Hs ACTA2 Vascular smooth muscle cells ACTSA 0.035 actin, alpha 2, smooth muscle, aorta protein-coding gene NA Mesoderm Smooth muscle 0.0 1.0 0.0194236 0.0386368 +Mm Hs MYH11 Vascular smooth muscle cells SMMHC|SMHC 0.015 myosin heavy chain 11 protein-coding gene NA Mesoderm Smooth muscle 0.0 1.0 0.0162907 0.0146974 +Mm Hs PDGFRB Vascular smooth muscle cells JTK12|CD140b|PDGFR1|PDGFR 0.033 platelet derived growth factor receptor beta protein-coding gene NA Mesoderm Smooth muscle 0.0 0.75 0.0363409 0.0332456 +Mm Hs SEMA3D Vascular smooth muscle cells coll-2|Sema-Z2 0.005 semaphorin 3D protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.00125313 0.0 +Mm Hs TBX18 Vascular smooth muscle cells NA 0.004 T-box 18 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.000313283 0.0 +Mm Hs WT1 Vascular smooth muscle cells WIT-2|AWT1|NPHS4|GUD 0.01 Wilms tumor 1 protein-coding gene NA Mesoderm Smooth muscle 0.0 0.0 0.0225564 0.0 From b0749ec7cf9db0406056f24c78ae69d1c1073da1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 20 Jul 2023 12:24:45 -0500 Subject: [PATCH 023/268] newline --- config/reference_paths.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/reference_paths.config b/config/reference_paths.config index e1b9be0a..5d95132e 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -9,4 +9,4 @@ barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references celltype_ref_dir = "${params.ref_rootdir}/celltype" celltype_ref_metadata = "${projectDir}/references/celltype-reference-metadata.tsv" -panglao_marker_genes = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" \ No newline at end of file +panglao_marker_genes = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" From 0e40c1c637ff576af164e8d68f2881c306a0ec2e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 21 Jul 2023 09:40:03 -0500 Subject: [PATCH 024/268] update input to train singleR --- build-celltype-ref.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index a7877cea..b82f9fba 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -10,7 +10,7 @@ process save_singler_refs { input: tuple val(ref_name), val(ref_database) output: - path ref_file + tuple val(ref_name), path(ref_file) script: ref_file = "${ref_database}-${ref_name}.rds" """ @@ -32,7 +32,7 @@ process train_singler_models { label 'cpus_4' label 'mem_16' input: - tuple val(ref_name), path(celltype_ref) + tuple val(ref_name), path(ref_file) path tx2gene output: path celltype_model @@ -40,7 +40,7 @@ process train_singler_models { celltype_model = "${ref_name}_model.rds" """ train_SingleR.R \ - --ref_file ${celltype_ref} \ + --ref_file ${ref_file} \ --output_file ${celltype_model} \ --fry_tx2gene ${tx2gene} \ --label_name ${params.label_name} \ From bac32db00ff5b78bed2d247115ec086e98dbef76 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 21 Jul 2023 16:49:35 -0500 Subject: [PATCH 025/268] Apply suggestions from code review Co-authored-by: Stephanie --- build-celltype-ref.nf | 12 ++++++------ config/reference_paths.config | 2 +- references/celltype-reference-metadata.tsv | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index b82f9fba..6550e745 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -8,18 +8,18 @@ process save_singler_refs { publishDir "${params.celltype_ref_dir}/singler_references" label 'mem_8' input: - tuple val(ref_name), val(ref_database) + tuple val(ref_name), val(ref_source) output: tuple val(ref_name), path(ref_file) script: - ref_file = "${ref_database}-${ref_name}.rds" + ref_file = "${ref_source}-${ref_name}.rds" """ save_singler_refs.R \ --ref_name ${ref_name} \ --ref_file ${ref_file} """ stub: - ref_file = "${ref_database}-${ref_name}.rds" + ref_file = "${ref_source}-${ref_name}.rds" """ touch ${ref_file} """ @@ -68,7 +68,7 @@ workflow build_celltype_ref { singler_refs_ch = celltype_refs_ch.singler .map{[ ref_name: it.celltype_ref_name, - ref_database: it.celltype_ref_database + ref_source: it.celltype_ref_source ]} // download and save reference files @@ -79,10 +79,10 @@ workflow build_celltype_ref { // cellassign refs cellassign_refs_ch = celltype_refs_ch.cellassign - // create a channel with ref_name, database, organs + // create a channel with ref_name, source, organs .map{[ ref_name: it.celltype_ref_name, - ref_database: it.celltype_ref_database, + ref_source: it.celltype_ref_source, organs: it.organs ]} } diff --git a/config/reference_paths.config b/config/reference_paths.config index 5d95132e..a70c793e 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -9,4 +9,4 @@ barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references celltype_ref_dir = "${params.ref_rootdir}/celltype" celltype_ref_metadata = "${projectDir}/references/celltype-reference-metadata.tsv" -panglao_marker_genes = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" +panglao_marker_genes_file = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" diff --git a/references/celltype-reference-metadata.tsv b/references/celltype-reference-metadata.tsv index 8ac944fc..dee416a7 100644 --- a/references/celltype-reference-metadata.tsv +++ b/references/celltype-reference-metadata.tsv @@ -1,4 +1,4 @@ -celltype_ref_name celltype_ref_database celltype_method organs +celltype_ref_name celltype_ref_source celltype_method organs BlueprintEncodeData celldex SingleR NA DatabaseImmuneCellExpressionData celldex SingleR NA HumanPrimaryCellAtlasData celldex SingleR NA From 4b536a57117e221078418a52d86629929329bbf1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 21 Jul 2023 16:50:14 -0500 Subject: [PATCH 026/268] initial process for creating marker gene refs --- bin/generate_cellassign_refs.R | 87 ++++++++++++++++++++++++++++++++++ build-celltype-ref.nf | 24 ++++++++++ 2 files changed, 111 insertions(+) create mode 100644 bin/generate_cellassign_refs.R diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R new file mode 100644 index 00000000..449bc438 --- /dev/null +++ b/bin/generate_cellassign_refs.R @@ -0,0 +1,87 @@ +#!/usr/bin/env Rscript + +# this script is used to create binary gene x cell marker genes matrices +# for use as references with CellAssign + +library(optparse) + +option_list <- list( + make_option( + opt_str = c("--organs"), + type = "character", + help = "Comma separated list of organs to include in gene x cell matrix" + ), + make_option( + opt_str = c("--marker_gene_file"), + type = "character", + help = "File containing a list of marker genes for all cell types and all organs. + Must contain the `organ`, `cell_type_column` and `gene_id_column` columns. " + ), + make_option( + opt_str = c("--cell_type_column"), + type = "character", + default = "cell type" + ), + make_option( + opt_str = c("--gene_id_column"), + type = "character", + default = "official gene symbol" + ), + make_option( + opt_str = c("--gtf"), + type = "character", + help = "reference gtf to use" + ), + make_option( + opt_str = c("--ref_file"), + type = "character", + help = "path to save reference file" + ) +) + + +if(!file.exists(opt$marker_gene_file)){ + stop("Provided `marker_gene_file` does not exist.") +} + +marker_gene_df <- readr::read_tsv(opt$marker_gene_file) + +organs <- stringr::str_split(opt$organs, ",") |> + unlist() |> + stringr::str_trim() + +if(!all(organs %in% marker_gene_df$organ)){ + stop("`organs` must be present in `organ` column of `marker_gene_file`.") +} + +cell_type_column <- opt$cell_type_column +gene_id_column <- opt$gene_id_column + +if(!(cell_type_column %in% colnames(marker_gene_df))){ + stop("Specified `cell_type_column` does not exist as a column in `marker_gene_file`") +} + +if(!(gene_id_column %in% colnames(marker_gene_df))){ + stop("Specified `gene_id_column` does not exist as a column in `marker_gene_file`") +} + +organ_gene_df <- marker_gene_df |> + dplyr::filter(organ %in% organs) |> + dplyr::select(cell_type_column, gene_id_column) + +# combine with ensembl gene id + +# create a binary matrix of genes by cell type markers +binary_mtx <- organ_gene_df |> + tidyr::pivot_wider(id_cols = ensembl_id, + names_from = celltype_column, + values_from = celltype_column, + values_fn = length, + values_fill = 0) |> + tibble::column_to_rownames(ensembl_id) |> + # add a column with no marker genes + # cell assign will assign cells to "other" when no other cell types are appropriate + dplyr::mutate(other = 0) + +# replace length with 1 +binary_mtx[binary_mtx > 1] <- 1 diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index b82f9fba..e2e12dae 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -54,6 +54,30 @@ process train_singler_models { """ } +process generate_cellassign_refs { + container params.SCPCATOOLS_CONTAINER + publishDir "${params.celltype_ref_dir}/cellassign_references" + label 'mem_8' + input: + tuple val(ref_name), val(ref_database), val(organs) + path(marker_gene_file) + output: + path ref_file + script: + ref_file="${ref_database}-${ref_name}.tsv" + """ + generate_cellassign_refs.R \ + --organs "${organs}" \ + --marker_gene_file ${marker_gene_file} \ + --ref_file ${ref_file} + """ + stub: + ref_file="${ref_database}-${ref_name}.tsv" + """ + touch ${ref_file} + """ +} + workflow build_celltype_ref { // create channel of cell type ref files and names From 2b3c2e02a8e0530f2587d1cb72b32240ef33cacf Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 21 Jul 2023 16:54:40 -0500 Subject: [PATCH 027/268] add output directories as params --- build-celltype-ref.nf | 4 ++-- config/reference_paths.config | 8 +++++++- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 6550e745..0b090cce 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -5,7 +5,7 @@ params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotatio process save_singler_refs { container params.SCPCATOOLS_CONTAINER - publishDir "${params.celltype_ref_dir}/singler_references" + publishDir "${params.singler_references_dir}" label 'mem_8' input: tuple val(ref_name), val(ref_source) @@ -28,7 +28,7 @@ process save_singler_refs { process train_singler_models { container params.SCPCATOOLS_CONTAINER - publishDir "${params.celltype_ref_dir}/singler_models" + publishDir "${params.singler_models_dir}" label 'cpus_4' label 'mem_16' input: diff --git a/config/reference_paths.config b/config/reference_paths.config index a70c793e..38ec9d41 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -6,7 +6,13 @@ ref_rootdir = 's3://scpca-references' // barcode files barcode_dir = "${params.ref_rootdir}/barcodes/10X" -// cell type references +// cell type references directories celltype_ref_dir = "${params.ref_rootdir}/celltype" +// output from save_singler_refs() process +singler_references_dir = "${params.celltype_ref_dir}/singler_references" +// output from train_singler_models() process +singler_models_dir = "${params.celltype_ref_dir}/singler_models" + +// cell type metadata celltype_ref_metadata = "${projectDir}/references/celltype-reference-metadata.tsv" panglao_marker_genes_file = "${projectDir}/references/PanglaoDB_markers_27_Mar_2020.tsv" From 4f531a4ec8c88470c8dff61a8e1a7662061bd55a Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 24 Jul 2023 13:18:05 -0500 Subject: [PATCH 028/268] script for creating binary matrix --- bin/generate_cellassign_refs.R | 53 +++++++++++++++++++++++++++------- 1 file changed, 43 insertions(+), 10 deletions(-) diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R index 449bc438..c90f0ba9 100644 --- a/bin/generate_cellassign_refs.R +++ b/bin/generate_cellassign_refs.R @@ -15,7 +15,7 @@ option_list <- list( opt_str = c("--marker_gene_file"), type = "character", help = "File containing a list of marker genes for all cell types and all organs. - Must contain the `organ`, `cell_type_column` and `gene_id_column` columns. " + Must contain the `organ` column, `--cell_type_column` and `--gene_id_column`. " ), make_option( opt_str = c("--cell_type_column"), @@ -28,17 +28,20 @@ option_list <- list( default = "official gene symbol" ), make_option( - opt_str = c("--gtf"), + opt_str = c("--gtf_file"), type = "character", help = "reference gtf to use" ), make_option( - opt_str = c("--ref_file"), + opt_str = c("--ref_mtx_file"), type = "character", help = "path to save reference file" ) ) +opt <- parse_args(OptionParser(option_list = option_list)) + +# Set up ----------------------------------------------------------------------- if(!file.exists(opt$marker_gene_file)){ stop("Provided `marker_gene_file` does not exist.") @@ -65,23 +68,53 @@ if(!(gene_id_column %in% colnames(marker_gene_df))){ stop("Specified `gene_id_column` does not exist as a column in `marker_gene_file`") } +# Create marker gene matrix ---------------------------------------------------- + +# grab marker genes for specified organs from marker gene reference organ_gene_df <- marker_gene_df |> dplyr::filter(organ %in% organs) |> - dplyr::select(cell_type_column, gene_id_column) - -# combine with ensembl gene id + dplyr::select({{cell_type_column}}, {{gene_id_column}}) # create a binary matrix of genes by cell type markers binary_mtx <- organ_gene_df |> - tidyr::pivot_wider(id_cols = ensembl_id, - names_from = celltype_column, - values_from = celltype_column, + tidyr::pivot_wider(id_cols = gene_id_column, + names_from = cell_type_column, + values_from = cell_type_column, values_fn = length, values_fill = 0) |> - tibble::column_to_rownames(ensembl_id) |> + tibble::column_to_rownames(gene_id_column) |> # add a column with no marker genes # cell assign will assign cells to "other" when no other cell types are appropriate dplyr::mutate(other = 0) # replace length with 1 binary_mtx[binary_mtx > 1] <- 1 + +# Add ensembl ids -------------------------------------------------------------- + +# combine with ensembl gene id +# read in gtf file (genes only for speed) +gtf <- rtracklayer::import(opt$gtf_file, feature.type = "gene") + +# create a data frame with ensembl id and gene symbol +gene_id_map <- gtf |> + as.data.frame() |> + dplyr::select( + "ensembl_id" = "gene_id", + "gene_symbol" = "gene_name" + ) |> + dplyr::filter(.data$gene_symbol != "NA") |> + dplyr::distinct() |> + ## in case there are any duplicate gene_ids (there shouldn't be!) + dplyr::group_by(.data$ensembl_id) |> + dplyr::summarise(gene_symbol = paste(.data$gene_symbol, collapse = ";")) + +# replace gene symbols with ensembl id +binary_mtx <- binary_mtx |> + tibble::rownames_to_column("gene_symbol") |> + dplyr::left_join(gene_id_map, by = "gene_symbol") |> + # drop any rows where there is no ensembl id + tidyr::drop_na(ensembl_id) |> + dplyr::select(ensembl_id, everything(), -gene_symbol) + +readr::write_tsv(binary_mtx, opt$ref_mtx_file) From f6924902734a7124a115bf05eeb04201e187a226 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 24 Jul 2023 13:18:15 -0500 Subject: [PATCH 029/268] add gtf param --- build-celltype-ref.nf | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 399f8f00..dbf1fc40 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -2,6 +2,7 @@ nextflow.enable.dsl=2 params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv" +params.ref_gtf = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.gtf.gz" process save_singler_refs { container params.SCPCATOOLS_CONTAINER @@ -61,6 +62,7 @@ process generate_cellassign_refs { input: tuple val(ref_name), val(ref_database), val(organs) path(marker_gene_file) + path(ref_gtf) output: path ref_file script: @@ -69,7 +71,8 @@ process generate_cellassign_refs { generate_cellassign_refs.R \ --organs "${organs}" \ --marker_gene_file ${marker_gene_file} \ - --ref_file ${ref_file} + --gtf_file ${ref_gtf} \ + --ref_mtx_file ${ref_file} """ stub: ref_file="${ref_database}-${ref_name}.tsv" @@ -109,6 +112,9 @@ workflow build_celltype_ref { ref_source: it.celltype_ref_source, organs: it.organs ]} + + generate_cellassign_refs(cellassign_refs_ch, params.panglao_marker_genes_file, params.ref_gtf) + } workflow { From 9ed6f146313369e5a8820bac3bb219ea2c71f511 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 24 Jul 2023 15:45:04 -0500 Subject: [PATCH 030/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/generate_cellassign_refs.R | 8 ++++---- build-celltype-ref.nf | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R index c90f0ba9..e124fcf5 100644 --- a/bin/generate_cellassign_refs.R +++ b/bin/generate_cellassign_refs.R @@ -35,7 +35,7 @@ option_list <- list( make_option( opt_str = c("--ref_mtx_file"), type = "character", - help = "path to save reference file" + help = "path to save reference binary matrix file" ) ) @@ -103,11 +103,11 @@ gene_id_map <- gtf |> "ensembl_id" = "gene_id", "gene_symbol" = "gene_name" ) |> - dplyr::filter(.data$gene_symbol != "NA") |> + dplyr::filter(gene_symbol != "NA") |> dplyr::distinct() |> ## in case there are any duplicate gene_ids (there shouldn't be!) - dplyr::group_by(.data$ensembl_id) |> - dplyr::summarise(gene_symbol = paste(.data$gene_symbol, collapse = ";")) + dplyr::group_by(ensembl_id) |> + dplyr::summarize(gene_symbol = paste(gene_symbol, collapse = ";")) # replace gene symbols with ensembl id binary_mtx <- binary_mtx |> diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index dbf1fc40..ebdd1fac 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -60,13 +60,13 @@ process generate_cellassign_refs { publishDir "${params.celltype_ref_dir}/cellassign_references" label 'mem_8' input: - tuple val(ref_name), val(ref_database), val(organs) + tuple val(ref_name), val(ref_source), val(organs) path(marker_gene_file) path(ref_gtf) output: path ref_file script: - ref_file="${ref_database}-${ref_name}.tsv" + ref_file="${ref_source}-${ref_name}.tsv" """ generate_cellassign_refs.R \ --organs "${organs}" \ @@ -75,7 +75,7 @@ process generate_cellassign_refs { --ref_mtx_file ${ref_file} """ stub: - ref_file="${ref_database}-${ref_name}.tsv" + ref_file="${ref_source}-${ref_name}.tsv" """ touch ${ref_file} """ From 1695174df903c73296fc4e24f9ad27ef6fd9c88e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 24 Jul 2023 15:47:44 -0500 Subject: [PATCH 031/268] add missing help messages --- bin/generate_cellassign_refs.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R index e124fcf5..8e40fabe 100644 --- a/bin/generate_cellassign_refs.R +++ b/bin/generate_cellassign_refs.R @@ -20,12 +20,14 @@ option_list <- list( make_option( opt_str = c("--cell_type_column"), type = "character", - default = "cell type" + default = "cell type", + help = "Column name in `marker_gene_file` containing cell types." ), make_option( opt_str = c("--gene_id_column"), type = "character", - default = "official gene symbol" + default = "official gene symbol", + help = "Column name in `marker_gene_file` containing the gene symbols." ), make_option( opt_str = c("--gtf_file"), From f9684465e2a49520d929baed37b495ff1123c15b Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 28 Jul 2023 10:09:41 -0400 Subject: [PATCH 032/268] cellassign process to workflow --- add-celltypes.nf | 10 ++-- bin/classify_cellassign.py | 96 +++++++++++++++++++++++++++++++++++ modules/classify-celltypes.nf | 47 +++++++++++++++-- 3 files changed, 145 insertions(+), 8 deletions(-) create mode 100644 bin/classify_cellassign.py diff --git a/add-celltypes.nf b/add-celltypes.nf index 8a641a06..ea97da24 100644 --- a/add-celltypes.nf +++ b/add-celltypes.nf @@ -52,10 +52,12 @@ workflow { || (it.submitter == params.project) || (it.project_id == params.project) } - // tuple of meta, processed rds file to use as input to cell type annotation - .map{meta -> tuple(meta, - file("${params.results_dir}/${meta.project_id}/${meta.sample_id}/${meta.library_id}_processed.rds") - )} + // tuple of meta, processed RDS file to use as input to singleR + .map{meta -> tuple(meta, + file("${params.results_dir}/${meta.project_id}/${meta.sample_id}/${meta.library_id}_processed.rds"), + file("${params.results_dir}/${meta.project_id}/${meta.sample_id}/${meta.library_id}_processed_rna.hdf5") + )} annotate_celltypes(processed_sce_ch) + } diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py new file mode 100644 index 00000000..7b346a6d --- /dev/null +++ b/bin/classify_cellassign.py @@ -0,0 +1,96 @@ +#!/usr/bin/env python3 + +# This script takes an AnnData object and a reference marker gene matrix +# where genes are rows and columns are cell types +# CellAssign is run and the predictions matrix is returned + + +import os +import anndata as adata +import scvi +from scvi.external import CellAssign +from scvi import settings +import pandas as pd +import numpy as np +import argparse +import re + +parser = argparse.ArgumentParser() +parser.add_argument('-i', '--input_anndata', + dest = 'input_anndata', + required = True, + help = 'Path to HDF5 file with processed AnnData object to annotate') +parser.add_argument('-o', '--output_predictions', + dest = 'output_predictions', + required = True, + help = 'Path to directory to save the predictions, should end in tsv') +parser.add_argument('-r', '--reference', + dest = 'reference', + required = True, + help = 'Path to marker by cell type reference file') +parser.add_argument('-s', '--seed', + dest = 'seed', + type=int, + default = None, + help = 'Random seed to set for scvi.') +parser.add_argument('-t', '--threads', + dest = 'threads', + default = 1, + type = int, + help = 'Number of threads to use when training the CellAssign model') + +args = parser.parse_args() + +# set seed +scvi.settings.seed = args.seed + +# define the number of threads to use +settings.num_threads = args.threads + +# compile extension regex +file_ext = re.compile(r"\.hdf5$|.h5$", re.IGNORECASE) + +# check that input file exists, if it does exist, make sure it's an h5 file +if not os.path.exists(args.input_anndata): + raise FileExistsError("--input_anndata file not found.") +elif not file_ext.search(args.input_anndata): + raise ValueError("--input_anndata must end in either .hdf5 or .h5 and contain a processed AnnData object.") + +# check that marker file exists and make sure its a csv +if not os.path.exists(args.reference): + raise FileExistsError("--reference file not found.") +elif not ".csv" in args.reference: + raise ValueError("--reference must be a csv file") + +# make sure output file path is tsv file +if not ".tsv" in args.output_predictions: + raise ValueError("--output_predictions must provide a file path ending in tsv") + +# check that output file directory exists and create directory if doesn't exist +predictions_dir = os.path.dirname(args.output_predictions) +os.makedirs(predictions_dir, exist_ok = True) + +# read in references as marker gene tables +ref_matrix = pd.read_csv(args.reference, sep = "\t", index_col='ensembl_id') + +# file path to annotated sce +annotated_adata = adata.read_h5ad(args.input_anndata) + +# subset anndata to contain only genes in the reference file +# note that the gene names must be the rownames of the reference matrix +subset_adata = annotated_adata[:, ref_matrix.index].copy() +subset_adata.X = subset_adata.X.tocsr() + +# add size factor to subset adata (calculated from full data) +lib_size = annotated_adata.X.sum(1) +subset_adata.obs["size_factor"] = lib_size / np.mean(lib_size) + +# train and assign cell types +scvi.external.CellAssign.setup_anndata(subset_adata, size_factor_key="size_factor") +model = CellAssign(subset_adata, ref_matrix) +model.train() +predictions = model.predict() +predictions['barcode'] = subset_adata.obs_names + +# write out predictions as tsv +predictions.to_csv(args.output_predictions, sep = "\t", index = False) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 0fb7918c..ef438b63 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -26,6 +26,30 @@ process classify_singleR { """ } +process predict_cellassign { + container params.SCPCATOOLS_CONTAINER + label 'mem_8' + label 'cpus_4' + input: + tuple val(meta), path(processed_hdf5), path(cellassign_reference_mtx) + output: + tuple val(meta), path(cellassign_predictions) + script: + cellassign_predictions = "${meta.library_id}_predictions.tsv" + """ + classify_cellassign.py \ + --input_hdf5_file ${processed_hdf5} \ + --output_predictions ${cellassign_predictions} \ + --reference ${cellassign_reference_mtx} \ + --threads ${task.cpus} + """ + stub: + cellassign_predictions = "${meta.library_id}_predictions.tsv" + """ + touch "${cellassign_predictions}" + """ +} + workflow annotate_celltypes { take: processed_sce_channel main: @@ -34,7 +58,8 @@ workflow annotate_celltypes { .splitCsv(header: true, sep: '\t') .map{[ project_id = it.scpca_project_id, - singler_model_file = "${params.celltype_model_dir}/${it.celltype_ref_name}_model.rds" + singler_model_file = "${params.singler_models_dir}/${it.singler_ref_file}", + cellassign_ref_file = "${params.cellassign_ref_dir}/${it.cellassign_ref_file}" ]} // create channel grouped_celltype_ch as: [meta, processed sce object, SingleR reference model] @@ -43,10 +68,24 @@ workflow annotate_celltypes { .map{[it[0]["project_id"]] + it} .combine(celltype_ch, by: 0) .map{it.drop(1)} // remove extra project ID - // creates [meta, processed, SingleR reference model] - .map{ it[0..2] } - classify_singleR(grouped_celltype_ch) + // creates [meta, processed, SingleR reference model] + singler_input_ch = grouped_celltype_ch + .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file -> tuple(meta, + processed_rds, + singler_model_file + )} + + cellassign_input_ch = grouped_celltype_ch + .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file -> tuple(meta, + processed_hdf5, + cellassign_ref_file + )} + + + classify_singleR(singler_input_ch) + + predict_cellassign(cellassign_input_ch) emit: classify_singleR.out From 0e86eeb1be991639c8039ac5b66bb399321668d9 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 28 Jul 2023 10:09:48 -0400 Subject: [PATCH 033/268] update some references --- build-celltype-ref.nf | 2 +- config/reference_paths.config | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index ebdd1fac..938fc870 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -57,7 +57,7 @@ process train_singler_models { process generate_cellassign_refs { container params.SCPCATOOLS_CONTAINER - publishDir "${params.celltype_ref_dir}/cellassign_references" + publishDir "${cellassign_ref_dir}" label 'mem_8' input: tuple val(ref_name), val(ref_source), val(organs) diff --git a/config/reference_paths.config b/config/reference_paths.config index 38ec9d41..159d8eef 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -12,6 +12,8 @@ celltype_ref_dir = "${params.ref_rootdir}/celltype" singler_references_dir = "${params.celltype_ref_dir}/singler_references" // output from train_singler_models() process singler_models_dir = "${params.celltype_ref_dir}/singler_models" +// output from generating cell assign reference matrices +cellassign_ref_dir = "${params.celltype_ref_dir}/cellassign_references" // cell type metadata celltype_ref_metadata = "${projectDir}/references/celltype-reference-metadata.tsv" From ead5afd2500b6c0aaf2c3792ee553fb603db70a0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 28 Jul 2023 12:08:27 -0400 Subject: [PATCH 034/268] remove output directory creation --- bin/classify_cellassign.py | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py index 7b346a6d..9107ab28 100644 --- a/bin/classify_cellassign.py +++ b/bin/classify_cellassign.py @@ -16,8 +16,8 @@ import re parser = argparse.ArgumentParser() -parser.add_argument('-i', '--input_anndata', - dest = 'input_anndata', +parser.add_argument('-i', '--input_hdf5_file', + dest = 'input_hdf5_file', required = True, help = 'Path to HDF5 file with processed AnnData object to annotate') parser.add_argument('-o', '--output_predictions', @@ -51,30 +51,24 @@ file_ext = re.compile(r"\.hdf5$|.h5$", re.IGNORECASE) # check that input file exists, if it does exist, make sure it's an h5 file -if not os.path.exists(args.input_anndata): - raise FileExistsError("--input_anndata file not found.") -elif not file_ext.search(args.input_anndata): - raise ValueError("--input_anndata must end in either .hdf5 or .h5 and contain a processed AnnData object.") +if not os.path.exists(args.input_hdf5_file): + raise FileExistsError("--input_hdf5_file file not found.") +elif not file_ext.search(args.input_hdf5_file): + raise ValueError("--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object.") # check that marker file exists and make sure its a csv if not os.path.exists(args.reference): raise FileExistsError("--reference file not found.") -elif not ".csv" in args.reference: - raise ValueError("--reference must be a csv file") # make sure output file path is tsv file if not ".tsv" in args.output_predictions: raise ValueError("--output_predictions must provide a file path ending in tsv") -# check that output file directory exists and create directory if doesn't exist -predictions_dir = os.path.dirname(args.output_predictions) -os.makedirs(predictions_dir, exist_ok = True) - # read in references as marker gene tables ref_matrix = pd.read_csv(args.reference, sep = "\t", index_col='ensembl_id') # file path to annotated sce -annotated_adata = adata.read_h5ad(args.input_anndata) +annotated_adata = adata.read_h5ad(args.input_hdf5_file) # subset anndata to contain only genes in the reference file # note that the gene names must be the rownames of the reference matrix From f966fdca66b16d10dde4ef024b00558a8f0bcc64 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 31 Jul 2023 10:28:25 -0400 Subject: [PATCH 035/268] grab shared genes for subsetting --- bin/classify_cellassign.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py index 9107ab28..89f12cf0 100644 --- a/bin/classify_cellassign.py +++ b/bin/classify_cellassign.py @@ -72,7 +72,9 @@ # subset anndata to contain only genes in the reference file # note that the gene names must be the rownames of the reference matrix -subset_adata = annotated_adata[:, ref_matrix.index].copy() +# first get a list of shared genes +shared_genes = list(set(ref_matrix.index) & set(annotated_adata.var_names)) +subset_adata = annotated_adata[:, shared_genes].copy() subset_adata.X = subset_adata.X.tocsr() # add size factor to subset adata (calculated from full data) From 715e0e11226a5d0ff1bc3fe2ec7b253ba560e6c8 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 31 Jul 2023 10:28:37 -0400 Subject: [PATCH 036/268] increase memory and add a seed --- modules/classify-celltypes.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index ef438b63..35f129dc 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -28,8 +28,8 @@ process classify_singleR { process predict_cellassign { container params.SCPCATOOLS_CONTAINER - label 'mem_8' - label 'cpus_4' + label 'mem_32' + label 'cpus_12' input: tuple val(meta), path(processed_hdf5), path(cellassign_reference_mtx) output: @@ -41,6 +41,7 @@ process predict_cellassign { --input_hdf5_file ${processed_hdf5} \ --output_predictions ${cellassign_predictions} \ --reference ${cellassign_reference_mtx} \ + --seed ${params.seed} \ --threads ${task.cpus} """ stub: From baf6fb035a21114eb97cc16a8c426af3610c47a4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 1 Aug 2023 09:29:08 -0400 Subject: [PATCH 037/268] accept _R1_ or _R1 --- modules/af-features.nf | 4 ++-- modules/af-rna.nf | 4 ++-- modules/bulk-salmon.nf | 4 ++-- modules/bulk-star.nf | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/af-features.nf b/modules/af-features.nf index 515df47d..05a8e96d 100644 --- a/modules/af-features.nf +++ b/modules/af-features.nf @@ -156,8 +156,8 @@ workflow map_quant_feature{ // We start by including the feature_barcode file so we can combine with the indices, but that will be removed .map{meta -> tuple(meta.feature_barcode_file, meta, - file("${meta.files_directory}/*_R1_*.fastq.gz"), - file("${meta.files_directory}/*_R2_*.fastq.gz") + file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz") )} .combine(index_feature.out, by: 0) // combine by the feature_barcode_file (reused indices, so combine is needed) .map{it.drop(1)} // remove the first element (feature_barcode_file) diff --git a/modules/af-rna.nf b/modules/af-rna.nf index 9cd598e6..5a7bce6e 100644 --- a/modules/af-rna.nf +++ b/modules/af-rna.nf @@ -120,8 +120,8 @@ workflow map_quant_rna { // If we need to create rad files, create a new channel with tuple of (metadata map, [Read1 files], [Read2 files]) rna_reads_ch = rna_channel.make_rad .map{meta -> tuple(meta, - file("${meta.files_directory}/*_R1_*.fastq.gz"), - file("${meta.files_directory}/*_R2_*.fastq.gz"), + file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz"), file("${meta.salmon_splici_index}") )} diff --git a/modules/bulk-salmon.nf b/modules/bulk-salmon.nf index 9f3e176c..eab3de77 100644 --- a/modules/bulk-salmon.nf +++ b/modules/bulk-salmon.nf @@ -139,8 +139,8 @@ workflow bulk_quant_rna { // If we need to run salmon, create tuple of (metadata map, [Read 1 files], [Read 2 files]) bulk_reads_ch = bulk_channel.make_quants .map{meta -> tuple(meta, - file("${meta.files_directory}/*_R1_*.fastq.gz"), - file("${meta.files_directory}/*_R2_*.fastq.gz") + file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz") )} // run fastp and salmon for libraries that are not skipping salmon diff --git a/modules/bulk-star.nf b/modules/bulk-star.nf index 9a12c35b..016a975d 100644 --- a/modules/bulk-star.nf +++ b/modules/bulk-star.nf @@ -37,8 +37,8 @@ workflow star_bulk{ // create tuple of (metadata map, [Read 1 files], [Read 2 files]) bulk_reads_ch = bulk_channel .map{meta -> tuple(meta, - file("${meta.files_directory}/*_R1_*.fastq.gz"), - file("${meta.files_directory}/*_R2_*.fastq.gz"), + file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz"), file("${meta.star_index}"))} // map and index bulkmap_star(bulk_reads_ch) \ From 8c3d154cfe03c5bfe0df7e80251f218ad272dbfe Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Tue, 1 Aug 2023 13:02:16 -0400 Subject: [PATCH 038/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/classify_cellassign.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py index 89f12cf0..cc39417d 100644 --- a/bin/classify_cellassign.py +++ b/bin/classify_cellassign.py @@ -61,7 +61,7 @@ raise FileExistsError("--reference file not found.") # make sure output file path is tsv file -if not ".tsv" in args.output_predictions: +if not args.output_predictions.endswith(".tsv"): raise ValueError("--output_predictions must provide a file path ending in tsv") # read in references as marker gene tables From 4ce5ce5801ee6c5bb18a6181a0d4da36a2f41b0e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 1 Aug 2023 13:07:19 -0400 Subject: [PATCH 039/268] update comments and process output --- add-celltypes.nf | 2 +- bin/classify_cellassign.py | 7 +++---- modules/classify-celltypes.nf | 2 +- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/add-celltypes.nf b/add-celltypes.nf index ea97da24..80c804f0 100644 --- a/add-celltypes.nf +++ b/add-celltypes.nf @@ -52,7 +52,7 @@ workflow { || (it.submitter == params.project) || (it.project_id == params.project) } - // tuple of meta, processed RDS file to use as input to singleR + // tuple of meta, processed RDS file, processed hdf5 file to use as input to classifying celltypes .map{meta -> tuple(meta, file("${params.results_dir}/${meta.project_id}/${meta.sample_id}/${meta.library_id}_processed.rds"), file("${params.results_dir}/${meta.project_id}/${meta.sample_id}/${meta.library_id}_processed_rna.hdf5") diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py index cc39417d..11363a8e 100644 --- a/bin/classify_cellassign.py +++ b/bin/classify_cellassign.py @@ -9,7 +9,6 @@ import anndata as adata import scvi from scvi.external import CellAssign -from scvi import settings import pandas as pd import numpy as np import argparse @@ -23,11 +22,11 @@ parser.add_argument('-o', '--output_predictions', dest = 'output_predictions', required = True, - help = 'Path to directory to save the predictions, should end in tsv') + help = 'Path to file to save the predictions, should end in tsv') parser.add_argument('-r', '--reference', dest = 'reference', required = True, - help = 'Path to marker by cell type reference file') + help = 'Path to marker by cell type reference file, should end in tsv') parser.add_argument('-s', '--seed', dest = 'seed', type=int, @@ -56,7 +55,7 @@ elif not file_ext.search(args.input_hdf5_file): raise ValueError("--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object.") -# check that marker file exists and make sure its a csv +# check that marker file exists and make sure its a tsv if not os.path.exists(args.reference): raise FileExistsError("--reference file not found.") diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 35f129dc..bcc130c2 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -88,6 +88,6 @@ workflow annotate_celltypes { predict_cellassign(cellassign_input_ch) - emit: classify_singleR.out + emit: tuple(classify_singleR.out, predict_cellassign.out) } From 9bb0545a3be8feb87fad0e78db88ec5129dfbdd8 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 1 Aug 2023 13:07:45 -0400 Subject: [PATCH 040/268] call scvi for settings --- bin/classify_cellassign.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/classify_cellassign.py b/bin/classify_cellassign.py index 11363a8e..169c25d7 100644 --- a/bin/classify_cellassign.py +++ b/bin/classify_cellassign.py @@ -44,7 +44,7 @@ scvi.settings.seed = args.seed # define the number of threads to use -settings.num_threads = args.threads +scvi.settings.num_threads = args.threads # compile extension regex file_ext = re.compile(r"\.hdf5$|.h5$", re.IGNORECASE) From 2b7ddf5e77bf7fd2f87c91ccc904bbb638e65b9e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 1 Aug 2023 13:11:17 -0400 Subject: [PATCH 041/268] emit multiple outputs --- modules/classify-celltypes.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index bcc130c2..e5999d18 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -88,6 +88,8 @@ workflow annotate_celltypes { predict_cellassign(cellassign_input_ch) - emit: tuple(classify_singleR.out, predict_cellassign.out) + emit: + classify_singleR.out + predict_cellassign.out } From 166a6114ca1601971ae377f483b3fc2d2cb918e4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 1 Aug 2023 13:31:22 -0400 Subject: [PATCH 042/268] use main scpca-refs.json to define ref files in building celltype refs --- add-celltypes.nf | 2 ++ build-celltype-ref.nf | 28 ++++++++++++++-------------- config/reference_paths.config | 1 + 3 files changed, 17 insertions(+), 14 deletions(-) diff --git a/add-celltypes.nf b/add-celltypes.nf index 80c804f0..8d798410 100644 --- a/add-celltypes.nf +++ b/add-celltypes.nf @@ -30,6 +30,8 @@ workflow { log.info("Executing workflow for all runs in the run metafile.") } + celltype_ref_paths = Utils.readMeta(file(params.celltype_ref_json)) + // read in metadata file and filter to libraries/ projects of interest processed_sce_ch = Channel.fromPath(params.run_metafile) .splitCsv(header: true, sep: '\t') diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 938fc870..68b9677d 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -1,17 +1,14 @@ #!/usr/bin/env nextflow nextflow.enable.dsl=2 -params.t2g_3col_path = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.spliced_intron.tx2gene_3col.tsv" -params.ref_gtf = "s3://scpca-references/homo_sapiens/ensembl-104/annotation/Homo_sapiens.GRCh38.104.gtf.gz" - process save_singler_refs { container params.SCPCATOOLS_CONTAINER publishDir "${params.singler_references_dir}" label 'mem_8' input: - tuple val(ref_name), val(ref_source) + tuple val(ref_name), val(ref_source), path(t2g_3col_path) output: - tuple val(ref_name), path(ref_file) + tuple val(ref_name), path(ref_file), path(t2g_3col_path) script: ref_file = "${ref_source}-${ref_name}.rds" """ @@ -33,8 +30,7 @@ process train_singler_models { label 'cpus_4' label 'mem_16' input: - tuple val(ref_name), path(ref_file) - path tx2gene + tuple val(ref_name), path(ref_file), path(tx2gene) output: path celltype_model script: @@ -60,9 +56,8 @@ process generate_cellassign_refs { publishDir "${cellassign_ref_dir}" label 'mem_8' input: - tuple val(ref_name), val(ref_source), val(organs) - path(marker_gene_file) - path(ref_gtf) + tuple val(ref_name), val(ref_source), val(organs), path(ref_gtf) + path marker_gene_file output: path ref_file script: @@ -83,6 +78,9 @@ process generate_cellassign_refs { workflow build_celltype_ref { + // read in json file with all reference paths + ref_paths = Utils.getMetaVal(file(params.ref_json), "Homo_sapiens.GRCh38.104") + // create channel of cell type ref files and names celltype_refs_ch = Channel.fromPath(params.celltype_ref_metadata) .splitCsv(header: true, sep: '\t') @@ -95,14 +93,15 @@ workflow build_celltype_ref { singler_refs_ch = celltype_refs_ch.singler .map{[ ref_name: it.celltype_ref_name, - ref_source: it.celltype_ref_source + ref_source: it.celltype_ref_source, + t2g_3col_path: file("${params.ref_rootdir}/${ref_paths["t2g_3col_path"]}") ]} // download and save reference files save_singler_refs(singler_refs_ch) // train cell type references using SingleR - train_singler_models(save_singler_refs.out, params.t2g_3col_path) + train_singler_models(save_singler_refs.out) // cellassign refs cellassign_refs_ch = celltype_refs_ch.cellassign @@ -110,10 +109,11 @@ workflow build_celltype_ref { .map{[ ref_name: it.celltype_ref_name, ref_source: it.celltype_ref_source, - organs: it.organs + organs: it.organs, + ref_gtf: file("${params.ref_rootdir}/${ref_paths["ref_gtf"]}") ]} - generate_cellassign_refs(cellassign_refs_ch, params.panglao_marker_genes_file, params.ref_gtf) + generate_cellassign_refs(cellassign_refs_ch, params.panglao_marker_genes_file) } diff --git a/config/reference_paths.config b/config/reference_paths.config index 159d8eef..135af255 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -7,6 +7,7 @@ ref_rootdir = 's3://scpca-references' barcode_dir = "${params.ref_rootdir}/barcodes/10X" // cell type references directories +celltype_organism = "Homo_sapiens.GRCh38.104" celltype_ref_dir = "${params.ref_rootdir}/celltype" // output from save_singler_refs() process singler_references_dir = "${params.celltype_ref_dir}/singler_references" From 12177ea913b8529ac5fe2a52a46efe20aa9e9ab0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 7 Aug 2023 10:31:01 -0500 Subject: [PATCH 043/268] Apply suggestions from code review Co-authored-by: Stephanie --- build-celltype-ref.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 68b9677d..dc3c03dc 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -79,7 +79,7 @@ process generate_cellassign_refs { workflow build_celltype_ref { // read in json file with all reference paths - ref_paths = Utils.getMetaVal(file(params.ref_json), "Homo_sapiens.GRCh38.104") + ref_paths = Utils.getMetaVal(file(params.ref_json), params.celltype_organism) // create channel of cell type ref files and names celltype_refs_ch = Channel.fromPath(params.celltype_ref_metadata) From f7d64e058eedeeb38f6d868cc43b6ab412799964 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 7 Aug 2023 10:36:17 -0500 Subject: [PATCH 044/268] update comment --- config/reference_paths.config | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/config/reference_paths.config b/config/reference_paths.config index 135af255..45e7779f 100644 --- a/config/reference_paths.config +++ b/config/reference_paths.config @@ -6,8 +6,11 @@ ref_rootdir = 's3://scpca-references' // barcode files barcode_dir = "${params.ref_rootdir}/barcodes/10X" -// cell type references directories +// organism name to use for cell type annotation +// name must match one of the keys in ref_json celltype_organism = "Homo_sapiens.GRCh38.104" + +// cell type references directories celltype_ref_dir = "${params.ref_rootdir}/celltype" // output from save_singler_refs() process singler_references_dir = "${params.celltype_ref_dir}/singler_references" From e7a5e0e93787191722700e72c8558c54bec166c4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 7 Aug 2023 10:36:27 -0500 Subject: [PATCH 045/268] remove extra json loading --- add-celltypes.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/add-celltypes.nf b/add-celltypes.nf index 8d798410..80c804f0 100644 --- a/add-celltypes.nf +++ b/add-celltypes.nf @@ -30,8 +30,6 @@ workflow { log.info("Executing workflow for all runs in the run metafile.") } - celltype_ref_paths = Utils.readMeta(file(params.celltype_ref_json)) - // read in metadata file and filter to libraries/ projects of interest processed_sce_ch = Channel.fromPath(params.run_metafile) .splitCsv(header: true, sep: '\t') From a6e2e4a287b3e398f5e418133c8a9ccef43c30ca Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Mon, 7 Aug 2023 10:37:42 -0500 Subject: [PATCH 046/268] use t2g_3col_path everywhere --- build-celltype-ref.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index dc3c03dc..9cb21ccb 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -30,7 +30,7 @@ process train_singler_models { label 'cpus_4' label 'mem_16' input: - tuple val(ref_name), path(ref_file), path(tx2gene) + tuple val(ref_name), path(ref_file), path(t2g_3col_path) output: path celltype_model script: @@ -39,7 +39,7 @@ process train_singler_models { train_SingleR.R \ --ref_file ${ref_file} \ --output_file ${celltype_model} \ - --fry_tx2gene ${tx2gene} \ + --fry_tx2gene ${t2g_3col_path} \ --label_name ${params.label_name} \ --seed ${params.seed} \ --threads ${task.cpus} From 92b5a476dce4a47075d7ddd30ff9c5bc42cd5ec1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Tue, 8 Aug 2023 09:13:58 -0500 Subject: [PATCH 047/268] fix publish directory Co-authored-by: Stephanie --- build-celltype-ref.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 9cb21ccb..9192d455 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -53,7 +53,7 @@ process train_singler_models { process generate_cellassign_refs { container params.SCPCATOOLS_CONTAINER - publishDir "${cellassign_ref_dir}" + publishDir "${params.cellassign_ref_dir}" label 'mem_8' input: tuple val(ref_name), val(ref_source), val(organs), path(ref_gtf) From 8841d77a99139b933105f4a3a464e42e410cee28 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 12:10:05 -0500 Subject: [PATCH 048/268] initial cell type assignments script and process --- bin/classify_cellassign.R | 61 +++++++++++++++++ ...fy_cellassign.py => predict_cellassign.py} | 0 modules/classify-celltypes.nf | 65 ++++++++++++++----- 3 files changed, 109 insertions(+), 17 deletions(-) create mode 100644 bin/classify_cellassign.R rename bin/{classify_cellassign.py => predict_cellassign.py} (100%) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R new file mode 100644 index 00000000..e1a981ad --- /dev/null +++ b/bin/classify_cellassign.R @@ -0,0 +1,61 @@ +#!/usr/bin/env Rscript + +# This script is used to read in the predictions from CellAssign and assign cell types + +# import libraries +suppressPackageStartupMessages({ + library(optparse) + library(SingleCellExperiment) +}) + +# set up arguments +option_list <- list( + make_option( + opt_str = c("-i", "--input_sce_file"), + type = "character", + help = "path to rds file with input sce object" + ), + make_option( + opt_str = c("-o", "--output_sce_file"), + type = "character", + help = "path to output rds file to store annotated sce object. Must end in .rds" + ), + make_option( + opt_str = c("--cellassign_predictions"), + type = "character", + help = "path to tsv file containing the prediction matrix returned by running CellAssign" + ), + make_option( + opt_str = c("--reference_name"), + type = "character", + help = "name referring to the marker gene reference used for CellAssign" + ) +) + +opt <- parse_args(OptionParser(option_list = option_list)) + +# check that input file file exists +if(!file.exists(opt$input_sce_file)){ + stop("Missing input SCE file") +} + +if(!file.exists(opt$cellassign_predictions)){ + stop("Missing CellAssign predictions file") +} + +# read in input files +sce <- readr::read_rds(opt$input_sce_file) +predictions <- readr::read_tsv(opt$cellassign_predictions) + +celltype_assignments <- predictions |> + tidyr::pivot_longer(!barcode, + names_to = "celltype", + values_to = "prediction") |> + dplyr::group_by(barcode) |> + dplyr::slice_max(prediction, n = 1) |> + dplyr::ungroup() + +sce$cellassign_celltype_annotation <- celltype_assignments + +metadata(sce)$cellassign_predictions <- predictions +metadata(sce)$cellassign_reference <- opt$reference_name diff --git a/bin/classify_cellassign.py b/bin/predict_cellassign.py similarity index 100% rename from bin/classify_cellassign.py rename to bin/predict_cellassign.py diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index e5999d18..a86db090 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -3,7 +3,6 @@ process classify_singleR { container params.SCPCATOOLS_CONTAINER label 'mem_8' label 'cpus_4' - publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(processed_rds), path(singler_model_file) output: @@ -28,16 +27,17 @@ process classify_singleR { process predict_cellassign { container params.SCPCATOOLS_CONTAINER + publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' label 'mem_32' label 'cpus_12' input: - tuple val(meta), path(processed_hdf5), path(cellassign_reference_mtx) + tuple val(meta), path(processed_hdf5), path(cellassign_reference_mtx), val(ref_name) output: - tuple val(meta), path(cellassign_predictions) + tuple val(meta), path(cellassign_predictions), val(ref_name) script: cellassign_predictions = "${meta.library_id}_predictions.tsv" """ - classify_cellassign.py \ + predict_cellassign.py \ --input_hdf5_file ${processed_hdf5} \ --output_predictions ${cellassign_predictions} \ --reference ${cellassign_reference_mtx} \ @@ -51,6 +51,27 @@ process predict_cellassign { """ } +process classify_cellassign { + container params.SCPCATOOLS_CONTAINER + publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' + label 'mem_4' + label 'cpus_2' + input: + tuple val(meta), path(cellassign_predictions), path(input_rds), val(ref_name) + output: + tuple val(meta), path(annotated_rds) + script: + annotated_rds = "${meta.library_id}_annotated.rds" + """ + classify_cellassign.R \ + --input_sce_file ${input_rds} \ + --output_sce_file ${annotated_rds} \ + --cellassign_predictions ${cellassign_predictions} \ + --reference_name ${ref_name} + + """ +} + workflow annotate_celltypes { take: processed_sce_channel main: @@ -60,7 +81,8 @@ workflow annotate_celltypes { .map{[ project_id = it.scpca_project_id, singler_model_file = "${params.singler_models_dir}/${it.singler_ref_file}", - cellassign_ref_file = "${params.cellassign_ref_dir}/${it.cellassign_ref_file}" + cellassign_ref_file = "${params.cellassign_ref_dir}/${it.cellassign_ref_file}", + cellassign_ref_name = it.cellassign_ref_name ]} // create channel grouped_celltype_ch as: [meta, processed sce object, SingleR reference model] @@ -72,24 +94,33 @@ workflow annotate_celltypes { // creates [meta, processed, SingleR reference model] singler_input_ch = grouped_celltype_ch - .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file -> tuple(meta, - processed_rds, - singler_model_file - )} + .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file, cellassign_ref_name -> tuple(meta, + processed_rds, + singler_model_file + )} + // creates [meta, processed hdf5, cellassign ref file, cell assign ref name] cellassign_input_ch = grouped_celltype_ch - .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file -> tuple(meta, - processed_hdf5, - cellassign_ref_file - )} - + .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file, cellassign_ref_name -> tuple(meta, + processed_hdf5, + cellassign_ref_file, + cellassign_ref_name + )} + // get SingleR cell type assignments and add them to SCE classify_singleR(singler_input_ch) + // get cellassign predictions file predict_cellassign(cellassign_input_ch) - emit: - classify_singleR.out - predict_cellassign.out + // add cellassign annotations to the object with singleR results + all_celltype_assignments_ch = classify_singleR.out + // combines using meta from both singleR and cellassign, they should be the same + // resulting tuple should be [meta, singleR annotated rds, cellassign predictions] + .combine(predict_cellassign.out, by: 0) + + classify_cellassign(all_celltype_assignments_ch) + + emit: classify_cellassign.out } From c11e1a98f6c31ced7c3273aac3637f13c62bd69e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 15:33:56 -0500 Subject: [PATCH 049/268] add sample metadata to unfiltered objects --- bin/generate_unfiltered_sce.R | 43 +++++++++++++++++++++++++++++++++++ config/profile_ccdl.config | 1 + main.nf | 7 +++++- modules/sce-processing.nf | 4 +++- nextflow.config | 1 + 5 files changed, 54 insertions(+), 2 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 22831c82..0ae78472 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -58,6 +58,11 @@ option_list <- list( type = "character", help = "sample id(s). If more than one, separated by commas and/or semicolons." ), + make_option( + opt_str = c("--sample_metadata_file"), + type = "character", + help = "path to tsv file containing sample metadata" + ), make_option( opt_str = c("--spliced_only"), action = "store_true", @@ -83,6 +88,11 @@ if(!file.exists(opt$gtf_file)){ stop("gtf file not found.") } +# check that sample metadata file exists +if(!file.exists(opt$sample_metadata_file)){ + stop("sample metadata file not found.") +} + # read in mitochondrial gene list mito_genes <- unique(scan(opt$mito_file, what = "character")) @@ -92,6 +102,10 @@ gtf <- rtracklayer::import(opt$gtf_file, feature.type = "gene") # parse sample id list sample_ids <- unlist(stringr::str_split(opt$sample_id, ",|;")) |> sort() +# read in sample metadata and filter to sample ids +sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> + dplyr::filter(scpca_sample_id %in% sample_ids) + # set include unspliced for non feature data include_unspliced <- !opt$spliced_only @@ -125,6 +139,35 @@ unfiltered_sce <- unfiltered_sce |> add_gene_symbols(gene_info = gtf) |> scuttle::addPerFeatureQCMetrics() +# get a list of sample metadata to add +# for each sample in the library, create an individual list of sample metadata +sample_metadata_list <- purrr::map(sample_ids, + \(sample){ + single_sample_df <- sample_metadata_df |> + dplyr::filter(scpca_sample_id %in% sample) + list( + age = paste(single_sample_df$age, collapse = ","), + sex = paste(single_sample_df$sex, collapse = ","), + diagnosis = paste(single_sample_df$sex, collapse = ","), + subdiagnosis = paste(single_sample_df$subdiagnosis, collapse = ","), + tissue_location = paste(single_sample_df$tissue_location, collapse = ","), + disease_timing = paste(single_sample_df$disease_timing, collapse = ","), + organism = paste(single_sample_df$organism, collapse = ","), + development_stage_ontology_term_id = paste(single_sample_df$development_stage_ontology_term_id, collapse = ","), + sex_ontology_term_id = paste(single_sample_df$sex_ontology_term_id, collapse = ","), + organism_ontology_id = paste(single_sample_df$organism_ontology_id, collapse = ","), + self_reported_ethnicity_ontology_term_id = paste(single_sample_df$self_reported_ethnicity_ontology_term_id, collapse = ","), + disease_ontology_term_id = paste(single_sample_df$disease_ontology_term_id, collapse = ","), + tissue_ontology_term_id = paste(single_sample_df$tissue_ontology_term_id, collapse = ",") + ) + }) |> + purrr::set_names(sample_ids) + +# add list of sample metadata +# access the list of sample metadata for each sample +# with metadata(unfiltered_sce)$sample_metadata[[sample_id]] +metadata(unfiltered_sce)$sample_metadata <- sample_metadata_list + # write to rds readr::write_rds(unfiltered_sce, opt$unfiltered_file, compress = "gz") diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index d3f35313..375feecc 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -2,6 +2,7 @@ params{ run_metafile = 's3://ccdl-scpca-data/sample_info/scpca-library-metadata.tsv' + sample_metafile = 's3://ccdl-scpca-data/sample_info/scpca-sample-metadata.tsv' cellhash_pool_file = 's3://ccdl-scpca-data/sample_info/scpca-multiplex-pools.tsv' outdir = "s3://nextflow-ccdl-results/scpca/processed" diff --git a/main.nf b/main.nf index 994f105e..b9f67259 100644 --- a/main.nf +++ b/main.nf @@ -36,7 +36,7 @@ include { map_quant_feature } from './modules/af-features.nf' addParams(cell_bar include { bulk_quant_rna } from './modules/bulk-salmon.nf' include { genetic_demux_vireo } from './modules/genetic-demux.nf' addParams(cell_barcodes: cell_barcodes, bulk_techs: bulk_techs) include { spaceranger_quant } from './modules/spaceranger.nf' -include { generate_sce; generate_merged_sce; cellhash_demux_sce; genetic_demux_sce; post_process_sce} from './modules/sce-processing.nf' +include { generate_sce; generate_merged_sce; cellhash_demux_sce; genetic_demux_sce; post_process_sce} from './modules/sce-processing.nf' addParams(sample_metafile: params.sample_metafile) include { sce_to_anndata } from './modules/export-anndata.nf' include { annotate_celltypes } from './modules/classify-celltypes.nf' include { sce_qc_report } from './modules/qc-report.nf' @@ -51,6 +51,11 @@ if (!file(params.run_metafile).exists()) { param_error = true } +if (!file(params.sample_metafile).exists()) { + log.error("The 'sample_metafile' file '${params.sample_metafile}' can not be found.") + param_error = true +} + resolution_strategies = ['cr-like', 'full', 'cr-like-em', 'parsimony', 'trivial'] if (!resolution_strategies.contains(params.af_resolution)) { log.error("'af_resolution' must be one of the following: ${resolution_strategies}") diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 90cbea59..5ba87894 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -7,6 +7,7 @@ process make_unfiltered_sce{ tag "${meta.library_id}" input: tuple val(meta), path(alevin_dir), path(mito_file), path(ref_gtf) + path sample_meta_file output: tuple val(meta), path(unfiltered_rds) script: @@ -20,6 +21,7 @@ process make_unfiltered_sce{ --technology ${meta.technology} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ + --sample_metadata_file ${sample_meta_file} \ ${params.spliced_only ? '--spliced_only' : ''} """ stub: @@ -198,7 +200,7 @@ workflow generate_sce { sce_ch = quant_channel .map{it.toList() + [file(it[0].mito_file), file(it[0].ref_gtf)]} - make_unfiltered_sce(sce_ch) + make_unfiltered_sce(sce_ch, params.sample_metafile) empty_file = file("${projectDir}/assets/NO_FILE.txt") diff --git a/nextflow.config b/nextflow.config index 90b68274..2ed20281 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,6 +12,7 @@ manifest{ params { // Input data table run_metafile = "run_metadata.tsv" + sample_metafile = "sample_metadata.tsv" // Output base directory outdir = "scpca_out" From 43a45260494ce1899e9e605a4cca2c664be504e0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 15:48:37 -0500 Subject: [PATCH 050/268] no collapsing --- bin/generate_unfiltered_sce.R | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 0ae78472..d92f649e 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -146,19 +146,19 @@ sample_metadata_list <- purrr::map(sample_ids, single_sample_df <- sample_metadata_df |> dplyr::filter(scpca_sample_id %in% sample) list( - age = paste(single_sample_df$age, collapse = ","), - sex = paste(single_sample_df$sex, collapse = ","), - diagnosis = paste(single_sample_df$sex, collapse = ","), - subdiagnosis = paste(single_sample_df$subdiagnosis, collapse = ","), - tissue_location = paste(single_sample_df$tissue_location, collapse = ","), - disease_timing = paste(single_sample_df$disease_timing, collapse = ","), - organism = paste(single_sample_df$organism, collapse = ","), - development_stage_ontology_term_id = paste(single_sample_df$development_stage_ontology_term_id, collapse = ","), - sex_ontology_term_id = paste(single_sample_df$sex_ontology_term_id, collapse = ","), - organism_ontology_id = paste(single_sample_df$organism_ontology_id, collapse = ","), - self_reported_ethnicity_ontology_term_id = paste(single_sample_df$self_reported_ethnicity_ontology_term_id, collapse = ","), - disease_ontology_term_id = paste(single_sample_df$disease_ontology_term_id, collapse = ","), - tissue_ontology_term_id = paste(single_sample_df$tissue_ontology_term_id, collapse = ",") + age = single_sample_df$age, + sex = single_sample_df$sex, + diagnosis = single_sample_df$sex, + subdiagnosis = single_sample_df$subdiagnosis, + tissue_location = single_sample_df$tissue_location, + disease_timing = single_sample_df$disease_timing, + organism = single_sample_df$organism, + development_stage_ontology_term_id = single_sample_df$development_stage_ontology_term_id, + sex_ontology_term_id = single_sample_df$sex_ontology_term_id, + organism_ontology_id = single_sample_df$organism_ontology_id, + self_reported_ethnicity_ontology_term_id = single_sample_df$self_reported_ethnicity_ontology_term_id, + disease_ontology_term_id = single_sample_df$disease_ontology_term_id, + tissue_ontology_term_id = single_sample_df$tissue_ontology_term_id ) }) |> purrr::set_names(sample_ids) From 23647a2126d7ac5d363b48fa25be40e6647749f5 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 15:58:40 -0500 Subject: [PATCH 051/268] update stub tests with sample metadata --- config/profile_stub.config | 3 ++- test/{stub-metadata.tsv => stub-run-metadata.tsv} | 0 test/stub-sample-metadata.tsv | 10 ++++++++++ 3 files changed, 12 insertions(+), 1 deletion(-) rename test/{stub-metadata.tsv => stub-run-metadata.tsv} (100%) create mode 100644 test/stub-sample-metadata.tsv diff --git a/config/profile_stub.config b/config/profile_stub.config index 36380f9b..16858515 100644 --- a/config/profile_stub.config +++ b/config/profile_stub.config @@ -7,7 +7,8 @@ params{ max_cpus = 2 max_memory = 1.GB - run_metafile = 'test/stub-metadata.tsv' + run_metafile = 'test/stub-run-metadata.tsv' + sample_metafile = 'test/stub-sample-metadata.tsv' cellhash_pool_file = 'test/stub-pools.tsv' outdir = "test/output" run_ids = "All" diff --git a/test/stub-metadata.tsv b/test/stub-run-metadata.tsv similarity index 100% rename from test/stub-metadata.tsv rename to test/stub-run-metadata.tsv diff --git a/test/stub-sample-metadata.tsv b/test/stub-sample-metadata.tsv new file mode 100644 index 00000000..50711208 --- /dev/null +++ b/test/stub-sample-metadata.tsv @@ -0,0 +1,10 @@ +scpca_sample_id age sex diagnosis subdiagnosis tissue_location disease_timing organism disease_ontology_term_id tissue_ontology_term_id development_stage_ontology_term_id sex_ontology_term_id organism_ontology_id self_reported_ethnicity_ontology_term_id +STUBS01 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS02 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS02 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS04 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS05 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS06 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS07 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS10 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS11 NA NA NA NA NA NA NA NA NA NA NA NA NA From 471faba97878db9b1cbb42fc0aacdae33775c049 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 16:08:23 -0500 Subject: [PATCH 052/268] stubl12 and stubl13 to sample metadata --- test/stub-sample-metadata.tsv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/stub-sample-metadata.tsv b/test/stub-sample-metadata.tsv index 50711208..a9f4c915 100644 --- a/test/stub-sample-metadata.tsv +++ b/test/stub-sample-metadata.tsv @@ -8,3 +8,5 @@ STUBS06 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS07 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS10 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS11 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS12 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS13 NA NA NA NA NA NA NA NA NA NA NA NA NA From b12ef464190866d47e26fdfea0d731a3e71593ce Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 16:17:49 -0500 Subject: [PATCH 053/268] remove an extra 0 --- test/stub-pools.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/stub-pools.tsv b/test/stub-pools.tsv index 277f369c..2331d900 100644 --- a/test/stub-pools.tsv +++ b/test/stub-pools.tsv @@ -1,5 +1,5 @@ scpca_library_id scpca_sample_id barcode_id -STUBL010 STUBS010 TAG01 -STUBL010 STUBS011 TAG02 -STUBL011 STUBS012 TAG01 -STUBL011 STUBS013 TAG02 +STUBL10 STUBS10 TAG01 +STUBL10 STUBS11 TAG02 +STUBL11 STUBS12 TAG01 +STUBL11 STUBS13 TAG02 From 3fd79cac709a89916d97b32a5dac0d935188a882 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 10 Aug 2023 16:17:49 -0500 Subject: [PATCH 054/268] Revert "remove an extra 0" This reverts commit b12ef464190866d47e26fdfea0d731a3e71593ce. --- test/stub-pools.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/stub-pools.tsv b/test/stub-pools.tsv index 2331d900..277f369c 100644 --- a/test/stub-pools.tsv +++ b/test/stub-pools.tsv @@ -1,5 +1,5 @@ scpca_library_id scpca_sample_id barcode_id -STUBL10 STUBS10 TAG01 -STUBL10 STUBS11 TAG02 -STUBL11 STUBS12 TAG01 -STUBL11 STUBS13 TAG02 +STUBL010 STUBS010 TAG01 +STUBL010 STUBS011 TAG02 +STUBL011 STUBS012 TAG01 +STUBL011 STUBS013 TAG02 From d8240987b78b0a20bbf8656fa98bc0300dc50e45 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 11 Aug 2023 10:07:17 -0400 Subject: [PATCH 055/268] Add `file()` and fix log uploads The `cat` step in GHA wasn't running, so logs weren't uploading on failure --- .github/workflows/nextflow-stub-check.yaml | 7 ++++--- modules/sce-processing.nf | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/nextflow-stub-check.yaml b/.github/workflows/nextflow-stub-check.yaml index 5c226c0a..f710430e 100644 --- a/.github/workflows/nextflow-stub-check.yaml +++ b/.github/workflows/nextflow-stub-check.yaml @@ -24,12 +24,13 @@ jobs: uses: docker://nextflow/nextflow:21.10.6 with: args: nextflow -log checkpoint-run.log run main.nf -stub -profile stub -ansi-log false - + - name: Join log files + if: ${{ !cancelled() }} run: cat stub-run.log checkpoint-run.log > nextflow-runs.log - + - name: Upload nextflow log - if: ${{ always() }} + if: ${{ !cancelled() }} uses: actions/upload-artifact@v3 with: name: nextflow-log diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 5ba87894..fe143f4c 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -200,7 +200,7 @@ workflow generate_sce { sce_ch = quant_channel .map{it.toList() + [file(it[0].mito_file), file(it[0].ref_gtf)]} - make_unfiltered_sce(sce_ch, params.sample_metafile) + make_unfiltered_sce(sce_ch, file(params.sample_metafile)) empty_file = file("${projectDir}/assets/NO_FILE.txt") From 33d391240f1f8e6d24515d4fa59597b762730401 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 10:19:57 -0500 Subject: [PATCH 056/268] add sample metadata as dataframe --- bin/generate_unfiltered_sce.R | 34 ++++++---------------------------- 1 file changed, 6 insertions(+), 28 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index d92f649e..5413cda2 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -139,34 +139,12 @@ unfiltered_sce <- unfiltered_sce |> add_gene_symbols(gene_info = gtf) |> scuttle::addPerFeatureQCMetrics() -# get a list of sample metadata to add -# for each sample in the library, create an individual list of sample metadata -sample_metadata_list <- purrr::map(sample_ids, - \(sample){ - single_sample_df <- sample_metadata_df |> - dplyr::filter(scpca_sample_id %in% sample) - list( - age = single_sample_df$age, - sex = single_sample_df$sex, - diagnosis = single_sample_df$sex, - subdiagnosis = single_sample_df$subdiagnosis, - tissue_location = single_sample_df$tissue_location, - disease_timing = single_sample_df$disease_timing, - organism = single_sample_df$organism, - development_stage_ontology_term_id = single_sample_df$development_stage_ontology_term_id, - sex_ontology_term_id = single_sample_df$sex_ontology_term_id, - organism_ontology_id = single_sample_df$organism_ontology_id, - self_reported_ethnicity_ontology_term_id = single_sample_df$self_reported_ethnicity_ontology_term_id, - disease_ontology_term_id = single_sample_df$disease_ontology_term_id, - tissue_ontology_term_id = single_sample_df$tissue_ontology_term_id - ) - }) |> - purrr::set_names(sample_ids) - -# add list of sample metadata -# access the list of sample metadata for each sample -# with metadata(unfiltered_sce)$sample_metadata[[sample_id]] -metadata(unfiltered_sce)$sample_metadata <- sample_metadata_list +# filter the sample metadata to only include samples present in the library +sample_metadata <- sample_metadata_df |> + dplyr::filter(scpca_sample_id %in% sample_ids) + +# add dataframe with sample metadata to sce metadata +metadata(unfiltered_sce)$sample_metadata <- sample_metadata # write to rds readr::write_rds(unfiltered_sce, opt$unfiltered_file, compress = "gz") From e65169e37558f5f2fd796f08e2e67a985e54ee99 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 10:31:34 -0500 Subject: [PATCH 057/268] switch order of inputs --- modules/classify-celltypes.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index a86db090..8737ecd6 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -57,7 +57,7 @@ process classify_cellassign { label 'mem_4' label 'cpus_2' input: - tuple val(meta), path(cellassign_predictions), path(input_rds), val(ref_name) + tuple val(meta), path(input_rds), path(cellassign_predictions), val(ref_name) output: tuple val(meta), path(annotated_rds) script: From 91715783868306db5cf044b2b83c445d8355f4e9 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 11:43:20 -0500 Subject: [PATCH 058/268] make sure cell type assignments are in the right order --- bin/classify_cellassign.R | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index e1a981ad..5a7ad862 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -43,9 +43,9 @@ if(!file.exists(opt$cellassign_predictions)){ stop("Missing CellAssign predictions file") } -# read in input files +# read in input files sce <- readr::read_rds(opt$input_sce_file) -predictions <- readr::read_tsv(opt$cellassign_predictions) +predictions <- readr::read_tsv(opt$cellassign_predictions) celltype_assignments <- predictions |> tidyr::pivot_longer(!barcode, @@ -55,7 +55,13 @@ celltype_assignments <- predictions |> dplyr::slice_max(prediction, n = 1) |> dplyr::ungroup() -sce$cellassign_celltype_annotation <- celltype_assignments +# join by barcode to make sure assignments are in the right order +celltype_assignments <- data.frame(barcode = sce$barcodes) |> + dplyr::left_join(celltype_assignments, by = "barcode") + +# add into sce +sce$cellassign_celltype_annotation <- celltype_assignments$celltype +sce$cellassign_max_prediction <- celltype_assignments$prediction metadata(sce)$cellassign_predictions <- predictions metadata(sce)$cellassign_reference <- opt$reference_name From d48ec60b31ab2d40935255ec788001be85738ad2 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 11:43:37 -0500 Subject: [PATCH 059/268] publish predictions to checkpoints directory --- modules/classify-celltypes.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 8737ecd6..c13f291a 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -27,7 +27,7 @@ process classify_singleR { process predict_cellassign { container params.SCPCATOOLS_CONTAINER - publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' + publishDir "${params.checkpoints_dir}/celltype/${meta.library_id}", mode: 'copy' label 'mem_32' label 'cpus_12' input: From a8289788f502d7d17d5183fd16232a6b5b3838e4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 11 Aug 2023 14:50:46 -0500 Subject: [PATCH 060/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/classify_cellassign.R | 13 +++++++++++-- modules/classify-celltypes.nf | 1 + 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 5a7ad862..70e0f6bd 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -1,6 +1,6 @@ #!/usr/bin/env Rscript -# This script is used to read in the predictions from CellAssign and assign cell types +# This script is used to read in the predictions from CellAssign and assign cell types in the annotated RDS file # import libraries suppressPackageStartupMessages({ @@ -34,15 +34,24 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) -# check that input file file exists +# check that input file exists if(!file.exists(opt$input_sce_file)){ stop("Missing input SCE file") } +# check that cellassign predictions file was provided if(!file.exists(opt$cellassign_predictions)){ stop("Missing CellAssign predictions file") } +# check that reference_name was provided +if (is.null(opt$reference_name)) { + stop("Missing reference name") +} +# check that output file ends in rds +if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ + stop("output sce file name must end in .rds") +} # read in input files sce <- readr::read_rds(opt$input_sce_file) predictions <- readr::read_tsv(opt$cellassign_predictions) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index c13f291a..f26f83b5 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -119,6 +119,7 @@ workflow annotate_celltypes { // resulting tuple should be [meta, singleR annotated rds, cellassign predictions] .combine(predict_cellassign.out, by: 0) + // get CellAssign cell type predictions and add them to SCE classify_cellassign(all_celltype_assignments_ch) emit: classify_cellassign.out From 9719001ba9a281b3cd992af5ff5036aaeb063283 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 14:54:14 -0500 Subject: [PATCH 061/268] export rds --- bin/classify_cellassign.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 70e0f6bd..4b096295 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -68,9 +68,13 @@ celltype_assignments <- predictions |> celltype_assignments <- data.frame(barcode = sce$barcodes) |> dplyr::left_join(celltype_assignments, by = "barcode") -# add into sce -sce$cellassign_celltype_annotation <- celltype_assignments$celltype +# add cell type and prediction to colData +sce$cellassign_celltype_annotation <- celltype_assignments sce$cellassign_max_prediction <- celltype_assignments$prediction +# add entire predictions matrix and ref name to metadata metadata(sce)$cellassign_predictions <- predictions metadata(sce)$cellassign_reference <- opt$reference_name + +# export annotated object with cellassign assignments +readr::write_rds(sce, opt$output_sce_file) From a3a8d5234d9f39e8f46c4eb69e851a849facf9b3 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 14:55:12 -0500 Subject: [PATCH 062/268] add output file check to classify SingleR --- bin/classify_SingleR.R | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 870081c8..fc46e2ed 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -56,6 +56,11 @@ if(!file.exists(opt$input_sce_file)){ stop("Missing input SCE file") } +# check that output file ends in rds +if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ + stop("output sce file name must end in .rds") +} + # check that references all exist singler_model_file <- opt$singler_model_file if(!file.exists(singler_model_file)) { From 6449ca11f6a9307b33abdb5323fce1f8ef89086b Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 11 Aug 2023 14:57:20 -0500 Subject: [PATCH 063/268] update comments --- modules/classify-celltypes.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index f26f83b5..07c757db 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -82,6 +82,8 @@ workflow annotate_celltypes { project_id = it.scpca_project_id, singler_model_file = "${params.singler_models_dir}/${it.singler_ref_file}", cellassign_ref_file = "${params.cellassign_ref_dir}/${it.cellassign_ref_file}", + // add ref name for cellassign since we cannot store it in the cellassign output + // singler ref name does not need to be added because it is stored in the singler model cellassign_ref_name = it.cellassign_ref_name ]} @@ -92,14 +94,14 @@ workflow annotate_celltypes { .combine(celltype_ch, by: 0) .map{it.drop(1)} // remove extra project ID - // creates [meta, processed, SingleR reference model] + // creates input for singleR [meta, processed, SingleR reference model] singler_input_ch = grouped_celltype_ch .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file, cellassign_ref_name -> tuple(meta, processed_rds, singler_model_file )} - // creates [meta, processed hdf5, cellassign ref file, cell assign ref name] + // creates input for cellassign [meta, processed hdf5, cellassign ref file, cell assign ref name] cellassign_input_ch = grouped_celltype_ch .map{meta, processed_rds, processed_hdf5, singler_model_file, cellassign_ref_file, cellassign_ref_name -> tuple(meta, processed_hdf5, From 9c97aeea74e49f61f02adea55e051a66c5748d7a Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 14 Aug 2023 11:38:22 -0500 Subject: [PATCH 064/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/classify_SingleR.R | 2 +- bin/classify_cellassign.R | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index fc46e2ed..2365753d 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -57,7 +57,7 @@ if(!file.exists(opt$input_sce_file)){ } # check that output file ends in rds -if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))){ stop("output sce file name must end in .rds") } diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 4b096295..02ba3f99 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -35,12 +35,12 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that input file exists -if(!file.exists(opt$input_sce_file)){ +if (!file.exists(opt$input_sce_file)){ stop("Missing input SCE file") } # check that cellassign predictions file was provided -if(!file.exists(opt$cellassign_predictions)){ +if (!file.exists(opt$cellassign_predictions)){ stop("Missing CellAssign predictions file") } # check that reference_name was provided From 0b1b04aec606ed7b0ef46b53d39d267c6dc5cc80 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 14:54:19 +0000 Subject: [PATCH 065/268] Add initial script to perform clustering on and SCE object --- bin/cluster_sce.R | 87 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 bin/cluster_sce.R diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R new file mode 100644 index 00000000..67af6976 --- /dev/null +++ b/bin/cluster_sce.R @@ -0,0 +1,87 @@ +#!/usr/bin/env Rscript + +# Script used to perform clustering on a given SCE object +# +# This script reads in an RDS file containing an SCE, and performed +# graph-based clustering using the specified algorithm. Cluster identities are +# stored in the SCE's colData slot, and the SCE is written back out to the +# original RDS file. + +# import libraries +library(optparse) +library(SingleCellExperiment) + +# Set up optparse options +option_list <- list( + make_option( + opt_str = c("-i", "--sce_file"), + type = "character", + help = "Path to RDS file that contains the SCE object to cluster." + ), + make_option( + opt_str = c("--pca_name"), + type = "character", + default = "PCA", + help = "Name of the PCA reduced dimensionality representation to perform + clustering on." + ), + make_option( + opt_str = c("--cluster_algorithm"), + type = "character", + default = "leiden", + help = "Clustering algorithm to use. Must be one of the options available in bluster. + Default is 'leiden'." + ), + make_option( + opt_str = c("--nn"), + type = "integer", + default = 15, + help = "Nearest neighbors parameter to set for graph-based clustering." + ), + make_option( + opt_str = c("--seed"), + type = "integer", + help = "random seed to set during clustering." + ) +) + +# Setup ------------------------------ +# Parse options +opt <- parse_args(OptionParser(option_list = option_list)) + +set.seed(opt$seed) + +# check and read in SCE file +if (!file.exists(opt$sce_file)) { + stop("Input `sce_file` is missing.") +} +sce <- readr::read_rds(opt$sce_file) + + +# check pca_name is present +if (!opt$pca_name %in% reducedDimNames(sce)) { + stop("Provided `pca_name` is not present in the SCE object.") +} + +# Perform clustering ---------------- + +# extract the principal components matrix +pca_matrix <- reducedDim(sce, opt$pca_name) + +# cluster with specified algorithm +clusters <- bluster::clusterRows( + pca_matrix, + bluster::SNNGraphParam( + k = opt$nn, + cluster.fun = opt$cluster_algorithm + ) +) + +# add clusters and associated parameters to SCE object +sce$clusters <- clusters +metadata(sce)$cluster_algorithm <- opt$cluster_algorithm +metadata(sce)$cluster_nn <- opt$nn + + +# export ------------------- +readr::write_rds(sce, opt$sce_file) From 3a27f0c3bfa6fbd8c0fb2db597c755cbd0786da4 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 15:14:45 +0000 Subject: [PATCH 066/268] add clustering config parameters --- nextflow.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nextflow.config b/nextflow.config index 90b68274..d0d7d7e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -45,6 +45,10 @@ params { gene_cutoff = 200 // minimum number of genes per cell cutoff used for filtering cells num_hvg = 2000 // number of high variance genes to use for dimension reduction num_pcs = 50 // number of principal components to retain in the returned SingleCellExperiment object + + // SCE clustering options + cluster_algorithm = "leiden" // default graph-based clustering algorithm + nearest_neighbors = 15 // number of nearest neighbors parameter for graph-based clustering // Docker container images includeConfig 'config/containers.config' From 13d308e753568924721ec1afff1c63d96f7e740f Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 16:30:15 +0000 Subject: [PATCH 067/268] add cluster process and update/debug R script accordingly --- bin/cluster_sce.R | 25 +++++++++++++------------ modules/cluster-sce.nf | 27 +++++++++++++++++++++++++++ 2 files changed, 40 insertions(+), 12 deletions(-) create mode 100644 modules/cluster-sce.nf diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index 67af6976..993d429b 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -14,9 +14,10 @@ library(SingleCellExperiment) # Set up optparse options option_list <- list( make_option( - opt_str = c("-i", "--sce_file"), + opt_str = c("-i", "--processed_sce_file"), type = "character", - help = "Path to RDS file that contains the SCE object to cluster." + default = "~/sce.rds", + help = "Path to RDS file that contains the processedsce SCE object to cluster." ), make_option( opt_str = c("--pca_name"), @@ -33,13 +34,13 @@ option_list <- list( Default is 'leiden'." ), make_option( - opt_str = c("--nn"), + opt_str = c("--nearest_neighbors"), type = "integer", default = 15, help = "Nearest neighbors parameter to set for graph-based clustering." ), make_option( - opt_str = c("--seed"), + opt_str = c("--random_seed"), type = "integer", help = "random seed to set during clustering." ) @@ -52,10 +53,10 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$seed) # check and read in SCE file -if (!file.exists(opt$sce_file)) { +if (!file.exists(opt$processed_sce_file)) { stop("Input `sce_file` is missing.") } -sce <- readr::read_rds(opt$sce_file) +sce <- readr::read_rds(opt$processed_sce_file) # check pca_name is present @@ -71,17 +72,17 @@ pca_matrix <- reducedDim(sce, opt$pca_name) # cluster with specified algorithm clusters <- bluster::clusterRows( pca_matrix, - bluster::SNNGraphParam( - k = opt$nn, + bluster::NNGraphParam( + k = opt$nearest_neighbors, cluster.fun = opt$cluster_algorithm ) -) +) +# TODO: may wish to modify additional cluster parameters depending on cluster algorithm # add clusters and associated parameters to SCE object sce$clusters <- clusters metadata(sce)$cluster_algorithm <- opt$cluster_algorithm -metadata(sce)$cluster_nn <- opt$nn - +metadata(sce)$cluster_nn <- opt$nearest_neighbors # export ------------------- -readr::write_rds(sce, opt$sce_file) +readr::write_rds(sce, opt$processed_sce_file) diff --git a/modules/cluster-sce.nf b/modules/cluster-sce.nf new file mode 100644 index 00000000..cca98409 --- /dev/null +++ b/modules/cluster-sce.nf @@ -0,0 +1,27 @@ +// perform graph-based clustering on a processed SCE object +// this process also does the RDS file export to the publishDir + + +process cluster_sce{ + container params.SCPCATOOLS_CONTAINER + label 'mem_8' + tag "${meta.library_id}" + publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' + input: + tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) + output: + tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) + script: + """ + cluster_sce.R \ + --processed_sce_file ${processed_rds} \ + --cluster_algorithm ${params.cluster_algorithm} \ + --nearest_neighbors ${params.nearest_neighbors} \ + ${params.seed ? "--random_seed ${params.seed}" : ""} + """ + stub: + processed_rds = "${meta.library_id}_processed.rds" + """ + touch ${processed_rds} + """ +} From ac4180ebc6374e8f46b1bdc58c7ef5a3e260031a Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 16:30:37 +0000 Subject: [PATCH 068/268] Incorporate cluster_sce process, and update publishDir --- main.nf | 9 ++++++--- modules/sce-processing.nf | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 994f105e..42b1a1a3 100644 --- a/main.nf +++ b/main.nf @@ -40,7 +40,7 @@ include { generate_sce; generate_merged_sce; cellhash_demux_sce; genetic_demux_s include { sce_to_anndata } from './modules/export-anndata.nf' include { annotate_celltypes } from './modules/classify-celltypes.nf' include { sce_qc_report } from './modules/qc-report.nf' - +include { cluster_sce } from './modules/cluster-sce.nf' // parameter checks @@ -206,12 +206,15 @@ workflow { // **** Post processing and generate QC reports **** // combine all SCE outputs - // Make channel for all library sce files & run QC report + // Make channel for all library sce files all_sce_ch = sce_ch.no_genetic.mix(genetic_demux_sce.out) post_process_sce(all_sce_ch) + + // Cluster SCE and export RDS files to publishDir + cluster_sce(post_process_sce.out) // generate QC reports - sce_qc_report(post_process_sce.out, report_template_tuple) + sce_qc_report(cluster_sce.out, report_template_tuple) // convert RNA component of SCE object to anndata sce_to_anndata(post_process_sce.out) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 90cbea59..92b88661 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -167,7 +167,7 @@ process post_process_sce{ container params.SCPCATOOLS_CONTAINER label 'mem_8' tag "${meta.library_id}" - publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' + publishDir "${params.checkpoints_dir}/post_processed/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(unfiltered_rds), path(filtered_rds) output: From 71c11edb5d261895fe7ef1935aa57e8df7e90255 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 16:37:58 +0000 Subject: [PATCH 069/268] remove my testing default value for processed_sce_file arg --- bin/cluster_sce.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index 993d429b..c6897cf2 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -16,8 +16,7 @@ option_list <- list( make_option( opt_str = c("-i", "--processed_sce_file"), type = "character", - default = "~/sce.rds", - help = "Path to RDS file that contains the processedsce SCE object to cluster." + help = "Path to RDS file that contains the processed sce SCE object to cluster." ), make_option( opt_str = c("--pca_name"), From 3be2fc38a4e9af4066f8be5c8f65474344746f00 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 15 Aug 2023 13:33:13 -0400 Subject: [PATCH 070/268] Apply suggestions from code review Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- bin/cluster_sce.R | 4 ++-- modules/cluster-sce.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index c6897cf2..a9e48d47 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -2,7 +2,7 @@ # Script used to perform clustering on a given SCE object # -# This script reads in an RDS file containing an SCE, and performed +# This script reads in an RDS file containing an SCE, and performs # graph-based clustering using the specified algorithm. Cluster identities are # stored in the SCE's colData slot, and the SCE is written back out to the # original RDS file. @@ -14,7 +14,7 @@ library(SingleCellExperiment) # Set up optparse options option_list <- list( make_option( - opt_str = c("-i", "--processed_sce_file"), + opt_str = c("-i", "--input_sce_file"), type = "character", help = "Path to RDS file that contains the processed sce SCE object to cluster." ), diff --git a/modules/cluster-sce.nf b/modules/cluster-sce.nf index cca98409..dc3f7726 100644 --- a/modules/cluster-sce.nf +++ b/modules/cluster-sce.nf @@ -14,7 +14,7 @@ process cluster_sce{ script: """ cluster_sce.R \ - --processed_sce_file ${processed_rds} \ + --input_sce_file ${processed_rds} \ --cluster_algorithm ${params.cluster_algorithm} \ --nearest_neighbors ${params.nearest_neighbors} \ ${params.seed ? "--random_seed ${params.seed}" : ""} From f6711f89e6f9c3248ebd715ef8a0db8a49c8a743 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 17:34:42 +0000 Subject: [PATCH 071/268] Use louvain default algorithm and add jaccard. Ensure use of input_sce_file option name throughout --- bin/cluster_sce.R | 14 ++++++++------ nextflow.config | 2 +- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index a9e48d47..5177fbd7 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -28,9 +28,9 @@ option_list <- list( make_option( opt_str = c("--cluster_algorithm"), type = "character", - default = "leiden", + default = "louvain", help = "Clustering algorithm to use. Must be one of the options available in bluster. - Default is 'leiden'." + Default is 'louvain'." ), make_option( opt_str = c("--nearest_neighbors"), @@ -52,10 +52,10 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$seed) # check and read in SCE file -if (!file.exists(opt$processed_sce_file)) { - stop("Input `sce_file` is missing.") +if (!file.exists(opt$input_sce_file)) { + stop("Input `input_sce_file` is missing.") } -sce <- readr::read_rds(opt$processed_sce_file) +sce <- readr::read_rds(opt$input_sce_file) # check pca_name is present @@ -73,6 +73,7 @@ clusters <- bluster::clusterRows( pca_matrix, bluster::NNGraphParam( k = opt$nearest_neighbors, + type = "jaccard", cluster.fun = opt$cluster_algorithm ) ) @@ -84,4 +85,5 @@ metadata(sce)$cluster_algorithm <- opt$cluster_algorithm metadata(sce)$cluster_nn <- opt$nearest_neighbors # export ------------------- -readr::write_rds(sce, opt$processed_sce_file) +# we are overwriting the input file here: +readr::write_rds(sce, opt$input_sce_file) diff --git a/nextflow.config b/nextflow.config index d0d7d7e9..c078b627 100644 --- a/nextflow.config +++ b/nextflow.config @@ -47,7 +47,7 @@ params { num_pcs = 50 // number of principal components to retain in the returned SingleCellExperiment object // SCE clustering options - cluster_algorithm = "leiden" // default graph-based clustering algorithm + cluster_algorithm = "louvain" // default graph-based clustering algorithm nearest_neighbors = 15 // number of nearest neighbors parameter for graph-based clustering // Docker container images From abb1ac05b09d6bc9031c5ae182c47b180afd2f1d Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 17:37:15 +0000 Subject: [PATCH 072/268] remove checkpoint publishing from post_process_sce --- modules/sce-processing.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 92b88661..dc182d3c 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -167,7 +167,6 @@ process post_process_sce{ container params.SCPCATOOLS_CONTAINER label 'mem_8' tag "${meta.library_id}" - publishDir "${params.checkpoints_dir}/post_processed/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(unfiltered_rds), path(filtered_rds) output: From 580124061a19db4e82842e38ca0158ff412d5f12 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 15 Aug 2023 15:14:56 -0400 Subject: [PATCH 073/268] Update bin/cluster_sce.R Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- bin/cluster_sce.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index 5177fbd7..d9d43b6f 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -16,7 +16,8 @@ option_list <- list( make_option( opt_str = c("-i", "--input_sce_file"), type = "character", - help = "Path to RDS file that contains the processed sce SCE object to cluster." + help = "Path to RDS file that contains the processed SCE object to cluster. + Must contain a PCA matrix to calculate clusters from." ), make_option( opt_str = c("--pca_name"), From c636e67c1544ec25e0c002a8aa147fe7c541439a Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 19:29:50 +0000 Subject: [PATCH 074/268] bump nn to 20 and add weighting param --- nextflow.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index c078b627..5b03726b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -48,7 +48,8 @@ params { // SCE clustering options cluster_algorithm = "louvain" // default graph-based clustering algorithm - nearest_neighbors = 15 // number of nearest neighbors parameter for graph-based clustering + cluster_weighting = "jaccard" // default weighting scheme for graph-based clustering + nearest_neighbors = 20 // default nearest neighbors parameter for graph-based clustering // Docker container images includeConfig 'config/containers.config' From c911580a50a6e1e70edeb3c44bf8f309bbe1fbea Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 19:30:32 +0000 Subject: [PATCH 075/268] Back to processed_sce_file, bump nn to 20, and add option for cluster_weighting which also gets saved in metadata --- bin/cluster_sce.R | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index d9d43b6f..9d77fdd4 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -14,7 +14,7 @@ library(SingleCellExperiment) # Set up optparse options option_list <- list( make_option( - opt_str = c("-i", "--input_sce_file"), + opt_str = c("--processed_sce_file"), type = "character", help = "Path to RDS file that contains the processed SCE object to cluster. Must contain a PCA matrix to calculate clusters from." @@ -33,11 +33,18 @@ option_list <- list( help = "Clustering algorithm to use. Must be one of the options available in bluster. Default is 'louvain'." ), + make_option( + opt_str = c("--cluster_weighting"), + type = "character", + default = "jaccard", + help = "The type of weighting scheme to use for shared neighbors when performing + graph-based clustering. Default is 'jaccard'." + ), make_option( opt_str = c("--nearest_neighbors"), type = "integer", - default = 15, - help = "Nearest neighbors parameter to set for graph-based clustering." + default = 20, + help = "Nearest neighbors parameter to set for graph-based clustering. Default is 20." ), make_option( opt_str = c("--random_seed"), @@ -53,10 +60,10 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$seed) # check and read in SCE file -if (!file.exists(opt$input_sce_file)) { - stop("Input `input_sce_file` is missing.") +if (!file.exists(opt$processed_sce_file)) { + stop("Input `processed_sce_file` is missing.") } -sce <- readr::read_rds(opt$input_sce_file) +sce <- readr::read_rds(opt$processed_sce_file) # check pca_name is present @@ -74,7 +81,7 @@ clusters <- bluster::clusterRows( pca_matrix, bluster::NNGraphParam( k = opt$nearest_neighbors, - type = "jaccard", + type = opt$cluster_weighting, cluster.fun = opt$cluster_algorithm ) ) @@ -83,8 +90,9 @@ clusters <- bluster::clusterRows( # add clusters and associated parameters to SCE object sce$clusters <- clusters metadata(sce)$cluster_algorithm <- opt$cluster_algorithm +metadata(sce)$cluster_weighting <- opt$cluster_weighting metadata(sce)$cluster_nn <- opt$nearest_neighbors # export ------------------- -# we are overwriting the input file here: -readr::write_rds(sce, opt$input_sce_file) +# we are overwriting the `processed_sce_file` here +readr::write_rds(sce, opt$processed_sce_file) From b3fe032dbdc4555fe43753163f32cc4c08d51246 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 19:31:11 +0000 Subject: [PATCH 076/268] back to processed_sce_file and use the new cluster_weighting param --- modules/cluster-sce.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/cluster-sce.nf b/modules/cluster-sce.nf index dc3f7726..ae0db5ca 100644 --- a/modules/cluster-sce.nf +++ b/modules/cluster-sce.nf @@ -14,8 +14,9 @@ process cluster_sce{ script: """ cluster_sce.R \ - --input_sce_file ${processed_rds} \ + --processed_sce_file ${processed_rds} \ --cluster_algorithm ${params.cluster_algorithm} \ + --cluster_weighting ${params.cluster_weighting} \ --nearest_neighbors ${params.nearest_neighbors} \ ${params.seed ? "--random_seed ${params.seed}" : ""} """ From 673e542fbc6dd164531a0fbd3533f3045a73d5e3 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 15 Aug 2023 14:48:12 -0500 Subject: [PATCH 077/268] add celltype ref files to internal docs --- internal-instructions.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/internal-instructions.md b/internal-instructions.md index af3b32a7..8949b3de 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -67,6 +67,17 @@ See [instructions for adding additional organisms](#adding-additional-organisms) For each supported reference, a list of all the reference files that are needed to run `scpca-nf` will be included. This file is required as input to `scpca-nf`. +3. `celltype-reference-metadata.tsv`: Each row of this TSV file corresponds to a supported cell type reference available for cell type assignment using `add-celltypes.nf`. +For all references, the following columns will be populated: `celltype_ref_name`, `celltype_ref_source` (e.g., `celldex`), supported `celltype_method` (e.g., `SingleR`). +For all references obtained from the `PanglaoDB` source also require an `organs` column containing the list of supported `PanglaoDB` organs to include when building the reference. +This should be a comma separated list of all organs to include. +To find all possible organs, see the `organs` column of `PanglaoDB_markers_27_Mar_2020.tsv`. +This file is required as input to the `build-celltype-ref.nf` workflow, which will create all required cell type references for `add-celltypes.nf`. + +4. `PanglaoDB_markers_27_Mar_2020.tsv`: This file is used to build the cell type references from `PanglaoDB`. +This file was obtained from clicking the `get tsv file` button on the [PanglaoDB Dataset page](https://panglaodb.se/markers.html?cell_type=%27choose%27). +This file is required as input to the `build-celltype-ref.nf` workflow, which will create all required cell type references for `add-celltypes.nf`. + ### Adding additional organisms Follow the below steps to add support for additional references: From 55327f0acfd1a670ca1f3f4606bec01ed259c199 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 15 Aug 2023 19:52:14 +0000 Subject: [PATCH 078/268] Use scran::clusterCells instead of bluster::clusterRows; tested successfully --- bin/cluster_sce.R | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index 9d77fdd4..a6153ff8 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -74,18 +74,15 @@ if (!opt$pca_name %in% reducedDimNames(sce)) { # Perform clustering ---------------- # extract the principal components matrix -pca_matrix <- reducedDim(sce, opt$pca_name) - -# cluster with specified algorithm -clusters <- bluster::clusterRows( - pca_matrix, - bluster::NNGraphParam( +clusters <- scran::clusterCells( + sce, + use.dimred = opt$pca_name, + BLUSPARAM = bluster::NNGraphParam( k = opt$nearest_neighbors, type = opt$cluster_weighting, cluster.fun = opt$cluster_algorithm ) -) -# TODO: may wish to modify additional cluster parameters depending on cluster algorithm +) # add clusters and associated parameters to SCE object sce$clusters <- clusters From bc9868530db5584fd27d9e3a9ad97d296ddfb48c Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 16 Aug 2023 10:58:37 -0500 Subject: [PATCH 079/268] Apply suggestions from code review Co-authored-by: Stephanie --- internal-instructions.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/internal-instructions.md b/internal-instructions.md index 8949b3de..3f625e8b 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -69,8 +69,8 @@ This file is required as input to `scpca-nf`. 3. `celltype-reference-metadata.tsv`: Each row of this TSV file corresponds to a supported cell type reference available for cell type assignment using `add-celltypes.nf`. For all references, the following columns will be populated: `celltype_ref_name`, `celltype_ref_source` (e.g., `celldex`), supported `celltype_method` (e.g., `SingleR`). -For all references obtained from the `PanglaoDB` source also require an `organs` column containing the list of supported `PanglaoDB` organs to include when building the reference. -This should be a comma separated list of all organs to include. +All references obtained from the `PanglaoDB` source also require an `organs` column containing the list of supported `PanglaoDB` organs to include when building the reference. +This should be a comma-separated list of all organs to include. To find all possible organs, see the `organs` column of `PanglaoDB_markers_27_Mar_2020.tsv`. This file is required as input to the `build-celltype-ref.nf` workflow, which will create all required cell type references for `add-celltypes.nf`. From 590f9ae0782377f43f8d40f49d106877fa693940 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 16 Aug 2023 11:04:23 -0500 Subject: [PATCH 080/268] add instructions for adding new cell type refs --- internal-instructions.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/internal-instructions.md b/internal-instructions.md index 3f625e8b..e8c17ddf 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -73,6 +73,7 @@ All references obtained from the `PanglaoDB` source also require an `organs` col This should be a comma-separated list of all organs to include. To find all possible organs, see the `organs` column of `PanglaoDB_markers_27_Mar_2020.tsv`. This file is required as input to the `build-celltype-ref.nf` workflow, which will create all required cell type references for `add-celltypes.nf`. +See [instructions for adding additional cell type references](#adding-additional-cell-type-references) for more details. 4. `PanglaoDB_markers_27_Mar_2020.tsv`: This file is used to build the cell type references from `PanglaoDB`. This file was obtained from clicking the `get tsv file` button on the [PanglaoDB Dataset page](https://panglaodb.se/markers.html?cell_type=%27choose%27). @@ -99,3 +100,11 @@ homo_sapiens 3. Generate an updated `scpca-refs.json` by running the script, `create-reference-json.R`, located in the `scripts` directory. 4. Generate the index files using `nextflow run build-index.nf -profile ccdl,batch` from the root directory of this repository. 5. Ensure that the new reference files are public and in the correct location on S3 (`s3://scpca-references`). + +## Adding additional cell type references + +Follow the below steps to add suppor for additional cell type references: + +1. Add the `celltype_ref_name`, `celltype_ref_source`, `celltype_method`, and `organs` (if applicable) for the new reference to `celltype-reference-metadata.tsv`. +2. Generate the new cell type references using `nextflow run build-celltype-ref.nf -profile ccdl,batch` from the root directory of this repository. +3. Ensure that the new reference files are public and in the correct location on S3 (`s3://scpca-references/celltype`). From 84d12a088e987af4c2e7693ceb161a7118db02ba Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 16 Aug 2023 11:19:05 -0500 Subject: [PATCH 081/268] Apply suggestions from code review Co-authored-by: Stephanie --- internal-instructions.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/internal-instructions.md b/internal-instructions.md index e8c17ddf..a70e4333 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -103,7 +103,8 @@ homo_sapiens ## Adding additional cell type references -Follow the below steps to add suppor for additional cell type references: +Follow the below steps to add support for additional cell type references. +We currently only support `celldex` and `PanglaoDB` for reference sources. 1. Add the `celltype_ref_name`, `celltype_ref_source`, `celltype_method`, and `organs` (if applicable) for the new reference to `celltype-reference-metadata.tsv`. 2. Generate the new cell type references using `nextflow run build-celltype-ref.nf -profile ccdl,batch` from the root directory of this repository. From 72f5acae095dc2a7564b3889a1c804ca09202e30 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 22 Aug 2023 12:46:23 -0500 Subject: [PATCH 082/268] use add_sample_metadata function --- bin/generate_unfiltered_sce.R | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 5413cda2..f0743006 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -102,10 +102,6 @@ gtf <- rtracklayer::import(opt$gtf_file, feature.type = "gene") # parse sample id list sample_ids <- unlist(stringr::str_split(opt$sample_id, ",|;")) |> sort() -# read in sample metadata and filter to sample ids -sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> - dplyr::filter(scpca_sample_id %in% sample_ids) - # set include unspliced for non feature data include_unspliced <- !opt$spliced_only @@ -139,12 +135,14 @@ unfiltered_sce <- unfiltered_sce |> add_gene_symbols(gene_info = gtf) |> scuttle::addPerFeatureQCMetrics() -# filter the sample metadata to only include samples present in the library -sample_metadata <- sample_metadata_df |> - dplyr::filter(scpca_sample_id %in% sample_ids) +# read in sample metadata and filter to sample ids +sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> + # rename sample id column + dplyr::rename(sample_id = "scpca_sample_id") # add dataframe with sample metadata to sce metadata -metadata(unfiltered_sce)$sample_metadata <- sample_metadata +unfiltered_sce <- add_sample_metadata(sce = unfiltered_sce, + metadata_df = sample_metadata_df) # write to rds readr::write_rds(unfiltered_sce, opt$unfiltered_file, compress = "gz") From ba144431041618f1dbcd2b714a5a05b656b86a1e Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Tue, 22 Aug 2023 14:54:46 -0500 Subject: [PATCH 083/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- bin/generate_unfiltered_sce.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index f0743006..b225570b 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -138,7 +138,7 @@ unfiltered_sce <- unfiltered_sce |> # read in sample metadata and filter to sample ids sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> # rename sample id column - dplyr::rename(sample_id = "scpca_sample_id") + dplyr::rename("sample_id" = "scpca_sample_id") # add dataframe with sample metadata to sce metadata unfiltered_sce <- add_sample_metadata(sce = unfiltered_sce, From ebf6ea44713fb82f4f6f526939ac1f844904098e Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 22 Aug 2023 15:36:36 -0500 Subject: [PATCH 084/268] remove passing param to workflow --- main.nf | 8 ++++---- modules/sce-processing.nf | 18 ++++++++++++------ 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/main.nf b/main.nf index 809b6f5b..56f35cec 100644 --- a/main.nf +++ b/main.nf @@ -36,7 +36,7 @@ include { map_quant_feature } from './modules/af-features.nf' addParams(cell_bar include { bulk_quant_rna } from './modules/bulk-salmon.nf' include { genetic_demux_vireo } from './modules/genetic-demux.nf' addParams(cell_barcodes: cell_barcodes, bulk_techs: bulk_techs) include { spaceranger_quant } from './modules/spaceranger.nf' -include { generate_sce; generate_merged_sce; cellhash_demux_sce; genetic_demux_sce; post_process_sce} from './modules/sce-processing.nf' addParams(sample_metafile: params.sample_metafile) +include { generate_sce; generate_merged_sce; cellhash_demux_sce; genetic_demux_sce; post_process_sce} from './modules/sce-processing.nf' include { sce_to_anndata } from './modules/export-anndata.nf' include { annotate_celltypes } from './modules/classify-celltypes.nf' include { sce_qc_report } from './modules/qc-report.nf' @@ -164,7 +164,7 @@ workflow { rna_quant_ch = map_quant_rna.out .filter{it[0]["library_id"] in rna_only_libs.getVal()} // make rds for rna only - rna_sce_ch = generate_sce(rna_quant_ch) + rna_sce_ch = generate_sce(rna_quant_ch, file(params.sample_metafile)) // **** Process feature data **** @@ -177,7 +177,7 @@ workflow { .join(map_quant_rna.out.map{[it[0]["library_id"]] + it }, by: 0, failOnDuplicate: true, failOnMismatch: false) .map{it.drop(1)} // remove library_id index // make rds for merged RNA and feature quants - feature_sce_ch = generate_merged_sce(feature_rna_quant_ch) + feature_sce_ch = generate_merged_sce(feature_rna_quant_ch, file(params.sample_metafile)) .branch{ // branch cellhash libs cellhash: it[0]["feature_meta"]["technology"] in cellhash_techs single: true @@ -214,7 +214,7 @@ workflow { // Make channel for all library sce files all_sce_ch = sce_ch.no_genetic.mix(genetic_demux_sce.out) post_process_sce(all_sce_ch) - + // Cluster SCE and export RDS files to publishDir cluster_sce(post_process_sce.out) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 05603aa6..5598e3de 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -7,7 +7,7 @@ process make_unfiltered_sce{ tag "${meta.library_id}" input: tuple val(meta), path(alevin_dir), path(mito_file), path(ref_gtf) - path sample_meta_file + path sample_metafile output: tuple val(meta), path(unfiltered_rds) script: @@ -21,7 +21,7 @@ process make_unfiltered_sce{ --technology ${meta.technology} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ - --sample_metadata_file ${sample_meta_file} \ + --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} """ stub: @@ -41,6 +41,7 @@ process make_merged_unfiltered_sce{ tuple val(feature_meta), path(feature_alevin_dir), val (meta), path(alevin_dir), path(mito_file), path(ref_gtf) + path sample_metafile output: tuple val(meta), path(unfiltered_rds) script: @@ -65,6 +66,7 @@ process make_merged_unfiltered_sce{ --technology ${meta.technology} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ + --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} """ stub: @@ -194,12 +196,14 @@ process post_process_sce{ workflow generate_sce { // generate rds files for RNA-only samples - take: quant_channel + take: + quant_channel + sample_metafile main: sce_ch = quant_channel .map{it.toList() + [file(it[0].mito_file), file(it[0].ref_gtf)]} - make_unfiltered_sce(sce_ch, file(params.sample_metafile)) + make_unfiltered_sce(sce_ch, sample_metafile) empty_file = file("${projectDir}/assets/NO_FILE.txt") @@ -216,13 +220,15 @@ workflow generate_sce { workflow generate_merged_sce { // generate rds files for feature + quant samples // input is a channel with feature_meta, feature_quantdir, rna_meta, rna_quantdir - take: feature_quant_channel + take: + feature_quant_channel + sample_metafile main: feature_sce_ch = feature_quant_channel // RNA meta is in the third slot here .map{it.toList() + [file(it[2].mito_file), file(it[2].ref_gtf)]} - make_merged_unfiltered_sce(feature_sce_ch) + make_merged_unfiltered_sce(feature_sce_ch, sample_metafile) // append the feature barcode file unfiltered_merged_sce_ch = make_merged_unfiltered_sce.out From b1c2e5ee8d1ebf073c4bf810bafacb547aa47473 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 23 Aug 2023 09:29:43 -0500 Subject: [PATCH 085/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- main.nf | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 56f35cec..9701b474 100644 --- a/main.nf +++ b/main.nf @@ -51,7 +51,8 @@ if (!file(params.run_metafile).exists()) { param_error = true } -if (!file(params.sample_metafile).exists()) { +sample_metafile = file(params.sample_metafile) +if (!sample_metafile.exists()) { log.error("The 'sample_metafile' file '${params.sample_metafile}' can not be found.") param_error = true } @@ -164,7 +165,7 @@ workflow { rna_quant_ch = map_quant_rna.out .filter{it[0]["library_id"] in rna_only_libs.getVal()} // make rds for rna only - rna_sce_ch = generate_sce(rna_quant_ch, file(params.sample_metafile)) + rna_sce_ch = generate_sce(rna_quant_ch, sample_metafile) // **** Process feature data **** @@ -177,7 +178,7 @@ workflow { .join(map_quant_rna.out.map{[it[0]["library_id"]] + it }, by: 0, failOnDuplicate: true, failOnMismatch: false) .map{it.drop(1)} // remove library_id index // make rds for merged RNA and feature quants - feature_sce_ch = generate_merged_sce(feature_rna_quant_ch, file(params.sample_metafile)) + feature_sce_ch = generate_merged_sce(feature_rna_quant_ch, sample_metafile) .branch{ // branch cellhash libs cellhash: it[0]["feature_meta"]["technology"] in cellhash_techs single: true From e43c8b9a4e5961affba53470a94ad2b154290782 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 24 Aug 2023 15:11:03 -0500 Subject: [PATCH 086/268] rename library id column in sample metadata --- bin/generate_unfiltered_sce.R | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index b225570b..28fa8565 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -136,9 +136,10 @@ unfiltered_sce <- unfiltered_sce |> scuttle::addPerFeatureQCMetrics() # read in sample metadata and filter to sample ids -sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> +sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> # rename sample id column - dplyr::rename("sample_id" = "scpca_sample_id") + dplyr::rename("sample_id" = "scpca_sample_id", + "library_id" = "scpca_library_id") # add dataframe with sample metadata to sce metadata unfiltered_sce <- add_sample_metadata(sce = unfiltered_sce, From 22b64228c4f4ef137529958df0b4f3dd91205d24 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 24 Aug 2023 15:11:22 -0500 Subject: [PATCH 087/268] incorporate sample metadata to coldata --- bin/sce_to_anndata.R | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index ec3a9a65..c3c1a801 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -28,7 +28,7 @@ option_list <- list( make_option( opt_str = c("--output_feature_h5"), type = "character", - help = "path to output hdf5 file to store feature counts as AnnData object. + help = "path to output hdf5 file to store feature counts as AnnData object. Only used if the input SCE contains an altExp. Must end in .hdf5 or .h5" ) ) @@ -52,32 +52,41 @@ if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ # read in sce sce <- readr::read_rds(opt$input_sce_file) +# add library id as a column to the sce object +sce$library_id <- metadata(sce)$library_id + +# add sample metadata to sce +sce <- scpcaTools::metadata_to_coldata(sce, + batch_column = "library_id") +# remove sample metadata from metadata, otherwise conflicts with converting object +metadata(sce) <- metadata(sce)[!names(metadata(sce)) %in% "sample_metadata"] + # export sce as anndata object scpcaTools::sce_to_anndata( sce, anndata_file = opt$output_rna_h5 ) -# if feature data exists, grab it and export to AnnData +# if feature data exists, grab it and export to AnnData if(!is.null(opt$feature_name)){ - - # make sure the feature data is present + + # make sure the feature data is present if(!(opt$feature_name %in% altExpNames(sce))){ stop("feature_name must match name of altExp in provided SCE object.") } - - # check for output file + + # check for output file if(!(stringr::str_ends(opt$output_feature_h5, ".hdf5|.h5"))){ stop("output feature file name must end in .hdf5 or .h5") } - - # extract altExp + + # extract altExp alt_sce <- altExp(sce, opt$feature_name) - + # export altExp sce as anndata object scpcaTools::sce_to_anndata( alt_sce, anndata_file = opt$output_feature_h5 ) - + } From e2d3137f25333daee70857031d6cb80b45fbfd95 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 28 Aug 2023 16:52:38 -0500 Subject: [PATCH 088/268] reformat sample metadata before adding it --- bin/generate_unfiltered_sce.R | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 28fa8565..4a99f5df 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -113,7 +113,6 @@ unfiltered_sce <- read_alevin(quant_dir = opt$alevin_dir, library_id = opt$library_id, sample_id = sample_ids) - # read and merge feature counts if present if (opt$feature_dir != ""){ feature_sce <- read_alevin(quant_dir = opt$feature_dir, @@ -128,22 +127,25 @@ if (opt$feature_dir != ""){ altExp(unfiltered_sce, opt$feature_name) <- scuttle::addPerFeatureQCMetrics(altExp(unfiltered_sce, opt$feature_name)) } -# add per cell and per gene statistics to colData and rowData -unfiltered_sce <- unfiltered_sce |> - add_cell_mito_qc(mito = mito_genes) |> - # add gene symbols to rowData - add_gene_symbols(gene_info = gtf) |> - scuttle::addPerFeatureQCMetrics() # read in sample metadata and filter to sample ids sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> # rename sample id column - dplyr::rename("sample_id" = "scpca_sample_id", - "library_id" = "scpca_library_id") + dplyr::rename("sample_id" = "scpca_sample_id") |> + # add library ID as column in sample metadata + # we need this so we are able to merge sample metadata with colData later + dplyr::mutate(library_id = opt$library_id) |> + # remove upload date as we don't provide this on the portal + dplyr::select(-upload_date) -# add dataframe with sample metadata to sce metadata -unfiltered_sce <- add_sample_metadata(sce = unfiltered_sce, - metadata_df = sample_metadata_df) +# add per cell and per gene statistics to colData and rowData +unfiltered_sce <- unfiltered_sce |> + add_cell_mito_qc(mito = mito_genes) |> + # add gene symbols to rowData + add_gene_symbols(gene_info = gtf) |> + scuttle::addPerFeatureQCMetrics() |> + # add dataframe with sample metadata to sce metadata + add_sample_metadata(metadata_df = sample_metadata_df) # write to rds readr::write_rds(unfiltered_sce, opt$unfiltered_file, compress = "gz") From 4e5e541a3f727ca34f9959f936d9de8441119bd4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 28 Aug 2023 16:52:59 -0500 Subject: [PATCH 089/268] account for cite seq and skip anndata creation for cell hashing --- bin/sce_to_anndata.R | 22 +++++++++++++++++++--- main.nf | 7 +++++-- 2 files changed, 24 insertions(+), 5 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index c3c1a801..faf8b114 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -52,14 +52,17 @@ if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ # read in sce sce <- readr::read_rds(opt$input_sce_file) +# grab sample metadata +sample_metadata <- metadata(sce)$sample_metadata + # add library id as a column to the sce object sce$library_id <- metadata(sce)$library_id -# add sample metadata to sce +# add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, - batch_column = "library_id") + join_columns = "library_id") # remove sample metadata from metadata, otherwise conflicts with converting object -metadata(sce) <- metadata(sce)[!names(metadata(sce)) %in% "sample_metadata"] +metadata(sce) <- metadata(sce)[!metadata(sce) %in% sample_metadata] # export sce as anndata object scpcaTools::sce_to_anndata( @@ -83,6 +86,19 @@ if(!is.null(opt$feature_name)){ # extract altExp alt_sce <- altExp(sce, opt$feature_name) + # add library ID to colData + metadata(alt_sce)$library_id <- metadata(sce)$library_id + + # add sample metadata to alt sce metadata + metadata(alt_sce)$sample_metadata <- sample_metadata + + # add sample metadata to alt sce coldata + alt_sce <- scpcaTools::metadata_to_coldata(alt_sce, + join_columns = "library_id") + + # remove sample metadata from metadata, otherwise conflicts with converting object + metadata(sce) <- metadata(sce)[!metadata(sce) %in% sample_metadata] + # export altExp sce as anndata object scpcaTools::sce_to_anndata( alt_sce, diff --git a/main.nf b/main.nf index 9701b474..04679425 100644 --- a/main.nf +++ b/main.nf @@ -222,8 +222,11 @@ workflow { // generate QC reports sce_qc_report(cluster_sce.out, report_template_tuple) - // convert RNA component of SCE object to anndata - sce_to_anndata(post_process_sce.out) + // convert SCE object to anndata + // do this for everything but multiplexed libraries + anndata_ch = post_process_sce.out + .filter{!(it[0]["library_id"] in genetic_multiplex_libs.getVal())} + sce_to_anndata(anndata_ch) // **** Process Spatial Transcriptomics data **** spaceranger_quant(runs_ch.spatial) From 93cad76dbfbcd498665ccf1ec532cf783f7ec59b Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Tue, 29 Aug 2023 15:44:20 +0000 Subject: [PATCH 090/268] extract celltype column --- bin/classify_cellassign.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 02ba3f99..05a80ce2 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -69,7 +69,7 @@ celltype_assignments <- data.frame(barcode = sce$barcodes) |> dplyr::left_join(celltype_assignments, by = "barcode") # add cell type and prediction to colData -sce$cellassign_celltype_annotation <- celltype_assignments +sce$cellassign_celltype_annotation <- celltype_assignments$celltype sce$cellassign_max_prediction <- celltype_assignments$prediction # add entire predictions matrix and ref name to metadata From 64c30b947d0318d3b57feae3b3382388441250f5 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 12:47:46 -0400 Subject: [PATCH 091/268] initiate celltype qc report with tables --- templates/qc_report/celltypes_qc.rmd | 87 ++++++++++++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 templates/qc_report/celltypes_qc.rmd diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd new file mode 100644 index 00000000..949d37ab --- /dev/null +++ b/templates/qc_report/celltypes_qc.rmd @@ -0,0 +1,87 @@ +# Celltype annotation results + +This section details results from performing celltype annotation. +Two complementary methods were used to perform celltyping: + +* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. +The [`BlueprintEncode` reference](https://rdrr.io/github/LTLA/celldex/man/BlueprintEncodeData.html) from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) was used as the reference dataset. +This reference contains stroma and immune cells identified by Blueprint and Encode. +* [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. +Marker genes for celltyping were obtained from [PanglaoDB](https://panglaodb.se/). + +Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. + +If available, these results will be compared to celltype annotations provided by the data's originating research group. + +## Celltype annotation summary + +```{r} +# Create data frame of celltypes +celltype_df <- colData(processed_sce) |> + as.data.frame() |> + # barcodes to a column + tibble::rownames_to_column(var = "barcode") |> + # `celltype_cols` was defined in the main qc_report.rmd + dplyr::select(barcode, all_of(celltype_cols)) + + +# Define a helper function to create tables for singler and cellassign annotations +create_celltype_n_table <- function(df, celltype_column) { + df |> + # create column with better name + dplyr::rename(`Annotated celltype` = {{celltype_column}}) |> + # unified name for unknown cells + dplyr::mutate(`Annotated celltype` = ifelse( + # singler gives NA and cellassign (as we wrote it) gives "other" for unknown + is.na(`Annotated celltype`) | `Annotated celltype` == "other", + "Unknown cell type", + `Annotated celltype`) + ) |> + dplyr::count(`Annotated celltype`) |> + dplyr::arrange(-n) |> + # make this column a factor with unknown at the end + dplyr::mutate( + # Add percentage column + `Percent of cells` = paste0(round(n/sum(n) * 100, digits = 2), "%"), + # set column order in descending order of n, but with unknown at the end + `Annotated celltype` = forcats::fct_reorder(`Annotated celltype`, n, .desc=TRUE), + `Annotated celltype` = forcats::fct_relevel(`Annotated celltype`, + "Unknown cell type", + after = Inf) + ) |> + # arrange on `Annotated celltype` + dplyr::arrange(`Annotated celltype`) |> + # set column order + dplyr::select( + `Annotated celltype`, + `Number of cells` = n, + `Percent of cells` + ) |> + # kable formatting + knitr::kable(align = 'r') |> + kableExtra::kable_styling(bootstrap_options = "striped", + full_width = FALSE, + position = "left") |> + kableExtra::column_spec(2, monospace = TRUE) +} +``` + +##### `SingleR` + +```{r} +create_celltype_n_table(celltype_df, singler_celltype_annotation) +``` + + +##### `CellAssign` + +```{r} +create_celltype_n_table(celltype_df, cellassign_celltype_annotation) +``` + + +```{r, eval = has_submitter_celltypes} +asis_output("##### Submitter-provided annotations\n") +# TODO: check column name once submitter annotations are actually added to workflow +create_celltype_n_table(celltype_df, submitter_celltype_annotation) +``` \ No newline at end of file From 370b66401a08c2fd91e20f992a9cf909e2b7f99e Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 12:50:51 -0400 Subject: [PATCH 092/268] header size tweak --- templates/qc_report/celltypes_qc.rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 949d37ab..d601a747 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -11,7 +11,7 @@ Marker genes for celltyping were obtained from [PanglaoDB](https://panglaodb.se/ Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. -If available, these results will be compared to celltype annotations provided by the data's originating research group. +If available, these results will be compared to celltype annotations provided by the data's originating research group ("submitter-provided celltype annotations".) ## Celltype annotation summary @@ -66,14 +66,14 @@ create_celltype_n_table <- function(df, celltype_column) { } ``` -##### `SingleR` +### `SingleR` celltype annotations ```{r} create_celltype_n_table(celltype_df, singler_celltype_annotation) ``` -##### `CellAssign` +### `CellAssign` celltype annotations ```{r} create_celltype_n_table(celltype_df, cellassign_celltype_annotation) @@ -81,7 +81,7 @@ create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ```{r, eval = has_submitter_celltypes} -asis_output("##### Submitter-provided annotations\n") +asis_output("### Submitter-provided celltype annotations\n") # TODO: check column name once submitter annotations are actually added to workflow create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` \ No newline at end of file From 8c2401f817e5941e45a13ef0071c351457d77374 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 12:51:57 -0400 Subject: [PATCH 093/268] Add celltyping to be called from qc_report and set up has_celltypes variable --- templates/qc_report/qc_report.rmd | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 191cce7a..56f8e739 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -101,12 +101,25 @@ if (has_cellhash) { modalities <- c(modalities, "Multiplex") } -# check for umap, need to be sure that processed_sce exists first +# check for umap and celltypes, but need to be sure that processed_sce exists first +# for celltypes, we expect these four columns. +# TODO: do we need to check for all 4? +celltype_cols <- c("singler_celltype_ontology", + "singler_celltype_annotation", + "cellassign_celltype_annotation", + "cellassign_max_prediction") if (has_processed) { has_umap <- "UMAP" %in% reducedDimNames(processed_sce) + has_celltypes <- all(celltype_cols %in% names(colData(processed_sce))) + } else { has_umap <- FALSE + has_celltypes <- FALSE } + +# Note: later, we will also check for submitter-provided annotations +# for now, we will say this is false +has_submitter_celltypes <- FALSE ``` @@ -498,6 +511,11 @@ The raw counts from all cells that remain after filtering low quality cells (RNA ``` + +```{r, child='celltypes_qc.rmd', eval = has_celltypes} + +``` + # Session Info
From 7c1672eeec295b3066191fc8521f9f1cdc95ffa6 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 13:13:53 -0400 Subject: [PATCH 094/268] move up code that converts NA/other to unknown since we want the rest of the report to use it too; confirmed still knits the same --- templates/qc_report/celltypes_qc.rmd | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index d601a747..c8b36068 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -22,21 +22,26 @@ celltype_df <- colData(processed_sce) |> # barcodes to a column tibble::rownames_to_column(var = "barcode") |> # `celltype_cols` was defined in the main qc_report.rmd - dplyr::select(barcode, all_of(celltype_cols)) - - + dplyr::select(barcode, all_of(celltype_cols)) |> + # change NA/other to "Unknown cell type" + dplyr::mutate( + singler_celltype_annotation = ifelse( + is.na(singler_celltype_annotation), + "Unknown cell type", + singler_celltype_annotation + ), + cellassign_celltype_annotation = ifelse( + cellassign_celltype_annotation == "other", + "Unknown cell type", + cellassign_celltype_annotation + ) + ) + # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { df |> # create column with better name dplyr::rename(`Annotated celltype` = {{celltype_column}}) |> - # unified name for unknown cells - dplyr::mutate(`Annotated celltype` = ifelse( - # singler gives NA and cellassign (as we wrote it) gives "other" for unknown - is.na(`Annotated celltype`) | `Annotated celltype` == "other", - "Unknown cell type", - `Annotated celltype`) - ) |> dplyr::count(`Annotated celltype`) |> dplyr::arrange(-n) |> # make this column a factor with unknown at the end From 4bef14c561b92c1c838f3bd906aa5351689b27ac Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Tue, 29 Aug 2023 12:51:26 -0500 Subject: [PATCH 095/268] make sure library id is present in alt experiments --- bin/sce_to_anndata.R | 4 ++-- main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index faf8b114..b3baef61 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -62,7 +62,7 @@ sce$library_id <- metadata(sce)$library_id sce <- scpcaTools::metadata_to_coldata(sce, join_columns = "library_id") # remove sample metadata from metadata, otherwise conflicts with converting object -metadata(sce) <- metadata(sce)[!metadata(sce) %in% sample_metadata] +metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] # export sce as anndata object scpcaTools::sce_to_anndata( @@ -87,7 +87,7 @@ if(!is.null(opt$feature_name)){ alt_sce <- altExp(sce, opt$feature_name) # add library ID to colData - metadata(alt_sce)$library_id <- metadata(sce)$library_id + alt_sce$library_id <- metadata(sce)$library_id # add sample metadata to alt sce metadata metadata(alt_sce)$sample_metadata <- sample_metadata diff --git a/main.nf b/main.nf index 04679425..2243af5e 100644 --- a/main.nf +++ b/main.nf @@ -225,7 +225,7 @@ workflow { // convert SCE object to anndata // do this for everything but multiplexed libraries anndata_ch = post_process_sce.out - .filter{!(it[0]["library_id"] in genetic_multiplex_libs.getVal())} + .filter{!(it[0]["library_id"] in multiplex_libs.getVal())} sce_to_anndata(anndata_ch) // **** Process Spatial Transcriptomics data **** From a0b5b033f18353cfbcac71e483ce89162715c197 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 14:17:43 -0400 Subject: [PATCH 096/268] Add section for celltypes with 'draft-level' formatting --- templates/qc_report/celltypes_qc.rmd | 61 ++++++++++++++++++++++++++-- 1 file changed, 58 insertions(+), 3 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index c8b36068..3837c0b5 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -21,8 +21,9 @@ celltype_df <- colData(processed_sce) |> as.data.frame() |> # barcodes to a column tibble::rownames_to_column(var = "barcode") |> - # `celltype_cols` was defined in the main qc_report.rmd - dplyr::select(barcode, all_of(celltype_cols)) |> + # keep only cell name, celltyping, and clusters + # note that `celltype_cols` was defined in the main qc_report.rmd + dplyr::select(barcode, all_of(celltype_cols), clusters) |> # change NA/other to "Unknown cell type" dplyr::mutate( singler_celltype_annotation = ifelse( @@ -89,4 +90,58 @@ create_celltype_n_table(celltype_df, cellassign_celltype_annotation) asis_output("### Submitter-provided celltype annotations\n") # TODO: check column name once submitter annotations are actually added to workflow create_celltype_n_table(celltype_df, submitter_celltype_annotation) -``` \ No newline at end of file +``` + + +## Celltype annotations and clusters + +Below, we show heatmaps comparing celltype annotations (along the y-axis) to clustering results (along the x-axis). +Clusters were obtained using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. + +```{r} +# Helper function for making a heatmap +create_celltype_cluster_heatmap <- function(celltype_vector, + cluster_vector, + title) { + + # Ensure factor order: descending order with unknown at the end + celltype_vector <- celltype_vector |> + forcats::fct_infreq() |> + forcats::fct_relevel("Unknown cell type", after = Inf) + + # build a matrix with cluster identity as rows and celltype as columns + label_mtx <- table(celltype_vector, + cluster_vector, + useNA = "ifany") |> + log1p() # log transform for visualization + + # heatmap + ComplexHeatmap::pheatmap(label_mtx, + # TODO: cluster or specify row order based on number of cells? + cluster_rows = FALSE, + cluster_cols = FALSE, + row_order = rownames(label_mtx), # use factor levels + row_names_side = "left", # show cell type labels on left + fontsize_col = 12, # font size for clusters types + fontsize_row = 7, # font size for celltypes + angle_col = "0", # don't rotate column names (clusters) + heatmap_legend_param = list(title = "Log(Number of cells)", + legend_height = unit(4, "cm")), + main = title) +} +``` + + +```{r fig.height=5, fig.width=7} +create_celltype_cluster_heatmap( + celltype_df$singler_celltype_annotation, + celltype_df$clusters, + "SingleR annotations" +) + +create_celltype_cluster_heatmap( + celltype_df$cellassign_celltype_annotation, + celltype_df$clusters, + "CellAssign annotations" +) +``` From 33c60ef38b3d8eba7684e76e9265ba3a036e0f72 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 14:23:52 -0400 Subject: [PATCH 097/268] chunk for submitter annotations --- templates/qc_report/celltypes_qc.rmd | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 3837c0b5..cb508528 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -145,3 +145,13 @@ create_celltype_cluster_heatmap( "CellAssign annotations" ) ``` + +```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} +create_celltype_cluster_heatmap( + celltype_df$submitter_celltype_annotation, + celltype_df$clusters, + "Submitter-provided annotations" +) + +``` + From aa2d124102bbd45c622a632d740fa3362db0c0fc Mon Sep 17 00:00:00 2001 From: Stephanie Date: Tue, 29 Aug 2023 14:24:47 -0400 Subject: [PATCH 098/268] rm extra line --- templates/qc_report/celltypes_qc.rmd | 1 - 1 file changed, 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index cb508528..cd6e3451 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -152,6 +152,5 @@ create_celltype_cluster_heatmap( celltype_df$clusters, "Submitter-provided annotations" ) - ``` From 016878052fde8b818be2cb1eec9de2f514f71b01 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 09:41:08 -0400 Subject: [PATCH 099/268] Apply suggestions from code review Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- templates/qc_report/celltypes_qc.rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index c8b36068..2a45e8d0 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -1,4 +1,4 @@ -# Celltype annotation results +# Celltype Annotation Summary This section details results from performing celltype annotation. Two complementary methods were used to perform celltyping: @@ -13,7 +13,7 @@ Cells annotated as "Unknown cell type" represent cells which could not be confid If available, these results will be compared to celltype annotations provided by the data's originating research group ("submitter-provided celltype annotations".) -## Celltype annotation summary +## Celltype Annotation Statistics ```{r} # Create data frame of celltypes From 9afdabdc1e34b08b71f3b1089803a694652b7c38 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 09:43:05 -0400 Subject: [PATCH 100/268] Add metadata indicator variables that singler and cellassign are present. --- bin/classify_SingleR.R | 3 ++- bin/classify_cellassign.R | 4 +++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 2365753d..3c60dfcd 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -115,7 +115,8 @@ if (opt$label_name == "label.ont") { metadata(sce)$singler_results <- singler_results metadata(sce)$singler_reference <- singler_model$reference_name metadata(sce)$singler_reference_label <- singler_model$reference_label - +# add indicator variable that singler predictions are present +metadata(sce)$has_singler <- TRUE # export sce with annotations added readr::write_rds(sce, diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 02ba3f99..5fa3e140 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -75,6 +75,8 @@ sce$cellassign_max_prediction <- celltype_assignments$prediction # add entire predictions matrix and ref name to metadata metadata(sce)$cellassign_predictions <- predictions metadata(sce)$cellassign_reference <- opt$reference_name +# add indicator variable that cellassign predictions are present +metadata(sce)$has_cellassign <- TRUE -# export annotated object with cellassign assignments +# export annotated object with cellassign assignments readr::write_rds(sce, opt$output_sce_file) From b90b72c540fe1e890d2532b66ccae557d85bb934 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 09:47:04 -0400 Subject: [PATCH 101/268] Change check for celltypes to be the indicator columns --- templates/qc_report/qc_report.rmd | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 56f8e739..56907b05 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -102,16 +102,10 @@ if (has_cellhash) { } # check for umap and celltypes, but need to be sure that processed_sce exists first -# for celltypes, we expect these four columns. -# TODO: do we need to check for all 4? -celltype_cols <- c("singler_celltype_ontology", - "singler_celltype_annotation", - "cellassign_celltype_annotation", - "cellassign_max_prediction") if (has_processed) { has_umap <- "UMAP" %in% reducedDimNames(processed_sce) - has_celltypes <- all(celltype_cols %in% names(colData(processed_sce))) - + # these metadata fields are only present if celltyping has been performed: + has_celltypes <- all(c("has_singler", "has_cellassign") %in% names(metadata(processed_sce))) } else { has_umap <- FALSE has_celltypes <- FALSE From 8b18aab4345c80966c25c112565c8d7c2ec4d3e8 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 30 Aug 2023 08:47:17 -0500 Subject: [PATCH 102/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/sce_to_anndata.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index b3baef61..edc625e0 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -61,7 +61,7 @@ sce$library_id <- metadata(sce)$library_id # add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, join_columns = "library_id") -# remove sample metadata from metadata, otherwise conflicts with converting object +# remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] # export sce as anndata object From ebb74070a0baa8a0aef89a37b022b2724b32b2bb Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 09:50:38 -0400 Subject: [PATCH 103/268] Change check - should be separate for each method --- templates/qc_report/qc_report.rmd | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 56907b05..e9ba60a6 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -104,11 +104,14 @@ if (has_cellhash) { # check for umap and celltypes, but need to be sure that processed_sce exists first if (has_processed) { has_umap <- "UMAP" %in% reducedDimNames(processed_sce) + # these metadata fields are only present if celltyping has been performed: - has_celltypes <- all(c("has_singler", "has_cellassign") %in% names(metadata(processed_sce))) + has_singler <- "has_singler" %in% names(metadata(processed_sce)) + has_cellassign <- "has_cellassign" %in% names(metadata(processed_sce)) + } else { has_umap <- FALSE - has_celltypes <- FALSE + has_celltypes <- FALSE # use overall variable here for QC report logic } # Note: later, we will also check for submitter-provided annotations From 998b61bc2d457573275aa074656a87c6abbeb52e Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 10:26:03 -0400 Subject: [PATCH 104/268] Split up text with asis logic, and celltype -> cell type. Still needs some formatting --- templates/qc_report/celltypes_qc.rmd | 71 ++++++++++++++++------------ 1 file changed, 42 insertions(+), 29 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 2a45e8d0..89e5451d 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -1,28 +1,43 @@ -# Celltype Annotation Summary +# Cell type Annotation Summary -This section details results from performing celltype annotation. -Two complementary methods were used to perform celltyping: +This section details results from performing cell type annotation. +The following method(s) were used to perform cell typing: + + +```{r, eval = has_singler} +knitr::asis_output( +" * [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. -The [`BlueprintEncode` reference](https://rdrr.io/github/LTLA/celldex/man/BlueprintEncodeData.html) from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) was used as the reference dataset. -This reference contains stroma and immune cells identified by Blueprint and Encode. +The folllowing reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used: +") +metadata(processed_sce)$singler_reference # TODO: format?? +``` + +```{r, eval = has_cellassign} +knitr::asis_output( +" * [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. Marker genes for celltyping were obtained from [PanglaoDB](https://panglaodb.se/). +") +``` + Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. -If available, these results will be compared to celltype annotations provided by the data's originating research group ("submitter-provided celltype annotations".) +If available, these results will be compared to cell type annotations provided by the data's originating research group ("submitter-provided cell type annotations".) -## Celltype Annotation Statistics +## Cell type Annotation Statistics ```{r} -# Create data frame of celltypes +# Create data frame of cell types celltype_df <- colData(processed_sce) |> as.data.frame() |> # barcodes to a column tibble::rownames_to_column(var = "barcode") |> - # `celltype_cols` was defined in the main qc_report.rmd - dplyr::select(barcode, all_of(celltype_cols)) |> + dplyr::select(barcode, + contains("singler"), + contains("cellassign")) |> # change NA/other to "Unknown cell type" dplyr::mutate( singler_celltype_annotation = ifelse( @@ -40,25 +55,24 @@ celltype_df <- colData(processed_sce) |> # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { df |> - # create column with better name - dplyr::rename(`Annotated celltype` = {{celltype_column}}) |> - dplyr::count(`Annotated celltype`) |> - dplyr::arrange(-n) |> + # rename column with user-facing name + dplyr::rename(`Annotated cell type` = {{celltype_column}}) |> + dplyr::count(`Annotated cell type`) |> # make this column a factor with unknown at the end dplyr::mutate( # Add percentage column `Percent of cells` = paste0(round(n/sum(n) * 100, digits = 2), "%"), # set column order in descending order of n, but with unknown at the end - `Annotated celltype` = forcats::fct_reorder(`Annotated celltype`, n, .desc=TRUE), - `Annotated celltype` = forcats::fct_relevel(`Annotated celltype`, + `Annotated cell type` = forcats::fct_reorder(`Annotated cell type`, n, .desc=TRUE), + `Annotated cell type` = forcats::fct_relevel(`Annotated cell type`, "Unknown cell type", after = Inf) ) |> - # arrange on `Annotated celltype` - dplyr::arrange(`Annotated celltype`) |> + # arrange on `Annotated cell type` now that factor levels have been specified + dplyr::arrange(`Annotated cell type`) |> # set column order dplyr::select( - `Annotated celltype`, + `Annotated cell type`, `Number of cells` = n, `Percent of cells` ) |> @@ -71,22 +85,21 @@ create_celltype_n_table <- function(df, celltype_column) { } ``` -### `SingleR` celltype annotations -```{r} + +```{r, eval = has_singler} +knitr::asis_output("### `SingleR` cell type annotations\n") create_celltype_n_table(celltype_df, singler_celltype_annotation) ``` - -### `CellAssign` celltype annotations - -```{r} +```{r, eval = has_cellassign} +knitr::asis_output("### `CellAssign` cell type annotations\n") create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ``` - ```{r, eval = has_submitter_celltypes} -asis_output("### Submitter-provided celltype annotations\n") -# TODO: check column name once submitter annotations are actually added to workflow +knitr::asis_output("### Submitter-provided cell type annotations\n") +# Note: submitter annotations have not yet been added to the workflow, +# so this variable name `submitter_celltype_annotation` is just a placeholder create_celltype_n_table(celltype_df, submitter_celltype_annotation) -``` \ No newline at end of file +``` From 1a2d53c3df0f059c96c513bb1e4bc37448186362 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 10:26:35 -0400 Subject: [PATCH 105/268] fix has_celltypes variable --- templates/qc_report/qc_report.rmd | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index e9ba60a6..e9d25f7a 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -108,10 +108,14 @@ if (has_processed) { # these metadata fields are only present if celltyping has been performed: has_singler <- "has_singler" %in% names(metadata(processed_sce)) has_cellassign <- "has_cellassign" %in% names(metadata(processed_sce)) + if (has_singler | has_cellassign) { + # use overall variable here for QC report logic + has_celltypes <- TRUE + } } else { has_umap <- FALSE - has_celltypes <- FALSE # use overall variable here for QC report logic + has_celltypes <- FALSE } # Note: later, we will also check for submitter-provided annotations From 6d2b20fce81c2660a55166ca8e92ea16c9d4a09f Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 10:46:55 -0400 Subject: [PATCH 106/268] Much better print formatting for asis parts using glue::glue --- templates/qc_report/celltypes_qc.rmd | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 89e5451d..464e4581 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -7,19 +7,22 @@ The following method(s) were used to perform cell typing: ```{r, eval = has_singler} knitr::asis_output( -" -* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. -The folllowing reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used: -") -metadata(processed_sce)$singler_reference # TODO: format?? + glue::glue( + "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. + The `{metadata(processed_sce)$singler_reference}` reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used for cell typing." + ) +) ``` + ```{r, eval = has_cellassign} knitr::asis_output( -" -* [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. -Marker genes for celltyping were obtained from [PanglaoDB](https://panglaodb.se/). -") + glue::glue( + " + * [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. + Marker genes associated with `{metadata(processed_sce)$cellassign_reference}` tissue were obtained from [PanglaoDB](https://panglaodb.se/). + ") +) ``` From 5d8b746172dd30df504bf00a3925efff729afbcb Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 30 Aug 2023 09:50:30 -0500 Subject: [PATCH 107/268] check names of metadata --- bin/sce_to_anndata.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index edc625e0..50857907 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -97,7 +97,7 @@ if(!is.null(opt$feature_name)){ join_columns = "library_id") # remove sample metadata from metadata, otherwise conflicts with converting object - metadata(sce) <- metadata(sce)[!metadata(sce) %in% sample_metadata] + metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] # export altExp sce as anndata object scpcaTools::sce_to_anndata( From 88b63d93e9d06a9e6d81e628a24ad3d03448e3da Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 11:56:54 -0400 Subject: [PATCH 108/268] Overhaul heatmap code to use ComplexHeatmap, including using hierarchical clustering --- templates/qc_report/celltypes_qc.rmd | 75 +++++++++++++++------------- 1 file changed, 41 insertions(+), 34 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 41be4447..0fe507d5 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -110,63 +110,70 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` -## Celltype annotations and clusters +## Cell type annotations and clusters -Below, we show heatmaps comparing celltype annotations (along the y-axis) to clustering results (along the x-axis). +Below, we show heat maps comparing cell type annotations (along the y-axis) to clustering results (along the x-axis). Clusters were obtained using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. ```{r} # Helper function for making a heatmap create_celltype_cluster_heatmap <- function(celltype_vector, - cluster_vector, - title) { + cluster_vector) { - # Ensure factor order: descending order with unknown at the end - celltype_vector <- celltype_vector |> - forcats::fct_infreq() |> - forcats::fct_relevel("Unknown cell type", after = Inf) - - # build a matrix with cluster identity as rows and celltype as columns - label_mtx <- table(celltype_vector, - cluster_vector, - useNA = "ifany") |> - log1p() # log transform for visualization + # build a matrix with cluster identity as rows and celltype as columns + celltype_cluster_mtx <- table(celltype_vector, + cluster_vector) |> + log1p() # log transform for visualization - # heatmap - ComplexHeatmap::pheatmap(label_mtx, - # TODO: cluster or specify row order based on number of cells? - cluster_rows = FALSE, - cluster_cols = FALSE, - row_order = rownames(label_mtx), # use factor levels - row_names_side = "left", # show cell type labels on left - fontsize_col = 12, # font size for clusters types - fontsize_row = 7, # font size for celltypes - angle_col = "0", # don't rotate column names (clusters) - heatmap_legend_param = list(title = "Log(Number of cells)", - legend_height = unit(4, "cm")), - main = title) + # Define CVD-friendly palette + # TODO: what palette? + heatmap_palette <- RColorBrewer::brewer.pal(n = 7, name = "BrBG") + + # heatmap + heat <- ComplexHeatmap::Heatmap(celltype_cluster_mtx, + # Overall heatmap parameters + col = heatmap_palette, + # Column parameters + column_title = "Clusters", + column_title_side = "bottom", + column_dend_side = "top", + column_names_rot = 0, + # Row parameters + row_dend_side = "left", + row_names_gp = grid::gpar(fontsize = 8), + # Legend parameters + heatmap_legend_param = list( + title = "Log(Number of cells)", + title_position = "leftcenter-rot", + legend_height = unit(4, "cm") + ) + ) + # draw with legend on left for spacing + ComplexHeatmap::draw(heat, heatmap_legend_side = "left") } ``` -```{r fig.height=5, fig.width=7} +```{r, eval = has_singler, fig.height=5, fig.width=7} +knitr::asis_output("### `SingleR` cluster and cell type heatmap\n") create_celltype_cluster_heatmap( celltype_df$singler_celltype_annotation, - celltype_df$clusters, - "SingleR annotations" + celltype_df$clusters ) +``` +```{r, eval = has_cellassign, fig.height=5, fig.width=7} +knitr::asis_output("### `CellAssign` cluster and cell type heatmap\n") create_celltype_cluster_heatmap( celltype_df$cellassign_celltype_annotation, - celltype_df$clusters, - "CellAssign annotations" + celltype_df$clusters ) ``` ```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} +knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") create_celltype_cluster_heatmap( celltype_df$submitter_celltype_annotation, - celltype_df$clusters, - "Submitter-provided annotations" + celltype_df$clusters ) ``` From d09acee2b125540632fa6bf6c88ed3db6d2a309c Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 12:09:25 -0400 Subject: [PATCH 109/268] change approach to cell type method indicator in metadata --- bin/classify_SingleR.R | 8 ++++++-- bin/classify_cellassign.R | 7 +++++-- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index 3c60dfcd..e1966069 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -115,8 +115,12 @@ if (opt$label_name == "label.ont") { metadata(sce)$singler_results <- singler_results metadata(sce)$singler_reference <- singler_model$reference_name metadata(sce)$singler_reference_label <- singler_model$reference_label -# add indicator variable that singler predictions are present -metadata(sce)$has_singler <- TRUE + +# add singler as celltype method +# note that if `metadata(sce)$celltype_methods` doesn't exist yet, this will +# come out to just the string "singler" +metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "singler") + # export sce with annotations added readr::write_rds(sce, diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 0add3796..8b7a9c18 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -75,8 +75,11 @@ sce$cellassign_max_prediction <- celltype_assignments$prediction # add entire predictions matrix and ref name to metadata metadata(sce)$cellassign_predictions <- predictions metadata(sce)$cellassign_reference <- opt$reference_name -# add indicator variable that cellassign predictions are present -metadata(sce)$has_cellassign <- TRUE + +# add cellassign as celltype method +# note that if `metadata(sce)$celltype_methods` doesn't exist yet, this will +# come out to just the string "cellassign" +metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "cellassign") # export annotated object with cellassign assignments readr::write_rds(sce, opt$output_sce_file) From 6824e7aa6dec65536502cc4c21a8ec7ebaa0097c Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 12:19:54 -0400 Subject: [PATCH 110/268] update check for presence of celltypes in processed sce to use the celltype_methods metadata vector --- templates/qc_report/qc_report.rmd | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index e9d25f7a..b3700f1c 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -105,10 +105,15 @@ if (has_cellhash) { if (has_processed) { has_umap <- "UMAP" %in% reducedDimNames(processed_sce) - # these metadata fields are only present if celltyping has been performed: - has_singler <- "has_singler" %in% names(metadata(processed_sce)) - has_cellassign <- "has_cellassign" %in% names(metadata(processed_sce)) - if (has_singler | has_cellassign) { + has_singler <- "singler" %in% metadata(processed_sce)$celltype_methods + has_cellassign <- "cellassign" %in% metadata(processed_sce)$celltype_methods + + # Note: later, we will also check for submitter-provided annotations + # for now, we will say this is false + has_submitter_celltypes <- FALSE + + # If at least 1 is present, we have cell type annotations. + if ( any(c(has_singler, has_cellassign, has_submitter_celltypes))) { # use overall variable here for QC report logic has_celltypes <- TRUE } @@ -117,10 +122,6 @@ if (has_processed) { has_umap <- FALSE has_celltypes <- FALSE } - -# Note: later, we will also check for submitter-provided annotations -# for now, we will say this is false -has_submitter_celltypes <- FALSE ``` From 9ee5ff95d6e0148ac3431fdd0b721a81cb13fe6e Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 12:24:07 -0400 Subject: [PATCH 111/268] use if blocks for changing singler and cellassign unknown values --- templates/qc_report/celltypes_qc.rmd | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 464e4581..c167ecde 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -40,20 +40,29 @@ celltype_df <- colData(processed_sce) |> tibble::rownames_to_column(var = "barcode") |> dplyr::select(barcode, contains("singler"), - contains("cellassign")) |> - # change NA/other to "Unknown cell type" + contains("cellassign")) + +# Reformat NA (singler) and other (cellassign) to "Unknown cell type" +if (has_singler) { +celltype_df <- celltype_df |> dplyr::mutate( singler_celltype_annotation = ifelse( is.na(singler_celltype_annotation), "Unknown cell type", singler_celltype_annotation - ), + ) + ) +} +if (has_cellassign) { + celltype_df <- celltype_df |> + dplyr::mutate( cellassign_celltype_annotation = ifelse( cellassign_celltype_annotation == "other", "Unknown cell type", cellassign_celltype_annotation ) ) +} # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { From 911a1d5de303fb1e5cc336914f5137641fd55b77 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 12:49:47 -0400 Subject: [PATCH 112/268] Add spell check script for our file types and add workflow --- .github/workflows/spell-check.yml | 43 +++++++++++++++++++++++++++++++ components/dictionary.txt | 36 ++++++++++++++++++++++++++ scripts/spell-check.R | 28 ++++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 .github/workflows/spell-check.yml create mode 100644 components/dictionary.txt create mode 100644 scripts/spell-check.R diff --git a/.github/workflows/spell-check.yml b/.github/workflows/spell-check.yml new file mode 100644 index 00000000..a823c039 --- /dev/null +++ b/.github/workflows/spell-check.yml @@ -0,0 +1,43 @@ + +name: Spell check R Markdown and Markdown files + +# Controls when the action will run. +# Pull requests to development and main only. +on: + pull_request: + branches: + - development + - main + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "spell check" + spell-check: + runs-on: ubuntu-latest + container: + image: rocker/tidyverse:4.2.3 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + - uses: actions/checkout@v3 + + - name: Install packages + run: Rscript --vanilla -e "install.packages(c('spelling'), repos = c(CRAN = '$CRAN'))" + + - name: Run spell check + id: spell_check_run + run: | + results=$(Rscript --vanilla "scripts/spell-check.R") + echo "sp_chk_results=$results" >> $GITHUB_OUTPUT + cat spell_check_errors.tsv + + - name: Archive spelling errors + uses: actions/upload-artifact@v3 + with: + name: spell-check-results + path: spell_check_errors.tsv + + # If there are too many spelling errors, this will stop the workflow + - name: Check spell check results - fail if too many errors + if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }} + run: exit 1 diff --git a/components/dictionary.txt b/components/dictionary.txt new file mode 100644 index 00000000..bc1d3fb1 --- /dev/null +++ b/components/dictionary.txt @@ -0,0 +1,36 @@ +alevin +ALSF +AMI +barcode +cDNA +cellhash +config +customizable +demultiplexed +demultiplexing +Dockerfile +Ensembl +fastq +FASTQ +Github +glioblastoma +GRCh +HPC +intronic +nextflow +Nextflow +Nextflow's +nf +PanglaoDB +parallelizing +pre +reproducibly +scpca +ScPCA +transcriptome +transcriptomic +trancriptomics +TSV +UMAP +uri +Visium diff --git a/scripts/spell-check.R b/scripts/spell-check.R new file mode 100644 index 00000000..502b58db --- /dev/null +++ b/scripts/spell-check.R @@ -0,0 +1,28 @@ +#!/usr/bin/env Rscript +# +# Run spell check and save results +# Adapted from: https://github.com/AlexsLemonade/refinebio-examples/blob/33cdeff66d57f9fe8ee4fcb5156aea4ac2dce07f/scripts/spell-check.R + +# Find .git root directory +root_dir <- rprojroot::find_root(rprojroot::has_dir(".git")) + +# Read in dictionary +dictionary <- readLines(file.path(root_dir, 'components', 'dictionary.txt')) + +# Add emoji to dictionary +dictionary <- c(dictionary, spelling::spell_check_text("⚠️")$word) + +# The only files we want to check are R Markdown and Markdown files +files <- list.files(pattern = '\\.(Rmd|md|rmd)$', recursive = TRUE, full.names = TRUE) + +# Run spell check +spelling_errors <- spelling::spell_check_files(files, ignore = dictionary) |> + data.frame() |> + tidyr::unnest(cols = found) |> + tidyr::separate(found, into = c("file", "lines"), sep = ":") + +# Print out how many spell check errors +write(nrow(spelling_errors), stdout()) + +# Save spell errors to file temporarily +readr::write_tsv(spelling_errors, 'spell_check_errors.tsv') From 599c9d6179fb64f88c058aa32e675372374cdd6e Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 12:50:21 -0400 Subject: [PATCH 113/268] Add dictionary based on running spell check, and fix spelling errors along the way --- components/dictionary.txt | 12 +++++ external-instructions.md | 16 +++--- internal-instructions.md | 2 +- templates/qc_report/cite_qc.rmd | 88 ++++++++++++++++----------------- 4 files changed, 65 insertions(+), 53 deletions(-) diff --git a/components/dictionary.txt b/components/dictionary.txt index bc1d3fb1..e0bf9e2e 100644 --- a/components/dictionary.txt +++ b/components/dictionary.txt @@ -1,3 +1,6 @@ +ADT +ADTs +al alevin ALSF AMI @@ -6,21 +9,29 @@ cDNA cellhash config customizable +data's demultiplexed demultiplexing Dockerfile +embeddings Ensembl +et fastq FASTQ Github glioblastoma GRCh +Hippen +HTOs HPC intronic +Lun +miQC nextflow Nextflow Nextflow's nf +Oligos PanglaoDB parallelizing pre @@ -32,5 +43,6 @@ transcriptomic trancriptomics TSV UMAP +UMI uri Visium diff --git a/external-instructions.md b/external-instructions.md index ab5ab4f4..14703a5b 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -33,7 +33,7 @@ Here we provide an overview of the steps you will need to complete: 1. **Install the necessary dependencies.** You will need to make sure you have the following software installed on your HPC where you plan to execute the workflow: - - [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation), the main workflow engine that scpca-nf relies on. + - [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation), the main workflow engine that `scpca-nf` relies on. This can be downloaded and installed by any user, with minimal external requirements. - [Docker](https://docs.docker.com/get-docker/) or [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html#installation), which allows the use of container images that encapsulate other dependencies used by the workflow reproducibly. These usually require installation by system administrators, but most HPC systems have one available (usually Singularity). @@ -53,7 +53,7 @@ See the [section below on preparing a metadata file](#prepare-the-metadata-file) Create a configuration file that stores user defined parameters and a profile indicating the system and other system related settings to use for executing the workflow. See the [section below on configuring `scpca-nf` for your environment](#configuring-scpca-nf-for-your-environment) for more information on setting up the configuration files to run Nextflow on your system. -The standard configuration the `scpca-nf` workflow expects that compute nodes will have direct access to the internet, and will download reference files and container images with ane required software as required. +The standard configuration the `scpca-nf` workflow expects that compute nodes will have direct access to the internet, and will download reference files and container images with any required software as required. If your HPC system does not allow internet access from compute nodes, you will need to download the required reference files and software before running, [following the instructions we have provided](#using-scpca-nf-on-nodes-without-direct-internet-access). Once you have set up your environment and created the metadata and configuration files, you will be able to start your run as follows, adding any additional optional parameters that you may choose: @@ -72,7 +72,7 @@ Using the above command will run the workflow from the `main` branch of the work To update to the latest released version you can run `nextflow pull AlexsLemonade/scpca-nf` before the `nextflow run` command. To be sure that you are using a consistent version, you can specify use of a release tagged version of the workflow, set below with the `-r` flag. -Released versions can be found on the [`scpca-nf` repo releases page](https://github.com/AlexsLemonade/scpca-nf/releases). +Released versions can be found on the [`scpca-nf` repository releases page](https://github.com/AlexsLemonade/scpca-nf/releases). ```sh nextflow run AlexsLemonade/scpca-nf \ @@ -89,7 +89,7 @@ For a complete description of the expected output files, see the section describ You will need to have files organized so that all the sequencing files for each library are in their own directory or folder. Each folder should be named with a unique ID, corresponding to the [`scpca_run_id` column of the metadata file](#prepare-the-metadata-file). Any sequencing runs that contain multiple libraries must be demultiplexed and FASTQ files must be placed into separate distinct folders, with distinct run IDs as the folder name. -If the same sequencing library was sequenced across multiple flowcells (e.g., to increase coverage), all FASTQ files should be combined into the same folder. +If the same sequencing library was sequenced across multiple flow cells (e.g., to increase coverage), all FASTQ files should be combined into the same folder. If a library has a corresponding CITE-seq library and therefore a separate set of FASTQ files, the FASTQ files corresponding to the CITE-seq library should be in their own folder, with a unique run ID. ## Prepare the metadata file @@ -215,13 +215,13 @@ We encourage you to read the official Nextflow instructions for [running pipelin To run `scpca-nf`, you will need to set up at least one batch queue and an associated compute environment configured with a custom Amazon Machine Image (AMI) prepared according to the [Nextflow instructions](https://www.nextflow.io/docs/latest/awscloud.html#custom-ami). You will also need an [S3 bucket](https://aws.amazon.com/s3/) path to use as the Nextflow `work` directory for intermediate files. -As the intermediate files can get quite large, you will likely want to set up a [lifecycle rule](https://docs.aws.amazon.com/AmazonS3/latest/userguide/object-lifecycle-mgmt.html) to delete files from this location after a fixed period of time (e.g., 30 days). +As the intermediate files can get quite large, you will likely want to set up a [life cycle rule](https://docs.aws.amazon.com/AmazonS3/latest/userguide/object-lifecycle-mgmt.html) to delete files from this location after a fixed period of time (e.g., 30 days). In most Batch queue setups, each AWS compute node has a fixed amount of disk space. We found it useful to have two queues: one for general use and one for jobs that may require larger amounts of disk space. The two compute environments use the same AMI, but use [Launch Templates](https://docs.aws.amazon.com/batch/latest/userguide/launch-templates.html) to configure the nodes on launch with different amounts of disk space. -Currently, our default queue is configured with a disk size of 128 GB for each node, and our "bigdisk" queue has 1000 GB of disk space. +Currently, our default queue is configured with a disk size of 128 GB for each node, and our `"bigdisk"` queue has 1000 GB of disk space. The queue used by each process is determined by Nextflow labels and associated profile settings. The Data Lab's [AWS Batch config file](https://github.com/AlexsLemonade/scpca-nf/blob/main/config/profile_awsbatch.config) may be helpful as a reference for creating a profile for use with AWS, but note that the queues and file locations listed there are not publicly available, so these will need to be set to different values your own profile. @@ -267,7 +267,7 @@ The `ref_rootdir` parameter should *only* be specified in a parameter file or at #### Additional reference files -If you wil be performing genetic demultiplexing for hashed samples, you will need STAR index files as well as the ones included by default. +If you will be performing genetic demultiplexing for hashed samples, you will need STAR index files as well as the ones included by default. To obtain these files, you can add the `--star_index` flag: ```sh @@ -343,7 +343,7 @@ TAG03 GTAGCTCCAA target ``` If this third column is not provided, all antibodies will be treated as targets. -Similarly, if information in this column is _not_ one of the allowed values, a warning will be printed, and the given antibody/ies will be treated as target(s). +Similarly, if information in this column is _not_ one of the allowed values, a warning will be printed, and the given antibodies will be treated as target(s). If there are negative control antibodies, these will be taken into account during post-processing filtering and normalization. Positive controls are currently unused, but if provided, this label will be included in final output files. diff --git a/internal-instructions.md b/internal-instructions.md index a70e4333..936868ae 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -84,7 +84,7 @@ This file is required as input to the `build-celltype-ref.nf` workflow, which wi Follow the below steps to add support for additional references: 1. Download the desired `fasta` and `gtf` files for the organism of choice from `Ensembl`. -Add these to the `S3://scpca-references` bucket with the following directory structure, where the root directory here corresponds to the `organism` and the subdirectory corresponds to the ensembl `version`: +Add these to the `S3://scpca-references` bucket with the following directory structure, where the root directory here corresponds to the `organism` and the subdirectory corresponds to the `Ensembl` version: ``` homo_sapiens diff --git a/templates/qc_report/cite_qc.rmd b/templates/qc_report/cite_qc.rmd index 4f957a2a..bdcb9ffc 100644 --- a/templates/qc_report/cite_qc.rmd +++ b/templates/qc_report/cite_qc.rmd @@ -41,7 +41,7 @@ antibody_tags <- as.data.frame(rowData(adt_exp)) |> tibble::rownames_to_column("Antibody") |> # ensure `target` is the first level of target_type mutate(target_type = forcats::fct_relevel(target_type, "target")) |> - arrange(target_type, desc(mean)) |> + arrange(target_type, desc(mean)) |> select("Antibody", "Mean UMI count per cell" = mean, "Percent of cells detected" = detected, @@ -51,7 +51,7 @@ knitr::kable(antibody_tags, digits = 2) |> kableExtra::kable_styling(bootstrap_options = c("striped", "condensed"), full_width = FALSE, position = "left", - ) + ) ``` ## ADT Post-processing Statistics @@ -59,14 +59,14 @@ knitr::kable(antibody_tags, digits = 2) |> ```{r} if (has_processed) { - + basic_statistics <- tibble::tibble( "Method used to identify cells to filter" = format(processed_meta$adt_scpca_filter_method) ) - + if (!(processed_meta$adt_scpca_filter_method == "No filter")) { filtered_cell_count <- sum(processed_sce$adt_scpca_filter == "Keep") - + basic_statistics <- basic_statistics |> # Note that the adt_scpca_filter_method column is only present in the processed_sce object mutate("Number of cells that pass filtering threshold" = format(filtered_cell_count), @@ -77,7 +77,7 @@ if (has_processed) { mutate("Normalization method" = format(processed_meta$adt_normalization)) |> reformat_nulls() |> t() - + knitr::kable(basic_statistics, align = 'r') |> kableExtra::kable_styling(bootstrap_options = "striped", full_width = FALSE, @@ -99,22 +99,22 @@ if (has_processed) { ```{r fig.alt="Cell filtering based on both ADT and RNA counts", results='asis'} -if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { - +if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { + glue::glue(' - + Note that low-quality cells as identified by ADT counts are not actually filtered from the SCE object. Instead, cells that passed the filter threshold are labeled as `"Keep"` within the SCE object, and conversely cells that failed to pass the filtered are labeled as `"Remove"`. The plot below displays an overall view of cell filtering based on both ADT and RNA counts. Cells are labeled as one of the following: - + - "Keep": This cell is retained based on both RNA and ADT counts. - "Filter (RNA only)": This cell is filtered based on only RNA counts. - "Filter (ADT only)": This cell is filtered based on only ADT counts. - "Filter (RNA & ADT)": This cell is filtered based on both RNA and ADT counts. - + ') |> print() - + filter_levels <- c("Keep", "Filter (RNA & ADT)", "Filter (RNA only)", "Filter (ADT only)") filtered_coldata_df <- filtered_coldata_df |> # add column to represent filtering on both RNA and ADT counts @@ -128,11 +128,11 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { # now, add a count to each label and factor in count order # add `keep_column` for use in plotting for colors add_count(filter_summary) |> - mutate(filter_summary = glue::glue("{filter_summary}\nN={n}"), - filter_summary = forcats::fct_infreq(filter_summary), + mutate(filter_summary = glue::glue("{filter_summary}\nN={n}"), + filter_summary = forcats::fct_infreq(filter_summary), keep_column = ifelse( - stringr::str_starts(filter_summary, "Keep"), - "Keep", + stringr::str_starts(filter_summary, "Keep"), + "Keep", "Remove" )) |> select(-n) @@ -141,7 +141,7 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { stop("Processing error when evaluating CITE-seq filtering.") } - + ggplot(filtered_coldata_df, aes(x = detected, y = subsets_mito_percent, color = keep_column)) + geom_point(alpha = 0.5, size = 1) + geom_vline(xintercept = min_gene_cutoff, linetype = "dashed") + @@ -149,7 +149,7 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { y = "Mitochondrial percentage", title = "Combined RNA and ADT filters") + facet_wrap(vars(filter_summary)) + - theme(plot.title = element_text(hjust = 0.5), + theme(plot.title = element_text(hjust = 0.5), legend.position = "none") } else { glue::glue(" @@ -166,20 +166,20 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { ## Expression of highly variable ADTs -The plots in this section visualize the top four most variable ADTS in the library. +The plots in this section visualize the top four most variable ADTs in the library. ```{r} # Calculate ADT variance if (has_processed) { - + top_n <- 4 # we want the top 4 ADTs # Calculate variance for each ADT adt_var <- altExp(processed_sce) |> logcounts() |> - apply(1, var, na.rm=TRUE) - + apply(1, var, na.rm=TRUE) + # Get the top 4 top_adts <- adt_var[ order(adt_var, decreasing=TRUE)[1:top_n] ] |> names() @@ -201,12 +201,12 @@ if (has_processed) { ```{r fig.alt="Density plot showing normalized expression of highly variable ADTs", warning = FALSE, results='asis'} if (has_processed) { - + glue::glue( "The plot below displays normalized expression of these four ADTs, with one ADT shown per panel.\n" - ) |> print() + ) |> print() + - # grab expression for top ADTs from counts var_adt_exp_df <- logcounts(altExp(processed_sce))[top_adts,] |> # as.matrix needs to come _first_ @@ -214,52 +214,52 @@ if (has_processed) { t() |> as.data.frame() |> tibble::rownames_to_column("barcode") |> - # combine all ADTs into a single column for faceting + # combine all ADTs into a single column for faceting tidyr::pivot_longer(!barcode, names_to = "ADT", values_to = "adt_expression") - + # expression density plots - ggplot(var_adt_exp_df, aes(x = adt_expression, fill = ADT)) + - geom_density() + + ggplot(var_adt_exp_df, aes(x = adt_expression, fill = ADT)) + + geom_density() + facet_wrap(vars(ADT), nrow = 2) + labs(x = "Log-normalized ADT expression") + - theme(legend.position = "none") -} + theme(legend.position = "none") +} ``` ```{r fig.alt="UMAP calculated from RNA expression but colored by normalized expression of highly variable ADTs", fig.height = 6, results='asis'} if (has_processed) { - + # Extra blank line here keeps the plot in a separate paragraph glue::glue( "The plot below displays UMAP embeddings calculated from RNA expression, where each cell is colored by the expression level of the given ADT. - + " - ) |> print() + ) |> print() - - # create data frame of UMAPs and expression + + # create data frame of UMAPs and expression umap_df <- scuttle::makePerCellDF(processed_sce) |> tibble::rownames_to_column("barcode") |> - select(barcode, - UMAP1 = UMAP.1, - UMAP2 = UMAP.2) |> + select(barcode, + UMAP1 = UMAP.1, + UMAP2 = UMAP.2) |> # combine with gene expression left_join(var_adt_exp_df, by = "barcode") - - ggplot(umap_df, aes(x = UMAP1, y = UMAP2, color = adt_expression)) + - geom_point(alpha = 0.1, size = 0.1) + + + ggplot(umap_df, aes(x = UMAP1, y = UMAP2, color = adt_expression)) + + geom_point(alpha = 0.1, size = 0.1) + facet_wrap(vars(ADT)) + scale_color_viridis_c() + labs( color = "Log-normalized ADT expression" ) + # remove axis numbers and background grid - scale_x_continuous(labels = NULL, breaks = NULL) + - scale_y_continuous(labels = NULL, breaks = NULL) + + scale_x_continuous(labels = NULL, breaks = NULL) + + scale_y_continuous(labels = NULL, breaks = NULL) + coord_fixed() + theme(legend.position = "bottom", axis.title = element_text(size = 8, color = "black"), From cd03649fd0299c6344dcc5279577961506321629 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 16:30:11 -0400 Subject: [PATCH 114/268] Implemented initial framework for UMAPs, including lumping to n=8 --- templates/qc_report/celltypes_qc.rmd | 108 ++++++++++++++++++++++++++- 1 file changed, 107 insertions(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 1d33d3fa..77c6ad0f 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -119,10 +119,116 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` + + + ## Cell type annotations and clusters + +### UMAPs + +In this section, we show UMAPs colored by clusters and cell types, for each cell typing method used. +Clusters were calculated using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. + +For legibility, only the eight most common cell types are shown. +All other cell types are grouped together and labeled "Other cell type" (not to be confused with "Unknown cell types," which represent cells that could not be classified). + + +```{r} +# Create dataset for plotting UMAPs with collapsed cell types +n_celltypes <- 8 + +umap_df <- tibble::tibble( + UMAP1 = unname(reducedDim(processed_sce, "UMAP")[,1]), + UMAP2 = unname(reducedDim(processed_sce, "UMAP")[,2]), + clusters = processed_sce$clusters +) + +if (has_singler) { + umap_df <- umap_df |> + dplyr::mutate(singler = celltype_df$singler_celltype_annotation, + # lump the top 10 + singler = forcats::fct_lump_n(singler, n_celltypes, other_level = "Other cell type") + ) +} +if (has_cellassign) { + umap_df <- umap_df |> + dplyr::mutate(cellassign = celltype_df$cellassign_celltype_annotation, + # lump the top 10 + cellassign = forcats::fct_lump_n(cellassign, n_celltypes, other_level = "Other cell type") + ) +} +# Note that later, we will want to do this with submitter cell types too, if present. +``` + + +```{r} +# Define helper function for making UMAPs in this section +# this function uses the default palette, which can be customized when +# calling the function +plot_umap <- function(umap_df, + color_variable, + legend_title, + legend_nrow = 2) { + + ggplot(umap_df) + + aes(x = UMAP1, + y = UMAP2, + color = {{color_variable}}) + + geom_point(size = 0.3, + alpha = 0.5) + + # remove axis numbers and background grid + scale_x_continuous(labels = NULL, breaks = NULL) + + scale_y_continuous(labels = NULL, breaks = NULL) + + coord_fixed() + + guides( + color = guide_legend(title = legend_title, + nrow = legend_nrow, + # more visible points in legend + override.aes = list(alpha = 1, + size = 1.5))) + + theme(legend.position = "bottom") +} +``` + + +```{r message=FALSE, warning=FALSE} +plot_umap(umap_df, + clusters, + "Clusters") + + ggtitle("UMAP colored by clusters") +``` + + + +```{r eval=has_singler, message=FALSE, warning=FALSE} +plot_umap(umap_df, + singler, + "Cell types", + legend_nrow = 4) + + ggtitle("UMAP colored by SingleR annotations") +``` + + +```{r, eval = has_cellassign, message=FALSE, warning=FALSE} +knitr::asis_output("##### CellAssign cell types") + +plot_umap(umap_df, + cellassign, + "Cell types", + legend_nrow = 4) + + ggtitle("UMAP colored by SingleR annotations") +``` + + +```{r eval=has_submitter_celltypes, message=FALSE, warning=FALSE} +knitr::asis_output("#### Submitter-provided cell types") +# Nothing in this chunk yet - it's a placeholder +``` + +### Heatmaps + Below, we show heat maps comparing cell type annotations (along the y-axis) to clustering results (along the x-axis). -Clusters were obtained using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. ```{r} # Helper function for making a heatmap From d5ca6739f3724c648c5a291f27894967717c3667 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 16:30:43 -0400 Subject: [PATCH 115/268] remove leftover header and fix title --- templates/qc_report/celltypes_qc.rmd | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 77c6ad0f..65e3bd25 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -211,18 +211,15 @@ plot_umap(umap_df, ```{r, eval = has_cellassign, message=FALSE, warning=FALSE} -knitr::asis_output("##### CellAssign cell types") - plot_umap(umap_df, cellassign, "Cell types", legend_nrow = 4) + - ggtitle("UMAP colored by SingleR annotations") + ggtitle("UMAP colored by CellAssign annotations") ``` ```{r eval=has_submitter_celltypes, message=FALSE, warning=FALSE} -knitr::asis_output("#### Submitter-provided cell types") # Nothing in this chunk yet - it's a placeholder ``` From 15cb26457a1ad96007cd3005fe09d968b8f98524 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 16:31:56 -0400 Subject: [PATCH 116/268] indeed lowercase nextflow should cover it --- components/dictionary.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/components/dictionary.txt b/components/dictionary.txt index e0bf9e2e..64682d87 100644 --- a/components/dictionary.txt +++ b/components/dictionary.txt @@ -28,7 +28,6 @@ intronic Lun miQC nextflow -Nextflow Nextflow's nf Oligos From afaa4fc16ad468718c7116674907693deed28cf0 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 30 Aug 2023 16:46:27 -0400 Subject: [PATCH 117/268] add helper functions for lumping --- templates/qc_report/celltypes_qc.rmd | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 65e3bd25..50f6e763 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -135,28 +135,32 @@ All other cell types are grouped together and labeled "Other cell type" (not to ```{r} -# Create dataset for plotting UMAPs with collapsed cell types -n_celltypes <- 8 - +# Create dataset for plotting UMAPs with lumped cell types umap_df <- tibble::tibble( UMAP1 = unname(reducedDim(processed_sce, "UMAP")[,1]), UMAP2 = unname(reducedDim(processed_sce, "UMAP")[,2]), clusters = processed_sce$clusters ) -if (has_singler) { - umap_df <- umap_df |> - dplyr::mutate(singler = celltype_df$singler_celltype_annotation, +# helper function for lumping cell types +lump_celltypes <- function(umap_df, + orginal_column_string, + new_column, + n_celltypes = 8) { + umap_df |> + dplyr::mutate({{new_column}} := celltype_df[[orginal_column_string]], # lump the top 10 - singler = forcats::fct_lump_n(singler, n_celltypes, other_level = "Other cell type") + {{new_column}} := forcats::fct_lump_n({{new_column}}, + n_celltypes, + other_level = "Other cell type") ) } + +if (has_singler) { + umap_df <- lump_celltypes(umap_df, "singler_celltype_annotation", singler) +} if (has_cellassign) { - umap_df <- umap_df |> - dplyr::mutate(cellassign = celltype_df$cellassign_celltype_annotation, - # lump the top 10 - cellassign = forcats::fct_lump_n(cellassign, n_celltypes, other_level = "Other cell type") - ) + umap_df <- lump_celltypes(umap_df, "cellassign_celltype_annotation", cellassign) } # Note that later, we will want to do this with submitter cell types too, if present. ``` From 516a680e785d12275198903c0d98c59e4aee6c1c Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 30 Aug 2023 15:56:01 -0500 Subject: [PATCH 118/268] rename participant id --- bin/generate_unfiltered_sce.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 4a99f5df..6635e37f 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -136,7 +136,9 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> # we need this so we are able to merge sample metadata with colData later dplyr::mutate(library_id = opt$library_id) |> # remove upload date as we don't provide this on the portal - dplyr::select(-upload_date) + dplyr::select(-upload_date) |> + # rename to donor id + dplyr::rename("donor_id" = "participant_id") # add per cell and per gene statistics to colData and rowData unfiltered_sce <- unfiltered_sce |> From 30c613a88a9c0bbb8d0da97de956872e92c3c30a Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 30 Aug 2023 15:56:27 -0500 Subject: [PATCH 119/268] add is primary data, labeled dim reductions, and rowData filtering --- bin/sce_to_anndata.R | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 50857907..5b5e091d 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -58,12 +58,24 @@ sample_metadata <- metadata(sce)$sample_metadata # add library id as a column to the sce object sce$library_id <- metadata(sce)$library_id +# add is_primary_data column only needed for anndata objects +sce$is_primary_data <- FALSE + # add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, join_columns = "library_id") # remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] +# modify rowData +# we don't do any gene filtering between normalized and raw counts matrix +rowData(sce)$feature_is_filtered <- FALSE + +# paste X to reduced dim names if present +if(!is.null(reducedDimNames(sce))){ + reducedDimNames(sce) <- glue::glue("X_{reducedDimNames(sce)}") +} + # export sce as anndata object scpcaTools::sce_to_anndata( sce, @@ -97,7 +109,10 @@ if(!is.null(opt$feature_name)){ join_columns = "library_id") # remove sample metadata from metadata, otherwise conflicts with converting object - metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] + metadata(alt_sce) <- metadata(alt_sce)[names(metadata(alt_sce)) != "sample_metadata"] + + # add feature is filtered column + rowData(alt_sce)$feature_is_filtered <- FALSE # export altExp sce as anndata object scpcaTools::sce_to_anndata( From f834faeb3f49772066486a78a46d9b056bdff0c7 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 31 Aug 2023 09:50:57 -0500 Subject: [PATCH 120/268] czi comment --- bin/generate_unfiltered_sce.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 6635e37f..8aefc703 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -137,7 +137,7 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> dplyr::mutate(library_id = opt$library_id) |> # remove upload date as we don't provide this on the portal dplyr::select(-upload_date) |> - # rename to donor id + # rename to donor id for czi compliance dplyr::rename("donor_id" = "participant_id") # add per cell and per gene statistics to colData and rowData From ee3f095a4f61781b319eda5af98ba20fd4fe905c Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 31 Aug 2023 09:51:06 -0500 Subject: [PATCH 121/268] regroup all czi compliant steps --- bin/sce_to_anndata.R | 82 +++++++++++++++++++++++--------------------- 1 file changed, 43 insertions(+), 39 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 5b5e091d..c5289914 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -47,40 +47,43 @@ if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ stop("output rna file name must end in .hdf5 or .h5") } -# Convert to AnnData ----------------------------------------------------------- +# CZI compliance function ------------------------------------------------------ -# read in sce -sce <- readr::read_rds(opt$input_sce_file) +# this function applies any necessary reformatting or changes needed to make +# sure that the sce that is getting converted to AnnData is compliant with CZI +format_czi <- function(sce){ + + # add library id as a column to the sce object + sce$library_id <- metadata(sce)$library_id -# grab sample metadata -sample_metadata <- metadata(sce)$sample_metadata + # add is_primary_data column only needed for anndata objects + sce$is_primary_data <- FALSE -# add library id as a column to the sce object -sce$library_id <- metadata(sce)$library_id + # add sample metadata to colData sce + sce <- scpcaTools::metadata_to_coldata(sce, + join_columns = "library_id") -# add is_primary_data column only needed for anndata objects -sce$is_primary_data <- FALSE + # remove sample metadata from sce metadata, otherwise conflicts with converting object + metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] -# add sample metadata to colData sce -sce <- scpcaTools::metadata_to_coldata(sce, - join_columns = "library_id") -# remove sample metadata from sce metadata, otherwise conflicts with converting object -metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] + # modify rowData + # we don't do any gene filtering between normalized and raw counts matrix + # so everything gets set to false + rowData(sce)$feature_is_filtered <- FALSE -# modify rowData -# we don't do any gene filtering between normalized and raw counts matrix -rowData(sce)$feature_is_filtered <- FALSE + # paste X to reduced dim names if present + if(!is.null(reducedDimNames(sce))){ + reducedDimNames(sce) <- glue::glue("X_{reducedDimNames(sce)}") + } + + return(sce) -# paste X to reduced dim names if present -if(!is.null(reducedDimNames(sce))){ - reducedDimNames(sce) <- glue::glue("X_{reducedDimNames(sce)}") } -# export sce as anndata object -scpcaTools::sce_to_anndata( - sce, - anndata_file = opt$output_rna_h5 -) +# AltExp to AnnData ----------------------------------------------------------- + +# read in sce +sce <- readr::read_rds(opt$input_sce_file) # if feature data exists, grab it and export to AnnData if(!is.null(opt$feature_name)){ @@ -98,21 +101,11 @@ if(!is.null(opt$feature_name)){ # extract altExp alt_sce <- altExp(sce, opt$feature_name) - # add library ID to colData - alt_sce$library_id <- metadata(sce)$library_id - - # add sample metadata to alt sce metadata - metadata(alt_sce)$sample_metadata <- sample_metadata - - # add sample metadata to alt sce coldata - alt_sce <- scpcaTools::metadata_to_coldata(alt_sce, - join_columns = "library_id") + # add sample metadata from main sce to alt sce metadata + metadata(alt_sce)$sample_metadata <- metadata(sce)$sample_metadata - # remove sample metadata from metadata, otherwise conflicts with converting object - metadata(alt_sce) <- metadata(alt_sce)[names(metadata(alt_sce)) != "sample_metadata"] - - # add feature is filtered column - rowData(alt_sce)$feature_is_filtered <- FALSE + # make sce czi compliant + alt_sce <- format_czi(alt_sce) # export altExp sce as anndata object scpcaTools::sce_to_anndata( @@ -121,3 +114,14 @@ if(!is.null(opt$feature_name)){ ) } + +# MainExp to AnnData ----------------------------------------------------------- + +# make main sce czi compliant +sce <- format_czi(sce) + +# export sce as anndata object +scpcaTools::sce_to_anndata( + sce, + anndata_file = opt$output_rna_h5 +) From 0bcce91de2e923de7d0b77d0a1cc5f65b59285ba Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 10:57:40 -0400 Subject: [PATCH 122/268] Use inferno palette for now, and add sentence about heatmap colors per review --- templates/qc_report/celltypes_qc.rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 1d33d3fa..33fd8898 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -122,6 +122,7 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ## Cell type annotations and clusters Below, we show heat maps comparing cell type annotations (along the y-axis) to clustering results (along the x-axis). +Heatmap colors represent the log number of cells present in both the given cell type and cluster. Clusters were obtained using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. ```{r} @@ -135,8 +136,7 @@ create_celltype_cluster_heatmap <- function(celltype_vector, log1p() # log transform for visualization # Define CVD-friendly palette - # TODO: what palette? - heatmap_palette <- RColorBrewer::brewer.pal(n = 7, name = "BrBG") + heatmap_palette <- viridisLite::inferno(7, alpha = 1, begin = 0, end = 1, direction = 1) # heatmap heat <- ComplexHeatmap::Heatmap(celltype_cluster_mtx, From 08b20745941e27117f67ee784cdaf04493928d0b Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 31 Aug 2023 11:29:56 -0500 Subject: [PATCH 123/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/sce_to_anndata.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index c5289914..16fa45db 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -51,12 +51,13 @@ if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ # this function applies any necessary reformatting or changes needed to make # sure that the sce that is getting converted to AnnData is compliant with CZI +# CZI 3.0.0 requirements: https://github.com/chanzuckerberg/single-cell-curation/blob/b641130fe53b8163e50c39af09ee3fcaa14c5ea7/schema/3.0.0/schema.md format_czi <- function(sce){ - # add library id as a column to the sce object + # add library_id as an sce colData column sce$library_id <- metadata(sce)$library_id - # add is_primary_data column only needed for anndata objects + # add is_primary_data column; only needed for anndata objects sce$is_primary_data <- FALSE # add sample metadata to colData sce @@ -72,7 +73,7 @@ format_czi <- function(sce){ rowData(sce)$feature_is_filtered <- FALSE # paste X to reduced dim names if present - if(!is.null(reducedDimNames(sce))){ + if (!is.null(reducedDimNames(sce))) { reducedDimNames(sce) <- glue::glue("X_{reducedDimNames(sce)}") } From 490e24cb9dca40fb23704321c89fb0b9409d7256 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 31 Aug 2023 11:33:41 -0500 Subject: [PATCH 124/268] reorder main before alt --- bin/sce_to_anndata.R | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 16fa45db..37efefba 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -86,6 +86,21 @@ format_czi <- function(sce){ # read in sce sce <- readr::read_rds(opt$input_sce_file) +# grab sample metadata +# we need this if we have any feature data that we need to add it o +sample_metadata <- metadata(sce)$sample_metadata + +# MainExp to AnnData ----------------------------------------------------------- + +# make main sce czi compliant +sce <- format_czi(sce) + +# export sce as anndata object +scpcaTools::sce_to_anndata( + sce, + anndata_file = opt$output_rna_h5 +) + # if feature data exists, grab it and export to AnnData if(!is.null(opt$feature_name)){ @@ -103,7 +118,7 @@ if(!is.null(opt$feature_name)){ alt_sce <- altExp(sce, opt$feature_name) # add sample metadata from main sce to alt sce metadata - metadata(alt_sce)$sample_metadata <- metadata(sce)$sample_metadata + metadata(alt_sce)$sample_metadata <- sample_metadata # make sce czi compliant alt_sce <- format_czi(alt_sce) @@ -115,14 +130,3 @@ if(!is.null(opt$feature_name)){ ) } - -# MainExp to AnnData ----------------------------------------------------------- - -# make main sce czi compliant -sce <- format_czi(sce) - -# export sce as anndata object -scpcaTools::sce_to_anndata( - sce, - anndata_file = opt$output_rna_h5 -) From f4c8adbc7f45305ab712de692917be82fa7c4138 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 13:05:11 -0400 Subject: [PATCH 125/268] Use 7 cell types plus other. Update palettes: Set2 for clusters unless too many clusters, and Dark2 for cell types --- templates/qc_report/celltypes_qc.rmd | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 630d4b3c..bbff4eab 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -130,7 +130,7 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) In this section, we show UMAPs colored by clusters and cell types, for each cell typing method used. Clusters were calculated using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. -For legibility, only the eight most common cell types are shown. +For legibility, only the seven most common cell types are shown. All other cell types are grouped together and labeled "Other cell type" (not to be confused with "Unknown cell types," which represent cells that could not be classified). @@ -146,7 +146,7 @@ umap_df <- tibble::tibble( lump_celltypes <- function(umap_df, orginal_column_string, new_column, - n_celltypes = 8) { + n_celltypes = 7) { umap_df |> dplyr::mutate({{new_column}} := celltype_df[[orginal_column_string]], # lump the top 10 @@ -197,10 +197,21 @@ plot_umap <- function(umap_df, ```{r message=FALSE, warning=FALSE} -plot_umap(umap_df, +clusters_plot <- plot_umap(umap_df, clusters, "Clusters") + ggtitle("UMAP colored by clusters") + +# Determine palette based on number of levels. +# If we have <=8, we can use a CVD-friendly palette (they generally don't have more than 8 colors). +# Otherwise, we will use the default palette. +if (length(levels(umap_df$clusters)) <= 8) { + clusters_plot + + scale_color_brewer(palette = "Set2") +} else { + clusters_plot +} + ``` @@ -210,7 +221,8 @@ plot_umap(umap_df, singler, "Cell types", legend_nrow = 4) + - ggtitle("UMAP colored by SingleR annotations") + ggtitle("UMAP colored by SingleR annotations") + + scale_color_brewer(palette = "Dark2") ``` @@ -219,7 +231,8 @@ plot_umap(umap_df, cellassign, "Cell types", legend_nrow = 4) + - ggtitle("UMAP colored by CellAssign annotations") + ggtitle("UMAP colored by CellAssign annotations") + + scale_color_brewer(palette = "Dark2") ``` From 921090f69280b0ce27d45a7efddecf11fdd36912 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 14:23:46 -0400 Subject: [PATCH 126/268] Update earlier code to make factors from the very beginning. This simplifies downstream code which often needs those levels --- templates/qc_report/celltypes_qc.rmd | 71 ++++++++++++++-------------- 1 file changed, 36 insertions(+), 35 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index bbff4eab..6c60d168 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -32,6 +32,31 @@ If available, these results will be compared to cell type annotations provided b ## Cell type Annotation Statistics +```{r} +# This chunk defines a helper function to reformat annotations: +# * Annotations that are `NA`/"other" are changed to "Unknown cell type" +# * Annotations are converted to a factor ordered by frequency, but with +# "Unknown cell type" always last. +prepare_annotation_values <- function(df, annotation_column) { + df |> + dplyr::mutate( + {{annotation_column}} := dplyr::case_when( + # singler condition + is.na({{annotation_column}}) ~ "Unknown cell type", + # cellassign conditon + {{annotation_column}} == "other" ~ "Unknown cell type", + # otherwise, keep it + TRUE ~ {{annotation_column}} + + ), + {{annotation_column}} := forcats::fct_infreq({{annotation_column}}), + {{annotation_column}} := forcats::fct_relevel({{annotation_column}}, + "Unknown cell type", + after = Inf) + ) +} +``` + ```{r} # Create data frame of cell types celltype_df <- colData(processed_sce) |> @@ -44,49 +69,28 @@ celltype_df <- colData(processed_sce) |> contains("singler"), contains("cellassign")) -# Reformat NA (singler) and other (cellassign) to "Unknown cell type" + + if (has_singler) { -celltype_df <- celltype_df |> - dplyr::mutate( - singler_celltype_annotation = ifelse( - is.na(singler_celltype_annotation), - "Unknown cell type", - singler_celltype_annotation - ) - ) + celltype_df <- celltype_df |> + prepare_annotation_values(singler_celltype_annotation) } if (has_cellassign) { celltype_df <- celltype_df |> - dplyr::mutate( - cellassign_celltype_annotation = ifelse( - cellassign_celltype_annotation == "other", - "Unknown cell type", - cellassign_celltype_annotation - ) - ) -} + prepare_annotation_values(cellassign_celltype_annotation) +} # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { df |> - # rename column with user-facing name - dplyr::rename(`Annotated cell type` = {{celltype_column}}) |> - dplyr::count(`Annotated cell type`) |> - # make this column a factor with unknown at the end + dplyr::count({{celltype_column}}) |> + # Add percentage column dplyr::mutate( - # Add percentage column - `Percent of cells` = paste0(round(n/sum(n) * 100, digits = 2), "%"), - # set column order in descending order of n, but with unknown at the end - `Annotated cell type` = forcats::fct_reorder(`Annotated cell type`, n, .desc=TRUE), - `Annotated cell type` = forcats::fct_relevel(`Annotated cell type`, - "Unknown cell type", - after = Inf) + `Percent of cells` = paste0(round(n/sum(n) * 100, digits = 2), "%") ) |> - # arrange on `Annotated cell type` now that factor levels have been specified - dplyr::arrange(`Annotated cell type`) |> - # set column order + # set column order & rename dplyr::select( - `Annotated cell type`, + `Annotated cell type` = {{celltype_column}}, `Number of cells` = n, `Percent of cells` ) |> @@ -119,9 +123,6 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` - - - ## Cell type annotations and clusters From 2759eee957add047d18c24d9c42a76804a43df20 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 14:40:19 -0400 Subject: [PATCH 127/268] add seed, here for now --- templates/qc_report/qc_report.rmd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index b3700f1c..c02d8e35 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -44,6 +44,9 @@ reformat_nulls <- function(df) { ) ) } + +# Set seed +set.seed(2023) ``` ```{r sce_setup} From 8a83b7043ce3b8b7c39accc1229d6e619483422c Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 14:40:33 -0400 Subject: [PATCH 128/268] add section for delta median plot --- templates/qc_report/celltypes_qc.rmd | 66 ++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 6c60d168..fd646681 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -123,6 +123,72 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` +## Cell type annotation assessment + +In this section, we assess the reliability of cell type annotations using diagnostic plots. + + +```{r, eval = has_singler, warning=FALSE, fig.height = 6, fig.width = 9} +knitr::asis_output(" +### `SingleR` assessment + +`SingleR` assigns cell types using on score based on Spearman correlations across features in the reference dataset. +We evaluate the reliability of cell type annotations using the per-cell _delta median_ statistic, which is the difference between the score for the cell's assigned label and the median score of all labels for the given cell. +Higher _delta median_ values indicate more confidence in the cell type annotation. +For more information, refer to the [`Singler` book section on 'Annotation diagnostics'](https://bioconductor.org/packages/release/bioc/vignettes/SingleR/inst/doc/SingleR.html#4_Annotation_diagnostics). + +In the plot, each black point corresponds to the _delta median_ statistic a cell with the given cell type annotation. +The red points with error bars represent the median ± interquartile range (IQR). +") + +# Prepare SingleR scores for plot + +# extract scores into matrix +singler_scores <- metadata(processed_sce)$singler_result$scores |> + as.matrix() + + +# Create data frame for plotting with delta median and wrapped levels + delta_median_df <- celltype_df |> + dplyr::mutate( + delta_median = rowMaxs(singler_scores) - rowMedians(singler_scores) + ) + +delta_median_df$annotation_wrapped <- factor( + delta_median_df$singler_celltype_annotation, + levels = levels(delta_median_df$singler_celltype_annotation), + labels = stringr::str_wrap(levels(celltype_df$singler_celltype_annotation), 30) +) + +# Plot the scores across celltypes +ggplot(delta_median_df) + + aes(x = annotation_wrapped, y = delta_median) + + ggforce::geom_sina(size = 0.2, + alpha = 0.5) + + stat_summary( + color = "red", + # median and quartiles for point range + fun = "median", + fun.min = function(x) { + quantile(x, 0.25) + }, + fun.max = function(x) { + quantile(x, 0.75) + }, + geom = "pointrange", + position = position_dodge(width = 0.9), + size = 0.1 + ) + + labs( + x = "Cell type annotation", + y = "Delta median statistic" + ) + + theme( + axis.text.x = element_text(angle = 55, hjust = 1) + ) +``` + + ## Cell type annotations and clusters From 2a83ef637ac52c0b548a963f17901eeb9c5ab642 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 16:17:37 -0400 Subject: [PATCH 129/268] Update templates/qc_report/celltypes_qc.rmd Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- templates/qc_report/celltypes_qc.rmd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index bbff4eab..6b8b42ec 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -127,7 +127,8 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ### UMAPs -In this section, we show UMAPs colored by clusters and cell types, for each cell typing method used. +In this section, we show UMAPs colored by clusters and cell types. +A separate UMAP is shown for each cell typing method used. Clusters were calculated using the graph-based `r metadata(processed_sce)$cluster_algorithm` algorithm with `r metadata(processed_sce)$cluster_weighting` weights. For legibility, only the seven most common cell types are shown. From a674f4a854b94936233730e3e04ded2205274f5c Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 31 Aug 2023 16:26:54 -0400 Subject: [PATCH 130/268] simplify function to lump cell types --- templates/qc_report/celltypes_qc.rmd | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 6b8b42ec..9f1ce43e 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -145,23 +145,25 @@ umap_df <- tibble::tibble( # helper function for lumping cell types lump_celltypes <- function(umap_df, - orginal_column_string, - new_column, + celltype_df, + celltype_method, n_celltypes = 7) { + umap_df |> - dplyr::mutate({{new_column}} := celltype_df[[orginal_column_string]], - # lump the top 10 - {{new_column}} := forcats::fct_lump_n({{new_column}}, - n_celltypes, - other_level = "Other cell type") - ) + dplyr::mutate( + celltypes = celltype_df[[glue::glue("{celltype_method}_celltype_annotation")]], + celltypes = forcats::fct_lump_n(celltypes, + n_celltypes, + other_level = "Other cell type")) |> + # finally, rename temporary `celltypes` column to the provided method + dplyr::rename({{celltype_method}} := celltypes) } if (has_singler) { - umap_df <- lump_celltypes(umap_df, "singler_celltype_annotation", singler) + umap_df <- lump_celltypes(umap_df, celltype_df, "singler") } if (has_cellassign) { - umap_df <- lump_celltypes(umap_df, "cellassign_celltype_annotation", cellassign) + umap_df <- lump_celltypes(umap_df, celltype_df, "cellassign") } # Note that later, we will want to do this with submitter cell types too, if present. ``` From 4a32dbb424f548a342c1b789f05a76f67bd36b79 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 10:16:15 -0400 Subject: [PATCH 131/268] make the heatmap function more general so we can show annotations against one another --- templates/qc_report/celltypes_qc.rmd | 34 +++++++++++++++++----------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 072ac75f..f51b8d61 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -318,28 +318,31 @@ Heatmap colors represent the log number of cells present in both the given cell ```{r} # Helper function for making a heatmap -create_celltype_cluster_heatmap <- function(celltype_vector, - cluster_vector) { +create_celltype_heatmap <- function(x_vector, + y_vector, + x_label = "", + y_label = "") { - # build a matrix with cluster identity as rows and celltype as columns - celltype_cluster_mtx <- table(celltype_vector, - cluster_vector) |> + # build a matrix for making a heatmap + celltype_mtx <- table(x_vector, + y_vector) |> log1p() # log transform for visualization # Define CVD-friendly palette heatmap_palette <- viridisLite::inferno(7, alpha = 1, begin = 0, end = 1, direction = 1) # heatmap - heat <- ComplexHeatmap::Heatmap(celltype_cluster_mtx, + heat <- ComplexHeatmap::Heatmap(celltype_mtx, # Overall heatmap parameters col = heatmap_palette, # Column parameters - column_title = "Clusters", + column_title = y_label, column_title_side = "bottom", column_dend_side = "top", column_names_rot = 0, # Row parameters row_dend_side = "left", + row_title = x_label, row_names_gp = grid::gpar(fontsize = 8), # Legend parameters heatmap_legend_param = list( @@ -356,24 +359,29 @@ create_celltype_cluster_heatmap <- function(celltype_vector, ```{r, eval = has_singler, fig.height=5, fig.width=7} knitr::asis_output("### `SingleR` cluster and cell type heatmap\n") -create_celltype_cluster_heatmap( +create_celltype_heatmap( celltype_df$singler_celltype_annotation, - celltype_df$clusters + celltype_df$clusters, + "Clusters" ) ``` ```{r, eval = has_cellassign, fig.height=5, fig.width=7} knitr::asis_output("### `CellAssign` cluster and cell type heatmap\n") -create_celltype_cluster_heatmap( +create_celltype_heatmap( celltype_df$cellassign_celltype_annotation, - celltype_df$clusters + celltype_df$clusters, + "Clusters" ) ``` ```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") -create_celltype_cluster_heatmap( +create_celltype_heatmap( celltype_df$submitter_celltype_annotation, - celltype_df$clusters + celltype_df$clusters, + "Clusters" ) ``` + + From b041cda557bb79bb954e95bace3fc56432879d37 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 10:40:45 -0400 Subject: [PATCH 132/268] Add in heatmap for direct comparison, which involved a couple more heatmap function tweaks --- templates/qc_report/celltypes_qc.rmd | 47 +++++++++++++++++++++------- 1 file changed, 35 insertions(+), 12 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index f51b8d61..d3dd59c6 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -321,7 +321,10 @@ Heatmap colors represent the log number of cells present in both the given cell create_celltype_heatmap <- function(x_vector, y_vector, x_label = "", - y_label = "") { + y_label = "", + column_names_rotation = 0, + row_font_size = 8, + column_font_size = 10) { # build a matrix for making a heatmap celltype_mtx <- table(x_vector, @@ -339,11 +342,13 @@ create_celltype_heatmap <- function(x_vector, column_title = y_label, column_title_side = "bottom", column_dend_side = "top", - column_names_rot = 0, + column_names_rot = column_names_rotation, + column_names_gp = grid::gpar(fontsize = column_font_size), # Row parameters row_dend_side = "left", + row_title_side = "right", row_title = x_label, - row_names_gp = grid::gpar(fontsize = 8), + row_names_gp = grid::gpar(fontsize = row_font_size), # Legend parameters heatmap_legend_param = list( title = "Log(Number of cells)", @@ -360,28 +365,46 @@ create_celltype_heatmap <- function(x_vector, ```{r, eval = has_singler, fig.height=5, fig.width=7} knitr::asis_output("### `SingleR` cluster and cell type heatmap\n") create_celltype_heatmap( - celltype_df$singler_celltype_annotation, - celltype_df$clusters, - "Clusters" + x_vector = celltype_df$singler_celltype_annotation, + y_vector = celltype_df$clusters, + y_label = "Clusters" ) ``` ```{r, eval = has_cellassign, fig.height=5, fig.width=7} knitr::asis_output("### `CellAssign` cluster and cell type heatmap\n") create_celltype_heatmap( - celltype_df$cellassign_celltype_annotation, - celltype_df$clusters, - "Clusters" + x_vector = celltype_df$cellassign_celltype_annotation, + y_vector = celltype_df$clusters, + y_label = "Clusters" ) ``` ```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") create_celltype_heatmap( - celltype_df$submitter_celltype_annotation, - celltype_df$clusters, - "Clusters" + x_vector = celltype_df$submitter_celltype_annotation, + y_vector = celltype_df$clusters, + y_label = "Clusters" ) ``` + +```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} +knitr::asis_output(" +### Comparison between cell type annotations + +Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. +Note that due to different annotations references, these methods may use different names for similar cell types. +") + +create_celltype_heatmap( + x_vector = celltype_df$singler_celltype_annotation, + y_vector = celltype_df$cellassign_celltype_annotation, + x_label = "SingleR annotations", + y_label = "CellAssign annotations", + column_names_rotation = 55, + column_font_size = 8 +) +``` From 3fe242e41d13c2d6041cc46b429912ef67d50f4f Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 10:55:56 -0400 Subject: [PATCH 133/268] header tweaks: use caps and make this its own section --- templates/qc_report/celltypes_qc.rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index d3dd59c6..6241fb7e 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -123,7 +123,7 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` -## Cell type annotation assessment +## Cell type Annotation Assessment In this section, we assess the reliability of cell type annotations using diagnostic plots. @@ -189,7 +189,7 @@ ggplot(delta_median_df) + ``` -## Cell type annotations and clusters +## Cell type Annotations and Clusters ### UMAPs @@ -393,7 +393,7 @@ create_celltype_heatmap( ```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} knitr::asis_output(" -### Comparison between cell type annotations +## Cell Type Annotation Comparison Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. Note that due to different annotations references, these methods may use different names for similar cell types. From 6ed692b812385092b4d6130a89e27d65ffdf19b8 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 14:32:57 -0400 Subject: [PATCH 134/268] add a non-styled ridgeplot --- templates/qc_report/celltypes_qc.rmd | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 072ac75f..747c08ef 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -186,6 +186,20 @@ ggplot(delta_median_df) + theme( axis.text.x = element_text(angle = 55, hjust = 1) ) + + +# Now, as ridgeplot: +ggplot(delta_median_df) + + aes(x = delta_median, y = annotation_wrapped) + + ggridges::geom_density_ridges2() + + ggridges::stat_density_ridges(quantile_lines = TRUE, quantiles = 2) + + labs( + x = "Delta median statistic", + y = "Cell type annotation" + ) + + theme( + axis.text.y = element_text(size = 7) + ) ``` From ee728bd3b66603d52e58ccc28bd49045b3a01bce Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 14:35:13 -0400 Subject: [PATCH 135/268] shorten headers --- templates/qc_report/celltypes_qc.rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 6241fb7e..4793bf70 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -30,7 +30,7 @@ Cells annotated as "Unknown cell type" represent cells which could not be confid If available, these results will be compared to cell type annotations provided by the data's originating research group ("submitter-provided cell type annotations".) -## Cell type Annotation Statistics +## Statistics ```{r} # This chunk defines a helper function to reformat annotations: @@ -123,7 +123,7 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` -## Cell type Annotation Assessment +## Annotation Assessment In this section, we assess the reliability of cell type annotations using diagnostic plots. @@ -189,7 +189,7 @@ ggplot(delta_median_df) + ``` -## Cell type Annotations and Clusters +## Comparison with clusterss ### UMAPs @@ -393,7 +393,7 @@ create_celltype_heatmap( ```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} knitr::asis_output(" -## Cell Type Annotation Comparison +## Comparison between annotations Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. Note that due to different annotations references, these methods may use different names for similar cell types. From 48e4d538deeffd95f333b393442fa964ab32f7fa Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 1 Sep 2023 14:36:18 -0400 Subject: [PATCH 136/268] spelling and caps --- templates/qc_report/celltypes_qc.rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 4793bf70..3a1ad1ca 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -189,7 +189,7 @@ ggplot(delta_median_df) + ``` -## Comparison with clusterss +## Comparison with Clusters ### UMAPs @@ -393,7 +393,7 @@ create_celltype_heatmap( ```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} knitr::asis_output(" -## Comparison between annotations +## Comparison Between Annotations Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. Note that due to different annotations references, these methods may use different names for similar cell types. From ec33c950fb8330d19f045b4c492bf1c35e2e9e0f Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 09:59:38 -0400 Subject: [PATCH 137/268] Update singler delta median plot to color by pruning, and update overall plot paragraph --- templates/qc_report/celltypes_qc.rmd | 115 +++++++++++++++------------ 1 file changed, 63 insertions(+), 52 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 747c08ef..7ddbe2cc 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -79,7 +79,9 @@ if (has_cellassign) { celltype_df <- celltype_df |> prepare_annotation_values(cellassign_celltype_annotation) } - +``` + +```{r} # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { df |> @@ -128,81 +130,90 @@ create_celltype_n_table(celltype_df, submitter_celltype_annotation) In this section, we assess the reliability of cell type annotations using diagnostic plots. -```{r, eval = has_singler, warning=FALSE, fig.height = 6, fig.width = 9} +```{r, eval = has_singler} knitr::asis_output(" ### `SingleR` assessment `SingleR` assigns cell types using on score based on Spearman correlations across features in the reference dataset. We evaluate the reliability of cell type annotations using the per-cell _delta median_ statistic, which is the difference between the score for the cell's assigned label and the median score of all labels for the given cell. -Higher _delta median_ values indicate more confidence in the cell type annotation. -For more information, refer to the [`Singler` book section on 'Annotation diagnostics'](https://bioconductor.org/packages/release/bioc/vignettes/SingleR/inst/doc/SingleR.html#4_Annotation_diagnostics). +Higher _delta median_ values indicate more confidence in the cell type annotation, although there is no specific threshold for calling absolute high vs. low confidence. +For more information, refer to the [`SingleR` book section on 'Annotation diagnostics'](https://bioconductor.org/books/release/SingleRBook/annotation-diagnostics.html#annotation-diagnostics). -In the plot, each black point corresponds to the _delta median_ statistic a cell with the given cell type annotation. -The red points with error bars represent the median ± interquartile range (IQR). + +In the plot below, each point is the _delta median_ statistic of a given cell with the given cell type annotation. +Points (cells) are colored by `SingleR`'s internal confidence assessment: High-quality cell annotations are shown in black, and low-quality cell annotations are shown in red. +All red points correspond to cells labeled as `Unknown cell type` in the tables above. ") +``` + +```{r, eval = has_singler, warning=FALSE, fig.height = 6, fig.width = 8} # Prepare SingleR scores for plot # extract scores into matrix -singler_scores <- metadata(processed_sce)$singler_result$scores |> - as.matrix() +singler_scores <- metadata(processed_sce)$singler_result$scores + +# Create data frame for plotting with delta median and the full *non-pruned* cell labels +delta_median_df <- tibble::tibble( + delta_median = rowMaxs(singler_scores) - rowMedians(singler_scores), + # Need to grab the non-pruned label for this plot + ontology = metadata(processed_sce)$singler_result$labels, + # TRUE pruned values ==> low confidence + # so, negate for this variable: + confident = !is.na(metadata(processed_sce)$singler_result$pruned.labels) +) |> + # Map ontologies and celltype labels for plot labeling + # we use inner_join b/c the above tibble does NOT contain "Unknown cell type", which + # we do not want to display here + dplyr::inner_join( + tibble::tibble( + ontology = celltype_df$singler_celltype_ontology, + celltype = celltype_df$singler_celltype_annotation + ) |> dplyr::distinct() + ) |> + dplyr::select(celltype, confident, delta_median) + +# Ensure we have no "Unknown cell type" values left: +if (sum(delta_median_df$celltype == "Unknown cell type") > 0) { + stop("Failed to process SingleR data for diagnostic plot.") +} -# Create data frame for plotting with delta median and wrapped levels - delta_median_df <- celltype_df |> - dplyr::mutate( - delta_median = rowMaxs(singler_scores) - rowMedians(singler_scores) - ) - +# remove "Unknown cell type" from levels, and wrap the labels +new_levels <- levels(delta_median_df$celltype) +new_levels <- new_levels[-length(new_levels)] delta_median_df$annotation_wrapped <- factor( - delta_median_df$singler_celltype_annotation, - levels = levels(delta_median_df$singler_celltype_annotation), - labels = stringr::str_wrap(levels(celltype_df$singler_celltype_annotation), 30) + delta_median_df$celltype, + levels = new_levels, + labels = stringr::str_wrap(new_levels, 30) ) -# Plot the scores across celltypes +# Plot delta_median across celltypes colored by pruning ggplot(delta_median_df) + - aes(x = annotation_wrapped, y = delta_median) + - ggforce::geom_sina(size = 0.2, - alpha = 0.5) + - stat_summary( - color = "red", - # median and quartiles for point range - fun = "median", - fun.min = function(x) { - quantile(x, 0.25) - }, - fun.max = function(x) { - quantile(x, 0.75) - }, - geom = "pointrange", - position = position_dodge(width = 0.9), - size = 0.1 - ) + + aes(x = annotation_wrapped, + y = delta_median, + color = confident) + + ggforce::geom_sina(size = 0.5, + alpha = 0.5, + # Keep red points mostly in line with black + position = position_dodge(width = 0.05)) + labs( x = "Cell type annotation", - y = "Delta median statistic" + y = "Delta median statistic", + color = "Confident cell type assignment" ) + + scale_color_manual(values = c("red", "black")) + + guides( + color = guide_legend(override.aes = list(size = 1, alpha = 0.9)) + ) + theme( - axis.text.x = element_text(angle = 55, hjust = 1) - ) - - -# Now, as ridgeplot: -ggplot(delta_median_df) + - aes(x = delta_median, y = annotation_wrapped) + - ggridges::geom_density_ridges2() + - ggridges::stat_density_ridges(quantile_lines = TRUE, quantiles = 2) + - labs( - x = "Delta median statistic", - y = "Cell type annotation" - ) + - theme( - axis.text.y = element_text(size = 7) + axis.text.x = element_text(angle = 55, hjust = 1, size = rel(0.85)), + legend.title = element_text(size = rel(0.75)), + legend.text = element_text(size = rel(0.75)), + legend.position = "bottom" ) ``` - ## Cell type annotations and clusters From 5af423e401f3312bdc83f2ebe91c8130bebd1bf2 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 10:01:32 -0400 Subject: [PATCH 138/268] update text and turn off messages to hide the joining output --- templates/qc_report/celltypes_qc.rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 7ddbe2cc..3245daf1 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -142,12 +142,12 @@ For more information, refer to the [`SingleR` book section on 'Annotation diagno In the plot below, each point is the _delta median_ statistic of a given cell with the given cell type annotation. Points (cells) are colored by `SingleR`'s internal confidence assessment: High-quality cell annotations are shown in black, and low-quality cell annotations are shown in red. -All red points correspond to cells labeled as `Unknown cell type` in the tables above. +All red points correspond to cells labeled as `Unknown cell type` in the `SingleR` result table in the previous section. ") ``` -```{r, eval = has_singler, warning=FALSE, fig.height = 6, fig.width = 8} +```{r, eval = has_singler, warning=FALSE, message=FALSE,fig.height = 6, fig.width = 8} # Prepare SingleR scores for plot # extract scores into matrix From 08e6a07882307e69f446be6dbef7507f3b6302c9 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 10:08:29 -0400 Subject: [PATCH 139/268] fix extra words --- templates/qc_report/celltypes_qc.rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 3245daf1..5fefad51 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -134,7 +134,7 @@ In this section, we assess the reliability of cell type annotations using diagno knitr::asis_output(" ### `SingleR` assessment -`SingleR` assigns cell types using on score based on Spearman correlations across features in the reference dataset. +`SingleR` assigns cell type scores based on Spearman correlations across features in the reference dataset. We evaluate the reliability of cell type annotations using the per-cell _delta median_ statistic, which is the difference between the score for the cell's assigned label and the median score of all labels for the given cell. Higher _delta median_ values indicate more confidence in the cell type annotation, although there is no specific threshold for calling absolute high vs. low confidence. For more information, refer to the [`SingleR` book section on 'Annotation diagnostics'](https://bioconductor.org/books/release/SingleRBook/annotation-diagnostics.html#annotation-diagnostics). From 61546ed13f3bddd69ca187575c06175eda4f74a5 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 11:00:49 -0400 Subject: [PATCH 140/268] First go at CellAssign diagnostic paragraph and ridgeplot --- templates/qc_report/celltypes_qc.rmd | 105 +++++++++++++++++++++++++++ 1 file changed, 105 insertions(+) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 3245daf1..3c475469 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -214,6 +214,111 @@ ggplot(delta_median_df) + ) ``` + + + +```{r, eval = has_cellassign} +knitr::asis_output(" +### `CellAssign` assessment + +`CellAssign` computes the probability that each cell is one of the provided cell types and ultimately annotates cells based on the highest probability. +We therefore expect that cell-level probabilities that correspond to the annotated cell types will be high. +Conversely, we expect that cell-level probabilities that correspond to annotated cell types will be low. + +In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type (excluding unknown cell types). +Colors represent whether the probabilities correspond to a cell with that given annotation: Purple distributions represent probabilities for cells that _were not_ annotated as the given cell type. +Yellow distribution represent probabilies for cells that _were_ annotated as the given cell type. +For distributions with fewer than three points, density plots cannot be calculated. +In these cases, we directly show values for individual cell probabilities as points. +") +``` + + +```{r, eval = has_cellassign, warning=FALSE, message=FALSE,fig.height = 7, fig.width = 8} + +# Prepare CellAssign scores for plot +cellassign_prob_df <- metadata(processed_sce)$cellassign_predictions |> + tidyr::pivot_longer( + -barcode, + names_to = "celltype", + values_to = "probability" + ) |> + # remove cell types that were not annotated + # bonus: ths will also remove the "other" level, which we don't want to show anyways + dplyr::filter(celltype %in% celltype_df$cellassign_celltype_annotation) |> + # join with actual annotations + # but use inner_join to avoid bringing back the others + dplyr::inner_join( + tibble::tibble( + cellassign_celltype_annotation = celltype_df$cellassign_celltype_annotation, + barcode = colData(processed_sce)$barcodes # plural! + ) + ) |> + # remove all the unknown cell types from this plot + dplyr::filter( + cellassign_celltype_annotation != "Unknown cell type" + ) |> + # add indicator for whether the celltype matches the annotation + dplyr::mutate( + annotated = cellassign_celltype_annotation == celltype + ) + +# remove "Unknown cell type" from levels, and wrap the labels +new_levels <- levels(cellassign_prob_df$cellassign_celltype_annotation) +new_levels <- rev(new_levels[-length(new_levels)]) # reverse for ridgeplot +cellassign_prob_df$annotation_wrapped <- factor( + cellassign_prob_df$celltype, + levels = new_levels, + labels = stringr::str_wrap(new_levels, 30) +) + +# find groups with <=2 cells to add back into plot +# These will always be `annotated = TRUE` +celltypes_leq2_cells <- cellassign_prob_df |> + dplyr::count(annotation_wrapped, annotated) |> + dplyr::filter(n <= 2) |> + dplyr::pull(annotation_wrapped) + +# data frame for adding those points back +leq2_probabilities_df <- cellassign_prob_df |> + dplyr::filter( + annotation_wrapped %in% celltypes_leq2_cells, + annotated + ) |> + dplyr::select(annotation_wrapped, probability, annotated) + +# Finally, the plot: +ggplot(cellassign_prob_df) + + aes(x = probability, + y = annotation_wrapped, + fill = annotated) + + ggridges::stat_density_ridges(quantile_lines = TRUE, + quantiles = 2, + alpha = 0.6) + + scale_fill_viridis_d() + + labs( + x = "CellAssign probability", + y = "Annotated cell type", + fill = "Cell annotated as given cell type" + ) + + theme( + axis.text.y = element_text(size = 9) + ) + + # add back points for leq2 cells + geom_point( + data = leq2_probabilities_df, + aes( + x = probability, + y = annotation_wrapped + ), + size = 1.5, pch = 23, color = "black", linewidth = 0.1, + position = position_nudge(y = 0.075), # place point slightly above the axis line + show.legend = FALSE + ) +``` + + + ## Cell type annotations and clusters From 972a2539874d63a5ae537f358efbd5c75f735024 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 14:06:06 -0400 Subject: [PATCH 141/268] Simplify levels code for label wrapping --- templates/qc_report/celltypes_qc.rmd | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 5fefad51..b7d2f7d9 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -178,14 +178,11 @@ if (sum(delta_median_df$celltype == "Unknown cell type") > 0) { stop("Failed to process SingleR data for diagnostic plot.") } - -# remove "Unknown cell type" from levels, and wrap the labels -new_levels <- levels(delta_median_df$celltype) -new_levels <- new_levels[-length(new_levels)] +# add column with ordered levels with wrapped labels for visualization delta_median_df$annotation_wrapped <- factor( delta_median_df$celltype, - levels = new_levels, - labels = stringr::str_wrap(new_levels, 30) + levels = levels(delta_median_df$celltype), + labels = stringr::str_wrap(levels(delta_median_df$celltype), 30) ) # Plot delta_median across celltypes colored by pruning From 440adc5074cb3a540ecf0e95a7d7be66777d4263 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 14:42:49 -0400 Subject: [PATCH 142/268] Update plot: use blue pruned points and red crossbar overlay for median +iqr --- templates/qc_report/celltypes_qc.rmd | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index b7d2f7d9..7aae0ac2 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -141,8 +141,9 @@ For more information, refer to the [`SingleR` book section on 'Annotation diagno In the plot below, each point is the _delta median_ statistic of a given cell with the given cell type annotation. -Points (cells) are colored by `SingleR`'s internal confidence assessment: High-quality cell annotations are shown in black, and low-quality cell annotations are shown in red. -All red points correspond to cells labeled as `Unknown cell type` in the `SingleR` result table in the previous section. +Points (cells) are colored by `SingleR`'s internal confidence assessment: High-quality cell annotations are shown in black, and low-quality cell annotations are shown in blue. +All blue points correspond to cells labeled as `Unknown cell type` in the `SingleR` result table in the previous section. +The red overlayed boxes represent the median ± interquartile range (IQR), specifically for high-quality annotations. ") ``` @@ -184,13 +185,17 @@ delta_median_df$annotation_wrapped <- factor( levels = levels(delta_median_df$celltype), labels = stringr::str_wrap(levels(delta_median_df$celltype), 30) ) + +# Subset the data to just confident points for median+/-IQR +delta_median_confident_df <- delta_median_df |> + dplyr::filter(confident) # Plot delta_median across celltypes colored by pruning ggplot(delta_median_df) + aes(x = annotation_wrapped, y = delta_median, color = confident) + - ggforce::geom_sina(size = 0.5, + ggforce::geom_sina(size = 0.75, alpha = 0.5, # Keep red points mostly in line with black position = position_dodge(width = 0.05)) + @@ -199,7 +204,15 @@ ggplot(delta_median_df) + y = "Delta median statistic", color = "Confident cell type assignment" ) + - scale_color_manual(values = c("red", "black")) + + scale_color_manual(values = c("blue", "black")) + + # add median/IQR + stat_summary( + data = delta_median_confident_df, # only use black points for median + color = "red", + geom = "crossbar", + width = 0.4, + size = 0.2 + ) + guides( color = guide_legend(override.aes = list(size = 1, alpha = 0.9)) ) + From 601087b36b1ebef14ca5a6b8b02b8834de0c6adb Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 14:48:05 -0400 Subject: [PATCH 143/268] Add code we would need if we want to pass in the workflow seed; this requires scpcaTools changes --- bin/sce_qc_report.R | 9 ++++++++- modules/qc-report.nf | 3 ++- templates/qc_report/.DS_Store | Bin 0 -> 6148 bytes templates/qc_report/qc_report.rmd | 3 ++- 4 files changed, 12 insertions(+), 3 deletions(-) create mode 100644 templates/qc_report/.DS_Store diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R index 62be8c72..8961f19d 100755 --- a/bin/sce_qc_report.R +++ b/bin/sce_qc_report.R @@ -92,6 +92,12 @@ option_list <- list( type = "character", default = "vireo", help = "Demultiplexing method to use for multiplexed samples. One of `vireo`, `HTOdemux`, or `HashedDrops`" + ), + make_option( + opt_str = "--seed", + type = "integer", + default = NULL, + help = "Optional random seed used in certain QC report visualizations." ) ) @@ -224,6 +230,7 @@ scpcaTools::generate_qc_report( filtered_sce = filtered_sce, processed_sce = processed_sce, report_template = opt$report_template, - output = opt$qc_report_file + output = opt$qc_report_file, + seed = opt$seed ) diff --git a/modules/qc-report.nf b/modules/qc-report.nf index 0c2da616..6f649203 100644 --- a/modules/qc-report.nf +++ b/modules/qc-report.nf @@ -32,7 +32,8 @@ process sce_qc_report{ --genome_assembly "${meta.ref_assembly}" \ --workflow_url "${workflow_url}" \ --workflow_version "${workflow_version}" \ - --workflow_commit "${workflow.commitId}" + --workflow_commit "${workflow.commitId}" \ + --seed "${params.seed}" """ stub: qc_report = "${meta.library_id}_qc.html" diff --git a/templates/qc_report/.DS_Store b/templates/qc_report/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 Date: Wed, 6 Sep 2023 15:27:01 -0400 Subject: [PATCH 144/268] Update bin/sce_qc_report.R Co-authored-by: Joshua Shapiro --- bin/sce_qc_report.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R index 8961f19d..88da774c 100755 --- a/bin/sce_qc_report.R +++ b/bin/sce_qc_report.R @@ -231,6 +231,6 @@ scpcaTools::generate_qc_report( processed_sce = processed_sce, report_template = opt$report_template, output = opt$qc_report_file, - seed = opt$seed + extra_params = list(seed = opt$seed) ) From 6ba63513e8660998cea7e5e6ab876ef8a42d115e Mon Sep 17 00:00:00 2001 From: Stephanie Date: Wed, 6 Sep 2023 15:44:34 -0400 Subject: [PATCH 145/268] Add that new forcats code, and cover the condition where ontologies were NOT used for annotation --- templates/qc_report/celltypes_qc.rmd | 31 +++++++++++++++++----------- 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 7aae0ac2..632d13a3 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -47,12 +47,9 @@ prepare_annotation_values <- function(df, annotation_column) { {{annotation_column}} == "other" ~ "Unknown cell type", # otherwise, keep it TRUE ~ {{annotation_column}} - - ), - {{annotation_column}} := forcats::fct_infreq({{annotation_column}}), - {{annotation_column}} := forcats::fct_relevel({{annotation_column}}, - "Unknown cell type", - after = Inf) + ) |> + forcats::fct_infreq() |> + forcats::fct_relevel("Unknown cell type", after = Inf) ) } ``` @@ -158,21 +155,31 @@ singler_scores <- metadata(processed_sce)$singler_result$scores delta_median_df <- tibble::tibble( delta_median = rowMaxs(singler_scores) - rowMedians(singler_scores), # Need to grab the non-pruned label for this plot - ontology = metadata(processed_sce)$singler_result$labels, + full_labels = metadata(processed_sce)$singler_result$labels, # TRUE pruned values ==> low confidence # so, negate for this variable: confident = !is.na(metadata(processed_sce)$singler_result$pruned.labels) -) |> - # Map ontologies and celltype labels for plot labeling +) + +# If ontologies were used for `full_labels`, we'll need to map back to cell names +# for the plot itself. +if ("singler_celltype_ontology" %in% names(celltype_df)) { + # we use inner_join b/c the above tibble does NOT contain "Unknown cell type", which # we do not want to display here - dplyr::inner_join( + delta_median_df <- delta_median_df |> + dplyr::inner_join( tibble::tibble( - ontology = celltype_df$singler_celltype_ontology, + full_labels = celltype_df$singler_celltype_ontology, celltype = celltype_df$singler_celltype_annotation ) |> dplyr::distinct() ) |> - dplyr::select(celltype, confident, delta_median) + dplyr::select(-full_labels) +} else { + # otherwise, full_labels already contain what we want to plot, so just rename it + delta_median_df <- delta_median_df |> + dplyr::rename(celltype = full_labels) +} # Ensure we have no "Unknown cell type" values left: if (sum(delta_median_df$celltype == "Unknown cell type") > 0) { From 498f54efd86db73b82f4ae1970110c4658980362 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 6 Sep 2023 16:32:03 -0400 Subject: [PATCH 146/268] add explicit 'dir' types --- modules/af-features.nf | 2 +- modules/af-rna.nf | 4 ++-- modules/bulk-salmon.nf | 4 ++-- modules/bulk-star.nf | 5 +++-- modules/genetic-demux.nf | 2 +- modules/spaceranger.nf | 6 +++--- modules/starsolo.nf | 2 +- 7 files changed, 13 insertions(+), 12 deletions(-) diff --git a/modules/af-features.nf b/modules/af-features.nf index 05a8e96d..8f371fe0 100644 --- a/modules/af-features.nf +++ b/modules/af-features.nf @@ -166,7 +166,7 @@ workflow map_quant_feature{ // create tuple of metdata map (read from output) and rad_directory to be used directly as input to alevin-fry quantification feature_rad_ch = feature_ch.has_rad .map{meta -> tuple(Utils.readMeta(file("${meta.feature_rad_dir}/scpca-meta.json")), - file(meta.feature_rad_dir) + file(meta.feature_rad_dir, type: 'dir') )} // run Alevin on feature reads diff --git a/modules/af-rna.nf b/modules/af-rna.nf index 5a7bce6e..98dcc98b 100644 --- a/modules/af-rna.nf +++ b/modules/af-rna.nf @@ -122,14 +122,14 @@ workflow map_quant_rna { .map{meta -> tuple(meta, file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz"), - file("${meta.salmon_splici_index}") + file(meta.salmon_splici_index, type: 'dir') )} // if the rad directory has been created and repeat_mapping is set to false // create tuple of metdata map (read from output) and rad_directory to be used directly as input to alevin-fry quantification rna_rad_ch = rna_channel.has_rad .map{meta -> tuple(Utils.readMeta(file("${meta.rad_dir}/scpca-meta.json")), - file(meta.rad_dir) + file(meta.rad_dir, type: 'dir') )} // run Alevin for mapping on libraries that don't have RAD directory already created diff --git a/modules/bulk-salmon.nf b/modules/bulk-salmon.nf index eab3de77..c8956b19 100644 --- a/modules/bulk-salmon.nf +++ b/modules/bulk-salmon.nf @@ -133,14 +133,14 @@ workflow bulk_quant_rna { // create tuple of metadata map (read from output), salmon output directory to use as input to merge_bulk_quants quants_ch = bulk_channel.has_quants .map{meta -> tuple(Utils.readMeta(file("${meta.salmon_results_dir}/scpca-meta.json")), - file(meta.salmon_results_dir) + file(meta.salmon_results_dir, type: 'dir') )} // If we need to run salmon, create tuple of (metadata map, [Read 1 files], [Read 2 files]) bulk_reads_ch = bulk_channel.make_quants .map{meta -> tuple(meta, file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), - file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz") + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz") )} // run fastp and salmon for libraries that are not skipping salmon diff --git a/modules/bulk-star.nf b/modules/bulk-star.nf index 016a975d..bba51c65 100644 --- a/modules/bulk-star.nf +++ b/modules/bulk-star.nf @@ -38,8 +38,9 @@ workflow star_bulk{ bulk_reads_ch = bulk_channel .map{meta -> tuple(meta, file("${meta.files_directory}/*_{R1,R1_*}.fastq.gz"), - file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz"), - file("${meta.star_index}"))} + file("${meta.files_directory}/*_{R2,R2_*}.fastq.gz"), + file(meta.star_index, type: 'dir') + )} // map and index bulkmap_star(bulk_reads_ch) \ | index_bam diff --git a/modules/genetic-demux.nf b/modules/genetic-demux.nf index 9413092d..4788eed3 100644 --- a/modules/genetic-demux.nf +++ b/modules/genetic-demux.nf @@ -54,7 +54,7 @@ workflow genetic_demux_vireo{ demux_out = multiplex_ch.has_demux .map{meta -> tuple( Utils.readMeta(file("${meta.vireo_dir}/scpca-meta.json")), - file(meta.vireo_dir) + file(meta.vireo_dir, type: 'dir') )} .mix(cellsnp_vireo.out) diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf index 1cf8d03a..eca9718e 100644 --- a/modules/spaceranger.nf +++ b/modules/spaceranger.nf @@ -127,9 +127,9 @@ workflow spaceranger_quant{ // create tuple of [metadata, fastq dir, and path to image file] spaceranger_reads = spatial_channel.make_spatial .map{meta -> tuple(meta, - file("${meta.files_directory}"), + file(meta.files_directory, type: 'dir'), file("${meta.files_directory}/*.jpg"), - file("${meta.cellranger_index}") + file(meta.cellranger_index, type: 'dir') )} // run spaceranger @@ -139,7 +139,7 @@ workflow spaceranger_quant{ // make a tuple of metadata (read from prior output) and prior results directory spaceranger_quants_ch = spatial_channel.has_spatial .map{meta -> tuple(Utils.readMeta(file("${meta.spaceranger_results_dir}/scpca-meta.json")), - file("${meta.spaceranger_results_dir}") + file(meta.spaceranger_results_dir, type: 'dir') )} grouped_spaceranger_ch = spaceranger.out.mix(spaceranger_quants_ch) diff --git a/modules/starsolo.nf b/modules/starsolo.nf index 42921edd..9d0da459 100644 --- a/modules/starsolo.nf +++ b/modules/starsolo.nf @@ -62,7 +62,7 @@ workflow starsolo_map{ file("${meta.files_directory}/*_R1_*.fastq.gz"), file("${meta.files_directory}/*_R2_*.fastq.gz"), file("${params.barcode_dir}/${params.cell_barcodes[meta.technology]}"), - file("${meta.star_index}") + file(meta.star_index, type: 'dir') )} starsolo(sc_reads_ch) index_bam(starsolo.out.star_bam) From c9c80e110cf3619eae40452a6555249f97e4576b Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 6 Sep 2023 20:02:22 -0400 Subject: [PATCH 147/268] simplify celltype boolean and ensure it is set --- templates/qc_report/qc_report.rmd | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index b3700f1c..1e36c02b 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -113,11 +113,7 @@ if (has_processed) { has_submitter_celltypes <- FALSE # If at least 1 is present, we have cell type annotations. - if ( any(c(has_singler, has_cellassign, has_submitter_celltypes))) { - # use overall variable here for QC report logic - has_celltypes <- TRUE - } - + has_celltypes <- any(has_singler, has_cellassign, has_submitter_celltypes) } else { has_umap <- FALSE has_celltypes <- FALSE From 5141800781f36bf98d493f1882d7cdc7c948d207 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 7 Sep 2023 07:47:53 -0400 Subject: [PATCH 148/268] begone DS_Store --- templates/qc_report/.DS_Store | Bin 6148 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 templates/qc_report/.DS_Store diff --git a/templates/qc_report/.DS_Store b/templates/qc_report/.DS_Store deleted file mode 100644 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 Date: Thu, 7 Sep 2023 07:55:47 -0400 Subject: [PATCH 149/268] begone for everyone --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 1b8cd5ac..de1abeac 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,6 @@ scpca-references/ # ignore template htmls qc_report.html *_qc.html + +# ignore hidden `DS_Store` +.DS_Store From 11f3fe450219e036604fc498ff5026b81ce45975 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 7 Sep 2023 11:22:22 -0400 Subject: [PATCH 150/268] Apply suggestions from code review Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- templates/qc_report/celltypes_qc.rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 2afee6ad..b903d58c 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -237,13 +237,13 @@ ggplot(delta_median_df) + knitr::asis_output(" ### `CellAssign` assessment -`CellAssign` computes the probability that each cell is one of the provided cell types and ultimately annotates cells based on the highest probability. +`CellAssign` computes the probability that each cell in the library is one of the provided cell types in the reference and ultimately annotates cells by assigning the cell type with the highest probability. We therefore expect that cell-level probabilities that correspond to the annotated cell types will be high. Conversely, we expect that cell-level probabilities that correspond to annotated cell types will be low. In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type (excluding unknown cell types). -Colors represent whether the probabilities correspond to a cell with that given annotation: Purple distributions represent probabilities for cells that _were not_ annotated as the given cell type. -Yellow distribution represent probabilies for cells that _were_ annotated as the given cell type. +Colors represent whether the probabilities correspond to a cell with that given annotation: Yellow distribution represent probabilies for cells that _were_ annotated as the given cell type. +Purple distributions represent probabilities for cells that _were not_ annotated as the given cell type. For distributions with fewer than three points, density plots cannot be calculated. In these cases, we directly show values for individual cell probabilities as points. ") From fb75c45eec0530fb5e019e2e84df2cb61070a5ab Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 7 Sep 2023 11:24:10 -0400 Subject: [PATCH 151/268] plural yellow distributionS --- templates/qc_report/celltypes_qc.rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index b903d58c..9bb9079a 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -242,7 +242,7 @@ We therefore expect that cell-level probabilities that correspond to the annotat Conversely, we expect that cell-level probabilities that correspond to annotated cell types will be low. In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type (excluding unknown cell types). -Colors represent whether the probabilities correspond to a cell with that given annotation: Yellow distribution represent probabilies for cells that _were_ annotated as the given cell type. +Colors represent whether the probabilities correspond to a cell with that given annotation: Yellow distributions represent probabilies for cells that _were_ annotated as the given cell type. Purple distributions represent probabilities for cells that _were not_ annotated as the given cell type. For distributions with fewer than three points, density plots cannot be calculated. In these cases, we directly show values for individual cell probabilities as points. From 7e3a468af12002bf6be8dc2b28917f57bfd48d1d Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 10:25:29 -0500 Subject: [PATCH 152/268] add process for rearranging counts and logcounts in AnnData --- bin/move_counts_anndata.py | 46 ++++++++++++++++++++++++++++++++++++++ bin/sce_to_anndata.R | 6 ++--- modules/export-anndata.nf | 24 ++++++++++++++++++-- 3 files changed, 71 insertions(+), 5 deletions(-) create mode 100644 bin/move_counts_anndata.py diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py new file mode 100644 index 00000000..8657d2cf --- /dev/null +++ b/bin/move_counts_anndata.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 + +# This script takes an AnnData object and checks for the `logcounts` +# in layers. If present, `logcounts` is moved to `X` and `X` (which has the raw counts) +# is moved to `raw.X` + +import os +import anndata as adata +import argparse +import re + +parser = argparse.ArgumentParser() +parser.add_argument('-i', '--input_hdf5_file', + dest = 'input_hdf5_file', + required = True, + help = 'Path to HDF5 file(s) with processed AnnData object. If more than one file, separate with comma.') + +args = parser.parse_args() + +# separate input files +input_files = args.input_hdf5_file.split(",") + +# compile extension regex +file_ext = re.compile(r"\.hdf5$|.h5$", re.IGNORECASE) + +for file in input_files: + # check that input file exists, if it does exist, make sure it's an h5 file + if not os.path.exists(file): + raise FileExistsError("Make sure that all input_hdf5_file exist.") + elif not file_ext.search(file): + raise ValueError("--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object.") + + # read in anndata + object = adata.read_h5ad(file) + + # if logcounts is present + if "logcounts" in object.layers.keys(): + # move X to raw.X, first we need to initialize the raw.X + object.raw = object + object.raw.X = object.X + + # move logcounts to X + object.X = object.layers["logcounts"] + + # export object + object.write_h5ad(file) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 37efefba..f4d35b12 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -81,7 +81,7 @@ format_czi <- function(sce){ } -# AltExp to AnnData ----------------------------------------------------------- +# MainExp to AnnData ----------------------------------------------------------- # read in sce sce <- readr::read_rds(opt$input_sce_file) @@ -90,8 +90,6 @@ sce <- readr::read_rds(opt$input_sce_file) # we need this if we have any feature data that we need to add it o sample_metadata <- metadata(sce)$sample_metadata -# MainExp to AnnData ----------------------------------------------------------- - # make main sce czi compliant sce <- format_czi(sce) @@ -101,6 +99,8 @@ scpcaTools::sce_to_anndata( anndata_file = opt$output_rna_h5 ) +# AltExp to AnnData ----------------------------------------------------------- + # if feature data exists, grab it and export to AnnData if(!is.null(opt$feature_name)){ diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index d51dd2e0..79ccd0d7 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -29,6 +29,23 @@ process export_anndata{ """ } +process move_normalized_counts{ + container params.SCPCATOOLS_CONTAINER + label 'mem_4' + tag "${meta.library_id}" + publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' + input: + tuple val(meta), path(unfiltered_hdf5), path(filtered_hdf5), path(processed_hdf5) + output: + tuple val(meta), path(unfiltered_hdf5), path(filtered_hdf5), path(processed_hdf5) + script: + input_hdf5_files = processed_hdf5.join(',') + """ + move_counts_anndata.py \ + --input_hdf5_file ${input_hdf5_files} + """ +} + workflow sce_to_anndata{ take: @@ -48,13 +65,16 @@ workflow sce_to_anndata{ // creates anndata channel with [library_id, unfiltered, filtered, processed] anndata_ch = export_anndata.out .map{ meta, hdf5_files -> tuple( - meta.library_id, + meta.library_id, meta, hdf5_files )} .groupTuple(by: 0, size: 3, remainder: true) .map{ [it[1][0]] + it[2] } - emit: anndata_ch + // move any normalized counts to X in AnnData + move_normalized_counts(anndata_ch) + + emit: move_normalized_counts.out } From 2dd92399bb44048e1c382bf9a05b70faf63e023c Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 7 Sep 2023 11:46:32 -0400 Subject: [PATCH 153/268] Update plot in response to reviews, and other tweaks that might be useful --- templates/qc_report/celltypes_qc.rmd | 47 ++++++++++++++-------------- 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 9bb9079a..b3810ba7 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -241,47 +241,42 @@ knitr::asis_output(" We therefore expect that cell-level probabilities that correspond to the annotated cell types will be high. Conversely, we expect that cell-level probabilities that correspond to annotated cell types will be low. -In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type (excluding unknown cell types). -Colors represent whether the probabilities correspond to a cell with that given annotation: Yellow distributions represent probabilies for cells that _were_ annotated as the given cell type. -Purple distributions represent probabilities for cells that _were not_ annotated as the given cell type. +In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type. +Colors represent whether the probabilities correspond to a cell with that given annotation: Purple distributions represent probabilies for cells that _were_ annotated as the given cell type. +Yellow distributions represent probabilities for cells that _were not_ annotated as the given cell type. For distributions with fewer than three points, density plots cannot be calculated. -In these cases, we directly show values for individual cell probabilities as points. +In these cases, we directly show values for individual cell probabilities as line segments. ") ``` -```{r, eval = has_cellassign, warning=FALSE, message=FALSE,fig.height = 7, fig.width = 8} +```{r, eval = has_cellassign, warning=FALSE, message=FALSE, fig.height = 6, fig.width = 8} # Prepare CellAssign scores for plot cellassign_prob_df <- metadata(processed_sce)$cellassign_predictions |> + # Change "other" to "Unknown cell type" + dplyr::rename(`Unknown cell type` = other) |> tidyr::pivot_longer( -barcode, names_to = "celltype", values_to = "probability" ) |> # remove cell types that were not annotated - # bonus: ths will also remove the "other" level, which we don't want to show anyways dplyr::filter(celltype %in% celltype_df$cellassign_celltype_annotation) |> # join with actual annotations - # but use inner_join to avoid bringing back the others dplyr::inner_join( tibble::tibble( cellassign_celltype_annotation = celltype_df$cellassign_celltype_annotation, barcode = colData(processed_sce)$barcodes # plural! ) ) |> - # remove all the unknown cell types from this plot - dplyr::filter( - cellassign_celltype_annotation != "Unknown cell type" - ) |> # add indicator for whether the celltype matches the annotation dplyr::mutate( annotated = cellassign_celltype_annotation == celltype ) -# remove "Unknown cell type" from levels, and wrap the labels -new_levels <- levels(cellassign_prob_df$cellassign_celltype_annotation) -new_levels <- rev(new_levels[-length(new_levels)]) # reverse for ridgeplot +# reverse levels for ridgeplot layout, and wrap the labels +new_levels <- rev(levels(cellassign_prob_df$cellassign_celltype_annotation)) cellassign_prob_df$annotation_wrapped <- factor( cellassign_prob_df$celltype, levels = new_levels, @@ -299,7 +294,7 @@ celltypes_leq2_cells <- cellassign_prob_df |> leq2_probabilities_df <- cellassign_prob_df |> dplyr::filter( annotation_wrapped %in% celltypes_leq2_cells, - annotated + annotated ) |> dplyr::select(annotation_wrapped, probability, annotated) @@ -310,8 +305,10 @@ ggplot(cellassign_prob_df) + fill = annotated) + ggridges::stat_density_ridges(quantile_lines = TRUE, quantiles = 2, - alpha = 0.6) + - scale_fill_viridis_d() + + alpha = 0.6, + # avoid overlap to extent possible in a template - + scale = 0.85) + + scale_fill_viridis_d(direction = -1) + labs( x = "CellAssign probability", y = "Annotated cell type", @@ -320,17 +317,19 @@ ggplot(cellassign_prob_df) + theme( axis.text.y = element_text(size = 9) ) + - # add back points for leq2 cells - geom_point( + #### add line segment for N<3 distributions + geom_segment( data = leq2_probabilities_df, aes( x = probability, - y = annotation_wrapped + xend = probability, + y = annotation_wrapped, + yend = as.numeric(annotation_wrapped) + 0.25, + color = annotated ), - size = 1.5, pch = 23, color = "black", linewidth = 0.1, - position = position_nudge(y = 0.075), # place point slightly above the axis line show.legend = FALSE - ) + ) + + scale_color_viridis_d() ``` @@ -537,7 +536,7 @@ create_celltype_heatmap( ```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} knitr::asis_output(" -## Comparison Between Annotations +## Comparison between annotations Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. Note that due to different annotations references, these methods may use different names for similar cell types. From 3d49080cb474e8daf42bdc89364adf5e33fdf5c7 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 11:34:43 -0500 Subject: [PATCH 154/268] make sure only processed object is passed through --- modules/export-anndata.nf | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 79ccd0d7..32c0303d 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -8,7 +8,7 @@ process export_anndata{ input: tuple val(meta), path(sce_file), val(file_type) output: - tuple val(meta), path("${meta.library_id}_${file_type}*.hdf5") + tuple val(meta), path("${meta.library_id}_${file_type}*.hdf5"), val(file_type) script: rna_hdf5_file = "${meta.library_id}_${file_type}_rna.hdf5" feature_hdf5_file = "${meta.library_id}_${file_type}_${meta.feature_type}.hdf5" @@ -35,9 +35,9 @@ process move_normalized_counts{ tag "${meta.library_id}" publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: - tuple val(meta), path(unfiltered_hdf5), path(filtered_hdf5), path(processed_hdf5) + tuple val(meta), path(processed_hdf5), val(file_type) output: - tuple val(meta), path(unfiltered_hdf5), path(filtered_hdf5), path(processed_hdf5) + tuple val(meta), path(processed_hdf5), val(file_type) script: input_hdf5_files = processed_hdf5.join(',') """ @@ -61,10 +61,17 @@ workflow sce_to_anndata{ // export each anndata file export_anndata(sce_ch) + processed_anndata_ch = export_anndata.out + .filter{ it[2] == "processed"} + + // move any normalized counts to X in AnnData + move_normalized_counts(processed_anndata_ch) + // combine all anndata files by library id // creates anndata channel with [library_id, unfiltered, filtered, processed] anndata_ch = export_anndata.out - .map{ meta, hdf5_files -> tuple( + .join(move_normalized_counts.out, by: [0-2]) + .map{ meta, hdf5_files, file_type -> tuple( meta.library_id, meta, hdf5_files @@ -72,9 +79,6 @@ workflow sce_to_anndata{ .groupTuple(by: 0, size: 3, remainder: true) .map{ [it[1][0]] + it[2] } - // move any normalized counts to X in AnnData - move_normalized_counts(anndata_ch) - - emit: move_normalized_counts.out + emit: anndata_ch } From 5ea41a645f308435b5597f5accaf51d7d29fa416 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 11:35:23 -0500 Subject: [PATCH 155/268] rename x_name --- bin/move_counts_anndata.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index 8657d2cf..c1ff48db 100644 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -35,12 +35,12 @@ # if logcounts is present if "logcounts" in object.layers.keys(): - # move X to raw.X, first we need to initialize the raw.X + # move X to raw.X by creating the raw object object.raw = object - object.raw.X = object.X - # move logcounts to X + # move logcounts to X and rename object.X = object.layers["logcounts"] + object.uns["X_name"] = "logcounts" # export object object.write_h5ad(file) From cc49614a83afdda39fff6cc9b9773f88a10b1184 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 7 Sep 2023 13:16:34 -0400 Subject: [PATCH 156/268] Move legend to bottom and add sentence that there is a median line in the plot. Remove a DS_Store which somehow showed up?? --- templates/qc_report/.DS_Store | Bin 6148 -> 0 bytes templates/qc_report/celltypes_qc.rmd | 7 ++++--- 2 files changed, 4 insertions(+), 3 deletions(-) delete mode 100644 templates/qc_report/.DS_Store diff --git a/templates/qc_report/.DS_Store b/templates/qc_report/.DS_Store deleted file mode 100644 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 @@ -315,7 +315,8 @@ ggplot(cellassign_prob_df) + fill = "Cell annotated as given cell type" ) + theme( - axis.text.y = element_text(size = 9) + axis.text.y = element_text(size = 9), + legend.position = "bottom" ) + #### add line segment for N<3 distributions geom_segment( From 6901b46eb781b7d71b84e6555f7a1da8dce6a8f5 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 12:19:28 -0500 Subject: [PATCH 157/268] properly mix outputs --- modules/export-anndata.nf | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 32c0303d..a324f37e 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -31,7 +31,7 @@ process export_anndata{ process move_normalized_counts{ container params.SCPCATOOLS_CONTAINER - label 'mem_4' + label 'mem_8' tag "${meta.library_id}" publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: @@ -70,7 +70,10 @@ workflow sce_to_anndata{ // combine all anndata files by library id // creates anndata channel with [library_id, unfiltered, filtered, processed] anndata_ch = export_anndata.out - .join(move_normalized_counts.out, by: [0-2]) + // remove any files that were processed and went through reorganization + .filter{ it[2] != "processed" } + // mix with output from moving counts + .mix(move_normalized_counts.out) .map{ meta, hdf5_files, file_type -> tuple( meta.library_id, meta, From a7727de77613f77f6b04e3c08ad11ca2e7362fa7 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 12:22:00 -0500 Subject: [PATCH 158/268] make script executable --- bin/move_counts_anndata.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 bin/move_counts_anndata.py diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py old mode 100644 new mode 100755 From eaf2e5b45e96e3b618dc8fad502d6024b677f01f Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 7 Sep 2023 12:29:01 -0500 Subject: [PATCH 159/268] use python not python3 --- bin/move_counts_anndata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index c1ff48db..68971070 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python # This script takes an AnnData object and checks for the `logcounts` # in layers. If present, `logcounts` is moved to `X` and `X` (which has the raw counts) From a050ffdac9f6efb22627e6601f3f1d1d9bfedbcf Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 7 Sep 2023 14:08:00 -0400 Subject: [PATCH 160/268] Update templates/qc_report/celltypes_qc.rmd Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- templates/qc_report/celltypes_qc.rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 457b1f58..f2845831 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -239,7 +239,7 @@ knitr::asis_output(" `CellAssign` computes the probability that each cell in the library is one of the provided cell types in the reference and ultimately annotates cells by assigning the cell type with the highest probability. We therefore expect that cell-level probabilities that correspond to the annotated cell types will be high. -Conversely, we expect that cell-level probabilities that correspond to annotated cell types will be low. +Conversely, we expect that cell-level probabilities that correspond to unannotated cell types will be low. In the plot below, we show distributions of the `CellAssign` probabilities for each assigned cell type, where the median is shown as a vertical line in each. Colors represent whether the probabilities correspond to a cell with that given annotation: Purple distributions represent probabilies for cells that _were_ annotated as the given cell type. From bcf161890ed711a949ff2c85cdfcead479594e07 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 7 Sep 2023 16:13:51 -0500 Subject: [PATCH 161/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- bin/move_counts_anndata.py | 7 ++++--- modules/export-anndata.nf | 15 +++++++++++---- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index 68971070..b4ae24d1 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -1,14 +1,15 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # This script takes an AnnData object and checks for the `logcounts` # in layers. If present, `logcounts` is moved to `X` and `X` (which has the raw counts) # is moved to `raw.X` -import os -import anndata as adata import argparse +import os import re +import anndata as adata + parser = argparse.ArgumentParser() parser.add_argument('-i', '--input_hdf5_file', dest = 'input_hdf5_file', diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index a324f37e..229587b0 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -44,6 +44,10 @@ process move_normalized_counts{ move_counts_anndata.py \ --input_hdf5_file ${input_hdf5_files} """ + stub: + """ + # nothing to do since files don't move + """ } @@ -61,15 +65,18 @@ workflow sce_to_anndata{ // export each anndata file export_anndata(sce_ch) - processed_anndata_ch = export_anndata.out - .filter{ it[2] == "processed"} + anndata_ch = export_anndata.out + .branch{ + processed: it[2] == "processed" + other: true + } // move any normalized counts to X in AnnData - move_normalized_counts(processed_anndata_ch) + move_normalized_counts(anndata_ch.processed) // combine all anndata files by library id // creates anndata channel with [library_id, unfiltered, filtered, processed] - anndata_ch = export_anndata.out + anndata_ch = anndata_ch.other.mix(move_normalized_counts.out) // remove any files that were processed and went through reorganization .filter{ it[2] != "processed" } // mix with output from moving counts From 8dd6f611cb0473ddd476b68f16a52d207cd6245b Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 7 Sep 2023 16:33:26 -0500 Subject: [PATCH 162/268] change script to only take in one file at a time --- bin/move_counts_anndata.py | 48 +++++++++++++++++--------------------- modules/export-anndata.nf | 18 +++++++------- 2 files changed, 31 insertions(+), 35 deletions(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index b4ae24d1..bace86dc 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -11,37 +11,31 @@ import anndata as adata parser = argparse.ArgumentParser() -parser.add_argument('-i', '--input_hdf5_file', - dest = 'input_hdf5_file', +parser.add_argument('-i', '--anndata_file', + dest = 'anndata_file', required = True, - help = 'Path to HDF5 file(s) with processed AnnData object. If more than one file, separate with comma.') + help = 'Path to HDF5 file with processed AnnData object') args = parser.parse_args() -# separate input files -input_files = args.input_hdf5_file.split(",") - # compile extension regex file_ext = re.compile(r"\.hdf5$|.h5$", re.IGNORECASE) -for file in input_files: - # check that input file exists, if it does exist, make sure it's an h5 file - if not os.path.exists(file): - raise FileExistsError("Make sure that all input_hdf5_file exist.") - elif not file_ext.search(file): - raise ValueError("--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object.") - - # read in anndata - object = adata.read_h5ad(file) - - # if logcounts is present - if "logcounts" in object.layers.keys(): - # move X to raw.X by creating the raw object - object.raw = object - - # move logcounts to X and rename - object.X = object.layers["logcounts"] - object.uns["X_name"] = "logcounts" - - # export object - object.write_h5ad(file) +# check that input file exists, if it does exist, make sure it's an h5 file +if not os.path.exists(args.anndata_file): + raise FileExistsError("`input_anndata` does not exist.") +elif not file_ext.search(args.anndata_file): + raise ValueError("--input_anndata must end in either .hdf5 or .h5 and contain a processed AnnData object.") + +# read in anndata +object = adata.read_h5ad(args.anndata_file) + +# if logcounts is present +if "logcounts" in object.layers.keys(): + # move X to raw.X by creating the raw object + object.raw = object + # move logcounts to X and rename + object.X = object.layers["logcounts"] + object.uns["X_name"] = "logcounts" + # export object + object.write_h5ad(args.anndata_file) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 229587b0..e308e430 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -39,10 +39,11 @@ process move_normalized_counts{ output: tuple val(meta), path(processed_hdf5), val(file_type) script: - input_hdf5_files = processed_hdf5.join(',') """ - move_counts_anndata.py \ - --input_hdf5_file ${input_hdf5_files} + for file in ${processed_hdf5}; do + move_counts_anndata.py \ + --anndata_file \${file} + done """ stub: """ @@ -75,18 +76,19 @@ workflow sce_to_anndata{ move_normalized_counts(anndata_ch.processed) // combine all anndata files by library id - // creates anndata channel with [library_id, unfiltered, filtered, processed] anndata_ch = anndata_ch.other.mix(move_normalized_counts.out) - // remove any files that were processed and went through reorganization - .filter{ it[2] != "processed" } // mix with output from moving counts .mix(move_normalized_counts.out) .map{ meta, hdf5_files, file_type -> tuple( - meta.library_id, + meta.library_id, // pull out library id for grouping meta, - hdf5_files + hdf5_files // either rna.hdf5 or [ rna.hdf5, feature.hdf5 ] )} + // group by library id result is + // [library id, [meta, meta, meta], [hdf5 files]] .groupTuple(by: 0, size: 3, remainder: true) + // pull out just 1 meta object and hdf5 files + // [meta, [hdf5 files]] .map{ [it[1][0]] + it[2] } emit: anndata_ch From 281142ab58fd3fe86b2a5e8de4d6a001a1de3590 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 8 Sep 2023 11:38:24 -0400 Subject: [PATCH 163/268] change param name from label_name -> singler_label_name, since we have cellassign now too --- build-celltype-ref.nf | 2 +- config/profile_ccdl.config | 2 +- modules/classify-celltypes.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/build-celltype-ref.nf b/build-celltype-ref.nf index 9192d455..8730b8f4 100644 --- a/build-celltype-ref.nf +++ b/build-celltype-ref.nf @@ -40,7 +40,7 @@ process train_singler_models { --ref_file ${ref_file} \ --output_file ${celltype_model} \ --fry_tx2gene ${t2g_3col_path} \ - --label_name ${params.label_name} \ + --label_name ${params.singler_label_name} \ --seed ${params.seed} \ --threads ${task.cpus} """ diff --git a/config/profile_ccdl.config b/config/profile_ccdl.config index 375feecc..73f00976 100644 --- a/config/profile_ccdl.config +++ b/config/profile_ccdl.config @@ -15,7 +15,7 @@ params{ // cell type references and SingleR label of interest celltype_project_metafile = "s3://ccdl-scpca-data/sample_info/celltype_annotation/scpca-project-celltype-metadata.tsv" - label_name = "label.ont" + singler_label_name = "label.ont" // Private CCDL containers diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 07c757db..6c6217ed 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -14,7 +14,7 @@ process classify_singleR { --input_sce_file ${processed_rds} \ --output_sce_file ${annotated_rds} \ --singler_model_file ${singler_model_file} \ - --label_name ${params.label_name} \ + --label_name ${params.singler_label_name} \ --seed ${params.seed} \ --threads ${task.cpus} """ From ed55fc2a1d4efaf64573c000f2cdc6772e633ae8 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 8 Sep 2023 11:32:51 -0400 Subject: [PATCH 164/268] Add note to contributing doc on code styles --- CONTRIBUTING.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 95d5753d..e4fb53ed 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -25,7 +25,17 @@ When the changes in `development` merit a new release, a pull request will be fi All Nextflow processes should include a [`stub` block](https://www.nextflow.io/docs/latest/process.html#stub) with a minimal script that can be run quickly to produce files in the expected output locations. At this stage this is purely used to allow for testing of the main workflow logic rather than the internal logic of each process. -The [`test/stub-metadata.tsv`](test/stub-metadata.tsv) file is used to define input libraries that will be used for testing. +The [`test/stub-run-metadata.tsv`](test/stub-run-metadata.tsv) file is used to define input libraries that will be used for testing. Any additions to the overall workflow that will allow processing of a new library type should be added into `test/stub-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for that library type in the `test/runs/` directory. If a new reference type is needed, that should be defined in the [`test/stub-refs.json`](test/stub-refs.json) file. +## Code style + +While there is not necessarily an established code style for nextflow code, we try to keep code neat and readable. +Line length should generally be kept under 100 characters, and indentation should be consistent. + +For R code, we try to follow [tidyverse style conventions](https://style.tidyverse.org), and encourage the use of the [`styler`](https://styler.r-lib.org/) package to ensure that code is formatted consistently. + +For python code, we encourage the use of the `black` code formatter to ensure consistent formatting. +The `black` package can be installed with `pip install black`, and can be run on a file with `black `. +Alternatively, if you use VSCode, you can install the [black extension](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter). From 1d9511476a58bf6faef45f7d5f9071a06df19369 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 8 Sep 2023 11:55:43 -0400 Subject: [PATCH 165/268] format python & config files --- bin/predict_cellassign.py | 69 ++++++++++------ get_refs.py | 165 ++++++++++++++++++++++---------------- nextflow.config | 2 +- 3 files changed, 140 insertions(+), 96 deletions(-) diff --git a/bin/predict_cellassign.py b/bin/predict_cellassign.py index 169c25d7..49d905d1 100644 --- a/bin/predict_cellassign.py +++ b/bin/predict_cellassign.py @@ -15,28 +15,43 @@ import re parser = argparse.ArgumentParser() -parser.add_argument('-i', '--input_hdf5_file', - dest = 'input_hdf5_file', - required = True, - help = 'Path to HDF5 file with processed AnnData object to annotate') -parser.add_argument('-o', '--output_predictions', - dest = 'output_predictions', - required = True, - help = 'Path to file to save the predictions, should end in tsv') -parser.add_argument('-r', '--reference', - dest = 'reference', - required = True, - help = 'Path to marker by cell type reference file, should end in tsv') -parser.add_argument('-s', '--seed', - dest = 'seed', - type=int, - default = None, - help = 'Random seed to set for scvi.') -parser.add_argument('-t', '--threads', - dest = 'threads', - default = 1, - type = int, - help = 'Number of threads to use when training the CellAssign model') +parser.add_argument( + "-i", + "--input_hdf5_file", + dest="input_hdf5_file", + required=True, + help="Path to HDF5 file with processed AnnData object to annotate", +) +parser.add_argument( + "-o", + "--output_predictions", + dest="output_predictions", + required=True, + help="Path to file to save the predictions, should end in tsv", +) +parser.add_argument( + "-r", + "--reference", + dest="reference", + required=True, + help="Path to marker by cell type reference file, should end in tsv", +) +parser.add_argument( + "-s", + "--seed", + dest="seed", + type=int, + default=None, + help="Random seed to set for scvi.", +) +parser.add_argument( + "-t", + "--threads", + dest="threads", + default=1, + type=int, + help="Number of threads to use when training the CellAssign model", +) args = parser.parse_args() @@ -53,7 +68,9 @@ if not os.path.exists(args.input_hdf5_file): raise FileExistsError("--input_hdf5_file file not found.") elif not file_ext.search(args.input_hdf5_file): - raise ValueError("--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object.") + raise ValueError( + "--input_hdf5_file must end in either .hdf5 or .h5 and contain a processed AnnData object." + ) # check that marker file exists and make sure its a tsv if not os.path.exists(args.reference): @@ -64,7 +81,7 @@ raise ValueError("--output_predictions must provide a file path ending in tsv") # read in references as marker gene tables -ref_matrix = pd.read_csv(args.reference, sep = "\t", index_col='ensembl_id') +ref_matrix = pd.read_csv(args.reference, sep="\t", index_col="ensembl_id") # file path to annotated sce annotated_adata = adata.read_h5ad(args.input_hdf5_file) @@ -85,7 +102,7 @@ model = CellAssign(subset_adata, ref_matrix) model.train() predictions = model.predict() -predictions['barcode'] = subset_adata.obs_names +predictions["barcode"] = subset_adata.obs_names # write out predictions as tsv -predictions.to_csv(args.output_predictions, sep = "\t", index = False) +predictions.to_csv(args.output_predictions, sep="\t", index=False) diff --git a/get_refs.py b/get_refs.py index d51fd648..8820516c 100755 --- a/get_refs.py +++ b/get_refs.py @@ -20,34 +20,51 @@ from pathlib import Path parser = argparse.ArgumentParser() -parser.add_argument("--refdir", type=str, - default="scpca-references", - help = "destination directory for downloaded reference files") -parser.add_argument("--paramfile", type=str, - default="localref_params.yaml", - help = "path to nextflow param file to write (default: `localref_params.yaml`)") -parser.add_argument("--overwrite_refs", - action = "store_true", - help = "replace previously downloaded files") -parser.add_argument("-r", "--revision", type=str, - default="main", - metavar = "vX.X.X", - help = "tag for a specific workflow version (defaults to latest revision)") -parser.add_argument("--star_index", - action = "store_true", - help = "get STAR index (required for genetic demultiplexing)") -parser.add_argument("--cellranger_index", - action = "store_true", - help = "get Cell Ranger index (required for spatial data)") -parser.add_argument("--docker", - action = "store_true", - help = "pull and cache images for docker") -parser.add_argument("--singularity", - action = "store_true", - help = "pull and cache images for singularity") -parser.add_argument("--singularity_dir", type=str, - default = "singularity", - help = "directory to store singularity image files (default: `singularity`)") +parser.add_argument( + "--refdir", + type=str, + default="scpca-references", + help="destination directory for downloaded reference files", +) +parser.add_argument( + "--paramfile", + type=str, + default="localref_params.yaml", + help="path to nextflow param file to write (default: `localref_params.yaml`)", +) +parser.add_argument( + "--overwrite_refs", action="store_true", help="replace previously downloaded files" +) +parser.add_argument( + "-r", + "--revision", + type=str, + default="main", + metavar="vX.X.X", + help="tag for a specific workflow version (defaults to latest revision)", +) +parser.add_argument( + "--star_index", + action="store_true", + help="get STAR index (required for genetic demultiplexing)", +) +parser.add_argument( + "--cellranger_index", + action="store_true", + help="get Cell Ranger index (required for spatial data)", +) +parser.add_argument( + "--docker", action="store_true", help="pull and cache images for docker" +) +parser.add_argument( + "--singularity", action="store_true", help="pull and cache images for singularity" +) +parser.add_argument( + "--singularity_dir", + type=str, + default="singularity", + help="directory to store singularity image files (default: `singularity`)", +) args = parser.parse_args() # scpca-nf resource urls @@ -59,11 +76,13 @@ # download reference file print("Getting list of required reference files") try: - ref_file = urllib.request.urlopen(reffile_url) + ref_file = urllib.request.urlopen(reffile_url) json_file = urllib.request.urlopen(refjson_url) except urllib.error.URLError as e: print(e.reason) - print(f"The file download failed for {reffile_url} and/or {refjson_url}; please check the URLs for errors") + print( + f"The file download failed for {reffile_url} and/or {refjson_url}; please check the URLs for errors" + ) print(f"Is `{args.revision}` a valid release tag?") exit(1) @@ -75,21 +94,21 @@ for line in ref_file: match = ref_re.search(line.decode()) if match: - refs[match.group('id')] = match.group('loc') + refs[match.group("id")] = match.group("loc") # regular expressions for parameter expansion -root_re = re.compile(r'\$\{?(params.)?ref_rootdir\}?$') +root_re = re.compile(r"\$\{?(params.)?ref_rootdir\}?$") # get root location # split out protocol from the root URI -root_parts = refs.get("ref_rootdir").split('://', maxsplit = 1) -if root_parts[0] == 's3': +root_parts = refs.get("ref_rootdir").split("://", maxsplit=1) +if root_parts[0] == "s3": # if S3, convert bucket path to https:// url - bucket_path = root_parts[1].split("/", maxsplit = 1) + bucket_path = root_parts[1].split("/", maxsplit=1) url_root = f"https://{bucket_path[0]}.s3.amazonaws.com" if len(bucket_path) > 1: url_root += f"/{bucket_path[1]}" -elif root_parts[0] in ['http', 'https', 'ftp']: +elif root_parts[0] in ["http", "https", "ftp"]: # otherwise, just get the location url_root = refs.get("ref_rootdir") else: @@ -98,20 +117,17 @@ # single-file references # the keys here are the param variables we will be downloading -ref_keys =[ +ref_keys = [ "ref_fasta", "ref_fasta_index", "ref_gtf", "mito_file", "t2g_3col_path", - "t2g_bulk_path" + "t2g_bulk_path", ] # param variables that are salmon index directories -salmon_keys = [ - "splici_index", - "salmon_bulk_index" -] +salmon_keys = ["splici_index", "salmon_bulk_index"] # salmon index files within index dir (must be downloaded individually through http) salmon_index_files = [ @@ -129,7 +145,7 @@ "reflengths.bin", "refseq.bin", "seq.bin", - "versionInfo.json" + "versionInfo.json", ] # star index files within index dir (must be downloaded individually through http) @@ -149,7 +165,7 @@ "sjdbInfo.txt", "sjdbList.fromGTF.out.tab", "sjdbList.out.tab", - "transcriptInfo.tab" + "transcriptInfo.tab", ] # Cell Ranger index files within index dir (must be downloaded individually through http) @@ -172,7 +188,7 @@ "star/sjdbInfo.txt", "star/sjdbList.fromGTF.out.tab", "star/sjdbList.out.tab", - "star/transcriptInfo.tab" + "star/transcriptInfo.tab", ] # create a list of all paths for all assemblies listed in reference json file @@ -185,13 +201,17 @@ # get paths to salmon directories and add individual files sa_dir = [Path(assembly_refs.get(k)) for k in salmon_keys] for dir in sa_dir: - ref_paths += [dir / f for f in salmon_index_files] # add salmon files + ref_paths += [dir / f for f in salmon_index_files] # add salmon files # if cellranger and star index's are asked for, get individual files if args.cellranger_index: - ref_paths += [Path(assembly_refs.get("cellranger_index")) / f for f in cr_index_files] # add cellranger files + ref_paths += [ + Path(assembly_refs.get("cellranger_index")) / f for f in cr_index_files + ] # add cellranger files if args.star_index: - ref_paths += [Path(assembly_refs.get("star_index")) / f for f in star_index_files] # add star index files + ref_paths += [ + Path(assembly_refs.get("star_index")) / f for f in star_index_files + ] # add star index files # barcode paths are still kept in the reference config file, so add those separately # barcode files on S3 within the barcode_dir (must be downloaded individually through http) @@ -200,7 +220,7 @@ "737K-august-2016.txt", "cellranger_mit_license.txt", "visium-v1.txt", - "visium-v2.txt" + "visium-v2.txt", ] barcode_dir = Path(refs.get("barcode_dir")) if root_re.match(barcode_dir.parts[0]): @@ -215,32 +235,38 @@ continue print(f"Getting {path}") # make parents - outfile.parent.mkdir(exist_ok=True, parents = True) + outfile.parent.mkdir(exist_ok=True, parents=True) # download and write file_url = f"{url_root}/{path}" try: urllib.request.urlretrieve(file_url, outfile) except urllib.error.URLError as e: print(e.reason) - print(f"The file download failed for {file_url}; please check the URL for errors", - file = sys.stderr) + print( + f"The file download failed for {file_url}; please check the URL for errors", + file=sys.stderr, + ) exit(1) -print("Done with reference file downloads\n" - f"Reference files can be found at '{args.refdir}'\n") +print( + "Done with reference file downloads\n" + f"Reference files can be found at '{args.refdir}'\n" +) # write param file if requested if args.paramfile: pfile = Path(args.paramfile) # check if paramfile exists & move old if needed if pfile.exists(): - print(f"A file already exists at `{pfile}`; renaming previous file to `{pfile.name}.bak`") + print( + f"A file already exists at `{pfile}`; renaming previous file to `{pfile.name}.bak`" + ) shutil.move(pfile, str(pfile) + ".bak") # create parameter dictionary - nf_params = { - 'ref_rootdir': os.path.abspath(args.refdir) - } - with open(pfile, 'w') as f: - f.write("# local nextflow reference file parameters, generated by `get_refs.py`\n\n") + nf_params = {"ref_rootdir": os.path.abspath(args.refdir)} + with open(pfile, "w") as f: + f.write( + "# local nextflow reference file parameters, generated by `get_refs.py`\n\n" + ) for key, value in nf_params.items(): f.write(f"{key}: {value}\n") @@ -249,10 +275,12 @@ print("Getting list of required containers") containers = {} try: - container_file = urllib.request.urlopen(containerfile_url) + container_file = urllib.request.urlopen(containerfile_url) except urllib.error.URLError as e: print(e.reason) - print(f"The file download failed for {container_url}; please check the URL for errors") + print( + f"The file download failed for {containerfile_url}; please check the URL for errors" + ) print(f"Is `{args.revision}` a valid release tag?") exit(1) @@ -261,7 +289,7 @@ for line in container_file: match = container_re.search(line.decode()) if match: - containers[match.group('id')] = match.group('loc') + containers[match.group("id")] = match.group("loc") # pull docker images if requested if args.docker: @@ -283,11 +311,10 @@ print(image_path) if image_path.exists(): image_path.unlink() - subprocess.run([ - "singularity", "pull", - "--name", image_path, - f"docker://{loc}" - ]) + subprocess.run(["singularity", "pull", "--name", image_path, f"docker://{loc}"]) print("Done pulling singularity images") - print(f"Singularity images located at {image_dir.absolute()}; be sure to set `singularity.cacheDir` in your configuration file to this value") + print( + f"Singularity images located at {image_dir.absolute()}." + " Be sure to set `singularity.cacheDir` in your configuration file to this value" + ) print() diff --git a/nextflow.config b/nextflow.config index ff38d381..1b9652ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -46,7 +46,7 @@ params { gene_cutoff = 200 // minimum number of genes per cell cutoff used for filtering cells num_hvg = 2000 // number of high variance genes to use for dimension reduction num_pcs = 50 // number of principal components to retain in the returned SingleCellExperiment object - + // SCE clustering options cluster_algorithm = "louvain" // default graph-based clustering algorithm cluster_weighting = "jaccard" // default weighting scheme for graph-based clustering From b20fcb1174686e73ad3857b7e01e98ff86f83697 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 8 Sep 2023 12:03:13 -0400 Subject: [PATCH 166/268] Format R scripts --- bin/add_demux_sce.R | 34 ++++++------- bin/classify_SingleR.R | 23 +++++---- bin/classify_cellassign.R | 17 ++++--- bin/cluster_sce.R | 12 ++--- bin/filter_sce_rds.R | 39 +++++++-------- bin/generate_bulk_metadata.R | 61 +++++++++++++----------- bin/generate_cellassign_refs.R | 36 +++++++------- bin/generate_spaceranger_metadata.R | 37 ++++++++------- bin/generate_unfiltered_sce.R | 41 ++++++++-------- bin/integrate_sce.R | 32 +++++++------ bin/make_reference_fasta.R | 37 +++++++++------ bin/merge_counts_tximport.R | 8 ++-- bin/merge_sces.R | 74 ++++++++++++++++------------- bin/post_process_sce.R | 53 ++++++++++----------- bin/save_singler_refs.R | 6 +-- bin/sce_qc_report.R | 49 +++++++++++-------- bin/sce_to_anndata.R | 19 ++++---- bin/train_SingleR.R | 20 ++++---- 18 files changed, 321 insertions(+), 277 deletions(-) diff --git a/bin/add_demux_sce.R b/bin/add_demux_sce.R index 974fa083..bec58f61 100755 --- a/bin/add_demux_sce.R +++ b/bin/add_demux_sce.R @@ -58,30 +58,30 @@ opt <- parse_args(OptionParser(option_list = option_list)) # check that unfiltered file file exists -if(!file.exists(opt$sce_file)){ +if (!file.exists(opt$sce_file)) { stop("Can't find input SCE file") } # check that output file name ends in .rds -if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))) { stop("output file name must end in .rds") } # check for donor_ids file in vireo_dir -if(!is.null(opt$vireo_dir)){ +if (!is.null(opt$vireo_dir)) { vireo_file <- file.path(opt$vireo_dir, "donor_ids.tsv") - if(!file.exists(vireo_file)){ + if (!file.exists(vireo_file)) { stop("Can't find donor_ids.tsv file in vireo directory") } } -if(is.null(opt$cellhash_pool_file)){ +if (is.null(opt$cellhash_pool_file)) { cellhash_df <- NULL } else { - if(!file.exists(opt$cellhash_pool_file)){ + if (!file.exists(opt$cellhash_pool_file)) { stop("Can't find cellhash_pool_file") } - if(is.null(opt$library_id)){ + if (is.null(opt$library_id)) { stop("Must specify library_id with cellhash_pool_file") } cellhash_df <- readr::read_tsv(opt$cellhash_pool_file) |> @@ -93,12 +93,12 @@ if(is.null(opt$cellhash_pool_file)){ sce <- readRDS(opt$sce_file) # check for cellhash altExp if we will use it -if( opt$hash_demux || opt$seurat_demux ){ - if(!"cellhash" %in% altExpNames(sce)){ +if (opt$hash_demux || opt$seurat_demux) { + if (!"cellhash" %in% altExpNames(sce)) { stop("Can't process cellhash demulitplexing without a 'cellhash' altExp") } # add cellhash sample data to SCE if present - if(!is.null(cellhash_df)){ + if (!is.null(cellhash_df)) { sce <- scpcaTools::add_cellhash_ids(sce, cellhash_df, remove_unlabeled = TRUE) } } @@ -106,22 +106,22 @@ if( opt$hash_demux || opt$seurat_demux ){ cellhash_ids <- rownames(altExp(sce)) # only perform demultiplexing if more than one HTO is detected -if(length(cellhash_ids) > 1) { +if (length(cellhash_ids) > 1) { # add HashedDrops results - if(opt$hash_demux){ + if (opt$hash_demux) { sce <- scpcaTools::add_demux_hashedDrops(sce) } - + # add Seurat results - if(opt$seurat_demux){ + if (opt$seurat_demux) { sce <- scpcaTools::add_demux_seurat(sce) } - + # add vireo results - if(!is.null(opt$vireo_dir)){ + if (!is.null(opt$vireo_dir)) { vireo_table <- readr::read_tsv(vireo_file) sce <- scpcaTools::add_demux_vireo(sce, vireo_table) - } + } } # write filtered sce to output diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R index e1966069..f4ec9e63 100644 --- a/bin/classify_SingleR.R +++ b/bin/classify_SingleR.R @@ -52,26 +52,26 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$random_seed) # check that input file file exists -if(!file.exists(opt$input_sce_file)){ +if (!file.exists(opt$input_sce_file)) { stop("Missing input SCE file") } # check that output file ends in rds -if (!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))) { stop("output sce file name must end in .rds") } # check that references all exist singler_model_file <- opt$singler_model_file -if(!file.exists(singler_model_file)) { +if (!file.exists(singler_model_file)) { stop(glue::glue("Provided model file {singler_model_file} is missing.")) } # set up multiprocessing params -if(opt$threads > 1){ - bp_param = BiocParallel::MulticoreParam(opt$threads) +if (opt$threads > 1) { + bp_param <- BiocParallel::MulticoreParam(opt$threads) } else { - bp_param = BiocParallel::SerialParam() + bp_param <- BiocParallel::SerialParam() } # read in input rds file @@ -104,8 +104,6 @@ if (opt$label_name == "label.ont") { dplyr::rename(singler_celltype_annotation = ontology_cell_names) |> # make sure we keep rownames DataFrame(row.names = colData(sce)$barcodes) - - } else { # otherwise, just add cell names sce$singler_celltype_annotation <- singler_results$pruned.labels @@ -123,7 +121,8 @@ metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "singler") # export sce with annotations added -readr::write_rds(sce, - opt$output_sce_file, - compress = 'gz') - +readr::write_rds( + sce, + opt$output_sce_file, + compress = "gz" +) diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R index 8b7a9c18..af082b57 100644 --- a/bin/classify_cellassign.R +++ b/bin/classify_cellassign.R @@ -1,6 +1,7 @@ #!/usr/bin/env Rscript -# This script is used to read in the predictions from CellAssign and assign cell types in the annotated RDS file +# This script is used to read in the predictions from CellAssign +# and assign cell types in the annotated RDS file # import libraries suppressPackageStartupMessages({ @@ -35,12 +36,12 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that input file exists -if (!file.exists(opt$input_sce_file)){ +if (!file.exists(opt$input_sce_file)) { stop("Missing input SCE file") } # check that cellassign predictions file was provided -if (!file.exists(opt$cellassign_predictions)){ +if (!file.exists(opt$cellassign_predictions)) { stop("Missing CellAssign predictions file") } # check that reference_name was provided @@ -49,7 +50,7 @@ if (is.null(opt$reference_name)) { } # check that output file ends in rds -if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))) { stop("output sce file name must end in .rds") } # read in input files @@ -57,9 +58,11 @@ sce <- readr::read_rds(opt$input_sce_file) predictions <- readr::read_tsv(opt$cellassign_predictions) celltype_assignments <- predictions |> - tidyr::pivot_longer(!barcode, - names_to = "celltype", - values_to = "prediction") |> + tidyr::pivot_longer( + !barcode, + names_to = "celltype", + values_to = "prediction" + ) |> dplyr::group_by(barcode) |> dplyr::slice_max(prediction, n = 1) |> dplyr::ungroup() diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index a6153ff8..2bb67c34 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -1,9 +1,9 @@ #!/usr/bin/env Rscript # Script used to perform clustering on a given SCE object -# +# # This script reads in an RDS file containing an SCE, and performs -# graph-based clustering using the specified algorithm. Cluster identities are +# graph-based clustering using the specified algorithm. Cluster identities are # stored in the SCE's colData slot, and the SCE is written back out to the # original RDS file. @@ -25,7 +25,7 @@ option_list <- list( default = "PCA", help = "Name of the PCA reduced dimensionality representation to perform clustering on." - ), + ), make_option( opt_str = c("--cluster_algorithm"), type = "character", @@ -43,7 +43,7 @@ option_list <- list( make_option( opt_str = c("--nearest_neighbors"), type = "integer", - default = 20, + default = 20, help = "Nearest neighbors parameter to set for graph-based clustering. Default is 20." ), make_option( @@ -75,8 +75,8 @@ if (!opt$pca_name %in% reducedDimNames(sce)) { # extract the principal components matrix clusters <- scran::clusterCells( - sce, - use.dimred = opt$pca_name, + sce, + use.dimred = opt$pca_name, BLUSPARAM = bluster::NNGraphParam( k = opt$nearest_neighbors, type = opt$cluster_weighting, diff --git a/bin/filter_sce_rds.R b/bin/filter_sce_rds.R index 6e730036..217daf46 100755 --- a/bin/filter_sce_rds.R +++ b/bin/filter_sce_rds.R @@ -46,10 +46,10 @@ option_list <- list( help = "Name for the alternative experiment, if present, that contains ADT features" ), make_option( - opt_str = c("-r", "--random_seed"), - type = "integer", - help = "A random seed for reproducibility." - ) + opt_str = c("-r", "--random_seed"), + type = "integer", + help = "A random seed for reproducibility." + ) ) opt <- parse_args(OptionParser(option_list = option_list)) @@ -58,17 +58,17 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$random_seed) # check that unfiltered file file exists -if(!file.exists(opt$unfiltered_file)){ +if (!file.exists(opt$unfiltered_file)) { stop("Missing unfiltered.rds file") } # check that output file name ends in .rds -if(!(stringr::str_ends(opt$filtered_file, ".rds"))){ +if (!(stringr::str_ends(opt$filtered_file, ".rds"))) { stop("filtered file name must end in .rds") } # check that prob compromised cutoff is between 0-1 -if(!dplyr::between(opt$prob_compromised_cutoff, 0, 1)){ +if (!dplyr::between(opt$prob_compromised_cutoff, 0, 1)) { stop("--prob_compromised_cutoff must be a number between 0 to 1") } @@ -86,7 +86,7 @@ if (is.null(opt$adt_barcode_file)) { } # Calculate ambient profile from empty drops for later use, and save to altExp metadata - ambient_profile <- DropletUtils::ambientProfileEmpty( counts(altExp(unfiltered_sce, adt_exp)) ) + ambient_profile <- DropletUtils::ambientProfileEmpty(counts(altExp(unfiltered_sce, adt_exp))) metadata(altExp(unfiltered_sce, adt_exp))$ambient_profile <- ambient_profile } @@ -96,7 +96,7 @@ filtered_sce <- scpcaTools::filter_counts(unfiltered_sce) rm(unfiltered_sce) # need to remove old gene-level rowData statistics first -drop_cols <- colnames(rowData(filtered_sce)) %in% c('mean', 'detected') +drop_cols <- colnames(rowData(filtered_sce)) %in% c("mean", "detected") rowData(filtered_sce) <- rowData(filtered_sce)[!drop_cols] # recalculate rowData and add to filtered sce @@ -108,14 +108,15 @@ filtered_sce <- filtered_sce |> miQC_worked <- FALSE try({ filtered_sce <- scpcaTools::add_miQC(filtered_sce, - posterior_cutoff = opt$prob_compromised_cutoff, - enforce_left_cutoff = opt$enforce_left_cutoff) + posterior_cutoff = opt$prob_compromised_cutoff, + enforce_left_cutoff = opt$enforce_left_cutoff + ) metadata(filtered_sce)$prob_compromised_cutoff <- opt$prob_compromised_cutoff miQC_worked <- TRUE - }) +}) # set prob_compromised to NA if miQC failed -if (!miQC_worked){ +if (!miQC_worked) { warning("miQC failed. Setting `prob_compromised` to NA.") filtered_sce$prob_compromised <- NA_real_ filtered_sce$miQC_pass <- NA @@ -127,7 +128,7 @@ alt_names <- altExpNames(filtered_sce) for (alt in alt_names) { # remove old row data from unfiltered - drop_cols <- colnames(rowData(altExp(filtered_sce, alt))) %in% c('mean', 'detected') + drop_cols <- colnames(rowData(altExp(filtered_sce, alt))) %in% c("mean", "detected") rowData(altExp(filtered_sce, alt)) <- rowData(altExp(filtered_sce, alt))[!drop_cols] # add alt experiment features stats for filtered data @@ -137,7 +138,6 @@ for (alt in alt_names) { # calculate filtering QC from ADTs, if present if (!is.null(ambient_profile)) { - # Create data frame of ADTs and their target types # If `target_type` column is not present, assume all ADTs are targets adt_barcode_df <- readr::read_tsv( @@ -165,7 +165,7 @@ if (!is.null(ambient_profile)) { } # Check that barcode file ADTs match SCE ADTs - if ( !all.equal( sort(adt_barcode_df$name), sort(rownames(altExp(filtered_sce, adt_exp))) )) { + if (!all.equal(sort(adt_barcode_df$name), sort(rownames(altExp(filtered_sce, adt_exp))))) { stop("Mismatch between provided ADT barcode file and ADTs in SCE.") } @@ -190,8 +190,10 @@ if (!is.null(ambient_profile)) { } # Save QC stats to the altexp - colData(altExp(filtered_sce, adt_exp)) <- cbind(colData(altExp(filtered_sce, adt_exp)), - adt_qc_df) + colData(altExp(filtered_sce, adt_exp)) <- cbind( + colData(altExp(filtered_sce, adt_exp)), + adt_qc_df + ) # Add `target_type` to rowData rowData(altExp(filtered_sce, adt_exp))$target_type <- adt_barcode_df$target_type @@ -200,4 +202,3 @@ if (!is.null(ambient_profile)) { # write filtered sce to output readr::write_rds(filtered_sce, opt$filtered_file, compress = "gz") - diff --git a/bin/generate_bulk_metadata.R b/bin/generate_bulk_metadata.R index a55467df..ff56822b 100755 --- a/bin/generate_bulk_metadata.R +++ b/bin/generate_bulk_metadata.R @@ -59,35 +59,39 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check for project id -if(is.null(opt$project_id)){ +if (is.null(opt$project_id)) { stop("A `project_id` is required.") } # replace workflow url and commit if not provided -if (is.null(opt$workflow_url)){ +if (is.null(opt$workflow_url)) { opt$workflow_url <- NA } -if (is.null(opt$workflow_version)){ +if (is.null(opt$workflow_version)) { opt$workflow_version <- NA } -if (is.null(opt$workflow_commit)){ +if (is.null(opt$workflow_commit)) { opt$workflow_commit <- NA } -# read in library metadata file +# read in library metadata file library_metadata <- readr::read_tsv(opt$library_metadata_file) -# list of paths to salmon log files +# list of paths to salmon log files library_ids <- readLines(opt$salmon_dirs) -# subset library metadata to only contain libraries that are being processed -# only keep metadata columns of interest +# subset library metadata to only contain libraries that are being processed +# only keep metadata columns of interest bulk_metadata_df <- library_metadata |> - dplyr::filter(scpca_library_id %in% library_ids & - scpca_project_id %in% opt$project_id) |> - dplyr::select(scpca_sample_id, scpca_library_id, scpca_project_id, - technology, seq_unit) |> + dplyr::filter( + scpca_library_id %in% library_ids & + scpca_project_id %in% opt$project_id + ) |> + dplyr::select( + scpca_sample_id, scpca_library_id, scpca_project_id, + technology, seq_unit + ) |> # rename column names to match format of metadata files from other modalities dplyr::rename( sample_id = scpca_sample_id, @@ -95,30 +99,32 @@ bulk_metadata_df <- library_metadata |> project_id = scpca_project_id ) |> # add columns with processing information and date processed (same for all libraries ) - dplyr::mutate(genome_assembly = opt$genome_assembly, - workflow = opt$workflow_url, - workflow_version = opt$workflow_version, - workflow_commit = opt$workflow_commit) + dplyr::mutate( + genome_assembly = opt$genome_assembly, + workflow = opt$workflow_url, + workflow_version = opt$workflow_version, + workflow_commit = opt$workflow_commit + ) -# add salmon version, index, total_reads, mapped_reads for each library +# add salmon version, index, total_reads, mapped_reads for each library get_processing_info <- function(library_id) { - # read in json files for that library containing individual process information cmd_info_file <- file.path(library_id, "cmd_info.json") meta_info_file <- file.path(library_id, "aux_info", "meta_info.json") - + cmd_info <- jsonlite::read_json(cmd_info_file) meta_info <- jsonlite::read_json(meta_info_file) - + # add date processed from salmon in the format: "Mon Jan 03 15:13:14 2022" - date_processed <- lubridate::as_datetime(meta_info$end_time, - format = "%a %b %d %T %Y") + date_processed <- lubridate::as_datetime(meta_info$end_time, + format = "%a %b %d %T %Y" + ) # if meta_info is not recorded or the format has changed, use the modification time of the file - if (is.na(date_processed)){ + if (is.na(date_processed)) { date_processed <- file.info(meta_info_file)$mtime } - + library_processing <- data.frame( library_id = library_id, salmon_version = cmd_info$salmon_version, @@ -127,13 +133,14 @@ get_processing_info <- function(library_id) { mapped_reads = meta_info$num_mapped, date_processed = lubridate::format_ISO8601(date_processed, usetz = TRUE) ) - + + return(library_processing) } -bulk_processing_metadata <- purrr::map_dfr(library_ids, get_processing_info) +bulk_processing_metadata <- purrr::map_dfr(library_ids, get_processing_info) bulk_metadata_df <- bulk_metadata_df |> dplyr::left_join(bulk_processing_metadata, by = c("library_id")) -# write out file +# write out file readr::write_tsv(bulk_metadata_df, file = opt$metadata_output) diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R index 8e40fabe..8f97d3ac 100644 --- a/bin/generate_cellassign_refs.R +++ b/bin/generate_cellassign_refs.R @@ -1,6 +1,6 @@ #!/usr/bin/env Rscript -# this script is used to create binary gene x cell marker genes matrices +# this script is used to create binary gene x cell marker genes matrices # for use as references with CellAssign library(optparse) @@ -14,7 +14,7 @@ option_list <- list( make_option( opt_str = c("--marker_gene_file"), type = "character", - help = "File containing a list of marker genes for all cell types and all organs. + help = "File containing a list of marker genes for all cell types and all organs. Must contain the `organ` column, `--cell_type_column` and `--gene_id_column`. " ), make_option( @@ -45,7 +45,7 @@ opt <- parse_args(OptionParser(option_list = option_list)) # Set up ----------------------------------------------------------------------- -if(!file.exists(opt$marker_gene_file)){ +if (!file.exists(opt$marker_gene_file)) { stop("Provided `marker_gene_file` does not exist.") } @@ -55,18 +55,18 @@ organs <- stringr::str_split(opt$organs, ",") |> unlist() |> stringr::str_trim() -if(!all(organs %in% marker_gene_df$organ)){ +if (!all(organs %in% marker_gene_df$organ)) { stop("`organs` must be present in `organ` column of `marker_gene_file`.") } cell_type_column <- opt$cell_type_column gene_id_column <- opt$gene_id_column -if(!(cell_type_column %in% colnames(marker_gene_df))){ +if (!(cell_type_column %in% colnames(marker_gene_df))) { stop("Specified `cell_type_column` does not exist as a column in `marker_gene_file`") } -if(!(gene_id_column %in% colnames(marker_gene_df))){ +if (!(gene_id_column %in% colnames(marker_gene_df))) { stop("Specified `gene_id_column` does not exist as a column in `marker_gene_file`") } @@ -75,18 +75,20 @@ if(!(gene_id_column %in% colnames(marker_gene_df))){ # grab marker genes for specified organs from marker gene reference organ_gene_df <- marker_gene_df |> dplyr::filter(organ %in% organs) |> - dplyr::select({{cell_type_column}}, {{gene_id_column}}) + dplyr::select({{ cell_type_column }}, {{ gene_id_column }}) -# create a binary matrix of genes by cell type markers +# create a binary matrix of genes by cell type markers binary_mtx <- organ_gene_df |> - tidyr::pivot_wider(id_cols = gene_id_column, - names_from = cell_type_column, - values_from = cell_type_column, - values_fn = length, - values_fill = 0) |> + tidyr::pivot_wider( + id_cols = gene_id_column, + names_from = cell_type_column, + values_from = cell_type_column, + values_fn = length, + values_fill = 0 + ) |> tibble::column_to_rownames(gene_id_column) |> - # add a column with no marker genes - # cell assign will assign cells to "other" when no other cell types are appropriate + # add a column with no marker genes + # cell assign will assign cells to "other" when no other cell types are appropriate dplyr::mutate(other = 0) # replace length with 1 @@ -94,11 +96,11 @@ binary_mtx[binary_mtx > 1] <- 1 # Add ensembl ids -------------------------------------------------------------- -# combine with ensembl gene id +# combine with ensembl gene id # read in gtf file (genes only for speed) gtf <- rtracklayer::import(opt$gtf_file, feature.type = "gene") -# create a data frame with ensembl id and gene symbol +# create a data frame with ensembl id and gene symbol gene_id_map <- gtf |> as.data.frame() |> dplyr::select( diff --git a/bin/generate_spaceranger_metadata.R b/bin/generate_spaceranger_metadata.R index 46856de0..21cfedc6 100755 --- a/bin/generate_spaceranger_metadata.R +++ b/bin/generate_spaceranger_metadata.R @@ -1,6 +1,6 @@ #!/usr/bin/env Rscript -# This script generates the metadata.json file for Spatial Transcriptomics libraries. +# This script generates the metadata.json file for Spatial Transcriptomics libraries. # import libraries library(optparse) @@ -91,55 +91,57 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check for sample and library id -if(is.null(opt$library_id)){ +if (is.null(opt$library_id)) { stop("A `library_id` is required.") } -if(is.null(opt$sample_id)){ +if (is.null(opt$sample_id)) { stop("A `sample_id` is required.") } # check that barcode files exist -if(is.null(opt$unfiltered_barcodes_file) || !file.exists(opt$unfiltered_barcodes_file)){ +if (is.null(opt$unfiltered_barcodes_file) || !file.exists(opt$unfiltered_barcodes_file)) { stop("Unfiltered barcodes file missing or `unfiltered_barcodes_file` not specified.") } -if(is.null(opt$filtered_barcodes_file) || !file.exists(opt$filtered_barcodes_file)){ +if (is.null(opt$filtered_barcodes_file) || !file.exists(opt$filtered_barcodes_file)) { stop("Filtered barcodes file missing or `filtered_barcodes_file` not specified.") } -# check that metrics summary file exists -if(is.null(opt$metrics_summary_file) || !file.exists(opt$metrics_summary_file)){ +# check that metrics summary file exists +if (is.null(opt$metrics_summary_file) || !file.exists(opt$metrics_summary_file)) { stop("Metrics summary file missing or `metrics_summary_file` not specified.") } # check that version file exists -if(is.null(opt$spaceranger_versions_file) || !file.exists(opt$spaceranger_versions_file)){ +if (is.null(opt$spaceranger_versions_file) || !file.exists(opt$spaceranger_versions_file)) { stop("Versions file missing or `spaceranger_versions_file` not specified.") } # replace workflow url and commit if not provided -if (opt$workflow_url == "null"){ +if (opt$workflow_url == "null") { opt$workflow_url <- NA } -if (opt$workflow_version == "null"){ +if (opt$workflow_version == "null") { opt$workflow_version <- NA } -if (opt$workflow_commit == "null"){ +if (opt$workflow_commit == "null") { opt$workflow_commit <- NA } # read in barcode files unfiltered_barcodes <- readr::read_tsv(opt$unfiltered_barcodes_file, - col_names = c("barcode")) + col_names = c("barcode") +) filtered_barcodes <- readr::read_tsv(opt$filtered_barcodes_file, - col_names = c("barcode")) + col_names = c("barcode") +) -# read in metrics summary +# read in metrics summary metrics_summary <- readr::read_csv(opt$metrics_summary_file) -# read in versions file +# read in versions file spaceranger_versions <- jsonlite::read_json(opt$spaceranger_versions_file) -# compile metadata list +# compile metadata list metadata_list <- list( library_id = opt$library_id, sample_id = opt$sample_id, @@ -158,8 +160,7 @@ metadata_list <- list( workflow_version = opt$workflow_version, workflow_commit = opt$workflow_commit ) |> - purrr::map(~if(is.null(.)) NA else .) # convert any NULLS to NA + purrr::map(~ if (is.null(.)) NA else .) # convert any NULLS to NA # Output metadata as JSON jsonlite::write_json(metadata_list, path = opt$metadata_json, auto_unbox = TRUE) - diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 8aefc703..7d5c0186 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -74,22 +74,22 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that output file name ends in .rds -if(!(stringr::str_ends(opt$unfiltered_file, ".rds"))){ +if (!(stringr::str_ends(opt$unfiltered_file, ".rds"))) { stop("unfiltered file name must end in .rds") } # check that mitochondrial gene list exists -if(!file.exists(opt$mito_file)){ +if (!file.exists(opt$mito_file)) { stop("Mitochondrial gene list file not found.") } # check that gtf file exists -if(!file.exists(opt$gtf_file)){ +if (!file.exists(opt$gtf_file)) { stop("gtf file not found.") } # check that sample metadata file exists -if(!file.exists(opt$sample_metadata_file)){ +if (!file.exists(opt$sample_metadata_file)) { stop("sample metadata file not found.") } @@ -106,21 +106,25 @@ sample_ids <- unlist(stringr::str_split(opt$sample_id, ",|;")) |> sort() include_unspliced <- !opt$spliced_only # get unfiltered sce -unfiltered_sce <- read_alevin(quant_dir = opt$alevin_dir, - include_unspliced = include_unspliced, - fry_mode = TRUE, - tech_version = opt$technology, - library_id = opt$library_id, - sample_id = sample_ids) +unfiltered_sce <- read_alevin( + quant_dir = opt$alevin_dir, + include_unspliced = include_unspliced, + fry_mode = TRUE, + tech_version = opt$technology, + library_id = opt$library_id, + sample_id = sample_ids +) # read and merge feature counts if present -if (opt$feature_dir != ""){ - feature_sce <- read_alevin(quant_dir = opt$feature_dir, - include_unspliced = FALSE, - fry_mode = TRUE, - feature_data = TRUE, - library_id = opt$library_id, - sample_id = sample_ids) +if (opt$feature_dir != "") { + feature_sce <- read_alevin( + quant_dir = opt$feature_dir, + include_unspliced = FALSE, + fry_mode = TRUE, + feature_data = TRUE, + library_id = opt$library_id, + sample_id = sample_ids + ) unfiltered_sce <- merge_altexp(unfiltered_sce, feature_sce, opt$feature_name) # add alt experiment features stats @@ -143,7 +147,7 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> # add per cell and per gene statistics to colData and rowData unfiltered_sce <- unfiltered_sce |> add_cell_mito_qc(mito = mito_genes) |> - # add gene symbols to rowData + # add gene symbols to rowData add_gene_symbols(gene_info = gtf) |> scuttle::addPerFeatureQCMetrics() |> # add dataframe with sample metadata to sce metadata @@ -151,4 +155,3 @@ unfiltered_sce <- unfiltered_sce |> # write to rds readr::write_rds(unfiltered_sce, opt$unfiltered_file, compress = "gz") - diff --git a/bin/integrate_sce.R b/bin/integrate_sce.R index 8f163605..250d4140 100644 --- a/bin/integrate_sce.R +++ b/bin/integrate_sce.R @@ -61,31 +61,31 @@ set.seed(opt$seed) # Check and assign provided method based on available methods available_methods <- c("fastMNN", "harmony") -if(!(opt$method %in% available_methods)){ +if (!(opt$method %in% available_methods)) { stop("You must specify either `fastMNN` or `harmony` to the --method.") } # Check that provided input file exists and is an RDS file -if(is.null(opt$input_sce_file)) { +if (is.null(opt$input_sce_file)) { stop("You must provide the path to the RDS file with merged SCEs to --input_sce_file") } else { - if(!file.exists(opt$input_sce_file)) { + if (!file.exists(opt$input_sce_file)) { stop("Provided --input_sce_file file does not exist.") } } # set up multiprocessing params -if(opt$threads > 1){ - bp_param = BiocParallel::MulticoreParam(opt$threads) +if (opt$threads > 1) { + bp_param <- BiocParallel::MulticoreParam(opt$threads) } else { - bp_param = BiocParallel::SerialParam() + bp_param <- BiocParallel::SerialParam() } # Read in SCE file ------------------------------------------------------------- merged_sce <- readr::read_rds(opt$input_sce_file) # check that input contains a SCE object -if(!is(merged_sce, "SingleCellExperiment")){ +if (!is(merged_sce, "SingleCellExperiment")) { stop("The input RDS file must contain a SingleCellExperiment object.") } @@ -104,23 +104,25 @@ integration_args <- list( ) # append fastMNN only args -if(opt$method == "fastMNN"){ - integration_args <- append( +if (opt$method == "fastMNN") { + integration_args <- append( integration_args, list( subset.row = merged_hvgs, auto.merge = TRUE, BPPARAM = bp_param - )) + ) + ) } # append harmony only args -if(opt$method == "harmony"){ +if (opt$method == "harmony") { integration_arts <- append( integration_args, list( covariate_cols = opt$harmony_covariate_cols - )) + ) + ) } # perform integration @@ -128,8 +130,10 @@ integrated_sce <- do.call(scpcaTools::integrate_sces, integration_args) # calculate UMAP from corrected PCA integrated_sce <- integrated_sce |> - scater::runUMAP(dimred = glue::glue("{opt$method}_PCA"), - name = glue::glue("{opt$method}_UMAP")) + scater::runUMAP( + dimred = glue::glue("{opt$method}_PCA"), + name = glue::glue("{opt$method}_UMAP") + ) # add method to integrated sce existing_methods <- metadata(integrated_sce)$integration_methods diff --git a/bin/make_reference_fasta.R b/bin/make_reference_fasta.R index e6df3669..b198a91e 100755 --- a/bin/make_reference_fasta.R +++ b/bin/make_reference_fasta.R @@ -50,7 +50,7 @@ option_list <- list( help = "Prefix name containing organism and ensembl assembly version to be used for file naming" ), make_option( - opt_str = c("-l","--flank_length"), + opt_str = c("-l", "--flank_length"), type = "integer", default = 86, help = "Length of sequence flanking introns to be included in index, recommended to use read length minus 5." @@ -77,11 +77,15 @@ spliced_cdna_tx2gene_file <- paste0(opt$reference_name, ".spliced_cdna.tx2gene.t # splici output spliced_intron_fasta <- file.path(opt$fasta_output, spliced_intron_fasta_file) spliced_intron_gtf <- file.path(opt$annotation_output, spliced_intron_gtf_file) -spliced_intron_tx2gene <- file.path(opt$annotation_output, - spliced_intron_tx2gene_file) +spliced_intron_tx2gene <- file.path( + opt$annotation_output, + spliced_intron_tx2gene_file +) -spliced_intron_tx2gene_3col <- file.path(opt$annotation_output, - spliced_intron_tx2gene_3col_file) +spliced_intron_tx2gene_3col <- file.path( + opt$annotation_output, + spliced_intron_tx2gene_3col_file +) # spliced cDNA output spliced_cdna_fasta <- file.path(opt$fasta_output, spliced_cdna_fasta_file) @@ -134,7 +138,8 @@ splici_grl <- splici_grl[names(splici_seqs)] # write splici to fasta Biostrings::writeXStringSet( - splici_seqs, filepath = spliced_intron_fasta, compress = TRUE + splici_seqs, + filepath = spliced_intron_fasta, compress = TRUE ) # write the associated annotations to gtf @@ -151,12 +156,14 @@ splici_tx2gene_df <- eisaR::getTx2Gene(splici_grl) readr::write_tsv(splici_tx2gene_df, spliced_intron_tx2gene, col_names = FALSE) # make 3 column Tx2 gene needed for alevin-fry USA mode -splici_tx2gene_df_3col <- splici_tx2gene_df %>% +splici_tx2gene_df_3col <- splici_tx2gene_df %>% # add status column # remove extra -I* on gene ID - mutate(gene_id = stringr::word(gene_id,1,sep = '-'), - #if transcript_id contains an added -I*, then it is usnpliced - status = ifelse(stringr::str_detect(transcript_id, '-I'), 'U', 'S')) + mutate( + gene_id = stringr::word(gene_id, 1, sep = "-"), + # if transcript_id contains an added -I*, then it is usnpliced + status = ifelse(stringr::str_detect(transcript_id, "-I"), "U", "S") + ) # write 3 column tx2gene readr::write_tsv(splici_tx2gene_df_3col, spliced_intron_tx2gene_3col, col_names = FALSE) @@ -164,16 +171,16 @@ readr::write_tsv(splici_tx2gene_df_3col, spliced_intron_tx2gene_3col, col_names # reimport gtf to get list of mito genes gtf <- rtracklayer::import(spliced_intron_gtf) -mitogenes <- gtf[seqnames(gtf) == 'MT'] +mitogenes <- gtf[seqnames(gtf) == "MT"] # write out mitochondrial gene list writeLines(unique(mitogenes$gene_id), mito_out) # get list of all spliced transcript ID's -spliced_cdna_genes = metadata(grl)$featurelist$spliced +spliced_cdna_genes <- metadata(grl)$featurelist$spliced # subset sequences for only spliced cDNA -spliced_cdna_grl = grl[spliced_cdna_genes] +spliced_cdna_grl <- grl[spliced_cdna_genes] spliced_cdna_seqs <- GenomicFeatures::extractTranscriptSeqs( x = genome, @@ -182,7 +189,8 @@ spliced_cdna_seqs <- GenomicFeatures::extractTranscriptSeqs( # write spliced sequences only to fasta file Biostrings::writeXStringSet( - spliced_cdna_seqs, filepath = spliced_cdna_fasta, compress = TRUE + spliced_cdna_seqs, + filepath = spliced_cdna_fasta, compress = TRUE ) # write the associated annotations to gtf @@ -196,4 +204,3 @@ spliced_cdna_tx2gene_df <- eisaR::getTx2Gene(spliced_cdna_grl) # write out Tx2Gene for spliced transcripts readr::write_tsv(spliced_cdna_tx2gene_df, spliced_cdna_tx2gene, col_names = FALSE) - diff --git a/bin/merge_counts_tximport.R b/bin/merge_counts_tximport.R index 305cc799..87d9d56b 100755 --- a/bin/merge_counts_tximport.R +++ b/bin/merge_counts_tximport.R @@ -40,7 +40,7 @@ opt <- parse_args(OptionParser(option_list = option_list)) # read in tx2gene tx2gene <- readr::read_tsv(opt$tx2gene, col_names = c("transcript_id", "gene_id")) -# list of paths to salmon files +# list of paths to salmon files library_ids <- readLines(opt$salmon_dirs) salmon_files <- file.path(library_ids, "quant.sf") names(salmon_files) <- library_ids @@ -49,7 +49,7 @@ names(salmon_files) <- library_ids txi_salmon <- tximport(salmon_files, type = "salmon", tx2gene = tx2gene) # write counts matrix to txt file -txi_salmon$counts %>% - as.data.frame() %>% - tibble::rownames_to_column("gene_id") %>% +txi_salmon$counts |> + as.data.frame() |> + tibble::rownames_to_column("gene_id") |> readr::write_tsv(file = opt$output_file) diff --git a/bin/merge_sces.R b/bin/merge_sces.R index 8c2df16e..8402d3ca 100644 --- a/bin/merge_sces.R +++ b/bin/merge_sces.R @@ -42,29 +42,29 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that file extension for output file is correct -if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))) { stop("output file name must end in .rds") } # check that input files are provided and more than one are present for merging and integration -if(is.null(opt$input_sce_files)){ +if (is.null(opt$input_sce_files)) { stop("List of input files containing individual SCE objects to merge is missing.") } else { # list of paths to sce files - input_sce_files <- unlist(stringr::str_split(opt$input_sce_files, ',')) + input_sce_files <- unlist(stringr::str_split(opt$input_sce_files, ",")) } -if(length(input_sce_files) == 1){ +if (length(input_sce_files) == 1) { stop("Only 1 input file provided, no merging or integration will be performed for this group") } # use library ids to name list of input files -if(is.null(opt$input_library_ids)){ +if (is.null(opt$input_library_ids)) { # extract library ids from filename names(input_sce_files) <- stringr::word(basename(input_sce_files), 1, sep = "_") } else { # pull library ids from list - names(input_sce_files) <- unlist(stringr::str_split(opt$input_library_ids, ',')) + names(input_sce_files) <- unlist(stringr::str_split(opt$input_library_ids, ",")) } # sort inputs by library id @@ -72,7 +72,7 @@ input_sce_files <- input_sce_files[order(names(input_sce_files))] # check that input files exist missing_sce_files <- input_sce_files[which(!file.exists(input_sce_files))] -if(length(missing_sce_files) > 0){ +if (length(missing_sce_files) > 0) { stop( glue::glue( "\nCannot find input file: {missing_sce_files}." @@ -81,10 +81,10 @@ if(length(missing_sce_files) > 0){ } # set up multiprocessing params -if(opt$threads > 1){ - bp_param = BiocParallel::MulticoreParam(opt$threads) +if (opt$threads > 1) { + bp_param <- BiocParallel::MulticoreParam(opt$threads) } else { - bp_param = BiocParallel::SerialParam() + bp_param <- BiocParallel::SerialParam() } # Merge SCEs ------------------------------------------------------------------- @@ -93,9 +93,11 @@ if(opt$threads > 1){ sce_list <- purrr::map(input_sce_files, readr::read_rds) # check that all input RDS files contain SCE objects -sce_checks <- purrr::map(sce_list, - \(x) is(x, "SingleCellExperiment")) -if(!all(sce_checks)){ +sce_checks <- purrr::map( + sce_list, + \(x) is(x, "SingleCellExperiment") +) +if (!all(sce_checks)) { stop( "All input files must contain a `SingleCellExperiment` object." ) @@ -103,9 +105,10 @@ if(!all(sce_checks)){ # create combined SCE object merged_sce <- scpcaTools::merge_sce_list(sce_list, - batch_column = "library_id", - preserve_rowdata_cols = "gene_symbol", - cell_id_column = "cell_id") + batch_column = "library_id", + preserve_rowdata_cols = "gene_symbol", + cell_id_column = "cell_id" +) # HVG selection ---------------------------------------------------------------- @@ -114,35 +117,42 @@ merged_sce <- scpcaTools::merge_sce_list(sce_list, batch_column <- merged_sce$library_id # model gene variance -gene_var_block <- scran::modelGeneVar(merged_sce, - block = batch_column, - BPPARAM = bp_param) +gene_var_block <- scran::modelGeneVar( + merged_sce, + block = batch_column, + BPPARAM = bp_param +) # identify subset of variable genes hvg_list <- scran::getTopHVGs(gene_var_block, - n = opt$n_hvg) + n = opt$n_hvg +) metadata(merged_sce)$merged_hvgs <- hvg_list # Dim Reduction PCA and UMAP---------------------------------------------------- # multi batch PCA on merged object -multi_pca <- batchelor::multiBatchPCA(merged_sce, - subset.row = hvg_list, - batch = batch_column, - preserve.single = TRUE, - BPPARAM = bp_param) +multi_pca <- batchelor::multiBatchPCA( + merged_sce, + subset.row = hvg_list, + batch = batch_column, + preserve.single = TRUE, + BPPARAM = bp_param +) # add PCA results to merged SCE object reducedDim(merged_sce, "PCA") <- multi_pca[[1]] # add UMAP merged_sce <- scater::runUMAP(merged_sce, - dimred = "PCA", - BPPARAM = bp_param) + dimred = "PCA", + BPPARAM = bp_param +) # write out merged sce file -readr::write_rds(merged_sce, - opt$output_sce_file, - compress = "gz", - compression = 2) - +readr::write_rds( + merged_sce, + opt$output_sce_file, + compress = "gz", + compression = 2 +) diff --git a/bin/post_process_sce.R b/bin/post_process_sce.R index f0a7432e..3d4a7820 100755 --- a/bin/post_process_sce.R +++ b/bin/post_process_sce.R @@ -60,12 +60,12 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$random_seed) # check that filtered SCE file exists -if(!file.exists(opt$filtered_sce_file)){ +if (!file.exists(opt$filtered_sce_file)) { stop("Missing filtered.rds file") } # check that output file name ends in .rds -if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ +if (!(stringr::str_ends(opt$output_sce_file, ".rds"))) { stop("output file name must end in .rds") } @@ -73,7 +73,7 @@ if(!(stringr::str_ends(opt$output_sce_file, ".rds"))){ sce <- readr::read_rds(opt$filtered_sce_file) # create scpca_filter column ----------- -if(all(is.na(sce$miQC_pass))){ +if (all(is.na(sce$miQC_pass))) { sce$scpca_filter <- ifelse( sce$detected >= opt$gene_cutoff, "Keep", @@ -96,18 +96,17 @@ metadata(sce)$min_gene_cutoff <- opt$gene_cutoff # create adt_scpca_filter column, if CITEseq ---------- alt_exp <- opt$adt_name if (alt_exp %in% altExpNames(sce)) { - # set up filter with all Keep, and then override to Remove where necessary sce$adt_scpca_filter <- "Keep" sce$adt_scpca_filter[which(altExp(sce, alt_exp)$discard)] <- "Remove" # Warnings for different types of failure: fail_all_removed <- all(sce$adt_scpca_filter == "Remove") - fail_all_na <- all(is.na(altExp(sce, alt_exp)$discard)) - + fail_all_na <- all(is.na(altExp(sce, alt_exp)$discard)) + # handle failures - warnings and assign method as "No filter" - if (fail_all_removed | fail_all_na) { - metadata(sce)$adt_scpca_filter_method <- "No filter" + if (fail_all_removed || fail_all_na) { + metadata(sce)$adt_scpca_filter_method <- "No filter" if (fail_all_removed) { sce$adt_scpca_filter <- "Keep" warning("Filtering on ADTs attempted to remove all cells. No cells will be removed.") @@ -137,7 +136,7 @@ if (alt_exp %in% altExpNames(sce)) { processed_sce <- sce[, which(sce$scpca_filter == "Keep")] # replace existing stats with recalculated gene stats -drop_cols <- colnames(rowData(processed_sce, alt)) %in% c('mean', 'detected') +drop_cols <- colnames(rowData(processed_sce, alt)) %in% c("mean", "detected") rowData(processed_sce) <- rowData(processed_sce)[!drop_cols] processed_sce <- processed_sce |> @@ -146,7 +145,7 @@ processed_sce <- processed_sce |> # replace existing stats from altExp if any for (alt in altExpNames(processed_sce)) { # remove old row data - drop_cols <- colnames(rowData(altExp(processed_sce, alt))) %in% c('mean', 'detected') + drop_cols <- colnames(rowData(altExp(processed_sce, alt))) %in% c("mean", "detected") rowData(altExp(processed_sce, alt)) <- rowData(altExp(processed_sce, alt))[!drop_cols] # add alt experiment features stats for filtered data @@ -179,10 +178,8 @@ processed_sce <- scuttle::logNormCounts(processed_sce) # Try to normalize ADT counts, if present if (alt_exp %in% altExpNames(processed_sce)) { - - # need `all()` since,if present, this is an array - if( !all(is.null(metadata(altExp(processed_sce, alt_exp))$ambient_profile))){ + if (!all(is.null(metadata(altExp(processed_sce, alt_exp))$ambient_profile))) { # Calculate median size factors from the ambient profile altExp(processed_sce, alt_exp) <- scuttle::computeMedianFactors( altExp(processed_sce, alt_exp), @@ -192,32 +189,32 @@ if (alt_exp %in% altExpNames(processed_sce)) { # if ambient profile is not present, set sizeFactor to 0 for later warning. altExp(processed_sce, alt_exp)$sizeFactor <- 0 } - + adt_sce <- altExp(processed_sce, alt_exp) # Perform filtering specifically to allow for normalization if (!is.null(processed_sce$adt_scpca_filter)) { - adt_sce <- adt_sce[,processed_sce$adt_scpca_filter == "Keep"] + adt_sce <- adt_sce[, processed_sce$adt_scpca_filter == "Keep"] } - + # If any size factors are not positive or there was no filtering, simply use log1p - if ( any( adt_sce$sizeFactor <= 0 ) | metadata(processed_sce)$adt_scpca_filter_method == "No filter") { + if (any(adt_sce$sizeFactor <= 0) || metadata(processed_sce)$adt_scpca_filter_method == "No filter") { metadata(processed_sce)$adt_normalization <- "log-normalization" logcounts(adt_sce) <- log1p(counts(adt_sce)) } else { # Apply normalization using size factors metadata(processed_sce)$adt_normalization <- "median-based" - adt_sce <- scuttle::logNormCounts(adt_sce) + adt_sce <- scuttle::logNormCounts(adt_sce) } # Now that we have logcounts, add back to `processed_sce` but # with NA values for cells not included in normalization - + # first, get the counts matrix and make it NA result_matrix <- counts(altExp(processed_sce, alt_exp)) - result_matrix[,] <- NA - + result_matrix[, ] <- NA + # now get the computed logcounts & fill them in result_matrix[, colnames(adt_sce)] <- logcounts(adt_sce) - + # Check correct number of NAs: observed_na_count <- sum(is.na(result_matrix)) expected_na_count <- nrow(adt_sce) * (ncol(altExp(processed_sce, alt_exp)) - ncol(adt_sce)) @@ -243,14 +240,17 @@ metadata(processed_sce)$highly_variable_genes <- var_genes # dimensionality reduction # highly variable genes are used as input to PCA -processed_sce <- scater::runPCA(processed_sce, - ncomponents = opt$n_pcs, - subset_row = var_genes) +processed_sce <- scater::runPCA( + processed_sce, + ncomponents = opt$n_pcs, + subset_row = var_genes +) # calculate a UMAP matrix using the PCA results try({ processed_sce <- scater::runUMAP(processed_sce, - dimred = "PCA") + dimred = "PCA" + ) }) # Export -------------- @@ -260,4 +260,3 @@ readr::write_rds(sce, opt$filtered_sce_file, compress = "gz") # write out processed SCE readr::write_rds(processed_sce, opt$output_sce_file, compress = "gz") - diff --git a/bin/save_singler_refs.R b/bin/save_singler_refs.R index 1b2bce25..8c8718ee 100755 --- a/bin/save_singler_refs.R +++ b/bin/save_singler_refs.R @@ -22,12 +22,12 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that provided ref name is in celldex package -if(! opt$ref_name %in% ls("package:celldex")){ +if (!opt$ref_name %in% ls("package:celldex")) { stop(glue::glue("Provided `ref_name` `{opt$ref_name}` does not match a celldex dataset.")) -} +} # get a reference library from celldex: ref <- do.call(`::`, args = list("celldex", opt$ref_name))(ensembl = TRUE) -# export ref data +# export ref data readr::write_rds(ref, opt$ref_file, compress = "gz") diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R index 88da774c..cc574cca 100755 --- a/bin/sce_qc_report.R +++ b/bin/sce_qc_report.R @@ -102,33 +102,33 @@ option_list <- list( ) opt <- parse_args(OptionParser(option_list = option_list)) -if(is.null(opt$library_id)){ +if (is.null(opt$library_id)) { stop("A `library_id` is required.") } # check that template file, if given, exists -if(!is.null(opt$report_template) && !file.exists(opt$report_template)){ +if (!is.null(opt$report_template) && !file.exists(opt$report_template)) { stop("Specified `report_template` could not be found.") } -if(is.null(opt$unfiltered_sce) || !file.exists(opt$unfiltered_sce)){ +if (is.null(opt$unfiltered_sce) || !file.exists(opt$unfiltered_sce)) { stop("Unfiltered .rds file missing or `unfiltered_sce` not specified.") } -if(is.null(opt$filtered_sce) || !file.exists(opt$filtered_sce)){ +if (is.null(opt$filtered_sce) || !file.exists(opt$filtered_sce)) { stop("Filtered .rds file missing or `filtered_sce` not specified.") } demux_methods <- c("vireo", "HTODemux", "HashedDrops") -if(!opt$demux_method %in% demux_methods){ +if (!opt$demux_method %in% demux_methods) { stop("Unknown `demux_method` value. Must be one of `vireo`, `HTOdemux`, or `HashedDrops`") } -if (opt$workflow_url == "null"){ +if (opt$workflow_url == "null") { opt$workflow_url <- NA } -if (opt$workflow_version == "null"){ +if (opt$workflow_version == "null") { opt$workflow_version <- NA } -if (opt$workflow_commit == "null"){ +if (opt$workflow_commit == "null") { opt$workflow_commit <- NA } @@ -146,16 +146,20 @@ processed_sce_meta <- metadata(processed_sce) sample_ids <- unlist(stringr::str_split(opt$sample_id, ",|;")) |> sort() # check for multiplexing -multiplexed = if (length(sample_ids) > 1){TRUE} else {FALSE} +multiplexed <- if (length(sample_ids) > 1) { + TRUE +} else { + FALSE +} # sanity check ids -if (!is.null(sce_meta$sample_id)){ - if (!all.equal(sample_ids, sce_meta$sample_id)){ +if (!is.null(sce_meta$sample_id)) { + if (!all.equal(sample_ids, sce_meta$sample_id)) { stop("--sample_id does not match SCE metadata") } } -if (!is.null(sce_meta$library_id)){ - if (opt$library_id != sce_meta$library_id){ +if (!is.null(sce_meta$library_id)) { + if (opt$library_id != sce_meta$library_id) { stop("--library_id does not match SCE metadata") } } @@ -193,14 +197,18 @@ metadata_list <- list( workflow_version = opt$workflow_version, workflow_commit = opt$workflow_commit ) |> - purrr::map(\(x) {if(is.null(x)) NA else x}) # convert any NULLS to NA + purrr::map(\(x) { + if (is.null(x)) NA else x + }) # convert any NULLS to NA # add adt methods if citeseq if (has_citeseq) { metadata_list <- append( metadata_list, - list(adt_filtering_method = processed_sce_meta$adt_scpca_filter_method, - adt_normalization_method = processed_sce_meta$adt_normalization) + list( + adt_filtering_method = processed_sce_meta$adt_scpca_filter_method, + adt_normalization_method = processed_sce_meta$adt_normalization + ) ) } @@ -215,9 +223,11 @@ if (multiplexed) { # add demux info to the metadata list metadata_list <- append( metadata_list, - list(demux_method = opt$demux_method, - demux_samples = sample_ids, - sample_cell_estimates = demux_counts) + list( + demux_method = opt$demux_method, + demux_samples = sample_ids, + sample_cell_estimates = demux_counts + ) ) } @@ -233,4 +243,3 @@ scpcaTools::generate_qc_report( output = opt$qc_report_file, extra_params = list(seed = opt$seed) ) - diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 37efefba..39430522 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -38,12 +38,12 @@ opt <- parse_args(OptionParser(option_list = option_list)) # Set up ----------------------------------------------------------------------- # check that filtered SCE file exists -if(!file.exists(opt$input_sce_file)){ +if (!file.exists(opt$input_sce_file)) { stop(glue::glue("{opt$input_sce_file} does not exist.")) } # check that output file is h5 -if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ +if (!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))) { stop("output rna file name must end in .hdf5 or .h5") } @@ -52,8 +52,7 @@ if(!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))){ # this function applies any necessary reformatting or changes needed to make # sure that the sce that is getting converted to AnnData is compliant with CZI # CZI 3.0.0 requirements: https://github.com/chanzuckerberg/single-cell-curation/blob/b641130fe53b8163e50c39af09ee3fcaa14c5ea7/schema/3.0.0/schema.md -format_czi <- function(sce){ - +format_czi <- function(sce) { # add library_id as an sce colData column sce$library_id <- metadata(sce)$library_id @@ -62,7 +61,8 @@ format_czi <- function(sce){ # add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, - join_columns = "library_id") + join_columns = "library_id" + ) # remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] @@ -78,7 +78,6 @@ format_czi <- function(sce){ } return(sce) - } # AltExp to AnnData ----------------------------------------------------------- @@ -102,15 +101,14 @@ scpcaTools::sce_to_anndata( ) # if feature data exists, grab it and export to AnnData -if(!is.null(opt$feature_name)){ - +if (!is.null(opt$feature_name)) { # make sure the feature data is present - if(!(opt$feature_name %in% altExpNames(sce))){ + if (!(opt$feature_name %in% altExpNames(sce))) { stop("feature_name must match name of altExp in provided SCE object.") } # check for output file - if(!(stringr::str_ends(opt$output_feature_h5, ".hdf5|.h5"))){ + if (!(stringr::str_ends(opt$output_feature_h5, ".hdf5|.h5"))) { stop("output feature file name must end in .hdf5 or .h5") } @@ -128,5 +126,4 @@ if(!is.null(opt$feature_name)){ alt_sce, anndata_file = opt$output_feature_h5 ) - } diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R index ea97d803..19e12064 100644 --- a/bin/train_SingleR.R +++ b/bin/train_SingleR.R @@ -60,19 +60,19 @@ opt <- parse_args(OptionParser(option_list = option_list)) set.seed(opt$random_seed) # check that input files exist -if(!file.exists(opt$ref_file)){ +if (!file.exists(opt$ref_file)) { stop("Missing input file with cell type reference (`ref_file`).") } -if(!file.exists(opt$fry_tx2gene)){ +if (!file.exists(opt$fry_tx2gene)) { stop("Missing `fry_tx2gene` file.") } # set up multiprocessing params -if(opt$threads > 1){ - bp_param = BiocParallel::MulticoreParam(opt$threads) +if (opt$threads > 1) { + bp_param <- BiocParallel::MulticoreParam(opt$threads) } else { - bp_param = BiocParallel::SerialParam() + bp_param <- BiocParallel::SerialParam() } # read in model @@ -80,21 +80,23 @@ ref_data <- readr::read_rds(opt$ref_file) # check that ref data contains correct labels, and set up label column for later label_col <- opt$label_name -if(!label_col %in% colnames(colData(ref_data))){ +if (!label_col %in% colnames(colData(ref_data))) { stop( glue::glue("Reference dataset must contain `{label_col}` in `colData`.") ) } # read in tx2gene -tx2gene <- readr::read_tsv(opt$fry_tx2gene, - col_names = c("transcript", "gene", "transcript_type")) +tx2gene <- readr::read_tsv( + opt$fry_tx2gene, + col_names = c("transcript", "gene", "transcript_type") +) # select genes to use for model restriction gene_ids <- unique(tx2gene$gene) # check that genes aren't empty -if (length(gene_ids) == 0){ +if (length(gene_ids) == 0) { stop("Provided tx2gene tsv file does not contain any genes.") } From a4131a3651fa88b7fc3b7262183aad8576901049 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 8 Sep 2023 12:03:26 -0400 Subject: [PATCH 167/268] Format rmd files --- templates/integration-report.Rmd | 45 ++-- templates/qc_report/celltypes_qc.rmd | 318 ++++++++++++++------------- templates/qc_report/cite_qc.rmd | 149 +++++++------ templates/qc_report/multiplex_qc.rmd | 104 +++++---- templates/qc_report/qc_report.rmd | 227 ++++++++++--------- templates/qc_report/umap_qc.rmd | 95 ++++---- 6 files changed, 512 insertions(+), 426 deletions(-) diff --git a/templates/integration-report.Rmd b/templates/integration-report.Rmd index 5d7517b7..763da0a0 100644 --- a/templates/integration-report.Rmd +++ b/templates/integration-report.Rmd @@ -24,17 +24,19 @@ library(SingleCellExperiment) library(ggplot2) # Set default ggplot theme -theme_set(theme_bw() + - theme(plot.margin = margin(rep(20, 4)))) +theme_set( + theme_bw() + + theme(plot.margin = margin(rep(20, 4))) +) ``` ```{r} -# check that input files are provided -if(is.null(params$integrated_sce)){ +# check that input files are provided +if (is.null(params$integrated_sce)) { stop("Must provide a path to a RDS file containing a integrated SCE object.") } -# define batch column +# define batch column batch_column <- params$batch_column ``` @@ -53,28 +55,35 @@ UMAP showing batches before and after integration. ```{r, message=FALSE} # randomly shuffle cells prior to plotting col_order <- sample(ncol(integrated_sce)) -shuffled_sce <- integrated_sce[,col_order] +shuffled_sce <- integrated_sce[, col_order] -# set plot colors +# set plot colors num_colors <- length(unique(integrated_sce[[batch_column]])) plot_colors <- rainbow(n = num_colors) # list of batch umaps for all pre/post integration -batch_umaps <- purrr::map(umap_plot_names, \(name){ +batch_umaps <- umap_plot_names |> purrr::map(\(name) { scater::plotReducedDim(shuffled_sce, - dimred = name, - colour_by = batch_column, - point_size = 0.1, - point_alpha = 0.4) + - scale_color_manual(values = plot_colors, - name = batch_column) + + dimred = name, + colour_by = batch_column, + point_size = 0.1, + point_alpha = 0.4 + ) + + scale_color_manual( + values = plot_colors, + name = batch_column + ) + # relabel legend and resize dots - guides(color = guide_legend(override.aes = list(size = 3), - label.theme = element_text(size = 10))) + guides(color = guide_legend( + override.aes = list(size = 3), + label.theme = element_text(size = 10) + )) }) -patchwork::wrap_plots(batch_umaps, ncol = 2, - guides = "collect") +patchwork::wrap_plots(batch_umaps, + ncol = 2, + guides = "collect" +) ``` # Session Info diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index f2845831..04c3bfae 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -8,7 +8,7 @@ The following method(s) were used to perform cell typing: ```{r, eval = has_singler} knitr::asis_output( glue::glue( - "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. + "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. The `{metadata(processed_sce)$singler_reference}` reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used for cell typing." ) ) @@ -18,15 +18,16 @@ knitr::asis_output( ```{r, eval = has_cellassign} knitr::asis_output( glue::glue( - " + " * [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. Marker genes associated with `{metadata(processed_sce)$cellassign_reference}` tissue were obtained from [PanglaoDB](https://panglaodb.se/). - ") + " + ) ) ``` -Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. +Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. If available, these results will be compared to cell type annotations provided by the data's originating research group ("submitter-provided cell type annotations".) @@ -34,22 +35,22 @@ If available, these results will be compared to cell type annotations provided b ```{r} # This chunk defines a helper function to reformat annotations: -# * Annotations that are `NA`/"other" are changed to "Unknown cell type" -# * Annotations are converted to a factor ordered by frequency, but with +# * Annotations that are `NA`/"other" are changed to "Unknown cell type" +# * Annotations are converted to a factor ordered by frequency, but with # "Unknown cell type" always last. prepare_annotation_values <- function(df, annotation_column) { df |> dplyr::mutate( - {{annotation_column}} := dplyr::case_when( + {{ annotation_column }} := dplyr::case_when( # singler condition - is.na({{annotation_column}}) ~ "Unknown cell type", + is.na({{ annotation_column }}) ~ "Unknown cell type", # cellassign conditon - {{annotation_column}} == "other" ~ "Unknown cell type", + {{ annotation_column }} == "other" ~ "Unknown cell type", # otherwise, keep it - TRUE ~ {{annotation_column}} + TRUE ~ {{ annotation_column }} ) |> - forcats::fct_infreq() |> - forcats::fct_relevel("Unknown cell type", after = Inf) + forcats::fct_infreq() |> + forcats::fct_relevel("Unknown cell type", after = Inf) ) } ``` @@ -61,10 +62,12 @@ celltype_df <- colData(processed_sce) |> # barcodes to a column tibble::rownames_to_column(var = "barcode") |> # keep only cell name, celltyping, and clusters - dplyr::select(barcode, - clusters, - contains("singler"), - contains("cellassign")) + dplyr::select( + barcode, + clusters, + contains("singler"), + contains("cellassign") + ) @@ -75,29 +78,31 @@ if (has_singler) { if (has_cellassign) { celltype_df <- celltype_df |> prepare_annotation_values(cellassign_celltype_annotation) -} +} ``` ```{r} # Define a helper function to create tables for singler and cellassign annotations create_celltype_n_table <- function(df, celltype_column) { df |> - dplyr::count({{celltype_column}}) |> + dplyr::count({{ celltype_column }}) |> # Add percentage column dplyr::mutate( - `Percent of cells` = paste0(round(n/sum(n) * 100, digits = 2), "%") + `Percent of cells` = paste0(round(n / sum(n) * 100, digits = 2), "%") ) |> # set column order & rename dplyr::select( - `Annotated cell type` = {{celltype_column}}, + `Annotated cell type` = {{ celltype_column }}, `Number of cells` = n, `Percent of cells` ) |> # kable formatting - knitr::kable(align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> + knitr::kable(align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) } ``` @@ -116,7 +121,7 @@ create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ```{r, eval = has_submitter_celltypes} knitr::asis_output("### Submitter-provided cell type annotations\n") -# Note: submitter annotations have not yet been added to the workflow, +# Note: submitter annotations have not yet been added to the workflow, # so this variable name `submitter_celltype_annotation` is just a placeholder create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` @@ -137,7 +142,7 @@ Higher _delta median_ values indicate more confidence in the cell type annotatio For more information, refer to the [`SingleR` book section on 'Annotation diagnostics'](https://bioconductor.org/books/release/SingleRBook/annotation-diagnostics.html#annotation-diagnostics). -In the plot below, each point is the _delta median_ statistic of a given cell with the given cell type annotation. +In the plot below, each point is the _delta median_ statistic of a given cell with the given cell type annotation. Points (cells) are colored by `SingleR`'s internal confidence assessment: High-quality cell annotations are shown in black, and low-quality cell annotations are shown in blue. All blue points correspond to cells labeled as `Unknown cell type` in the `SingleR` result table in the previous section. The red overlayed boxes represent the median ± interquartile range (IQR), specifically for high-quality annotations. @@ -149,7 +154,7 @@ The red overlayed boxes represent the median ± interquartile range (IQR), speci # Prepare SingleR scores for plot # extract scores into matrix -singler_scores <- metadata(processed_sce)$singler_result$scores +singler_scores <- metadata(processed_sce)$singler_result$scores # Create data frame for plotting with delta median and the full *non-pruned* cell labels delta_median_df <- tibble::tibble( @@ -164,19 +169,18 @@ delta_median_df <- tibble::tibble( # If ontologies were used for `full_labels`, we'll need to map back to cell names # for the plot itself. if ("singler_celltype_ontology" %in% names(celltype_df)) { - # we use inner_join b/c the above tibble does NOT contain "Unknown cell type", which # we do not want to display here delta_median_df <- delta_median_df |> - dplyr::inner_join( - tibble::tibble( - full_labels = celltype_df$singler_celltype_ontology, - celltype = celltype_df$singler_celltype_annotation - ) |> dplyr::distinct() - ) |> + dplyr::inner_join( + tibble::tibble( + full_labels = celltype_df$singler_celltype_ontology, + celltype = celltype_df$singler_celltype_annotation + ) |> dplyr::distinct() + ) |> dplyr::select(-full_labels) } else { - # otherwise, full_labels already contain what we want to plot, so just rename it + # otherwise, full_labels already contain what we want to plot, so just rename it delta_median_df <- delta_median_df |> dplyr::rename(celltype = full_labels) } @@ -196,21 +200,25 @@ delta_median_df$annotation_wrapped <- factor( # Subset the data to just confident points for median+/-IQR delta_median_confident_df <- delta_median_df |> dplyr::filter(confident) - + # Plot delta_median across celltypes colored by pruning -ggplot(delta_median_df) + - aes(x = annotation_wrapped, - y = delta_median, - color = confident) + - ggforce::geom_sina(size = 0.75, - alpha = 0.5, - # Keep red points mostly in line with black - position = position_dodge(width = 0.05)) + +ggplot(delta_median_df) + + aes( + x = annotation_wrapped, + y = delta_median, + color = confident + ) + + ggforce::geom_sina( + size = 0.75, + alpha = 0.5, + # Keep red points mostly in line with black + position = position_dodge(width = 0.05) + ) + labs( x = "Cell type annotation", y = "Delta median statistic", color = "Confident cell type assignment" - ) + + ) + scale_color_manual(values = c("blue", "black")) + # add median/IQR stat_summary( @@ -219,12 +227,12 @@ ggplot(delta_median_df) + geom = "crossbar", width = 0.4, size = 0.2 - ) + + ) + guides( color = guide_legend(override.aes = list(size = 1, alpha = 0.9)) ) + theme( - axis.text.x = element_text(angle = 55, hjust = 1, size = rel(0.85)), + axis.text.x = element_text(angle = 55, hjust = 1, size = rel(0.85)), legend.title = element_text(size = rel(0.75)), legend.text = element_text(size = rel(0.75)), legend.position = "bottom" @@ -251,14 +259,13 @@ In these cases, we directly show values for individual cell probabilities as lin ```{r, eval = has_cellassign, warning=FALSE, message=FALSE, fig.height = 8, fig.width = 7} - # Prepare CellAssign scores for plot -cellassign_prob_df <- metadata(processed_sce)$cellassign_predictions |> +cellassign_prob_df <- metadata(processed_sce)$cellassign_predictions |> # Change "other" to "Unknown cell type" dplyr::rename(`Unknown cell type` = other) |> tidyr::pivot_longer( - -barcode, - names_to = "celltype", + -barcode, + names_to = "celltype", values_to = "probability" ) |> # remove cell types that were not annotated @@ -266,7 +273,7 @@ cellassign_prob_df <- metadata(processed_sce)$cellassign_predictions |> # join with actual annotations dplyr::inner_join( tibble::tibble( - cellassign_celltype_annotation = celltype_df$cellassign_celltype_annotation, + cellassign_celltype_annotation = celltype_df$cellassign_celltype_annotation, barcode = colData(processed_sce)$barcodes # plural! ) ) |> @@ -293,29 +300,33 @@ celltypes_leq2_cells <- cellassign_prob_df |> # data frame for adding those points back leq2_probabilities_df <- cellassign_prob_df |> dplyr::filter( - annotation_wrapped %in% celltypes_leq2_cells, - annotated + annotation_wrapped %in% celltypes_leq2_cells, + annotated ) |> dplyr::select(annotation_wrapped, probability, annotated) # Finally, the plot: ggplot(cellassign_prob_df) + - aes(x = probability, - y = annotation_wrapped, - fill = annotated) + - ggridges::stat_density_ridges(quantile_lines = TRUE, - quantiles = 2, - alpha = 0.6, - # avoid overlap to extent possible in a template - - scale = 0.85) + + aes( + x = probability, + y = annotation_wrapped, + fill = annotated + ) + + ggridges::stat_density_ridges( + quantile_lines = TRUE, + quantiles = 2, + alpha = 0.6, + # avoid overlap to extent possible in a template - + scale = 0.85 + ) + scale_fill_viridis_d(direction = -1) + labs( x = "CellAssign probability", - y = "Annotated cell type", + y = "Annotated cell type", fill = "Cell annotated as given cell type" ) + theme( - axis.text.y = element_text(size = 9), + axis.text.y = element_text(size = 9), legend.position = "bottom" ) + #### add line segment for N<3 distributions @@ -329,7 +340,7 @@ ggplot(cellassign_prob_df) + color = annotated ), show.legend = FALSE - ) + + ) + scale_color_viridis_d() ``` @@ -349,25 +360,26 @@ All other cell types are grouped together and labeled "Other cell type" (not to ```{r} # Create dataset for plotting UMAPs with lumped cell types umap_df <- tibble::tibble( - UMAP1 = unname(reducedDim(processed_sce, "UMAP")[,1]), - UMAP2 = unname(reducedDim(processed_sce, "UMAP")[,2]), + UMAP1 = unname(reducedDim(processed_sce, "UMAP")[, 1]), + UMAP2 = unname(reducedDim(processed_sce, "UMAP")[, 2]), clusters = processed_sce$clusters ) # helper function for lumping cell types -lump_celltypes <- function(umap_df, +lump_celltypes <- function(umap_df, celltype_df, celltype_method, n_celltypes = 7) { - umap_df |> dplyr::mutate( - celltypes = celltype_df[[glue::glue("{celltype_method}_celltype_annotation")]], - celltypes = forcats::fct_lump_n(celltypes, - n_celltypes, - other_level = "Other cell type")) |> + celltypes = celltype_df[[glue::glue("{celltype_method}_celltype_annotation")]] |> + forcats::fct_lump_n( + n_celltypes, + other_level = "Other cell type" + ) + ) |> # finally, rename temporary `celltypes` column to the provided method - dplyr::rename({{celltype_method}} := celltypes) + dplyr::rename({{ celltype_method }} := celltypes) } if (has_singler) { @@ -384,68 +396,79 @@ if (has_cellassign) { # Define helper function for making UMAPs in this section # this function uses the default palette, which can be customized when # calling the function -plot_umap <- function(umap_df, +plot_umap <- function(umap_df, color_variable, - legend_title, + legend_title, legend_nrow = 2) { - - ggplot(umap_df) + - aes(x = UMAP1, - y = UMAP2, - color = {{color_variable}}) + - geom_point(size = 0.3, - alpha = 0.5) + + ggplot(umap_df) + + aes( + x = UMAP1, + y = UMAP2, + color = {{ color_variable }} + ) + + geom_point( + size = 0.3, + alpha = 0.5 + ) + # remove axis numbers and background grid - scale_x_continuous(labels = NULL, breaks = NULL) + - scale_y_continuous(labels = NULL, breaks = NULL) + - coord_fixed() + + scale_x_continuous(labels = NULL, breaks = NULL) + + scale_y_continuous(labels = NULL, breaks = NULL) + + coord_fixed() + guides( - color = guide_legend(title = legend_title, - nrow = legend_nrow, - # more visible points in legend - override.aes = list(alpha = 1, - size = 1.5))) + + color = guide_legend( + title = legend_title, + nrow = legend_nrow, + # more visible points in legend + override.aes = list( + alpha = 1, + size = 1.5 + ) + ) + ) + theme(legend.position = "bottom") } ``` - + ```{r message=FALSE, warning=FALSE} -clusters_plot <- plot_umap(umap_df, - clusters, - "Clusters") + +clusters_plot <- plot_umap( + umap_df, + clusters, + "Clusters" +) + ggtitle("UMAP colored by clusters") # Determine palette based on number of levels. -# If we have <=8, we can use a CVD-friendly palette (they generally don't have more than 8 colors). +# If we have <=8, we can use a CVD-friendly palette (they generally don't have more than 8 colors). # Otherwise, we will use the default palette. if (length(levels(umap_df$clusters)) <= 8) { - clusters_plot + - scale_color_brewer(palette = "Set2") + clusters_plot + + scale_color_brewer(palette = "Set2") } else { clusters_plot } - ``` ```{r eval=has_singler, message=FALSE, warning=FALSE} -plot_umap(umap_df, - singler, - "Cell types", - legend_nrow = 4) + - ggtitle("UMAP colored by SingleR annotations") + +plot_umap(umap_df, + singler, + "Cell types", + legend_nrow = 4 +) + + ggtitle("UMAP colored by SingleR annotations") + scale_color_brewer(palette = "Dark2") ``` ```{r, eval = has_cellassign, message=FALSE, warning=FALSE} -plot_umap(umap_df, - cellassign, - "Cell types", - legend_nrow = 4) + - ggtitle("UMAP colored by CellAssign annotations") + +plot_umap(umap_df, + cellassign, + "Cell types", + legend_nrow = 4 +) + + ggtitle("UMAP colored by CellAssign annotations") + scale_color_brewer(palette = "Dark2") ``` @@ -463,43 +486,44 @@ Heatmap colors represent the log number of cells present in both the given cell ```{r} # Helper function for making a heatmap create_celltype_heatmap <- function(x_vector, - y_vector, + y_vector, x_label = "", - y_label = "", + y_label = "", column_names_rotation = 0, - row_font_size = 8, + row_font_size = 8, column_font_size = 10) { - # build a matrix for making a heatmap - celltype_mtx <- table(x_vector, - y_vector) |> + celltype_mtx <- table( + x_vector, + y_vector + ) |> log1p() # log transform for visualization - - # Define CVD-friendly palette + + # Define CVD-friendly palette heatmap_palette <- viridisLite::inferno(7, alpha = 1, begin = 0, end = 1, direction = 1) - + # heatmap heat <- ComplexHeatmap::Heatmap(celltype_mtx, - # Overall heatmap parameters - col = heatmap_palette, - # Column parameters - column_title = y_label, - column_title_side = "bottom", - column_dend_side = "top", - column_names_rot = column_names_rotation, - column_names_gp = grid::gpar(fontsize = column_font_size), - # Row parameters - row_dend_side = "left", - row_title_side = "right", - row_title = x_label, - row_names_gp = grid::gpar(fontsize = row_font_size), - # Legend parameters - heatmap_legend_param = list( - title = "Log(Number of cells)", - title_position = "leftcenter-rot", - legend_height = unit(4, "cm") - ) - ) + # Overall heatmap parameters + col = heatmap_palette, + # Column parameters + column_title = y_label, + column_title_side = "bottom", + column_dend_side = "top", + column_names_rot = column_names_rotation, + column_names_gp = grid::gpar(fontsize = column_font_size), + # Row parameters + row_dend_side = "left", + row_title_side = "right", + row_title = x_label, + row_names_gp = grid::gpar(fontsize = row_font_size), + # Legend parameters + heatmap_legend_param = list( + title = "Log(Number of cells)", + title_position = "leftcenter-rot", + legend_height = unit(4, "cm") + ) + ) # draw with legend on left for spacing ComplexHeatmap::draw(heat, heatmap_legend_side = "left") } @@ -509,8 +533,8 @@ create_celltype_heatmap <- function(x_vector, ```{r, eval = has_singler, fig.height=5, fig.width=7} knitr::asis_output("### `SingleR` cluster and cell type heatmap\n") create_celltype_heatmap( - x_vector = celltype_df$singler_celltype_annotation, - y_vector = celltype_df$clusters, + x_vector = celltype_df$singler_celltype_annotation, + y_vector = celltype_df$clusters, y_label = "Clusters" ) ``` @@ -518,8 +542,8 @@ create_celltype_heatmap( ```{r, eval = has_cellassign, fig.height=5, fig.width=7} knitr::asis_output("### `CellAssign` cluster and cell type heatmap\n") create_celltype_heatmap( - x_vector = celltype_df$cellassign_celltype_annotation, - y_vector = celltype_df$clusters, + x_vector = celltype_df$cellassign_celltype_annotation, + y_vector = celltype_df$clusters, y_label = "Clusters" ) ``` @@ -527,14 +551,14 @@ create_celltype_heatmap( ```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") create_celltype_heatmap( - x_vector = celltype_df$submitter_celltype_annotation, - y_vector = celltype_df$clusters, + x_vector = celltype_df$submitter_celltype_annotation, + y_vector = celltype_df$clusters, y_label = "Clusters" ) ``` - + ```{r, eval = has_cellassign & has_singler, fig.height=7, fig.width=8} knitr::asis_output(" ## Comparison between annotations @@ -544,8 +568,8 @@ Note that due to different annotations references, these methods may use differe ") create_celltype_heatmap( - x_vector = celltype_df$singler_celltype_annotation, - y_vector = celltype_df$cellassign_celltype_annotation, + x_vector = celltype_df$singler_celltype_annotation, + y_vector = celltype_df$cellassign_celltype_annotation, x_label = "SingleR annotations", y_label = "CellAssign annotations", column_names_rotation = 55, diff --git a/templates/qc_report/cite_qc.rmd b/templates/qc_report/cite_qc.rmd index bdcb9ffc..e0fd1015 100644 --- a/templates/qc_report/cite_qc.rmd +++ b/templates/qc_report/cite_qc.rmd @@ -6,7 +6,7 @@ This section details quality control statistics from the ADT (antibody-derived t ```{r} # add rowData if missing -if (is.null(rowData(adt_exp)$detected)){ +if (is.null(rowData(adt_exp)$detected)) { adt_exp <- scuttle::addPerFeatureQCMetrics(adt_exp) } @@ -14,24 +14,26 @@ cell_adt_counts <- Matrix::colSums(counts(adt_exp)) adt_information <- tibble::tibble( "Number of ADTs assayed" = - format(nrow(adt_exp), big.mark = ',', scientific = FALSE), + format(nrow(adt_exp), big.mark = ",", scientific = FALSE), "Number of reads sequenced" = - format(adt_meta$total_reads, big.mark = ',', scientific = FALSE), + format(adt_meta$total_reads, big.mark = ",", scientific = FALSE), "Percent reads mapped to ADTs" = - paste0(round(adt_meta$mapped_reads/adt_meta$total_reads * 100, digits = 2), "%"), + paste0(round(adt_meta$mapped_reads / adt_meta$total_reads * 100, digits = 2), "%"), "Percent of ADTs in cells" = - paste0(round(sum(cell_adt_counts)/adt_meta$mapped_reads * 100, digits = 2), "%"), + paste0(round(sum(cell_adt_counts) / adt_meta$mapped_reads * 100, digits = 2), "%"), "Percent of cells with ADTs" = - paste0(round(sum(cell_adt_counts > 0)/length(cell_adt_counts) * 100, digits = 2), "%"), + paste0(round(sum(cell_adt_counts > 0) / length(cell_adt_counts) * 100, digits = 2), "%"), "Median ADT UMIs per cell" = - format(median(cell_adt_counts), big.mark = ',', scientific = FALSE) - )|> + format(median(cell_adt_counts), big.mark = ",", scientific = FALSE) +) |> t() -knitr::kable(adt_information, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> +knitr::kable(adt_information, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) ``` @@ -43,34 +45,35 @@ antibody_tags <- as.data.frame(rowData(adt_exp)) |> mutate(target_type = forcats::fct_relevel(target_type, "target")) |> arrange(target_type, desc(mean)) |> select("Antibody", - "Mean UMI count per cell" = mean, - "Percent of cells detected" = detected, - "ADT target type" = target_type) + "Mean UMI count per cell" = mean, + "Percent of cells detected" = detected, + "ADT target type" = target_type + ) knitr::kable(antibody_tags, digits = 2) |> - kableExtra::kable_styling(bootstrap_options = c("striped", "condensed"), - full_width = FALSE, - position = "left", - ) + kableExtra::kable_styling( + bootstrap_options = c("striped", "condensed"), + full_width = FALSE, + position = "left", + ) ``` ## ADT Post-processing Statistics ```{r} - if (has_processed) { - basic_statistics <- tibble::tibble( - "Method used to identify cells to filter" = format(processed_meta$adt_scpca_filter_method) - ) + "Method used to identify cells to filter" = format(processed_meta$adt_scpca_filter_method) + ) if (!(processed_meta$adt_scpca_filter_method == "No filter")) { filtered_cell_count <- sum(processed_sce$adt_scpca_filter == "Keep") basic_statistics <- basic_statistics |> # Note that the adt_scpca_filter_method column is only present in the processed_sce object - mutate("Number of cells that pass filtering threshold" = format(filtered_cell_count), - "Percent of cells that pass filtering threshold" = paste0(round( filtered_cell_count/ncol(processed_sce) * 100, digits = 2), "%") + mutate( + "Number of cells that pass filtering threshold" = format(filtered_cell_count), + "Percent of cells that pass filtering threshold" = paste0(round(filtered_cell_count / ncol(processed_sce) * 100, digits = 2), "%") ) } basic_statistics <- basic_statistics |> @@ -78,13 +81,15 @@ if (has_processed) { reformat_nulls() |> t() - knitr::kable(basic_statistics, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> + knitr::kable(basic_statistics, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) } else { - glue::glue(" + glue::glue("
No ADT post-processing was performed on this library. @@ -92,15 +97,13 @@ if (has_processed) {
") } - ``` ## Removing low quality cells based on ADT counts ```{r fig.alt="Cell filtering based on both ADT and RNA counts", results='asis'} -if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { - +if (has_processed && !(processed_meta$adt_scpca_filter_method == "No filter")) { glue::glue(' Note that low-quality cells as identified by ADT counts are not actually filtered from the SCE object. @@ -113,28 +116,30 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { - "Filter (ADT only)": This cell is filtered based on only ADT counts. - "Filter (RNA & ADT)": This cell is filtered based on both RNA and ADT counts. - ') |> print() + ') |> print() filter_levels <- c("Keep", "Filter (RNA & ADT)", "Filter (RNA only)", "Filter (ADT only)") filtered_coldata_df <- filtered_coldata_df |> # add column to represent filtering on both RNA and ADT counts mutate(filter_summary = case_when( - scpca_filter == "Keep" & adt_scpca_filter == "Keep" ~ filter_levels[1], + scpca_filter == "Keep" & adt_scpca_filter == "Keep" ~ filter_levels[1], scpca_filter == "Remove" & adt_scpca_filter == "Remove" ~ filter_levels[2], - scpca_filter == "Remove" & adt_scpca_filter == "Keep" ~ filter_levels[3], - scpca_filter == "Keep" & adt_scpca_filter == "Remove" ~ filter_levels[4], + scpca_filter == "Remove" & adt_scpca_filter == "Keep" ~ filter_levels[3], + scpca_filter == "Keep" & adt_scpca_filter == "Remove" ~ filter_levels[4], TRUE ~ "Error" - )) |> + )) |> # now, add a count to each label and factor in count order # add `keep_column` for use in plotting for colors add_count(filter_summary) |> - mutate(filter_summary = glue::glue("{filter_summary}\nN={n}"), - filter_summary = forcats::fct_infreq(filter_summary), - keep_column = ifelse( - stringr::str_starts(filter_summary, "Keep"), - "Keep", - "Remove" - )) |> + mutate( + filter_summary = glue::glue("{filter_summary}\nN={n}"), + filter_summary = forcats::fct_infreq(filter_summary), + keep_column = ifelse( + stringr::str_starts(filter_summary, "Keep"), + "Keep", + "Remove" + ) + ) |> select(-n) if (sum(stringr::str_detect(filtered_coldata_df$filter_summary, "Error")) != 0) { @@ -145,12 +150,16 @@ if (has_processed & !(processed_meta$adt_scpca_filter_method == "No filter")) { ggplot(filtered_coldata_df, aes(x = detected, y = subsets_mito_percent, color = keep_column)) + geom_point(alpha = 0.5, size = 1) + geom_vline(xintercept = min_gene_cutoff, linetype = "dashed") + - labs(x = "Number of genes detected", - y = "Mitochondrial percentage", - title = "Combined RNA and ADT filters") + + labs( + x = "Number of genes detected", + y = "Mitochondrial percentage", + title = "Combined RNA and ADT filters" + ) + facet_wrap(vars(filter_summary)) + - theme(plot.title = element_text(hjust = 0.5), - legend.position = "none") + theme( + plot.title = element_text(hjust = 0.5), + legend.position = "none" + ) } else { glue::glue("
@@ -172,18 +181,16 @@ The plots in this section visualize the top four most variable ADTs in the libra ```{r} # Calculate ADT variance if (has_processed) { - top_n <- 4 # we want the top 4 ADTs # Calculate variance for each ADT adt_var <- altExp(processed_sce) |> logcounts() |> - apply(1, var, na.rm=TRUE) + apply(1, var, na.rm = TRUE) # Get the top 4 - top_adts <- adt_var[ order(adt_var, decreasing=TRUE)[1:top_n] ] |> + top_adts <- adt_var[order(adt_var, decreasing = TRUE)[1:top_n]] |> names() - } else { # This warning also handles "else" conditions for the next two chunks glue::glue(" @@ -201,14 +208,13 @@ if (has_processed) { ```{r fig.alt="Density plot showing normalized expression of highly variable ADTs", warning = FALSE, results='asis'} if (has_processed) { - glue::glue( - "The plot below displays normalized expression of these four ADTs, with one ADT shown per panel.\n" + "The plot below displays normalized expression of these four ADTs, with one ADT shown per panel.\n" ) |> print() # grab expression for top ADTs from counts - var_adt_exp_df <- logcounts(altExp(processed_sce))[top_adts,] |> + var_adt_exp_df <- logcounts(altExp(processed_sce))[top_adts, ] |> # as.matrix needs to come _first_ as.matrix() |> t() |> @@ -216,8 +222,9 @@ if (has_processed) { tibble::rownames_to_column("barcode") |> # combine all ADTs into a single column for faceting tidyr::pivot_longer(!barcode, - names_to = "ADT", - values_to = "adt_expression") + names_to = "ADT", + values_to = "adt_expression" + ) # expression density plots ggplot(var_adt_exp_df, aes(x = adt_expression, fill = ADT)) + @@ -232,7 +239,6 @@ if (has_processed) { ```{r fig.alt="UMAP calculated from RNA expression but colored by normalized expression of highly variable ADTs", fig.height = 6, results='asis'} if (has_processed) { - # Extra blank line here keeps the plot in a separate paragraph glue::glue( "The plot below displays UMAP embeddings calculated from RNA expression, where each cell is colored by the expression level of the given ADT. @@ -242,11 +248,12 @@ if (has_processed) { # create data frame of UMAPs and expression - umap_df <- scuttle::makePerCellDF(processed_sce) |> - tibble::rownames_to_column("barcode") |> - select(barcode, - UMAP1 = UMAP.1, - UMAP2 = UMAP.2) |> + umap_df <- scuttle::makePerCellDF(processed_sce) |> + tibble::rownames_to_column("barcode") |> + select(barcode, + UMAP1 = UMAP.1, + UMAP2 = UMAP.2 + ) |> # combine with gene expression left_join(var_adt_exp_df, by = "barcode") @@ -261,11 +268,13 @@ if (has_processed) { scale_x_continuous(labels = NULL, breaks = NULL) + scale_y_continuous(labels = NULL, breaks = NULL) + coord_fixed() + - theme(legend.position = "bottom", - axis.title = element_text(size = 8, color = "black"), - strip.text = element_text(size = 8), - legend.title = element_text(size = 9), - legend.text = element_text(size = 8)) + + theme( + legend.position = "bottom", + axis.title = element_text(size = 8, color = "black"), + strip.text = element_text(size = 8), + legend.title = element_text(size = 9), + legend.text = element_text(size = 8) + ) + guides(colour = guide_colorbar(title.position = "bottom", title.hjust = 0.5)) } ``` diff --git a/templates/qc_report/multiplex_qc.rmd b/templates/qc_report/multiplex_qc.rmd index fe3db2b8..b56db91a 100644 --- a/templates/qc_report/multiplex_qc.rmd +++ b/templates/qc_report/multiplex_qc.rmd @@ -4,32 +4,34 @@ ```{r} # add rowData if missing -if (is.null(rowData(multiplex_exp)$detected)){ +if (is.null(rowData(multiplex_exp)$detected)) { multiplex_exp <- scuttle::addPerFeatureQCMetrics(multiplex_exp) } cell_hto_counts <- Matrix::colSums(counts(multiplex_exp)) hto_information <- tibble::tibble( - "Number of HTOs assayed" = - format(nrow(multiplex_exp), big.mark = ',', scientific = FALSE), - "Multiplex reads sequenced" = - format(multiplex_meta$total_reads, big.mark = ',', scientific = FALSE), - "Percent multiplex reads mapped to ADTs" = - paste0(round(multiplex_meta$mapped_reads/multiplex_meta$total_reads * 100, digits = 2), "%"), - "Percent of HTOs in cells" = - paste0(round(sum(cell_hto_counts)/multiplex_meta$mapped_reads * 100, digits = 2), "%"), - "Percent of cells with HTOs" = - paste0(round(sum(cell_hto_counts > 0)/length(cell_hto_counts) * 100, digits = 2), "%"), - "Median HTO UMIs per cell" = - format(median(cell_hto_counts), big.mark = ',', scientific = FALSE) - )|> + "Number of HTOs assayed" = + format(nrow(multiplex_exp), big.mark = ",", scientific = FALSE), + "Multiplex reads sequenced" = + format(multiplex_meta$total_reads, big.mark = ",", scientific = FALSE), + "Percent multiplex reads mapped to ADTs" = + paste0(round(multiplex_meta$mapped_reads / multiplex_meta$total_reads * 100, digits = 2), "%"), + "Percent of HTOs in cells" = + paste0(round(sum(cell_hto_counts) / multiplex_meta$mapped_reads * 100, digits = 2), "%"), + "Percent of cells with HTOs" = + paste0(round(sum(cell_hto_counts > 0) / length(cell_hto_counts) * 100, digits = 2), "%"), + "Median HTO UMIs per cell" = + format(median(cell_hto_counts), big.mark = ",", scientific = FALSE) +) |> t() -knitr::kable(hto_information, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> +knitr::kable(hto_information, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) ``` @@ -40,63 +42,69 @@ hto_tags <- as.data.frame(rowData(multiplex_exp)) |> tibble::rownames_to_column("Hashtag Oligo (HTO)") |> arrange(desc(mean)) |> select("Hashtag Oligo (HTO)", - "Mean UMI count per cell" = mean, - "Percent of cells detected" = detected) + "Mean UMI count per cell" = mean, + "Percent of cells detected" = detected + ) knitr::kable(hto_tags, digits = 2) |> - kableExtra::kable_styling(bootstrap_options = c("striped", "condensed"), - full_width = FALSE, - position = "left", - ) |> - kableExtra::column_spec(2:3, monospace = TRUE) + kableExtra::kable_styling( + bootstrap_options = c("striped", "condensed"), + full_width = FALSE, + position = "left", + ) |> + kableExtra::column_spec(2:3, monospace = TRUE) ``` -## Demultiplexing Sample Calls +## Demultiplexing Sample Calls Demultiplexing was performed using both [`DropletUtils::hashedDrops()`](https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html) and [`Seurat::HTOdemux()`](https://rdrr.io/github/satijalab/seurat/man/HTODemux.html) only on the _filtered_ cells, using default parameters for each. -For multiplex libraries where bulk RNA-seq data is available for the individual samples, we also performed demultiplexing analysis using genotype data following the methods described in [Weber _et al._ (2021)](https://doi.org/10.1093/gigascience/giab062). -The genetic demultiplexing results are reported under the `vireo` column in the below table. +For multiplex libraries where bulk RNA-seq data is available for the individual samples, we also performed demultiplexing analysis using genotype data following the methods described in [Weber _et al._ (2021)](https://doi.org/10.1093/gigascience/giab062). +The genetic demultiplexing results are reported under the `vireo` column in the below table. -**Note:** We have reported the demultiplexed sample calls for each of the above mentioned algorithms, but the multiplexed library has not been separated into individual samples. +**Note:** We have reported the demultiplexed sample calls for each of the above mentioned algorithms, but the multiplexed library has not been separated into individual samples. ```{r, results='asis'} # grab columns that have demuxing results as not all methods could be present -# e.g. vireo is only used if a matching bulk RNA seq library is there, +# e.g. vireo is only used if a matching bulk RNA seq library is there, # otherwise those calls will not be present demux_methods <- c("hashedDrops_sampleid", "HTODemux_sampleid", "vireo_sampleid") demux_columns <- colnames(colData(filtered_sce)) %in% demux_methods -if(any(demux_columns)){ - # create a table summarizing demuxing calls for each method used +if (any(demux_columns)) { + # create a table summarizing demuxing calls for each method used demux_calls <- as.data.frame(colData(filtered_sce)[, demux_columns]) |> # remove _sampleid at the end of the column names - dplyr::rename_with(~stringr::str_remove(., "_sampleid")) |> - tidyr::pivot_longer(cols = everything(), - names_to = "demux_method", - values_to = "Sample") |> + dplyr::rename_with(~ stringr::str_remove(., "_sampleid")) |> + tidyr::pivot_longer( + cols = everything(), + names_to = "demux_method", + values_to = "Sample" + ) |> dplyr::count(Sample, demux_method) |> - tidyr::pivot_wider(names_from = demux_method, - values_from = n) - - + tidyr::pivot_wider( + names_from = demux_method, + values_from = n + ) + + knitr::kable(demux_calls, digits = 2) |> - kableExtra::kable_styling(bootstrap_options = c("striped", "condensed"), - full_width = FALSE, - position = "left", + kableExtra::kable_styling( + bootstrap_options = c("striped", "condensed"), + full_width = FALSE, + position = "left", ) |> - kableExtra::column_spec(2:ncol(demux_calls), monospace = TRUE) -}else{ + kableExtra::column_spec(2:ncol(demux_calls), monospace = TRUE) +} else { glue::glue("
- + Demultiplexing was not applied to this library using any of the above mentioned methods. Sample calls cannot be reported. - +
") } - ``` diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 509ed88f..0413c795 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -33,8 +33,10 @@ library(ggplot2) # Set default ggplot theme theme_set( theme_bw() + - theme(plot.margin = margin(rep(20, 4)), - strip.background = element_rect(fill = 'transparent')) + theme( + plot.margin = margin(rep(20, 4)), + strip.background = element_rect(fill = "transparent") + ) ) # Helper function to change NULL -> "N/A" in a data frame @@ -61,33 +63,33 @@ has_filtered <- !is.null(filtered_sce) has_processed <- !is.null(processed_sce) # if there is no filtered sce, use the unfiltered for both -if (!has_filtered){ +if (!has_filtered) { filtered_sce <- unfiltered_sce } # grab sample id from filtered sce, if missing set sample id to NA -if(is.null(metadata(filtered_sce)$sample_id)){ +if (is.null(metadata(filtered_sce)$sample_id)) { sample_id <- NA } else { sample_id <- metadata(filtered_sce)$sample_id } # add cell stats if missing -if (is.null(unfiltered_sce$sum)){ +if (is.null(unfiltered_sce$sum)) { unfiltered_sce <- scuttle::addPerCellQCMetrics(unfiltered_sce) } -if (is.null(filtered_sce$sum)){ +if (is.null(filtered_sce$sum)) { filtered_sce <- scuttle::addPerCellQCMetrics(filtered_sce) } -if (is.null(filtered_sce$subsets_mito_percent)){ +if (is.null(filtered_sce$subsets_mito_percent)) { filtered_sce$subsets_mito_percent <- NA_real_ skip_miQC <- TRUE -}else{ +} else { skip_miQC <- FALSE } # try to add miQC if it is missing -if (is.null(metadata(filtered_sce)$miQC_model) & !skip_miQC){ +if (is.null(metadata(filtered_sce)$miQC_model) && !skip_miQC) { filtered_sce <- scpcaTools::add_miQC(filtered_sce) } @@ -108,14 +110,14 @@ if (has_cellhash) { # check for umap and celltypes, but need to be sure that processed_sce exists first if (has_processed) { has_umap <- "UMAP" %in% reducedDimNames(processed_sce) - + has_singler <- "singler" %in% metadata(processed_sce)$celltype_methods has_cellassign <- "cellassign" %in% metadata(processed_sce)$celltype_methods - + # Note: later, we will also check for submitter-provided annotations # for now, we will say this is false has_submitter_celltypes <- FALSE - + # If at least 1 is present, we have cell type annotations. has_celltypes <- any(has_singler, has_cellassign, has_submitter_celltypes) } else { @@ -133,7 +135,7 @@ has_multiplex <- length(sample_id) > 1 if (has_multiplex) { # convert sample id to bullet separated list - multiplex_samples <- paste0("
  • ", paste(sample_id, collapse = '
  • ', "
    • ")) + multiplex_samples <- paste0("
  • ", paste(sample_id, collapse = "
  • ", "
    • ")) glue::glue("
    @@ -145,7 +147,6 @@ if (has_multiplex) {
    ") } - ``` ## Raw Sample Metrics @@ -160,13 +161,13 @@ sample_information <- tibble::tibble( "Tech version" = format(unfiltered_meta$tech_version), # format to keep nulls "Data modalities" = paste(modalities, collapse = ", "), "Cells reported by alevin-fry" = - format(unfiltered_meta$af_num_cells, big.mark = ',', scientific = FALSE), + format(unfiltered_meta$af_num_cells, big.mark = ",", scientific = FALSE), "Number of genes assayed" = - format(nrow(unfiltered_sce), big.mark = ',', scientific = FALSE), + format(nrow(unfiltered_sce), big.mark = ",", scientific = FALSE), "Number of RNA-seq reads sequenced" = - format(unfiltered_meta$total_reads, big.mark = ',', scientific = FALSE), + format(unfiltered_meta$total_reads, big.mark = ",", scientific = FALSE), "Percent of RNA-seq reads mapped to transcripts" = - paste0(round((unfiltered_meta$mapped_reads/unfiltered_meta$total_reads) *100, 2), "%") + paste0(round((unfiltered_meta$mapped_reads / unfiltered_meta$total_reads) * 100, 2), "%") ) if (has_adt) { @@ -176,11 +177,11 @@ if (has_adt) { sample_information <- sample_information |> mutate( "Number of antibodies assayed" = - format(nrow(adt_exp), big.mark = ',', scientific = FALSE), + format(nrow(adt_exp), big.mark = ",", scientific = FALSE), "Number of ADT reads sequenced" = - format(adt_meta$total_reads, big.mark = ',', scientific = FALSE), + format(adt_meta$total_reads, big.mark = ",", scientific = FALSE), "Percent of ADT reads mapped to ADTs" = - paste0(round(adt_meta$mapped_reads/adt_meta$total_reads * 100, digits = 2), "%") + paste0(round(adt_meta$mapped_reads / adt_meta$total_reads * 100, digits = 2), "%") ) } @@ -191,11 +192,11 @@ if (has_cellhash) { sample_information <- sample_information |> mutate( "Number of HTOs assayed" = - format(nrow(multiplex_exp), big.mark = ',', scientific = FALSE), + format(nrow(multiplex_exp), big.mark = ",", scientific = FALSE), "Number of cellhash reads sequenced" = - format(multiplex_meta$total_reads, big.mark = ',', scientific = FALSE), + format(multiplex_meta$total_reads, big.mark = ",", scientific = FALSE), "Percent of cellhash reads mapped to HTOs" = - paste0(round(multiplex_meta$mapped_reads/multiplex_meta$total_reads * 100, digits = 2), "%") + paste0(round(multiplex_meta$mapped_reads / multiplex_meta$total_reads * 100, digits = 2), "%") ) } @@ -204,10 +205,12 @@ sample_information <- sample_information |> t() # make table with sample information -knitr::kable(sample_information, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> +knitr::kable(sample_information, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) ``` @@ -218,25 +221,28 @@ knitr::kable(sample_information, align = 'r') |> transcript_type <- paste(unfiltered_meta$transcript_type, collapse = " ") processing_info <- tibble::tibble( - "Salmon version" = format(unfiltered_meta$salmon_version), - "Alevin-fry version" = format(unfiltered_meta$alevinfry_version), - "Transcriptome index" = format(unfiltered_meta$reference_index), - "Alevin-fry droplet detection" = format(unfiltered_meta$af_permit_type), - "Resolution" = format(unfiltered_meta$af_resolution), + "Salmon version" = format(unfiltered_meta$salmon_version), + "Alevin-fry version" = format(unfiltered_meta$alevinfry_version), + "Transcriptome index" = format(unfiltered_meta$reference_index), + "Alevin-fry droplet detection" = format(unfiltered_meta$af_permit_type), + "Resolution" = format(unfiltered_meta$af_resolution), "Transcripts included" = dplyr::case_when( - transcript_type == "total spliced" ~ "Total and spliced only", - transcript_type == "spliced" ~ "Spliced only", - TRUE ~ transcript_type) - ) |> + transcript_type == "total spliced" ~ "Total and spliced only", + transcript_type == "spliced" ~ "Spliced only", + TRUE ~ transcript_type + ) +) |> reformat_nulls() |> t() # make table with processing information -knitr::kable(processing_info, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> +knitr::kable(processing_info, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) ``` @@ -248,11 +254,11 @@ knitr::kable(processing_info, align = 'r') |> basic_statistics <- tibble::tibble( "Method used to filter empty droplets" = metadata(filtered_sce)$filtering_method, "Number of cells post filtering empty droplets" = format(ncol(filtered_sce), big.mark = ","), - "Percent of reads in cells" = paste0(round((sum(filtered_sce$sum)/sum(unfiltered_sce$sum))*100,2),"%"), + "Percent of reads in cells" = paste0(round((sum(filtered_sce$sum) / sum(unfiltered_sce$sum)) * 100, 2), "%"), "Median UMI count per cell" = format(median(filtered_sce$sum), big.mark = ","), "Median genes detected per cell" = format(median(filtered_sce$detected), big.mark = ","), "Median percent reads mitochondrial" = paste0(round(median(filtered_sce$subsets_mito_percent), 2), "%") - ) +) # if processed sce exists add filtering and normalization table if (has_processed) { @@ -261,7 +267,7 @@ if (has_processed) { basic_statistics <- basic_statistics |> mutate( "Method used to filter low quality cells" = format(processed_meta$scpca_filter_method), - "Cells after filtering low quality cells" = format(dim(processed_sce)[2], big.mark = ',', scientific = FALSE), + "Cells after filtering low quality cells" = format(dim(processed_sce)[2], big.mark = ",", scientific = FALSE), "Normalization method" = format(processed_meta$normalization), "Minimum genes per cell cutoff" = format(processed_meta$min_gene_cutoff) ) @@ -278,17 +284,20 @@ basic_statistics <- basic_statistics |> t() # make table with basic statistics -knitr::kable(basic_statistics, align = 'r') |> - kableExtra::kable_styling(bootstrap_options = "striped", - full_width = FALSE, - position = "left") |> +knitr::kable(basic_statistics, align = "r") |> + kableExtra::kable_styling( + bootstrap_options = "striped", + full_width = FALSE, + position = "left" + ) |> kableExtra::column_spec(2, monospace = TRUE) - ``` ```{r, results='asis'} -if (has_filtered && - (metadata(filtered_sce)$filtering_method == "UMI cutoff")) { +if ( + has_filtered && + (metadata(filtered_sce)$filtering_method == "UMI cutoff") +) { glue::glue("
    @@ -303,8 +312,8 @@ if (has_filtered && ```{r, results='asis'} # check for number of filtered cells min_filtered <- 100 -if(has_filtered){ - if(ncol(filtered_sce) < min_filtered){ +if (has_filtered) { + if (ncol(filtered_sce) < min_filtered) { glue::glue("
    @@ -318,8 +327,8 @@ if(has_filtered){ # check for number of cells post processing min_processed <- 50 -if(has_processed){ - if(ncol(processed_sce) < min_processed){ +if (has_processed) { + if (ncol(processed_sce) < min_processed) { glue::glue("
    @@ -337,7 +346,7 @@ if(has_processed){ ```{r, fig.alt="Smoothed knee plot of filtered and unfiltered droplets"} unfiltered_celldata <- data.frame(colData(unfiltered_sce)) |> mutate( - rank = rank(- unfiltered_sce$sum, ties.method = "first"), # using full spec for clarity + rank = rank(-unfiltered_sce$sum, ties.method = "first"), # using full spec for clarity filter_pass = colnames(unfiltered_sce) %in% colnames(filtered_sce) ) |> select(sum, rank, filter_pass) |> @@ -345,7 +354,7 @@ unfiltered_celldata <- data.frame(colData(unfiltered_sce)) |> grouped_celldata <- unfiltered_celldata |> - mutate(rank_group = floor(rank / 100) )|> + mutate(rank_group = floor(rank / 100)) |> group_by(rank_group) |> summarize( med_sum = median(sum), @@ -358,25 +367,31 @@ top_celldata <- unfiltered_celldata |> mutate(filter_pct = ifelse(filter_pass, 100, 0)) ggplot(grouped_celldata, aes(x = med_rank, y = med_sum, color = pct_passed)) + - geom_point(mapping = aes(x = rank, y = sum, color = filter_pct), - data = top_celldata, - alpha = 0.5) + - geom_line(linewidth = 2, lineend = "round", linejoin= "round") + + geom_point( + mapping = aes(x = rank, y = sum, color = filter_pct), + data = top_celldata, + alpha = 0.5 + ) + + geom_line(linewidth = 2, lineend = "round", linejoin = "round") + scale_x_log10(labels = scales::label_number(accuracy = 1)) + scale_y_log10(labels = scales::label_number(accuracy = 1)) + - scale_color_gradient2(low = "grey70", - mid = "forestgreen", - high = "darkgreen", - midpoint = 50) + + scale_color_gradient2( + low = "grey70", + mid = "forestgreen", + high = "darkgreen", + midpoint = 50 + ) + labs( x = "Rank", y = "Total UMI count", color = "% passing\ncell filter" ) + - theme(legend.position = c(0, 0), - legend.justification = c(0,0), - legend.background = element_rect(color = "grey20", linewidth = 0.25), - legend.box.margin = margin(rep(5, 4))) + theme( + legend.position = c(0, 0), + legend.justification = c(0, 0), + legend.background = element_rect(color = "grey20", linewidth = 0.25), + legend.box.margin = margin(rep(5, 4)) + ) ``` The total UMI count of each droplet (barcode) plotted against the rank of that droplet allows visualization of the distribution of sequencing depth across droplets. @@ -389,21 +404,29 @@ The color in this plot indicates the percentage of droplets in a region passing ```{r, fig.alt="Total UMI x genes expressed"} filtered_celldata <- data.frame(colData(filtered_sce)) -ggplot(filtered_celldata, - aes (x = sum, - y = detected, - color = subsets_mito_percent)) + +ggplot( + filtered_celldata, + aes( + x = sum, + y = detected, + color = subsets_mito_percent + ) +) + geom_point(alpha = 0.3) + scale_color_viridis_c(limits = c(0, 100)) + scale_x_continuous(labels = scales::label_number(accuracy = 1)) + scale_y_continuous(labels = scales::label_number(accuracy = 1)) + - labs(x = "Total UMI count", - y = "Number of genes detected", - color = "Percent reads\nmitochondrial") + - theme(legend.position = c(0, 1), - legend.justification = c(0,1), - legend.background = element_rect(color = "grey20", linewidth = 0.25), - legend.box.margin = margin(rep(5, 4))) + labs( + x = "Total UMI count", + y = "Number of genes detected", + color = "Percent reads\nmitochondrial" + ) + + theme( + legend.position = c(0, 1), + legend.justification = c(0, 1), + legend.background = element_rect(color = "grey20", linewidth = 0.25), + legend.box.margin = margin(rep(5, 4)) + ) ``` The above plot of cell metrics includes only droplets which have passed the `emptyDropsCellRanger()` filter. @@ -428,14 +451,18 @@ if (skip_miQC) { } miQC_plot + - coord_cartesian(ylim = c(0,100)) + + coord_cartesian(ylim = c(0, 100)) + scale_x_continuous(labels = scales::label_number(accuracy = 1)) + - labs(x = "Number of genes detected", - y = "Percent reads mitochondrial") + - theme(legend.position = c(1, 1), - legend.justification = c(1,1), - legend.background = element_rect(color = "grey20", linewidth = 0.25), - legend.box.margin = margin(rep(5, 4))) + labs( + x = "Number of genes detected", + y = "Percent reads mitochondrial" + ) + + theme( + legend.position = c(1, 1), + legend.justification = c(1, 1), + legend.background = element_rect(color = "grey20", linewidth = 0.25), + legend.box.margin = margin(rep(5, 4)) + ) } ``` @@ -460,8 +487,7 @@ The dotted vertical line indicates the minimum gene cutoff used for filtering. ```{r results='asis'} -if (has_filtered & has_processed) { - +if (has_filtered && has_processed) { # grab cutoffs and filtering method from processed sce min_gene_cutoff <- processed_meta$min_gene_cutoff @@ -475,15 +501,19 @@ if (has_filtered & has_processed) { ggplot(filtered_coldata_df, aes(x = detected, y = subsets_mito_percent, color = scpca_filter)) + geom_point(alpha = 0.5, size = 1) + geom_vline(xintercept = min_gene_cutoff, linetype = "dashed") + - labs(x = "Number of genes detected", - y = "Mitochondrial percentage", - color = "Filter", - title = stringr::str_replace(filter_method, "_", " ")) + - theme(plot.title = element_text(hjust = 0.5), - legend.position = c(1, 1), - legend.justification = c(1,1), - legend.background = element_rect(color = "grey20", linewidth = 0.25), - legend.title = element_text(hjust = 0.5)) + labs( + x = "Number of genes detected", + y = "Mitochondrial percentage", + color = "Filter", + title = stringr::str_replace(filter_method, "_", " ") + ) + + theme( + plot.title = element_text(hjust = 0.5), + legend.position = c(1, 1), + legend.justification = c(1, 1), + legend.background = element_rect(color = "grey20", linewidth = 0.25), + legend.title = element_text(hjust = 0.5) + ) } else { glue::glue("
    @@ -528,7 +558,6 @@ if (requireNamespace("sessioninfo", quietly = TRUE)) { } else { sessionInfo() } - ```
    diff --git a/templates/qc_report/umap_qc.rmd b/templates/qc_report/umap_qc.rmd index a84c9978..2d477a80 100644 --- a/templates/qc_report/umap_qc.rmd +++ b/templates/qc_report/umap_qc.rmd @@ -1,18 +1,19 @@ -## Dimensionality Reduction +## Dimensionality Reduction The below plot shows the UMAP (Uniform Manifold Approximation and Projection) embeddings for each cell, coloring each cell by the total number of genes detected per cell. ```{r message=FALSE} -# create UMAP colored by number of genes detected +# create UMAP colored by number of genes detected scater::plotUMAP(processed_sce, - point_size = 0.3, - point_alpha = 0.5, - colour_by = "detected") + + point_size = 0.3, + point_alpha = 0.5, + colour_by = "detected" +) + scale_color_viridis_c() + # remove axis numbers and background grid - scale_x_continuous(labels = NULL, breaks = NULL) + - scale_y_continuous(labels = NULL, breaks = NULL) + - coord_fixed() + + scale_x_continuous(labels = NULL, breaks = NULL) + + scale_y_continuous(labels = NULL, breaks = NULL) + + coord_fixed() + guides( color = guide_colorbar(title = "Number of \ngenes detected") ) @@ -28,78 +29,84 @@ If gene symbols are not available, the Ensembl id will be shown. ```{r message=FALSE, results='asis', fig.height = 8} # only create plot if variable genes are present if (!is.null(processed_meta$highly_variable_genes)) { - - # select top genes to plot + # select top genes to plot top_genes <- processed_meta$highly_variable_genes |> - head( n = 12) - + head(n = 12) + # grab expression for top genes from counts - var_gene_exp <- logcounts(processed_sce[top_genes,]) |> + var_gene_exp <- logcounts(processed_sce[top_genes, ]) |> as.matrix() |> t() |> as.data.frame() |> tibble::rownames_to_column("barcode") - + # grab rowdata as data frame to later combine with gene expression data - # rowdata contains the mapped gene symbol so can use that to label plots instead of ensembl gene id from rownames + # rowdata contains the mapped gene symbol so can use that to label plots instead of ensembl gene id from rownames rowdata_df <- rowData(processed_sce) |> as.data.frame() |> tibble::rownames_to_column("ensembl_id") |> select(ensembl_id, gene_symbol) |> filter(ensembl_id %in% top_genes) |> - mutate(gene_symbol = ifelse(!is.na(gene_symbol), gene_symbol, ensembl_id), - ensembl_id = factor(ensembl_id, levels = top_genes)) |> + mutate( + gene_symbol = ifelse(!is.na(gene_symbol), gene_symbol, ensembl_id), + ensembl_id = factor(ensembl_id, levels = top_genes) + ) |> arrange(ensembl_id) |> mutate(gene_symbol = factor(gene_symbol, levels = gene_symbol)) - - + + # extract umap embeddings as a dataframe to join with gene expression and coldata for plotting umap_df <- reducedDim(processed_sce, "UMAP") |> as.data.frame() |> tibble::rownames_to_column("barcode") |> - rename("UMAP1" = "V1", - "UMAP2" = "V2") - + rename( + "UMAP1" = "V1", + "UMAP2" = "V2" + ) + # combine gene expression with coldata, umap embeddings, and rowdata and create data frame to use for plotting coldata_df <- colData(processed_sce) |> as.data.frame() |> tibble::rownames_to_column("barcode") |> # combine with gene expression left_join(var_gene_exp, by = "barcode") |> - # combine with umap embeddings + # combine with umap embeddings left_join(umap_df, by = "barcode") |> - # combine all genes into a single column for easy faceting - tidyr::pivot_longer(cols = starts_with("ENSG"), - names_to = "ensembl_id", - values_to = "gene_expression") |> - # join with row data to add in gene symbols + # combine all genes into a single column for easy faceting + tidyr::pivot_longer( + cols = starts_with("ENSG"), + names_to = "ensembl_id", + values_to = "gene_expression" + ) |> + # join with row data to add in gene symbols left_join(rowdata_df) - - - ggplot(coldata_df, aes(x = UMAP1, y = UMAP2, color = gene_expression)) + - geom_point(alpha = 0.1, size = 0.001) + + + + ggplot(coldata_df, aes(x = UMAP1, y = UMAP2, color = gene_expression)) + + geom_point(alpha = 0.1, size = 0.001) + facet_wrap(vars(gene_symbol)) + scale_color_viridis_c() + labs( color = "Log-normalized gene expression" ) + # remove axis numbers and background grid - scale_x_continuous(labels = NULL, breaks = NULL) + - scale_y_continuous(labels = NULL, breaks = NULL) + - coord_fixed() + - theme(legend.position = "bottom", - axis.title = element_text(size = 9, color = "black"), - strip.text = element_text(size = 8), - legend.title = element_text(size = 9), - legend.text = element_text(size = 8)) + + scale_x_continuous(labels = NULL, breaks = NULL) + + scale_y_continuous(labels = NULL, breaks = NULL) + + coord_fixed() + + theme( + legend.position = "bottom", + axis.title = element_text(size = 9, color = "black"), + strip.text = element_text(size = 8), + legend.title = element_text(size = 9), + legend.text = element_text(size = 8) + ) + guides(colour = guide_colorbar(title.position = "bottom", title.hjust = 0.5)) - } else { glue::glue("
    - - This library does not contain a set of highly variable genes. - + + This library does not contain a set of highly variable genes. +
    ") } From 7a88afdcfd1eca982613c9d2af43922d6702cc07 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 8 Sep 2023 12:51:06 -0400 Subject: [PATCH 168/268] Appease the spell checker --- CONTRIBUTING.md | 4 ++-- components/dictionary.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e4fb53ed..590cef9a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -34,8 +34,8 @@ If a new reference type is needed, that should be defined in the [`test/stub-ref While there is not necessarily an established code style for nextflow code, we try to keep code neat and readable. Line length should generally be kept under 100 characters, and indentation should be consistent. -For R code, we try to follow [tidyverse style conventions](https://style.tidyverse.org), and encourage the use of the [`styler`](https://styler.r-lib.org/) package to ensure that code is formatted consistently. +For R code, we try to follow [`tidyverse` style conventions](https://style.tidyverse.org), and encourage the use of the [`styler`](https://styler.r-lib.org/) package to ensure that code is formatted consistently. For python code, we encourage the use of the `black` code formatter to ensure consistent formatting. The `black` package can be installed with `pip install black`, and can be run on a file with `black `. -Alternatively, if you use VSCode, you can install the [black extension](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter). +Alternatively, if you use [Visual Studio Code](https://code.visualstudio.com), you can install the [`black` extension](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter). diff --git a/components/dictionary.txt b/components/dictionary.txt index 64682d87..bbfb9fe8 100644 --- a/components/dictionary.txt +++ b/components/dictionary.txt @@ -18,6 +18,7 @@ Ensembl et fastq FASTQ +formatter Github glioblastoma GRCh From ef9341eb08a5d0a8855ac8acd6e399ab4c46f6f9 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 8 Sep 2023 13:54:46 -0400 Subject: [PATCH 169/268] Bug fix: needed to add levels to the non-ontology x-axis variable --- templates/qc_report/celltypes_qc.rmd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index f2845831..64b33fc7 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -179,6 +179,9 @@ if ("singler_celltype_ontology" %in% names(celltype_df)) { # otherwise, full_labels already contain what we want to plot, so just rename it delta_median_df <- delta_median_df |> dplyr::rename(celltype = full_labels) + # still need to add levels though: + # unknown will still be present, but it's not in the data, so it won't matter + levels(delta_median_df$celltype) <- levels(celltype_df$singler_celltype_annotation) } # Ensure we have no "Unknown cell type" values left: From 9c963bfb48c5285216a55712fecaff8710a52c42 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 8 Sep 2023 14:48:06 -0500 Subject: [PATCH 170/268] use black and save schema --- bin/move_counts_anndata.py | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index bace86dc..91c7eb1b 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -11,10 +11,13 @@ import anndata as adata parser = argparse.ArgumentParser() -parser.add_argument('-i', '--anndata_file', - dest = 'anndata_file', - required = True, - help = 'Path to HDF5 file with processed AnnData object') +parser.add_argument( + "-i", + "--anndata_file", + dest="anndata_file", + required=True, + help="Path to HDF5 file with processed AnnData object", +) args = parser.parse_args() @@ -25,7 +28,9 @@ if not os.path.exists(args.anndata_file): raise FileExistsError("`input_anndata` does not exist.") elif not file_ext.search(args.anndata_file): - raise ValueError("--input_anndata must end in either .hdf5 or .h5 and contain a processed AnnData object.") + raise ValueError( + "--input_anndata must end in either .hdf5 or .h5 and contain a processed AnnData object." + ) # read in anndata object = adata.read_h5ad(args.anndata_file) @@ -37,5 +42,9 @@ # move logcounts to X and rename object.X = object.layers["logcounts"] object.uns["X_name"] = "logcounts" + + # add schema to uns + object.uns["schema_version"] = "3.0.0" + # export object object.write_h5ad(args.anndata_file) From 6493fed0b5ccfd3458a4905487437abe20536e7a Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 8 Sep 2023 16:33:13 -0400 Subject: [PATCH 171/268] fix typo - one package --- templates/qc_report/celltypes_qc.rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 64b33fc7..29fe5919 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -9,7 +9,7 @@ The following method(s) were used to perform cell typing: knitr::asis_output( glue::glue( "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. - The `{metadata(processed_sce)$singler_reference}` reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used for cell typing." + The `{metadata(processed_sce)$singler_reference}` reference dataset, obtained from the [`celldex`](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used for cell typing." ) ) ``` From 41e1654a3169dded86e4924dccf03063e0535ac1 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 8 Sep 2023 16:46:05 -0400 Subject: [PATCH 172/268] Crossbar -> boxplot --- templates/qc_report/celltypes_qc.rmd | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 29fe5919..7005acf7 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -216,12 +216,15 @@ ggplot(delta_median_df) + ) + scale_color_manual(values = c("blue", "black")) + # add median/IQR - stat_summary( + geom_boxplot( data = delta_median_confident_df, # only use black points for median color = "red", - geom = "crossbar", - width = 0.4, - size = 0.2 + width = 0.2, + size = 0.3, + alpha = 0, + # remove whiskers, outliers + outlier.shape = 0, + coef = 0 ) + guides( color = guide_legend(override.aes = list(size = 1, alpha = 0.9)) From 5d91afbb06c85f2cc1988f94b11a226110610e87 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 11 Sep 2023 09:14:36 -0500 Subject: [PATCH 173/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- bin/move_counts_anndata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index 91c7eb1b..780841c0 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -36,7 +36,7 @@ object = adata.read_h5ad(args.anndata_file) # if logcounts is present -if "logcounts" in object.layers.keys(): +if "logcounts" in object.layers: # move X to raw.X by creating the raw object object.raw = object # move logcounts to X and rename From 3a9dec6f48598d22a22b1866c93ed60d5f480908 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 12 Sep 2023 08:31:28 -0400 Subject: [PATCH 174/268] Apply suggestions from code review Co-authored-by: Stephanie --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 590cef9a..e1f7e5f9 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -26,7 +26,7 @@ All Nextflow processes should include a [`stub` block](https://www.nextflow.io/d At this stage this is purely used to allow for testing of the main workflow logic rather than the internal logic of each process. The [`test/stub-run-metadata.tsv`](test/stub-run-metadata.tsv) file is used to define input libraries that will be used for testing. -Any additions to the overall workflow that will allow processing of a new library type should be added into `test/stub-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for that library type in the `test/runs/` directory. +Any additions to the overall workflow that will allow processing of a new library type should be added into `test/stub-run-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for that library type in the `test/runs/` directory. If a new reference type is needed, that should be defined in the [`test/stub-refs.json`](test/stub-refs.json) file. ## Code style @@ -36,6 +36,6 @@ Line length should generally be kept under 100 characters, and indentation shoul For R code, we try to follow [`tidyverse` style conventions](https://style.tidyverse.org), and encourage the use of the [`styler`](https://styler.r-lib.org/) package to ensure that code is formatted consistently. -For python code, we encourage the use of the `black` code formatter to ensure consistent formatting. +For python code, we encourage the use of the [`black` code formatter](https://black.readthedocs.io/en/stable/) to ensure consistent formatting. The `black` package can be installed with `pip install black`, and can be run on a file with `black `. Alternatively, if you use [Visual Studio Code](https://code.visualstudio.com), you can install the [`black` extension](https://marketplace.visualstudio.com/items?itemName=ms-python.black-formatter). From 3a2f57a686adda166a364640ceb434ace7705e69 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 12 Sep 2023 08:37:55 -0400 Subject: [PATCH 175/268] Add the stub sample file to contributing docs --- CONTRIBUTING.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e1f7e5f9..3ed931bc 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -26,7 +26,9 @@ All Nextflow processes should include a [`stub` block](https://www.nextflow.io/d At this stage this is purely used to allow for testing of the main workflow logic rather than the internal logic of each process. The [`test/stub-run-metadata.tsv`](test/stub-run-metadata.tsv) file is used to define input libraries that will be used for testing. -Any additions to the overall workflow that will allow processing of a new library type should be added into `test/stub-run-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for that library type in the `test/runs/` directory. +Each sample ID in the `stub-run-metadata.tsv` file should have a corresponding entry in [`test/stub-sample-metadata.tsv`](test/stub-sample-metadata.tsv) (which can be filled with `NA` values). +Any additions to the overall workflow that will allow processing of a new library type should include adding new example data. +This will involve adding rows to `test/stub-run-metadata.tsv` and `test/stub-sample-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for each library in the `test/runs/` directory. If a new reference type is needed, that should be defined in the [`test/stub-refs.json`](test/stub-refs.json) file. ## Code style From 706673a4f10560a7b60ee0e25cf10a9b6918d2e6 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 12 Sep 2023 08:40:12 -0400 Subject: [PATCH 176/268] give the row name --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3ed931bc..d6377f84 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -26,7 +26,7 @@ All Nextflow processes should include a [`stub` block](https://www.nextflow.io/d At this stage this is purely used to allow for testing of the main workflow logic rather than the internal logic of each process. The [`test/stub-run-metadata.tsv`](test/stub-run-metadata.tsv) file is used to define input libraries that will be used for testing. -Each sample ID in the `stub-run-metadata.tsv` file should have a corresponding entry in [`test/stub-sample-metadata.tsv`](test/stub-sample-metadata.tsv) (which can be filled with `NA` values). +Each `scpca_sample_id` value in the `stub-run-metadata.tsv` file should have a corresponding entry in [`test/stub-sample-metadata.tsv`](test/stub-sample-metadata.tsv) (which can be filled with `NA` values). Any additions to the overall workflow that will allow processing of a new library type should include adding new example data. This will involve adding rows to `test/stub-run-metadata.tsv` and `test/stub-sample-metadata.tsv`, along with the appropriate input files (usually empty files with the expected names) for each library in the `test/runs/` directory. If a new reference type is needed, that should be defined in the [`test/stub-refs.json`](test/stub-refs.json) file. From 0495e6ba05726c5ee88e84b247bbd137919661ad Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 13 Sep 2023 15:39:44 +0000 Subject: [PATCH 177/268] submitter celltypes into meta params --- main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/main.nf b/main.nf index 2243af5e..6f5c6c84 100644 --- a/main.nf +++ b/main.nf @@ -96,6 +96,7 @@ workflow { submitter: it.submitter, technology: it.technology, seq_unit: it.seq_unit, + submitter_cell_types_file: it.submitter_cell_types_file, feature_barcode_file: it.feature_barcode_file, feature_barcode_geom: it.feature_barcode_geom, files_directory: it.files_directory, From 1bee360977258a3181a7acca6a1f1510e55d1ac3 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:51:25 -0500 Subject: [PATCH 178/268] add try block around model gene var, pca, and umap --- bin/post_process_sce.R | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/bin/post_process_sce.R b/bin/post_process_sce.R index 3d4a7820..6304d51f 100755 --- a/bin/post_process_sce.R +++ b/bin/post_process_sce.R @@ -229,14 +229,15 @@ if (alt_exp %in% altExpNames(processed_sce)) { # Perform dimension reduction -------------------- -# model gene variance using `scran:modelGeneVar()` -gene_variance <- scran::modelGeneVar(processed_sce) +try({ + # model gene variance using `scran:modelGeneVar()` + gene_variance <- scran::modelGeneVar(processed_sce) -# select the most variable genes -var_genes <- scran::getTopHVGs(gene_variance, n = opt$n_hvg) + # select the most variable genes + var_genes <- scran::getTopHVGs(gene_variance, n = opt$n_hvg) -# save the most variable genes to the metadata -metadata(processed_sce)$highly_variable_genes <- var_genes + # save the most variable genes to the metadata + metadata(processed_sce)$highly_variable_genes <- var_genes # dimensionality reduction # highly variable genes are used as input to PCA @@ -247,7 +248,6 @@ processed_sce <- scater::runPCA( ) # calculate a UMAP matrix using the PCA results -try({ processed_sce <- scater::runUMAP(processed_sce, dimred = "PCA" ) From 69bed7ac1915af20990925e45c1228402f4ec785 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 13 Sep 2023 20:07:49 +0000 Subject: [PATCH 179/268] R script for adding submitter annotations --- bin/add_submitter_annotations.R | 73 +++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 bin/add_submitter_annotations.R diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R new file mode 100644 index 00000000..ddfb29b9 --- /dev/null +++ b/bin/add_submitter_annotations.R @@ -0,0 +1,73 @@ +#!/usr/bin/env Rscript + +# This script adds submitter annotations, if provided, to the unfiltered SCE's colData. +# If the file was not provided, this script has no effect. + +# import libraries +suppressPackageStartupMessages({ + library(optparse) + library(SingleCellExperiment) +}) +# set up arguments +option_list <- list( + make_option( + opt_str = c("-u", "--unfiltered_file"), + type = "character", + help = "path to output unfiltered rds file. Must end in .rds" + ), + make_option( + opt_str = c("--library_id"), + type = "character", + help = "library id" + ), + make_option( + opt_str = c("--submitter_cell_types_file"), + type = "character", + help = "path to tsv file containing submitter-provided cell type annotations" + ) +) + +opt <- parse_args(OptionParser(option_list = option_list)) + +# check that output file name ends in .rds +if (!(stringr::str_ends(opt$unfiltered_file, ".rds"))) { + stop("unfiltered file name must end in .rds") +} + + +# check that submitter cell types file exists +if (!file.exists(opt$submitter_cell_types_file)) { + stop("submitter cell type annotations file not found.") +} + + +# Read in unfiltered sce +sce <- readr::read_rds(opt$unfiltered_file) + +# Read in celltypes, and filter to relevant information +submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> + dplyr::filter(scpca_library_id == opt$library_id) |> + dplyr::select( + barcodes = cell_barcode, + submitter_celltype_annotations = cell_type_assignment + ) |> + # in the event of NA values, change to "Unclassified cell" + dplyr::mutate( + submitter_celltype_annotations = dplyr::if_else( + is.na(submitter_celltype_annotations), + "Unclassified cell", + submitter_celltype_annotations + ) + ) + +# Join in submitter cell types +colData(sce) <- colData(sce) |> + as.data.frame() |> + dplyr::left_join( + submitter_cell_types_df + ) |> + # make sure we keep rownames + DataFrame(row.names = colData(sce)$barcodes) + +# Write unfiltered RDS back to file +readr::write_rds(sce, opt$unfiltered_file, compress = "gz") From b365c1bb99d265de6ffa0e2acb6ae4bff1b6bcb5 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 13 Sep 2023 20:08:26 +0000 Subject: [PATCH 180/268] Submitter annotations added for RNA-only libraries --- modules/sce-processing.nf | 30 +++++++++++++++++++++++------- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 5598e3de..eae9d52b 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -6,12 +6,13 @@ process make_unfiltered_sce{ label 'mem_8' tag "${meta.library_id}" input: - tuple val(meta), path(alevin_dir), path(mito_file), path(ref_gtf) + tuple val(meta), path(alevin_dir), path(mito_file), path(ref_gtf), path(submitter_cell_types_file) path sample_metafile output: tuple val(meta), path(unfiltered_rds) script: unfiltered_rds = "${meta.library_id}_unfiltered.rds" + """ generate_unfiltered_sce.R \ --alevin_dir ${alevin_dir} \ @@ -23,13 +24,22 @@ process make_unfiltered_sce{ --sample_id "${meta.sample_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} + + + # Only run script if annotations are available: + if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then + add_submitter_annotations.R \ + --unfiltered_file ${unfiltered_rds} \ + --library_id "${meta.library_id}" \ + --submitter_cell_types_file ${submitter_cell_types_file} + fi + """ stub: unfiltered_rds = "${meta.library_id}_unfiltered.rds" """ touch ${unfiltered_rds} """ - } // channels with RNA and feature data @@ -200,13 +210,19 @@ workflow generate_sce { quant_channel sample_metafile main: + + empty_file = file("${projectDir}/assets/NO_FILE.txt") + sce_ch = quant_channel - .map{it.toList() + [file(it[0].mito_file), file(it[0].ref_gtf)]} - + .map{it.toList() + [file(it[0].mito_file), + file(it[0].ref_gtf), + // either submitter cell type files, or empty file if not available + file(it[0].submitter_cell_types_file).exists() ? file(it[0].submitter_cell_types_file) : empty_file + ]} + + sce_ch.view() make_unfiltered_sce(sce_ch, sample_metafile) - - empty_file = file("${projectDir}/assets/NO_FILE.txt") - + // provide empty feature barcode file, since no features here unfiltered_sce_ch = make_unfiltered_sce.out .map{it.toList() + [empty_file]} From 4bb55883cc65a01ab514d074669cd1e6e9dc860f Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:01:10 -0500 Subject: [PATCH 181/268] account for no pca in clustering --- bin/cluster_sce.R | 43 ++++++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index 2bb67c34..a6a9e7aa 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -65,30 +65,35 @@ if (!file.exists(opt$processed_sce_file)) { } sce <- readr::read_rds(opt$processed_sce_file) +# only perform clustering if reduced dimension embeddings are present +# otherwise just return the object +if(length(reducedDimNames(sce)) > 0){ -# check pca_name is present -if (!opt$pca_name %in% reducedDimNames(sce)) { - stop("Provided `pca_name` is not present in the SCE object.") -} + # check pca_name is present + if (!opt$pca_name %in% reducedDimNames(sce)) { + stop("Provided `pca_name` is not present in the SCE object.") + } -# Perform clustering ---------------- + # Perform clustering ---------------- -# extract the principal components matrix -clusters <- scran::clusterCells( - sce, - use.dimred = opt$pca_name, - BLUSPARAM = bluster::NNGraphParam( - k = opt$nearest_neighbors, - type = opt$cluster_weighting, - cluster.fun = opt$cluster_algorithm + # extract the principal components matrix + clusters <- scran::clusterCells( + sce, + use.dimred = opt$pca_name, + BLUSPARAM = bluster::NNGraphParam( + k = opt$nearest_neighbors, + type = opt$cluster_weighting, + cluster.fun = opt$cluster_algorithm + ) ) -) -# add clusters and associated parameters to SCE object -sce$clusters <- clusters -metadata(sce)$cluster_algorithm <- opt$cluster_algorithm -metadata(sce)$cluster_weighting <- opt$cluster_weighting -metadata(sce)$cluster_nn <- opt$nearest_neighbors + # add clusters and associated parameters to SCE object + sce$clusters <- clusters + metadata(sce)$cluster_algorithm <- opt$cluster_algorithm + metadata(sce)$cluster_weighting <- opt$cluster_weighting + metadata(sce)$cluster_nn <- opt$nearest_neighbors + +} # export ------------------- # we are overwriting the `processed_sce_file` here From 6114344b399bcdad5866766bbf8fcbb10cb42c59 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 13 Sep 2023 21:08:01 +0000 Subject: [PATCH 182/268] Add code for generate_merged_sce; tested and runs --- modules/sce-processing.nf | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index eae9d52b..0d9a9647 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -220,7 +220,6 @@ workflow generate_sce { file(it[0].submitter_cell_types_file).exists() ? file(it[0].submitter_cell_types_file) : empty_file ]} - sce_ch.view() make_unfiltered_sce(sce_ch, sample_metafile) // provide empty feature barcode file, since no features here @@ -240,10 +239,16 @@ workflow generate_merged_sce { feature_quant_channel sample_metafile main: - feature_sce_ch = feature_quant_channel + empty_file = file("${projectDir}/assets/NO_FILE.txt") + + feature_sce_ch = feature_quant_channel // RNA meta is in the third slot here - .map{it.toList() + [file(it[2].mito_file), file(it[2].ref_gtf)]} - + .map{it.toList() + [file(it[2].mito_file), + file(it[2].ref_gtf), + // either submitter cell type files, or empty file if not available + file(it[2].submitter_cell_types_file).exists() ? file(it[2].submitter_cell_types_file) : empty_file + ]} + make_merged_unfiltered_sce(feature_sce_ch, sample_metafile) // append the feature barcode file From 14370d6b780a2e4193b37b1b6f8a4730f2591fb1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:48:21 -0500 Subject: [PATCH 183/268] add seq unit, project id, and tech ontology to SCE --- bin/generate_unfiltered_sce.R | 26 ++++++++++++++++++++++++-- main.nf | 1 + 2 files changed, 25 insertions(+), 2 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 7d5c0186..fc0a5eb5 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -48,6 +48,16 @@ option_list <- list( type = "character", help = "sequencing technology string to store in metadata" ), + make_option( + opt_str = c("--assay_ontology_term_id"), + type = "character", + help = "Experimental Factor Ontology term associated with provided tech_version" + ), + make_option( + opt_str = c("-s", "--seq_unit"), + type = "character", + help = "sequencing unit string to store in metadata (e.g., cell, nucleus)" + ), make_option( opt_str = c("--library_id"), type = "character", @@ -58,6 +68,11 @@ option_list <- list( type = "character", help = "sample id(s). If more than one, separated by commas and/or semicolons." ), + make_option( + opt_str = c("--project_id"), + type = "character", + help = "project id" + ), make_option( opt_str = c("--sample_metadata_file"), type = "character", @@ -111,8 +126,11 @@ unfiltered_sce <- read_alevin( include_unspliced = include_unspliced, fry_mode = TRUE, tech_version = opt$technology, + assay_ontology_term_id = opt$assay_ontology_term_id, + seq_unit = opt$seq_unit, library_id = opt$library_id, - sample_id = sample_ids + sample_id = sample_ids, + project_id = opt$project_id ) # read and merge feature counts if present @@ -122,8 +140,12 @@ if (opt$feature_dir != "") { include_unspliced = FALSE, fry_mode = TRUE, feature_data = TRUE, + tech_version = opt$technology, + assay_ontology_term_id = opt$assay_ontology_term_id, + seq_unit = opt$seq_unit, library_id = opt$library_id, - sample_id = sample_ids + sample_id = sample_ids, + project_id = project_id ) unfiltered_sce <- merge_altexp(unfiltered_sce, feature_sce, opt$feature_name) diff --git a/main.nf b/main.nf index 2243af5e..df5d6115 100644 --- a/main.nf +++ b/main.nf @@ -95,6 +95,7 @@ workflow { project_id: it.scpca_project_id?: "no_project", submitter: it.submitter, technology: it.technology, + assay_ontology_term_id: it.assay_ontology_term_id, seq_unit: it.seq_unit, feature_barcode_file: it.feature_barcode_file, feature_barcode_geom: it.feature_barcode_geom, From 155b47976433b8ca95c138095e1705d1a2e981fe Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:48:39 -0500 Subject: [PATCH 184/268] add arguments to sce processing --- modules/sce-processing.nf | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 5598e3de..b079eee7 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -19,8 +19,11 @@ process make_unfiltered_sce{ --mito_file ${mito_file} \ --gtf_file ${ref_gtf} \ --technology ${meta.technology} \ + --assay_ontology_term_id ${meta.assay_ontology_term_id} \ + --seq_unit ${meta.seq_unit} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ + --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} """ @@ -64,8 +67,11 @@ process make_merged_unfiltered_sce{ --mito_file ${mito_file} \ --gtf_file ${ref_gtf} \ --technology ${meta.technology} \ + --assay_ontology_term_id ${meta.assay_ontology_term_id} \ + --seq_unit ${meta.seq_unit} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ + --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} """ From 1c7d36c9eb02c417cc7a5db5265a7118e514b7ff Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:48:56 -0500 Subject: [PATCH 185/268] update anndata formatting --- bin/move_counts_anndata.py | 3 --- bin/sce_to_anndata.R | 16 ++++++++++++++++ modules/export-anndata.nf | 4 +++- 3 files changed, 19 insertions(+), 4 deletions(-) diff --git a/bin/move_counts_anndata.py b/bin/move_counts_anndata.py index 780841c0..4fff0783 100755 --- a/bin/move_counts_anndata.py +++ b/bin/move_counts_anndata.py @@ -43,8 +43,5 @@ object.X = object.layers["logcounts"] object.uns["X_name"] = "logcounts" - # add schema to uns - object.uns["schema_version"] = "3.0.0" - # export object object.write_h5ad(args.anndata_file) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 6474b93f..660ab3ad 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -30,6 +30,12 @@ option_list <- list( type = "character", help = "path to output hdf5 file to store feature counts as AnnData object. Only used if the input SCE contains an altExp. Must end in .hdf5 or .h5" + ), + make_option( + opt_str = c("--czi_schema_version"), + type = "character", + default = "3.0.0", + help = "Version number for CZI schema matching formatting of output AnnData objects" ) ) @@ -59,6 +65,16 @@ format_czi <- function(sce) { # add is_primary_data column; only needed for anndata objects sce$is_primary_data <- FALSE + # create columns for assay and suspension ontology terms + sce$assay_ontology_term_id <- metadata(sce)$assay_ontology_term_id + sce$suspension_type <- metadata(sce)$seq_unit + + # move project id to title slot in metadata list + metadata(sce)$title <- metadata(sce)$project_id + + # add schema version + metadata(sce)$schema_version <- opt$czi_schema_version + # add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, join_columns = "library_id" diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index e308e430..4ffebc2d 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -7,6 +7,7 @@ process export_anndata{ publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(sce_file), val(file_type) + val(czi_schema_version) output: tuple val(meta), path("${meta.library_id}_${file_type}*.hdf5"), val(file_type) script: @@ -18,6 +19,7 @@ process export_anndata{ --input_sce_file ${sce_file} \ --output_rna_h5 ${rna_hdf5_file} \ --output_feature_h5 ${feature_hdf5_file} \ + --czi_schema_version ${czi_schema_version} \ ${feature_present ? "--feature_name ${meta.feature_type}" : ''} """ stub: @@ -64,7 +66,7 @@ workflow sce_to_anndata{ ]} // export each anndata file - export_anndata(sce_ch) + export_anndata(sce_ch, params.czi_schema_version) anndata_ch = export_anndata.out .branch{ From 703544bb01a39e04b2a4b53a92182ba0828f8f11 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:49:04 -0500 Subject: [PATCH 186/268] param for czi schema --- nextflow.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nextflow.config b/nextflow.config index 1b9652ca..2c4fe935 100644 --- a/nextflow.config +++ b/nextflow.config @@ -52,6 +52,9 @@ params { cluster_weighting = "jaccard" // default weighting scheme for graph-based clustering nearest_neighbors = 20 // default nearest neighbors parameter for graph-based clustering + // anndata options + czi_schema_version = "3.0.0" + // Docker container images includeConfig 'config/containers.config' From 97c17771aa2361659202783be0354ab788ffc8e8 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 09:17:52 -0400 Subject: [PATCH 187/268] remove the renaming --- templates/qc_report/umap_qc.rmd | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/templates/qc_report/umap_qc.rmd b/templates/qc_report/umap_qc.rmd index 2d477a80..586d8d4b 100644 --- a/templates/qc_report/umap_qc.rmd +++ b/templates/qc_report/umap_qc.rmd @@ -58,11 +58,7 @@ if (!is.null(processed_meta$highly_variable_genes)) { # extract umap embeddings as a dataframe to join with gene expression and coldata for plotting umap_df <- reducedDim(processed_sce, "UMAP") |> as.data.frame() |> - tibble::rownames_to_column("barcode") |> - rename( - "UMAP1" = "V1", - "UMAP2" = "V2" - ) + tibble::rownames_to_column("barcode") # combine gene expression with coldata, umap embeddings, and rowdata and create data frame to use for plotting coldata_df <- colData(processed_sce) |> From c0ce9e0a1a77d485204b67fa63da920c2f12f6b3 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 13:35:12 +0000 Subject: [PATCH 188/268] save fact that submitter is present to metadata --- bin/add_submitter_annotations.R | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index ddfb29b9..c3d9a6e7 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -69,5 +69,9 @@ colData(sce) <- colData(sce) |> # make sure we keep rownames DataFrame(row.names = colData(sce)$barcodes) +# Indicate that we have submitter celltypes in metadata, +# saving in same spot as for actual celltyping +metadata(sce)$celltype_methods <- "submitter" + # Write unfiltered RDS back to file readr::write_rds(sce, opt$unfiltered_file, compress = "gz") From d67cfbe6404131b58b99e1b5bfba5ba1cd187158 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:21:56 +0000 Subject: [PATCH 189/268] Added relevant bits to make_merged_unfiltered_sce --- modules/sce-processing.nf | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 0d9a9647..ab1b4ce4 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -50,7 +50,7 @@ process make_merged_unfiltered_sce{ input: tuple val(feature_meta), path(feature_alevin_dir), val (meta), path(alevin_dir), - path(mito_file), path(ref_gtf) + path(mito_file), path(ref_gtf), path(submitter_cell_types_file) path sample_metafile output: tuple val(meta), path(unfiltered_rds) @@ -78,6 +78,15 @@ process make_merged_unfiltered_sce{ --sample_id "${meta.sample_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} + + # Only run script if annotations are available: + if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then + add_submitter_annotations.R \ + --unfiltered_file ${unfiltered_rds} \ + --library_id "${meta.library_id}" \ + --submitter_cell_types_file ${submitter_cell_types_file} + fi + """ stub: unfiltered_rds = "${meta.library_id}_unfiltered.rds" From 01a5e93a681788c6b63949eff3cb86b669b68e49 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 14 Sep 2023 09:45:46 -0500 Subject: [PATCH 190/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- bin/cluster_sce.R | 5 +++-- bin/post_process_sce.R | 3 ++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index a6a9e7aa..ba94bff7 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -67,8 +67,9 @@ sce <- readr::read_rds(opt$processed_sce_file) # only perform clustering if reduced dimension embeddings are present # otherwise just return the object -if(length(reducedDimNames(sce)) > 0){ - +if(length(reducedDimNames(sce)) == 0) { + warning("No reduced dimensions present, skipping clustering") +} else { # check pca_name is present if (!opt$pca_name %in% reducedDimNames(sce)) { stop("Provided `pca_name` is not present in the SCE object.") diff --git a/bin/post_process_sce.R b/bin/post_process_sce.R index 6304d51f..48c5edae 100755 --- a/bin/post_process_sce.R +++ b/bin/post_process_sce.R @@ -248,7 +248,8 @@ processed_sce <- scater::runPCA( ) # calculate a UMAP matrix using the PCA results - processed_sce <- scater::runUMAP(processed_sce, + processed_sce <- scater::runUMAP( + processed_sce, dimred = "PCA" ) }) From 6c255ab595a34db4a15276bcf6d4a1f7717bd2f0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 14 Sep 2023 09:47:52 -0500 Subject: [PATCH 191/268] switch to using pca name check --- bin/cluster_sce.R | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R index ba94bff7..c14788f5 100644 --- a/bin/cluster_sce.R +++ b/bin/cluster_sce.R @@ -67,13 +67,9 @@ sce <- readr::read_rds(opt$processed_sce_file) # only perform clustering if reduced dimension embeddings are present # otherwise just return the object -if(length(reducedDimNames(sce)) == 0) { - warning("No reduced dimensions present, skipping clustering") +if(!opt$pca_name %in% reducedDimNames(sce)) { + warning("No reduced dimensions present with provided `pca_name`, skipping clustering") } else { - # check pca_name is present - if (!opt$pca_name %in% reducedDimNames(sce)) { - stop("Provided `pca_name` is not present in the SCE object.") - } # Perform clustering ---------------- From d19801f0024b8db759d76ba02fd71136fa7d0377 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 14 Sep 2023 09:50:16 -0500 Subject: [PATCH 192/268] split up try block and print a warning if no reduced dimensions --- bin/post_process_sce.R | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/bin/post_process_sce.R b/bin/post_process_sce.R index 48c5edae..d8b6ffc4 100755 --- a/bin/post_process_sce.R +++ b/bin/post_process_sce.R @@ -232,28 +232,35 @@ if (alt_exp %in% altExpNames(processed_sce)) { try({ # model gene variance using `scran:modelGeneVar()` gene_variance <- scran::modelGeneVar(processed_sce) - + # select the most variable genes var_genes <- scran::getTopHVGs(gene_variance, n = opt$n_hvg) - + # save the most variable genes to the metadata metadata(processed_sce)$highly_variable_genes <- var_genes + + # dimensionality reduction + # highly variable genes are used as input to PCA + processed_sce <- scater::runPCA( + processed_sce, + ncomponents = opt$n_pcs, + subset_row = var_genes + ) +}) -# dimensionality reduction -# highly variable genes are used as input to PCA -processed_sce <- scater::runPCA( - processed_sce, - ncomponents = opt$n_pcs, - subset_row = var_genes -) - -# calculate a UMAP matrix using the PCA results +try({ + # calculate a UMAP matrix using the PCA results processed_sce <- scater::runUMAP( processed_sce, dimred = "PCA" ) }) +# print a warning if no embeddings present +if(length(reducedDimNames(processed_sce)) == 0){ + warning("Reduced dimensions could not be calculated for this object.") +} + # Export -------------- # write out _original_ filtered SCE with additional filtering column From b696aee8d097901805de70789e638612599d8f59 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:52:05 +0000 Subject: [PATCH 193/268] Update example_metadata.tsv --- examples/example_metadata.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/example_metadata.tsv b/examples/example_metadata.tsv index 3a7bff73..40743932 100644 --- a/examples/example_metadata.tsv +++ b/examples/example_metadata.tsv @@ -1,8 +1,8 @@ -scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number -run01 library01 sample01 project01 10Xv3.1 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 -run02 library01 sample01 project01 CITEseq_10Xv3 cell Homo_sapiens.GRCh38.104 example_fastqs/run02 example_barcode_files/cite_barcodes.tsv 2[1-15] -run03 library02 sample02 project01 visium spot Homo_sapiens.GRCh38.104 example_fastqs/run03 A1 VXXXX-XXX -run04 library03 sample03;sample04 project01 10Xv3.1 cell Mus_musculus.GRCm39.104 example_fastqs/run04 -run05 library03 sample03;sample04 project01 cellhash cell Mus_musculus.GRCm39.104 example_fastqs/run05 example_barcode_files/cellhash_barcodes.tsv 2[1-10] -run06 library04 sample05 project01 paired_end bulk Mus_musculus.GRCm39.104 example_fastqs/run06 - +scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number submitter_cell_types_file +run01 library01 sample01 project01 10Xv3.1 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 NA NA NA NA NA +run02 library01 sample01 project01 CITEseq_10Xv3 cell Homo_sapiens.GRCh38.104 example_fastqs/run02 example_barcode_files/cite_barcodes.tsv 2[1-15] NA NA NA +run03 library02 sample02 project01 visium spot Homo_sapiens.GRCh38.104 example_fastqs/run03 NA NA A1 VXXXX-XXX NA +run04 library03 sample03;sample04 project01 10Xv3.1 cell Mus_musculus.GRCm39.104 example_fastqs/run04 NA NA NA NA NA +run05 library03 sample03;sample04 project01 cellhash cell Mus_musculus.GRCm39.104 example_fastqs/run05 example_barcode_files/cellhash_barcodes.tsv 2[1-10] NA NA NA +run06 library04 sample05 project01 paired_end bulk Mus_musculus.GRCm39.104 example_fastqs/run06 NA NA NA NA NA +run07 library05 sample06 project01 10Xv3.1 cell Homo_sapiens.GRCh38.104 example_fastqs/run07 NA NA NA NA example_metadata_files/submitter_celltypes.tsv From 04011331eac0a681284ec3a93316b0686e25fa9c Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:54:30 +0000 Subject: [PATCH 194/268] update examples README --- examples/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/README.md b/examples/README.md index cba83f52..f33b9362 100644 --- a/examples/README.md +++ b/examples/README.md @@ -18,11 +18,11 @@ The fastq files for this example data can be downloaded from the following link Following download and unzipping of the fastq files, you will need to create a tab-separated values metadata file that looks like the following: -| scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | seq_unit | sample_reference | files_directory | -| ------------ | ---------------- | --------------- | ---------------- | ---------- | -------- | ---------------- | --------------- | -| run01 | library01 | sample01 | project01 | 10Xv3.1 | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | +| scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | seq_unit | sample_reference | files_directory | submitter_cell_types_file | +| ------------ | ---------------- | --------------- | ---------------- | ---------- | -------- | ---------------- | --------------- | ------------------------ | +| run01 | library01 | sample01 | project01 | 10Xv3.1 | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_tsv -Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column. +Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column, and similarly the full path for the `submitter_cell_types_file` column. The following command can then be used to test your configuration setup with the example data: From 806ecfb252cfe1db3944aa27948ff30e16a42eba Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:58:21 +0000 Subject: [PATCH 195/268] stub sample metadata --- test/stub-sample-metadata.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/test/stub-sample-metadata.tsv b/test/stub-sample-metadata.tsv index a9f4c915..deb42f92 100644 --- a/test/stub-sample-metadata.tsv +++ b/test/stub-sample-metadata.tsv @@ -10,3 +10,4 @@ STUBS10 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS11 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS12 NA NA NA NA NA NA NA NA NA NA NA NA NA STUBS13 NA NA NA NA NA NA NA NA NA NA NA NA NA +STUBS14 NA NA NA NA NA NA NA NA NA NA NA NA NA From 0207c0acb46d1db933a7a306a8e20e5fdda37378 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:58:54 +0000 Subject: [PATCH 196/268] Add in submitter celltypes, and fix one place where it said tests instead of test for the directory --- test/stub-run-metadata.tsv | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/test/stub-run-metadata.tsv b/test/stub-run-metadata.tsv index dc211a61..f3a60dac 100644 --- a/test/stub-run-metadata.tsv +++ b/test/stub-run-metadata.tsv @@ -1,14 +1,15 @@ -scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number -STUBR01 STUBL01 STUBS01 STUBP01 10Xv2 cell stub test/runs/STUBR01 NA NA NA NA -STUBR02 STUBL02 STUBS02 STUBP02 10Xv3.1 cell stub test/runs/STUBR02 NA NA NA NA -STUBR03 STUBL02 STUBS02 STUBP02 CITEseq_10Xv3 cell stub test/runs/STUBR03 test/references/barcodes/adt.stub.tsv 2[1-15] NA NA -STUBR04 STUBL04 STUBS04 STUBP02 paired_end bulk stub test/runs/STUBR04 NA NA NA NA -STUBR05 STUBL05 STUBS05 STUBP03 10Xv3 nucleus stub test/runs/STUBR05 NA NA NA NA -STUBR06 STUBL06 STUBS06 STUBP04 10Xv2_5prime cell stub test/runs/STUBR06 NA NA NA NA -STUBR07 STUBL07 STUBS07 STUBP05 visium spot stub tests/runs/STUBR07 NA NA A1 V10L14-093 -STUBR08 STUBL08 STUBS10 STUBP06 single_end bulk stub test/runs/STUBR08 NA NA NA NA -STUBR09 STUBL09 STUBS11 STUBP06 single_end bulk stub test/runs/STUBR09 NA NA NA NA -STUBR10 STUBL10 STUBS10,STUBS11 STUBP06 10Xv3.1 cell stub test/runs/STUBR10 NA NA NA NA -STUBR11 STUBL10 STUBS10,STUBS11 STUBP06 cellhash_10Xv3 cell stub test/runs/STUBR11 test/references/barcodes/cellhash.stub.tsv 2[1-15] NA NA -STUBR12 STUBL11 STUBS12,STUBS13 STUBP06 10Xv3.1 cell stub test/runs/STUBR12 NA NA NA NA -STUBR13 STUBL11 STUBS12,STUBS13 STUBP06 cellhash_10Xv3 cell stub test/runs/STUBR13 test/references/barcodes/cellhash.stub.tsv 2[1-15] NA NA +scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number submitter_cell_types_file +STUBR01 STUBL01 STUBS01 STUBP01 10Xv2 cell stub test/runs/STUBR01 NA NA NA NA NA +STUBR02 STUBL02 STUBS02 STUBP02 10Xv3.1 cell stub test/runs/STUBR02 NA NA NA NA NA +STUBR03 STUBL02 STUBS02 STUBP02 CITEseq_10Xv3 cell stub test/runs/STUBR03 test/references/barcodes/adt.stub.tsv 2[1-15] NA NA NA +STUBR04 STUBL04 STUBS04 STUBP02 paired_end bulk stub test/runs/STUBR04 NA NA NA NA NA +STUBR05 STUBL05 STUBS05 STUBP03 10Xv3 nucleus stub test/runs/STUBR05 NA NA NA NA NA +STUBR06 STUBL06 STUBS06 STUBP04 10Xv2_5prime cell stub test/runs/STUBR06 NA NA NA NA NA +STUBR07 STUBL07 STUBS07 STUBP05 visium spot stub tests/runs/STUBR07 NA NA A1 V10L14-093 NA +STUBR08 STUBL08 STUBS10 STUBP06 single_end bulk stub test/runs/STUBR08 NA NA NA NA NA +STUBR09 STUBL09 STUBS11 STUBP06 single_end bulk stub test/runs/STUBR09 NA NA NA NA NA +STUBR10 STUBL10 STUBS10,STUBS11 STUBP06 10Xv3.1 cell stub test/runs/STUBR10 NA NA NA NA NA +STUBR11 STUBL10 STUBS10,STUBS11 STUBP06 cellhash_10Xv3 cell stub test/runs/STUBR11 test/references/barcodes/cellhash.stub.tsv 2[1-15] NA NA NA +STUBR12 STUBL11 STUBS12,STUBS13 STUBP06 10Xv3.1 cell stub test/runs/STUBR12 NA NA NA NA NA +STUBR13 STUBL11 STUBS12,STUBS13 STUBP06 cellhash_10Xv3 cell stub test/runs/STUBR13 test/references/barcodes/cellhash.stub.tsv 2[1-15] NA NA NA +STUBR14 STUBL12 STUBS14 STUBP07 10Xv3.1 cell stub test/runs/STUBR14 NA NA NA NA test/celltypes/STUBL12-submitter-celltypes.tsv From 300e1b335c7b51d92dd78d9de740609f9cf0e21b Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 14:59:06 +0000 Subject: [PATCH 197/268] add stub empty submitter celltypes file --- test/celltypes/STUBL12-submitter-celltypes.tsv | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 test/celltypes/STUBL12-submitter-celltypes.tsv diff --git a/test/celltypes/STUBL12-submitter-celltypes.tsv b/test/celltypes/STUBL12-submitter-celltypes.tsv new file mode 100644 index 00000000..e69de29b From 37f01bc8655a5b8a57950e9e3b6ba910c17deb21 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 15:02:33 +0000 Subject: [PATCH 198/268] spelling --- examples/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/README.md b/examples/README.md index f33b9362..08e00c0d 100644 --- a/examples/README.md +++ b/examples/README.md @@ -20,7 +20,7 @@ Following download and unzipping of the fastq files, you will need to create a t | scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | seq_unit | sample_reference | files_directory | submitter_cell_types_file | | ------------ | ---------------- | --------------- | ---------------- | ---------- | -------- | ---------------- | --------------- | ------------------------ | -| run01 | library01 | sample01 | project01 | 10Xv3.1 | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_tsv +| run01 | library01 | sample01 | project01 | 10Xv3.1 | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_file Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column, and similarly the full path for the `submitter_cell_types_file` column. From 6aa628281d63fb4176ceaefa7c15395c90ca263f Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 11:07:51 -0400 Subject: [PATCH 199/268] Update main.nf Co-authored-by: Joshua Shapiro --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 6f5c6c84..e427b37c 100644 --- a/main.nf +++ b/main.nf @@ -96,7 +96,7 @@ workflow { submitter: it.submitter, technology: it.technology, seq_unit: it.seq_unit, - submitter_cell_types_file: it.submitter_cell_types_file, + submitter_cell_types_file: it.submitter_cell_types_file == "NA"? it.submitter_cell_types_file : "" feature_barcode_file: it.feature_barcode_file, feature_barcode_geom: it.feature_barcode_geom, files_directory: it.files_directory, From 208d4be206ab3acdadfedefdb753162d995422c8 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 14 Sep 2023 11:24:27 -0400 Subject: [PATCH 200/268] add parseNA function and use it --- lib/Utils.groovy | 11 +++++++++++ main.nf | 14 +++++++------- 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 430010f1..5e6a060a 100644 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -40,4 +40,15 @@ class Utils { def obj = new JsonSlurper().parse(file) return(obj[key]) } + + + /** + * Replace a string with an NA value with null + * + * @param str A string + * @return The input string unless it was NA or a variant thereof, in which case returns null + */ + static def parseNA(str) { + str.toLowerCase()in ["na","n/a","nan"]? null : str + } } diff --git a/main.nf b/main.nf index e427b37c..42570fc1 100644 --- a/main.nf +++ b/main.nf @@ -92,16 +92,16 @@ workflow { run_id: it.scpca_run_id, library_id: it.scpca_library_id, sample_id: it.scpca_sample_id.split(";").sort().join(","), - project_id: it.scpca_project_id?: "no_project", + project_id: Utils.parseNA(it.scpca_project_id)?: "no_project", submitter: it.submitter, technology: it.technology, seq_unit: it.seq_unit, - submitter_cell_types_file: it.submitter_cell_types_file == "NA"? it.submitter_cell_types_file : "" - feature_barcode_file: it.feature_barcode_file, - feature_barcode_geom: it.feature_barcode_geom, - files_directory: it.files_directory, - slide_serial_number: it.slide_serial_number, - slide_section: it.slide_section, + submitter_cell_types_file: Utils.parseNA(it.submitter_cell_types_file), + feature_barcode_file: Utils.parseNA(it.feature_barcode_file), + feature_barcode_geom: Utils.parseNA(it.feature_barcode_geom), + files_directory: Utils.parseNA(it.files_directory), + slide_serial_number: Utils.parseNA(it.slide_serial_number), + slide_section: Utils.parseNA(it.slide_section), ref_assembly: it.sample_reference, ref_fasta: params.ref_rootdir + "/" + sample_refs["ref_fasta"], ref_fasta_index: params.ref_rootdir + "/" + sample_refs["ref_fasta_index"], From 43d5dfd1a2e34c12fb68870d7515379aba4ac947 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 16:27:17 +0000 Subject: [PATCH 201/268] add comma --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index e427b37c..c0617ac9 100644 --- a/main.nf +++ b/main.nf @@ -96,7 +96,7 @@ workflow { submitter: it.submitter, technology: it.technology, seq_unit: it.seq_unit, - submitter_cell_types_file: it.submitter_cell_types_file == "NA"? it.submitter_cell_types_file : "" + submitter_cell_types_file: it.submitter_cell_types_file == "NA"? it.submitter_cell_types_file : "", feature_barcode_file: it.feature_barcode_file, feature_barcode_geom: it.feature_barcode_geom, files_directory: it.files_directory, From fee2c79f3a001732369d61732bbda856dc4e291b Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 16:27:49 +0000 Subject: [PATCH 202/268] Updated sce-processing to match changes in main; tested --- modules/sce-processing.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index ab1b4ce4..a94e6977 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -220,13 +220,14 @@ workflow generate_sce { sample_metafile main: + // used for both submitter cell types & feature barcode files empty_file = file("${projectDir}/assets/NO_FILE.txt") sce_ch = quant_channel .map{it.toList() + [file(it[0].mito_file), file(it[0].ref_gtf), // either submitter cell type files, or empty file if not available - file(it[0].submitter_cell_types_file).exists() ? file(it[0].submitter_cell_types_file) : empty_file + file(it[0].submitter_cell_types_file ?: empty_file) ]} make_unfiltered_sce(sce_ch, sample_metafile) @@ -248,14 +249,13 @@ workflow generate_merged_sce { feature_quant_channel sample_metafile main: - empty_file = file("${projectDir}/assets/NO_FILE.txt") - + feature_sce_ch = feature_quant_channel // RNA meta is in the third slot here .map{it.toList() + [file(it[2].mito_file), file(it[2].ref_gtf), // either submitter cell type files, or empty file if not available - file(it[2].submitter_cell_types_file).exists() ? file(it[2].submitter_cell_types_file) : empty_file + file(it[2].submitter_cell_types_file ?: file("${projectDir}/assets/NO_FILE.txt")) ]} make_merged_unfiltered_sce(feature_sce_ch, sample_metafile) From 3b057d95ab7794d0334adffc08ec4b4021595977 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 12:29:18 -0400 Subject: [PATCH 203/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- bin/add_submitter_annotations.R | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index c3d9a6e7..fc41b2f0 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -11,9 +11,9 @@ suppressPackageStartupMessages({ # set up arguments option_list <- list( make_option( - opt_str = c("-u", "--unfiltered_file"), + opt_str = c("-f", "--sce_file"), type = "character", - help = "path to output unfiltered rds file. Must end in .rds" + help = "path to SingleCellExperiment file to update. Must end in .rds" ), make_option( opt_str = c("--library_id"), @@ -51,13 +51,8 @@ submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> barcodes = cell_barcode, submitter_celltype_annotations = cell_type_assignment ) |> - # in the event of NA values, change to "Unclassified cell" - dplyr::mutate( - submitter_celltype_annotations = dplyr::if_else( - is.na(submitter_celltype_annotations), - "Unclassified cell", - submitter_celltype_annotations - ) + # in the event of NA values, change to "Unclassified cell" + tidyr::replace_na(list(submitter_celltype_annotations = "Unclassified cell")) ) # Join in submitter cell types @@ -71,7 +66,7 @@ colData(sce) <- colData(sce) |> # Indicate that we have submitter celltypes in metadata, # saving in same spot as for actual celltyping -metadata(sce)$celltype_methods <- "submitter" +metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "submitter") # Write unfiltered RDS back to file readr::write_rds(sce, opt$unfiltered_file, compress = "gz") From 9658a6c3b99a692ee2077f7f3a05e48602544352 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 16:30:12 +0000 Subject: [PATCH 204/268] use sce_file flag --- modules/sce-processing.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index a94e6977..71fe5507 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -29,7 +29,7 @@ process make_unfiltered_sce{ # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ - --unfiltered_file ${unfiltered_rds} \ + --sce_file ${unfiltered_rds} \ --library_id "${meta.library_id}" \ --submitter_cell_types_file ${submitter_cell_types_file} fi @@ -82,7 +82,7 @@ process make_merged_unfiltered_sce{ # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ - --unfiltered_file ${unfiltered_rds} \ + --sce_file ${unfiltered_rds} \ --library_id "${meta.library_id}" \ --submitter_cell_types_file ${submitter_cell_types_file} fi From 29c04ec8bc6e3f3e3bea7cc2afc9ca5b1c09e776 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 16:30:28 +0000 Subject: [PATCH 205/268] update comment --- bin/add_submitter_annotations.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index fc41b2f0..25ebfa42 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -1,7 +1,6 @@ #!/usr/bin/env Rscript -# This script adds submitter annotations, if provided, to the unfiltered SCE's colData. -# If the file was not provided, this script has no effect. +# This script adds submitter annotations, if provided, to the an SCE object's colData. # import libraries suppressPackageStartupMessages({ From 0eece14bd6534e3c927da514b482981be997d9ce Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 16:31:09 +0000 Subject: [PATCH 206/268] parens --- bin/add_submitter_annotations.R | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index 25ebfa42..97e3394b 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -50,8 +50,9 @@ submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> barcodes = cell_barcode, submitter_celltype_annotations = cell_type_assignment ) |> - # in the event of NA values, change to "Unclassified cell" - tidyr::replace_na(list(submitter_celltype_annotations = "Unclassified cell")) + # in the event of NA values, change to "Unclassified cell" + tidyr::replace_na( + list(submitter_celltype_annotations = "Unclassified cell") ) # Join in submitter cell types From ee4aedfb9a3e504e9ddc4acddddee6341a29ff6d Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 14 Sep 2023 13:09:19 -0500 Subject: [PATCH 207/268] remove czi schema param and fix formatting of NA --- bin/sce_to_anndata.R | 42 +++++++++++++++++++++------------------ modules/export-anndata.nf | 4 +--- nextflow.config | 3 --- 3 files changed, 24 insertions(+), 25 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 660ab3ad..70be4057 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -30,12 +30,6 @@ option_list <- list( type = "character", help = "path to output hdf5 file to store feature counts as AnnData object. Only used if the input SCE contains an altExp. Must end in .hdf5 or .h5" - ), - make_option( - opt_str = c("--czi_schema_version"), - type = "character", - default = "3.0.0", - help = "Version number for CZI schema matching formatting of output AnnData objects" ) ) @@ -60,26 +54,36 @@ if (!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))) { # CZI 3.0.0 requirements: https://github.com/chanzuckerberg/single-cell-curation/blob/b641130fe53b8163e50c39af09ee3fcaa14c5ea7/schema/3.0.0/schema.md format_czi <- function(sce) { # add library_id as an sce colData column + # need this column to join in the sample metadata with the colData sce$library_id <- metadata(sce)$library_id - # add is_primary_data column; only needed for anndata objects - sce$is_primary_data <- FALSE - - # create columns for assay and suspension ontology terms - sce$assay_ontology_term_id <- metadata(sce)$assay_ontology_term_id - sce$suspension_type <- metadata(sce)$seq_unit - - # move project id to title slot in metadata list - metadata(sce)$title <- metadata(sce)$project_id - - # add schema version - metadata(sce)$schema_version <- opt$czi_schema_version - # add sample metadata to colData sce sce <- scpcaTools::metadata_to_coldata(sce, join_columns = "library_id" ) + # modify colData to be AnnData and CZI compliant + coldata_df <- colData(sce) |> + as.data.frame() |> + # make sure all colData columns have the correct NA formatting if all NA + # python doesn't like character NA + dplyr::mutate(across(where(\(x) all(is.na(x))), as.logical), + # create columns for assay and suspension ontology terms + assay_ontology_term_id = metadata(sce)$assay_ontology_term_id, + suspension_type = metadata(sce)$seq_unit, + # move project id to title slot in metadata list + title = metadata(sce)$project_id, + # add is_primary_data column; only needed for anndata objects + is_primary_data = FALSE, + # add schema version + schema_version = "3.0.0") + + # add colData back to sce object + colData(sce) <- DataFrame( + coldata_df, + row.names = coldata_df$barcodes + ) + # remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 4ffebc2d..e308e430 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -7,7 +7,6 @@ process export_anndata{ publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(sce_file), val(file_type) - val(czi_schema_version) output: tuple val(meta), path("${meta.library_id}_${file_type}*.hdf5"), val(file_type) script: @@ -19,7 +18,6 @@ process export_anndata{ --input_sce_file ${sce_file} \ --output_rna_h5 ${rna_hdf5_file} \ --output_feature_h5 ${feature_hdf5_file} \ - --czi_schema_version ${czi_schema_version} \ ${feature_present ? "--feature_name ${meta.feature_type}" : ''} """ stub: @@ -66,7 +64,7 @@ workflow sce_to_anndata{ ]} // export each anndata file - export_anndata(sce_ch, params.czi_schema_version) + export_anndata(sce_ch) anndata_ch = export_anndata.out .branch{ diff --git a/nextflow.config b/nextflow.config index 2c4fe935..1b9652ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -52,9 +52,6 @@ params { cluster_weighting = "jaccard" // default weighting scheme for graph-based clustering nearest_neighbors = 20 // default nearest neighbors parameter for graph-based clustering - // anndata options - czi_schema_version = "3.0.0" - // Docker container images includeConfig 'config/containers.config' From 386d10133c71f6d7d074a2058298aec4b735a802 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 14 Sep 2023 13:23:01 -0500 Subject: [PATCH 208/268] remove NA handling --- bin/sce_to_anndata.R | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 70be4057..02fe1d18 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -65,18 +65,17 @@ format_czi <- function(sce) { # modify colData to be AnnData and CZI compliant coldata_df <- colData(sce) |> as.data.frame() |> - # make sure all colData columns have the correct NA formatting if all NA - # python doesn't like character NA - dplyr::mutate(across(where(\(x) all(is.na(x))), as.logical), - # create columns for assay and suspension ontology terms - assay_ontology_term_id = metadata(sce)$assay_ontology_term_id, - suspension_type = metadata(sce)$seq_unit, - # move project id to title slot in metadata list - title = metadata(sce)$project_id, - # add is_primary_data column; only needed for anndata objects - is_primary_data = FALSE, - # add schema version - schema_version = "3.0.0") + dplyr::mutate( + # create columns for assay and suspension ontology terms + assay_ontology_term_id = metadata(sce)$assay_ontology_term_id, + suspension_type = metadata(sce)$seq_unit, + # move project id to title slot in metadata list + title = metadata(sce)$project_id, + # add is_primary_data column; only needed for anndata objects + is_primary_data = FALSE, + # add schema version + schema_version = "3.0.0" + ) # add colData back to sce object colData(sce) <- DataFrame( From be54b8851570e73ed858cebd043ea7ec62f65239 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 18:28:35 +0000 Subject: [PATCH 209/268] more unfiltered_sce -> sce_file, add check for nrows, and a little rearrangment that makes sense with this new check --- bin/add_submitter_annotations.R | 38 ++++++++++++++++++++------------- 1 file changed, 23 insertions(+), 15 deletions(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index 97e3394b..d3c2f70a 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -29,8 +29,8 @@ option_list <- list( opt <- parse_args(OptionParser(option_list = option_list)) # check that output file name ends in .rds -if (!(stringr::str_ends(opt$unfiltered_file, ".rds"))) { - stop("unfiltered file name must end in .rds") +if (!(stringr::str_ends(opt$sce_file, ".rds"))) { + stop("SingleCellExperiment file name must end in .rds") } @@ -40,11 +40,12 @@ if (!file.exists(opt$submitter_cell_types_file)) { } -# Read in unfiltered sce -sce <- readr::read_rds(opt$unfiltered_file) +# Read in sce +sce <- readr::read_rds(opt$sce_file) -# Read in celltypes, and filter to relevant information +# Read in celltypes submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> + # filter to relevant information dplyr::filter(scpca_library_id == opt$library_id) |> dplyr::select( barcodes = cell_barcode, @@ -53,20 +54,27 @@ submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> # in the event of NA values, change to "Unclassified cell" tidyr::replace_na( list(submitter_celltype_annotations = "Unclassified cell") + ) |> + # join with colData + dplyr::right_join( + colData(sce) |> + as.data.frame() ) -# Join in submitter cell types -colData(sce) <- colData(sce) |> - as.data.frame() |> - dplyr::left_join( - submitter_cell_types_df - ) |> - # make sure we keep rownames - DataFrame(row.names = colData(sce)$barcodes) +# Check rows before sending back into the SCE object +if (nrow(submitter_cell_types_df) != ncol(sce)) { + stop("Could not add submitter annotations to SCE object. There should only be one annotation per cell.") +} + +# Rejoin with colData, making sure we keep rownames +colData(sce) <- DataFrame( + submitter_cell_types_df, + row.names = colData(sce)$barcodes +) # Indicate that we have submitter celltypes in metadata, # saving in same spot as for actual celltyping metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "submitter") -# Write unfiltered RDS back to file -readr::write_rds(sce, opt$unfiltered_file, compress = "gz") +# Write SCE back to file +readr::write_rds(sce, opt$sce_file, compress = "gz") From 73d9c6a19d1628c5537c776b0ff60734599e76a8 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 18:29:06 +0000 Subject: [PATCH 210/268] extra word --- bin/add_submitter_annotations.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index d3c2f70a..b40ba6d6 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -1,6 +1,6 @@ #!/usr/bin/env Rscript -# This script adds submitter annotations, if provided, to the an SCE object's colData. +# This script adds submitter annotations, if provided, to an SCE object's colData. # import libraries suppressPackageStartupMessages({ From d220a97bf910d331fde546edbdec4a6d4ea4b07a Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 14:48:01 -0400 Subject: [PATCH 211/268] WIP: adding submitter vs methods heatmaps --- templates/qc_report/celltypes_qc.rmd | 97 ++++++++++++++++++++++++---- templates/qc_report/qc_report.rmd | 12 ++-- 2 files changed, 90 insertions(+), 19 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index 05afa849..c679076a 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -1,14 +1,31 @@ # Cell type Annotation Summary -This section details results from performing cell type annotation. -The following method(s) were used to perform cell typing: + + + + +```{r, eval = has_submitter & !(has_singler | has_cellassign)} +knitr::asis_output( + print("This section details cell type annotations provided by the original lab ('submitter') which generated this data.") +) +``` + + + +```{r, eval = has_singler | has_cellassign} +knitr::asis_output( + print(" + This section details results from performing cell type annotation. + The following method(s) were used to perform cell typing: + ") +) +``` - ```{r, eval = has_singler} knitr::asis_output( glue::glue( - "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. + "* [`SingleR`](https://bioconductor.org/packages/release/bioc/html/SingleR.html), which uses a reference-based approach. The `{metadata(processed_sce)$singler_reference}` reference dataset, obtained from the [`celldex` package](http://bioconductor.org/packages/release/data/experiment/html/celldex.html) package, was used for cell typing." ) ) @@ -18,8 +35,7 @@ knitr::asis_output( ```{r, eval = has_cellassign} knitr::asis_output( glue::glue( - " - * [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. + "* [`CellAssign`](https://github.com/Irrationone/cellassign), which uses a marker-gene based approach. Marker genes associated with `{metadata(processed_sce)$cellassign_reference}` tissue were obtained from [PanglaoDB](https://panglaodb.se/). " ) @@ -27,12 +43,23 @@ knitr::asis_output( ``` -Cells annotated as "Unknown cell type" represent cells which could not be confidently identified using the given annotation method. + +```{r, eval = has_submitter & (has_singler | has_cellassign)} +knitr::asis_output( + glue::glue( + "* Cell type annotations were also provided by the original lab ('submitter') which generated this data. + * In these cell type annotations, the label 'Unclassified cell' indicates that submitters did not provide an annotation for the given cell. + " + ) +) +``` + -If available, these results will be compared to cell type annotations provided by the data's originating research group ("submitter-provided cell type annotations".) ## Statistics +Below, cells labeled as "Unknown cell type" are those which could not be confidently identified using the given annotation method. + ```{r} # This chunk defines a helper function to reformat annotations: # * Annotations that are `NA`/"other" are changed to "Unknown cell type" @@ -119,7 +146,7 @@ knitr::asis_output("### `CellAssign` cell type annotations\n") create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ``` -```{r, eval = has_submitter_celltypes} +```{r, eval = has_submitter} knitr::asis_output("### Submitter-provided cell type annotations\n") # Note: submitter annotations have not yet been added to the workflow, # so this variable name `submitter_celltype_annotation` is just a placeholder @@ -394,7 +421,9 @@ if (has_singler) { if (has_cellassign) { umap_df <- lump_celltypes(umap_df, celltype_df, "cellassign") } -# Note that later, we will want to do this with submitter cell types too, if present. +if (has_submitter) { + umap_df <- lump_celltypes(umap_df, celltype_df, "submitter") +} ``` @@ -479,8 +508,14 @@ plot_umap(umap_df, ``` -```{r eval=has_submitter_celltypes, message=FALSE, warning=FALSE} -# Nothing in this chunk yet - it's a placeholder +```{r eval = has_submitter, message=FALSE, warning=FALSE} +plot_umap(umap_df, + submitter, + "Cell types", + legend_nrow = 4 +) + + ggtitle("UMAP colored by submitter-provided annotations") + + scale_color_brewer(palette = "Dark2") ``` ### Heatmaps @@ -554,7 +589,7 @@ create_celltype_heatmap( ) ``` -```{r, eval = has_submitter_celltypes, fig.height=5, fig.width=7} +```{r, eval = has_submitter, fig.height=5, fig.width=7} knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") create_celltype_heatmap( x_vector = celltype_df$submitter_celltype_annotation, @@ -569,7 +604,7 @@ create_celltype_heatmap( knitr::asis_output(" ## Comparison between annotations -Below, we show a heatmap directly comparing `SingleR` and `CellAssign`cell type annotations. +Below, we show a heatmap directly comparing `SingleR` and `CellAssign` cell type annotations. Note that due to different annotations references, these methods may use different names for similar cell types. ") @@ -582,3 +617,37 @@ create_celltype_heatmap( column_font_size = 8 ) ``` + +```{r, eval = has_submitter & (has_cellassign | has_singler)} +knitr::asis_output(" +## Comparison with submitter annotations + +This section shows heatmap(s) directly comparing submitter-provided cell type annotations to cell type inferred with the given method(s). +Again, different annotations may use different names for similar cell types. +") +``` + + +```{r, eval = has_submitter & has_singler, fig.height=7, fig.width=8} + +create_celltype_heatmap( + x_vector = celltype_df$submitter_celltype_annotation, + y_vector = celltype_df$singler_celltype_annotation, + x_label = "Submitter-provided annotations", + y_label = "SingleR annotations", + column_names_rotation = 55, + column_font_size = 8 +) +``` + +```{r, eval = has_submitter & has_cellassign, fig.height=7, fig.width=8} + +create_celltype_heatmap( + x_vector = celltype_df$submitter_celltype_annotation, + y_vector = celltype_df$cellassign_celltype_annotation, + x_label = "Submitter-provided annotations", + y_label = "CellAssign annotations", + column_names_rotation = 55, + column_font_size = 8 +) +``` \ No newline at end of file diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 0413c795..00df0221 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -59,6 +59,11 @@ unfiltered_sce <- params$unfiltered_sce filtered_sce <- params$filtered_sce processed_sce <- params$processed_sce +library_id <- "SCPCL000295" +unfiltered_sce <- readRDS(glue::glue("{library_id}_unfiltered.rds")) +filtered_sce <- readRDS(glue::glue("{library_id}_filtered.rds")) +processed_sce <- readRDS(glue::glue("{library_id}_processed.rds")) + has_filtered <- !is.null(filtered_sce) has_processed <- !is.null(processed_sce) @@ -113,13 +118,10 @@ if (has_processed) { has_singler <- "singler" %in% metadata(processed_sce)$celltype_methods has_cellassign <- "cellassign" %in% metadata(processed_sce)$celltype_methods - - # Note: later, we will also check for submitter-provided annotations - # for now, we will say this is false - has_submitter_celltypes <- FALSE + has_submitter <- "submitter" %in% metadata(processed_sce)$celltype_methods # If at least 1 is present, we have cell type annotations. - has_celltypes <- any(has_singler, has_cellassign, has_submitter_celltypes) + has_celltypes <- any(has_singler, has_cellassign, has_submitter) } else { has_umap <- FALSE has_celltypes <- FALSE From 255a68ab96fc072996e5fae82ddb70a749dfa96a Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 18:59:13 +0000 Subject: [PATCH 212/268] column should be SINGULAR for consistency with singler, cellassign and use in QC report --- bin/add_submitter_annotations.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R index b40ba6d6..e4b6d45b 100644 --- a/bin/add_submitter_annotations.R +++ b/bin/add_submitter_annotations.R @@ -49,11 +49,11 @@ submitter_cell_types_df <- readr::read_tsv(opt$submitter_cell_types_file) |> dplyr::filter(scpca_library_id == opt$library_id) |> dplyr::select( barcodes = cell_barcode, - submitter_celltype_annotations = cell_type_assignment + submitter_celltype_annotation = cell_type_assignment ) |> # in the event of NA values, change to "Unclassified cell" tidyr::replace_na( - list(submitter_celltype_annotations = "Unclassified cell") + list(submitter_celltype_annotation = "Unclassified cell") ) |> # join with colData dplyr::right_join( From 996651644d8fa83ad2a7f559fdfd29a5099f9252 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 15:02:50 -0400 Subject: [PATCH 213/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- modules/sce-processing.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 71fe5507..863f267b 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -29,9 +29,9 @@ process make_unfiltered_sce{ # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ - --sce_file ${unfiltered_rds} \ + --sce_file "${unfiltered_rds}" \ --library_id "${meta.library_id}" \ - --submitter_cell_types_file ${submitter_cell_types_file} + --submitter_cell_types_file "${submitter_cell_types_file}" fi """ @@ -82,9 +82,9 @@ process make_merged_unfiltered_sce{ # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ - --sce_file ${unfiltered_rds} \ + --sce_file "${unfiltered_rds}" \ --library_id "${meta.library_id}" \ - --submitter_cell_types_file ${submitter_cell_types_file} + --submitter_cell_types_file "${submitter_cell_types_file}" fi """ @@ -221,7 +221,7 @@ workflow generate_sce { main: // used for both submitter cell types & feature barcode files - empty_file = file("${projectDir}/assets/NO_FILE.txt") + empty_file = "${projectDir}/assets/NO_FILE.txt" sce_ch = quant_channel .map{it.toList() + [file(it[0].mito_file), From abfaacc69e2a671091ff5492e0d6e88af1040b51 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Thu, 14 Sep 2023 19:03:51 +0000 Subject: [PATCH 214/268] file() in the places, and not in other places --- modules/sce-processing.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 863f267b..9ecd74d7 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -234,7 +234,7 @@ workflow generate_sce { // provide empty feature barcode file, since no features here unfiltered_sce_ch = make_unfiltered_sce.out - .map{it.toList() + [empty_file]} + .map{it.toList() + [file(empty_file)]} filter_sce(unfiltered_sce_ch) @@ -255,7 +255,7 @@ workflow generate_merged_sce { .map{it.toList() + [file(it[2].mito_file), file(it[2].ref_gtf), // either submitter cell type files, or empty file if not available - file(it[2].submitter_cell_types_file ?: file("${projectDir}/assets/NO_FILE.txt")) + file(it[2].submitter_cell_types_file ?: "${projectDir}/assets/NO_FILE.txt") ]} make_merged_unfiltered_sce(feature_sce_ch, sample_metafile) From 79cf961900db8fb74ef1eab0732244383171f908 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 14 Sep 2023 14:05:56 -0500 Subject: [PATCH 215/268] Apply suggestions from code review Co-authored-by: Stephanie --- bin/generate_unfiltered_sce.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index fc0a5eb5..5a89247f 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -145,7 +145,7 @@ if (opt$feature_dir != "") { seq_unit = opt$seq_unit, library_id = opt$library_id, sample_id = sample_ids, - project_id = project_id + project_id = opt$project_id ) unfiltered_sce <- merge_altexp(unfiltered_sce, feature_sce, opt$feature_name) From f06dd2a11ff0538be536a67a59dc1a44f079d89d Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 14 Sep 2023 14:10:38 -0500 Subject: [PATCH 216/268] note about schema at top of script --- bin/sce_to_anndata.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 02fe1d18..19b912ec 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -3,6 +3,8 @@ # This script takes a SingleCellExperiment stored in a .rds file and converts the main experiment # (usually RNA) to an AnnData object saved as an hdf5 file +# The AnnData object being exported by this script is formatted to fit CZI schema: 3.0.0 + # import libraries suppressPackageStartupMessages({ library(optparse) From 54695cdb83c3a867845ea3671b5fc68732105fff Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 15:31:59 -0400 Subject: [PATCH 217/268] remove temporary dev code --- templates/qc_report/qc_report.rmd | 5 ----- 1 file changed, 5 deletions(-) diff --git a/templates/qc_report/qc_report.rmd b/templates/qc_report/qc_report.rmd index 00df0221..7171a76f 100644 --- a/templates/qc_report/qc_report.rmd +++ b/templates/qc_report/qc_report.rmd @@ -59,11 +59,6 @@ unfiltered_sce <- params$unfiltered_sce filtered_sce <- params$filtered_sce processed_sce <- params$processed_sce -library_id <- "SCPCL000295" -unfiltered_sce <- readRDS(glue::glue("{library_id}_unfiltered.rds")) -filtered_sce <- readRDS(glue::glue("{library_id}_filtered.rds")) -processed_sce <- readRDS(glue::glue("{library_id}_processed.rds")) - has_filtered <- !is.null(filtered_sce) has_processed <- !is.null(processed_sce) From dcf7f229095b2600ce1b90af2cf3494a5fb5de61 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Thu, 14 Sep 2023 15:32:20 -0400 Subject: [PATCH 218/268] Text and formatting cleanups, other small debugs --- templates/qc_report/celltypes_qc.rmd | 29 +++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index c679076a..c57acf94 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -6,7 +6,9 @@ ```{r, eval = has_submitter & !(has_singler | has_cellassign)} knitr::asis_output( - print("This section details cell type annotations provided by the original lab ('submitter') which generated this data.") + glue::glue(" + This section details cell type annotations provided by the original lab ('submitter') which generated this data. + ") ) ``` @@ -14,7 +16,7 @@ knitr::asis_output( ```{r, eval = has_singler | has_cellassign} knitr::asis_output( - print(" + glue::glue(" This section details results from performing cell type annotation. The following method(s) were used to perform cell typing: ") @@ -47,8 +49,8 @@ knitr::asis_output( ```{r, eval = has_submitter & (has_singler | has_cellassign)} knitr::asis_output( glue::glue( - "* Cell type annotations were also provided by the original lab ('submitter') which generated this data. - * In these cell type annotations, the label 'Unclassified cell' indicates that submitters did not provide an annotation for the given cell. + "* Cell type annotations were also provided by the original lab (`submitter-provided`) which generated this data. + In these cell type annotations, the label `Unclassified cell` indicates that submitters did not provide an annotation for the given cell. " ) ) @@ -93,7 +95,8 @@ celltype_df <- colData(processed_sce) |> barcode, clusters, contains("singler"), - contains("cellassign") + contains("cellassign"), + contains("submitter") ) @@ -148,16 +151,17 @@ create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ```{r, eval = has_submitter} knitr::asis_output("### Submitter-provided cell type annotations\n") -# Note: submitter annotations have not yet been added to the workflow, -# so this variable name `submitter_celltype_annotation` is just a placeholder create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` +```{r, eval = has_singler | has_cellassign } +knitr::asis_output(" ## Annotation Assessment In this section, we assess the reliability of cell type annotations using diagnostic plots. - +") +``` ```{r, eval = has_singler} knitr::asis_output(" @@ -392,11 +396,10 @@ All other cell types are grouped together and labeled "Other cell type" (not to ```{r} # Create dataset for plotting UMAPs with lumped cell types -umap_df <- tibble::tibble( - UMAP1 = unname(reducedDim(processed_sce, "UMAP")[, 1]), - UMAP2 = unname(reducedDim(processed_sce, "UMAP")[, 2]), - clusters = processed_sce$clusters -) +umap_df <- tibble::as_tibble( + reducedDim(processed_sce, "UMAP") +) |> + dplyr::mutate(clusters = processed_sce$clusters) # helper function for lumping cell types lump_celltypes <- function(umap_df, From 26f9a2bdb2c2832da68bcf67b1ffdf4a7690b215 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 14 Sep 2023 14:40:01 -0500 Subject: [PATCH 219/268] v0.5.4 in docs --- external-instructions.md | 6 +++--- internal-instructions.md | 2 +- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/external-instructions.md b/external-instructions.md index 14703a5b..40dd2b5c 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -65,7 +65,7 @@ nextflow run AlexsLemonade/scpca-nf \ ``` Where `` is the **relative** path to the [configuration file](#configuration-files) that you have setup and `` is the name of the profile that you chose when [creating a profile](#setting-up-a-profile-in-the-configuration-file). -This command will pull the `scpca-nf` workflow directly from Github, using the `v0.5.3` version, and run it based on the settings in the configuration file that you have defined. +This command will pull the `scpca-nf` workflow directly from Github, using the `v0.5.4` version, and run it based on the settings in the configuration file that you have defined. **Note:** `scpca-nf` is under active development. Using the above command will run the workflow from the `main` branch of the workflow repository. @@ -76,7 +76,7 @@ Released versions can be found on the [`scpca-nf` repository releases page](http ```sh nextflow run AlexsLemonade/scpca-nf \ - -r v0.5.3 \ + -r v0.5.4 \ -config \ -profile ``` @@ -280,7 +280,7 @@ If you will be analyzing spatial expression data, you will also need the Cell Ra If your compute nodes do not have internet access, you will likely have to pre-pull the required container images as well. When doing this, it is important to be sure that you also specify the revision (version tag) of the `scpca-nf` workflow that you are using. -For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.5.3`, then you will want to set `-r v0.5.3` for `get_refs.py` as well to be sure you have the correct containers. +For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.5.4`, then you will want to set `-r v0.5.4` for `get_refs.py` as well to be sure you have the correct containers. By default, `get_refs.py` will download files and images associated with the latest release. If your system uses Docker, you can add the `--docker` flag: diff --git a/internal-instructions.md b/internal-instructions.md index 936868ae..67c3e6e7 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -33,7 +33,7 @@ nextflow run AlexsLemonade/scpca-nf -profile ccdl,batch When running the workflow for a project or group of samples that is ready to be released on ScPCA portal, please use the tag for the latest release: ``` -nextflow run AlexsLemonade/scpca-nf -r v0.5.3 -profile ccdl,batch --project SCPCP000000 +nextflow run AlexsLemonade/scpca-nf -r v0.5.4 -profile ccdl,batch --project SCPCP000000 ``` ### Processing example data diff --git a/nextflow.config b/nextflow.config index 1b9652ca..c126a1b3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest{ homePage = 'https://github.com/AlexsLemonade/scpca-nf' mainScript = 'main.nf' defaultBranch = 'main' - version = 'v0.5.3' + version = 'v0.5.4' } // global parameters for workflows From 2fa82ad88d5ad82ddf71ecbc736e4d580c45bb48 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 14 Sep 2023 20:38:38 -0400 Subject: [PATCH 220/268] use one empty_file for both workflows --- modules/sce-processing.nf | 45 ++++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index a1252b64..235b26a5 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -12,7 +12,7 @@ process make_unfiltered_sce{ tuple val(meta), path(unfiltered_rds) script: unfiltered_rds = "${meta.library_id}_unfiltered.rds" - + """ generate_unfiltered_sce.R \ --alevin_dir ${alevin_dir} \ @@ -27,8 +27,8 @@ process make_unfiltered_sce{ --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} - - + + # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ @@ -84,7 +84,7 @@ process make_merged_unfiltered_sce{ --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ ${params.spliced_only ? '--spliced_only' : ''} - + # Only run script if annotations are available: if [ ${submitter_cell_types_file.name} != "NO_FILE.txt" ]; then add_submitter_annotations.R \ @@ -219,25 +219,26 @@ process post_process_sce{ """ } + +// used when a given file is not defined in the below workflows +empty_file = "${projectDir}/assets/NO_FILE.txt" + workflow generate_sce { // generate rds files for RNA-only samples take: quant_channel sample_metafile main: - - // used for both submitter cell types & feature barcode files - empty_file = "${projectDir}/assets/NO_FILE.txt" - + sce_ch = quant_channel - .map{it.toList() + [file(it[0].mito_file), - file(it[0].ref_gtf), - // either submitter cell type files, or empty file if not available - file(it[0].submitter_cell_types_file ?: empty_file) - ]} - + .map{it.toList() + [file(it[0].mito_file), + file(it[0].ref_gtf), + // either submitter cell type files, or empty file if not available + file(it[0].submitter_cell_types_file ?: empty_file) + ]} + make_unfiltered_sce(sce_ch, sample_metafile) - + // provide empty feature barcode file, since no features here unfiltered_sce_ch = make_unfiltered_sce.out .map{it.toList() + [file(empty_file)]} @@ -256,14 +257,14 @@ workflow generate_merged_sce { sample_metafile main: - feature_sce_ch = feature_quant_channel + feature_sce_ch = feature_quant_channel // RNA meta is in the third slot here - .map{it.toList() + [file(it[2].mito_file), - file(it[2].ref_gtf), - // either submitter cell type files, or empty file if not available - file(it[2].submitter_cell_types_file ?: "${projectDir}/assets/NO_FILE.txt") - ]} - + .map{it.toList() + [file(it[2].mito_file), + file(it[2].ref_gtf), + // either submitter cell type files, or empty file if not available + file(it[2].submitter_cell_types_file ?: empty_file) + ]} + make_merged_unfiltered_sce(feature_sce_ch, sample_metafile) // append the feature barcode file From 1e4323f8b09b0fc865077a62cbbd4d3f193d3cb7 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 14 Sep 2023 20:39:03 -0400 Subject: [PATCH 221/268] whitespace --- modules/spaceranger.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf index eca9718e..c2b245ed 100644 --- a/modules/spaceranger.nf +++ b/modules/spaceranger.nf @@ -127,9 +127,9 @@ workflow spaceranger_quant{ // create tuple of [metadata, fastq dir, and path to image file] spaceranger_reads = spatial_channel.make_spatial .map{meta -> tuple(meta, - file(meta.files_directory, type: 'dir'), - file("${meta.files_directory}/*.jpg"), - file(meta.cellranger_index, type: 'dir') + file(meta.files_directory, type: 'dir'), + file("${meta.files_directory}/*.jpg"), + file(meta.cellranger_index, type: 'dir') )} // run spaceranger @@ -140,7 +140,7 @@ workflow spaceranger_quant{ spaceranger_quants_ch = spatial_channel.has_spatial .map{meta -> tuple(Utils.readMeta(file("${meta.spaceranger_results_dir}/scpca-meta.json")), file(meta.spaceranger_results_dir, type: 'dir') - )} + )} grouped_spaceranger_ch = spaceranger.out.mix(spaceranger_quants_ch) From 47ea085e6ed6d5c170c1ef727f9649af93042a35 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 14 Sep 2023 20:55:15 -0400 Subject: [PATCH 222/268] rehandle NAs --- modules/sce-processing.nf | 3 +-- modules/spaceranger.nf | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 235b26a5..7e9ae1c6 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -119,7 +119,6 @@ process filter_sce{ // - barcode file should exist // - barcode file should _not_ be the empty file NO_FILE.txt adt_present = meta.feature_type == 'adt' & - feature_barcode_file.exists() & feature_barcode_file.name != "NO_FILE.txt" """ @@ -269,7 +268,7 @@ workflow generate_merged_sce { // append the feature barcode file unfiltered_merged_sce_ch = make_merged_unfiltered_sce.out - .map{it.toList() + [file(it[0]["feature_meta"].feature_barcode_file)]} + .map{it.toList() + [file(it[0]["feature_meta"].feature_barcode_file ?: empty_file)]} filter_sce(unfiltered_merged_sce_ch) diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf index c2b245ed..54318a09 100644 --- a/modules/spaceranger.nf +++ b/modules/spaceranger.nf @@ -24,8 +24,8 @@ process spaceranger{ --localcores=${task.cpus} \ --localmem=${task.memory.toGiga()} \ --image=${image_file} \ - --slide=${meta.slide_serial_number} \ - --area=${meta.slide_section} + --slide=${meta.slide_serial_number ?: "NA"} \ + --area=${meta.slide_section ?: "NA"} # write metadata echo '${meta_json}' > ${out_id}/scpca-meta.json From 3adb55f8568f31d42d6d3f881b46e10e604ca6b8 Mon Sep 17 00:00:00 2001 From: Stephanie Date: Fri, 15 Sep 2023 11:01:09 -0400 Subject: [PATCH 223/268] respond to reviews --- templates/qc_report/celltypes_qc.rmd | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/templates/qc_report/celltypes_qc.rmd b/templates/qc_report/celltypes_qc.rmd index c57acf94..b02bc35e 100644 --- a/templates/qc_report/celltypes_qc.rmd +++ b/templates/qc_report/celltypes_qc.rmd @@ -50,7 +50,6 @@ knitr::asis_output( knitr::asis_output( glue::glue( "* Cell type annotations were also provided by the original lab (`submitter-provided`) which generated this data. - In these cell type annotations, the label `Unclassified cell` indicates that submitters did not provide an annotation for the given cell. " ) ) @@ -150,7 +149,11 @@ create_celltype_n_table(celltype_df, cellassign_celltype_annotation) ``` ```{r, eval = has_submitter} -knitr::asis_output("### Submitter-provided cell type annotations\n") +knitr::asis_output(' +### Submitter-provided cell type annotations\n + +Below, cells labeled "Unclassified cell" are those for which submitters did not provide an annotation. + ') create_celltype_n_table(celltype_df, submitter_celltype_annotation) ``` @@ -533,6 +536,7 @@ create_celltype_heatmap <- function(x_vector, y_vector, x_label = "", y_label = "", + y_title_location = "bottom", column_names_rotation = 0, row_font_size = 8, column_font_size = 10) { @@ -552,7 +556,7 @@ create_celltype_heatmap <- function(x_vector, col = heatmap_palette, # Column parameters column_title = y_label, - column_title_side = "bottom", + column_title_side = y_title_location, column_dend_side = "top", column_names_rot = column_names_rotation, column_names_gp = grid::gpar(fontsize = column_font_size), @@ -575,7 +579,7 @@ create_celltype_heatmap <- function(x_vector, ```{r, eval = has_singler, fig.height=5, fig.width=7} -knitr::asis_output("### `SingleR` cluster and cell type heatmap\n") +knitr::asis_output("### `SingleR` cell type and cluster heatmap\n") create_celltype_heatmap( x_vector = celltype_df$singler_celltype_annotation, y_vector = celltype_df$clusters, @@ -584,7 +588,7 @@ create_celltype_heatmap( ``` ```{r, eval = has_cellassign, fig.height=5, fig.width=7} -knitr::asis_output("### `CellAssign` cluster and cell type heatmap\n") +knitr::asis_output("### `CellAssign` cell type and cluster heatmap\n") create_celltype_heatmap( x_vector = celltype_df$cellassign_celltype_annotation, y_vector = celltype_df$clusters, @@ -593,7 +597,7 @@ create_celltype_heatmap( ``` ```{r, eval = has_submitter, fig.height=5, fig.width=7} -knitr::asis_output("### Submitter-provided cluster and cell type heatmap\n") +knitr::asis_output("### Submitter-provided cell type and cluster heatmap\n") create_celltype_heatmap( x_vector = celltype_df$submitter_celltype_annotation, y_vector = celltype_df$clusters, @@ -638,18 +642,22 @@ create_celltype_heatmap( y_vector = celltype_df$singler_celltype_annotation, x_label = "Submitter-provided annotations", y_label = "SingleR annotations", + y_title_location = "top", column_names_rotation = 55, column_font_size = 8 ) ``` -```{r, eval = has_submitter & has_cellassign, fig.height=7, fig.width=8} + +
    +```{r, eval = has_submitter & has_cellassign, fig.height=7, fig.width=8} create_celltype_heatmap( x_vector = celltype_df$submitter_celltype_annotation, y_vector = celltype_df$cellassign_celltype_annotation, x_label = "Submitter-provided annotations", y_label = "CellAssign annotations", + y_title_location = "top", column_names_rotation = 55, column_font_size = 8 ) From 066f97581b70dc2c7b84744fdea99370adc78639 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 15 Sep 2023 11:31:32 -0400 Subject: [PATCH 224/268] Update lib/Utils.groovy Co-authored-by: Stephanie --- lib/Utils.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 5e6a060a..fe527369 100644 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -49,6 +49,6 @@ class Utils { * @return The input string unless it was NA or a variant thereof, in which case returns null */ static def parseNA(str) { - str.toLowerCase()in ["na","n/a","nan"]? null : str + str.toLowerCase() in ["na","n/a","nan"]? null : str } } From c9d7019f38091b67cffb32fd47ec09caa44beb96 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Fri, 15 Sep 2023 11:35:55 -0400 Subject: [PATCH 225/268] Update sce-processing.nf comment --- modules/sce-processing.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 7e9ae1c6..0ef4bf7a 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -114,9 +114,8 @@ process filter_sce{ script: filtered_rds = "${meta.library_id}_filtered.rds" - // Three checks for whether we have ADT data: + // Checks for whether we have ADT data: // - feature_type should be adt - // - barcode file should exist // - barcode file should _not_ be the empty file NO_FILE.txt adt_present = meta.feature_type == 'adt' & feature_barcode_file.name != "NO_FILE.txt" From 026f478150b20d9b01404e58268d09a8745ab31e Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 18 Sep 2023 13:54:15 -0500 Subject: [PATCH 226/268] add processed cells to metadata.json --- bin/sce_qc_report.R | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R index cc574cca..69e6b56b 100755 --- a/bin/sce_qc_report.R +++ b/bin/sce_qc_report.R @@ -178,6 +178,7 @@ metadata_list <- list( is_multiplexed = multiplexed, has_citeseq = has_citeseq, has_cellhash = has_cellhash, + processed_cells = ncol(processed_sce), filtered_cells = ncol(filtered_sce), unfiltered_cells = ncol(unfiltered_sce), droplet_filtering_method = filtered_sce_meta$filtering_method, From ced5b6cf8613a4c9b885aa2db8cedd458ee4241f Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 18 Sep 2023 13:54:43 -0500 Subject: [PATCH 227/268] use clustering output and qc report output as input to anndata export --- main.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 5e001db4..fbdfefb0 100644 --- a/main.nf +++ b/main.nf @@ -225,8 +225,12 @@ workflow { sce_qc_report(cluster_sce.out, report_template_tuple) // convert SCE object to anndata - // do this for everything but multiplexed libraries - anndata_ch = post_process_sce.out + anndata_ch = cluster_sce.out + // join clustering output with qc report data + // we need to be able to grab the number of cells for each object from the metadata json (output from sce_qc_report) + // tuple of [meta, unfiltered, filtered, processed, qc report, metadata json] + .join(sce_qc_report.out, by: 0, failOnDuplicate: true, failOnMismatch: true) + // skip multiplexed libraries .filter{!(it[0]["library_id"] in multiplex_libs.getVal())} sce_to_anndata(anndata_ch) From 6275f7c8a6044110425303b8cad0864fdc46bdc0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 18 Sep 2023 13:55:03 -0500 Subject: [PATCH 228/268] filter sce objects to export based on number of cells --- modules/export-anndata.nf | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index e308e430..47e25c64 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -57,11 +57,20 @@ workflow sce_to_anndata{ sce_files_ch main: sce_ch = sce_files_ch - // make tuple of [meta, sce_file, type of file] - .flatMap{[[it[0], it[1], "unfiltered"], - [it[0], it[2], "filtered"], - [it[0], it[3], "processed"] + // make tuple of [meta, sce_file, type of file, metadata.json] + .flatMap{[[it[0], it[1], "unfiltered", it[5]], + [it[0], it[2], "filtered", it[5]], + [it[0], it[3], "processed", it[5]] ]} + // remove any sce files that don't have enough cells in the sce object + // number of cells are stored in each metadata.json file + .filter{ Utils.getMetaVal(file(it[3]), "${it[2]}_cells") > 1 } + // remove metadata.json file from tuple + .map{meta, sce_file, file_type, meta_json -> tuple( + meta, + sce_file, + file_type + )} // export each anndata file export_anndata(sce_ch) From 50599632b8306e3d623254531fccdcdff361046a Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 20 Sep 2023 10:15:45 -0400 Subject: [PATCH 229/268] Handle blank values in parseNA --- lib/Utils.groovy | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index fe527369..944a1db0 100644 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -48,7 +48,11 @@ class Utils { * @param str A string * @return The input string unless it was NA or a variant thereof, in which case returns null */ - static def parseNA(str) { - str.toLowerCase() in ["na","n/a","nan"]? null : str + static def parseNA(str) { + if (str){ + str.toLowerCase() in ["na","n/a","nan"]? null : str + } else { + null + } } } From d31c8cd16f58a7f7cd067a3efa86fe34bdd09870 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 20 Sep 2023 10:35:40 -0500 Subject: [PATCH 230/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- modules/export-anndata.nf | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 47e25c64..479d4232 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -66,11 +66,7 @@ workflow sce_to_anndata{ // number of cells are stored in each metadata.json file .filter{ Utils.getMetaVal(file(it[3]), "${it[2]}_cells") > 1 } // remove metadata.json file from tuple - .map{meta, sce_file, file_type, meta_json -> tuple( - meta, - sce_file, - file_type - )} + .map{it.dropRight(1)} // export each anndata file export_anndata(sce_ch) From ebe4e3df43b83629a4479156c38c349232a30ddd Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 20 Sep 2023 11:28:49 -0500 Subject: [PATCH 231/268] document anndata in main readme --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4c5aaadd..494fc533 100644 --- a/README.md +++ b/README.md @@ -4,10 +4,11 @@ This repository holds a [Nextflow](https://www.nextflow.io) workflow (`scpca-nf` All dependencies for the workflow outside of the Nextflow workflow engine itself are handled automatically; setup generally requires only organizing the input files and configuring Nextflow for your computing environment. Nextflow will also handle parallelizing sample processing as allowed by your environment, minimizing total run time. -The workflow processes fastq files from single-cell and single-nuclei RNA-seq samples using [alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) to create gene by cell matrices as [`SingleCellExperiment` objects](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). +The workflow processes fastq files from single-cell and single-nuclei RNA-seq samples using [alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) to create gene by cell matrices. +The workflow outputs gene expression data stored as both [`SingleCellExperiment` objects](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) and [`AnnData` objects](https://anndata.readthedocs.io/en/latest/). Reads from samples are aligned using selective alignment, to an index with transcripts corresponding to spliced cDNA and to intronic regions, denoted by alevin-fry as `splici`. These matrices are filtered and additional processing is performed to calculate quality control statistics, create reduced-dimension transformations, and create output reports. -`scpca-nf` can also process CITE-seq, bulk RNA-seq, and spatial transcriptomics samples. +`scpca-nf` can also process libraries with ADT tags (e.g., CITE-seq), bulk RNA-seq, and spatial transcriptomics samples. For more information on the contents of the output files and the processing of all modalities, please see the [ScPCA Portal docs](https://scpca.readthedocs.io/en/latest/). From fee4b157d9564762996d1f976ae8c134e10c6fbd Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 20 Sep 2023 11:29:07 -0500 Subject: [PATCH 232/268] update output to include anndata output and switch CITE -> ADT --- external-instructions.md | 39 ++++++++++++++++++++++++--------------- 1 file changed, 24 insertions(+), 15 deletions(-) diff --git a/external-instructions.md b/external-instructions.md index 40dd2b5c..76246f25 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -15,7 +15,7 @@ - [Downloading container images](#downloading-container-images) - [Repeating mapping steps](#repeating-mapping-steps) - [Special considerations for specific data types](#special-considerations-for-specific-data-types) - - [Libraries with additional feature data (CITE-seq or cellhash)](#libraries-with-additional-feature-data-cite-seq-or-cellhash) + - [Libraries with additional feature data (ADT tags or cellhash)](#libraries-with-additional-feature-data-adt-tags-or-cellhash) - [Multiplexed (cellhash) libraries](#multiplexed-cellhash-libraries) - [Spatial transcriptomics libraries](#spatial-transcriptomics-libraries) - [Output files](#output-files) @@ -90,7 +90,7 @@ You will need to have files organized so that all the sequencing files for each Each folder should be named with a unique ID, corresponding to the [`scpca_run_id` column of the metadata file](#prepare-the-metadata-file). Any sequencing runs that contain multiple libraries must be demultiplexed and FASTQ files must be placed into separate distinct folders, with distinct run IDs as the folder name. If the same sequencing library was sequenced across multiple flow cells (e.g., to increase coverage), all FASTQ files should be combined into the same folder. -If a library has a corresponding CITE-seq library and therefore a separate set of FASTQ files, the FASTQ files corresponding to the CITE-seq library should be in their own folder, with a unique run ID. +If a library has a corresponding ADT library and therefore a separate set of FASTQ files, the FASTQ files corresponding to the ADT library should be in their own folder, with a unique run ID. ## Prepare the metadata file @@ -102,7 +102,7 @@ See [the section on file organization above for more information](#file-organiza The library ID will be unique for each set of cells that have been isolated from a sample and have undergone droplet generation. For single-cell/single-nuclei RNA-seq runs, the library ID should be unique for each sequencing run. -For libraries that have corresponding CITE-seq or cellhash runs, they should share the same library ID as the associated single-cell/single-nuclei RNA-seq run, indicating that the sequencing data has been generated from the same group of cells. +For libraries that have corresponding ADT or cellhash runs, they should share the same library ID as the associated single-cell/single-nuclei RNA-seq run, indicating that the sequencing data has been generated from the same group of cells. Finally, the sample ID will indicate the unique tissue or source from which a sample was collected. If you have two libraries that have been generated from the same original tissue, then they will share the same sample ID. @@ -120,7 +120,7 @@ To run the workflow, you will need to create a tab separated values (TSV) metada | `scpca_library_id`| A unique library ID for each unique set of cells | | `scpca_sample_id` | A unique sample ID for each tissue or unique source.
    For multiplexed libraries, separate multiple samples with semicolons (`;`) | | `scpca_project_id` | A unique ID for each group of related samples. All results for samples with the same project ID will be returned in the same folder labeled with the project ID. | -| `technology` | Sequencing/library technology used
    For single-cell/single-nuclei libraries use either `10Xv2`, `10Xv2_5prime`, `10Xv3`, or `10Xv31`.
    For CITE-seq libraries use either `CITEseq_10Xv2`, `CITEseq_10Xv3`, or `CITEseq_10Xv3.1`
    For cellhash libraries use either `cellhash_10Xv2`, `cellhash_10Xv3`, or `cellhash_10Xv3.1`
    For bulk RNA-seq use either `single_end` or `paired_end`.
    For spatial transcriptomics use `visium` | +| `technology` | Sequencing/library technology used
    For single-cell/single-nuclei libraries use either `10Xv2`, `10Xv2_5prime`, `10Xv3`, or `10Xv31`.
    For ADT or CITE-seq libraries use either `CITEseq_10Xv2`, `CITEseq_10Xv3`, or `CITEseq_10Xv3.1`
    For cellhash libraries use either `cellhash_10Xv2`, `cellhash_10Xv3`, or `cellhash_10Xv3.1`
    For bulk RNA-seq use either `single_end` or `paired_end`.
    For spatial transcriptomics use `visium` | | `seq_unit` | Sequencing unit (one of: `cell`, `nucleus`, `bulk`, or `spot`)| | `sample_reference`| The name of the reference to use for mapping, available references include: `Homo_sapiens.GRCh38.104` and `Mus_musculus.GRCm39.104` | | `files_directory` | path/uri to directory containing fastq files (unique per run) | @@ -129,8 +129,8 @@ The following columns may be necessary for running other data modalities (CITE-s | column_id | contents | |-----------------|----------------------------------------------------------------| -| `feature_barcode_file` | path/uri to file containing the feature barcode sequences (only required for CITE-seq and cellhash samples); for CITE-seq samples, this file can optionally indicate whether antibodies are targets or controls. | -| `feature_barcode_geom` | A salmon `--read-geometry` layout string.
    See https://github.com/COMBINE-lab/salmon/releases/tag/v1.4.0 for details (only required for CITE-seq and cellhash samples) | +| `feature_barcode_file` | path/uri to file containing the feature barcode sequences (only required for ADT and cellhash samples); for samples with ADT tags, this file can optionally indicate whether antibodies are targets or controls. | +| `feature_barcode_geom` | A salmon `--read-geometry` layout string.
    See https://github.com/COMBINE-lab/salmon/releases/tag/v1.4.0 for details (only required for ADT and cellhash samples) | | `slide_section` | The slide section for spatial transcriptomics samples (only required for spatial transcriptomics) | | `slide_serial_number`| The slide serial number for spatial transcriptomics samples (only required for spatial transcriptomics) | @@ -314,9 +314,9 @@ nextflow run AlexsLemonade/scpca-nf \ ## Special considerations for specific data types -### Libraries with additional feature data (CITE-seq or cellhash) +### Libraries with additional feature data (ADT or cellhash) -Libraries processed using multiple modalities, such as those that include runs of CITE-seq or cellhash tags, will require a file containing the barcode IDs and sequences. +Libraries processed using multiple modalities, such as those that include runs with ADT or cellhash tags, will require a file containing the barcode IDs and sequences. The file location should be specified in the `feature_barcode_file` for each library as listed in the [metadata file](#prepare-the-metadata-file); multiple libraries can and should use the same `feature_barcode_file` if the same feature barcode sequences are expected. The `feature_barcode_file` itself is a tab separated file with one line per barcode and no header. @@ -328,7 +328,7 @@ TAG01 CATGTGAGCT TAG02 TGTGAGGGTG ``` -For CITE-seq data, you can optionally include a third column in the `feature_barcode_file` to indicate the purpose of each antibody, which can take one of the following three values: +For libraries with ADT tags, you can optionally include a third column in the `feature_barcode_file` to indicate the purpose of each antibody, which can take one of the following three values: - `target`: antibody is a true target - `neg_control`: a negative control antibody @@ -410,8 +410,14 @@ Within the `outdir`, two folders will be present, `results` and `checkpoints`. The `results` folder will contain the final output files produced by the workflow and the files that are typically available for download on the ScPCA portal. Within the `results` folder, all files pertaining to a specific sample will be nested within a folder labeled with the sample ID. -All files in that folder will be prefixed by library ID, with the following suffixes: `_unfiltered.rds`, `_filtered.rds`, `_processed.rds`, `_metadata.json`, and `_qc.html`. -The `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` files contain the quantified gene expression data as a [`SingleCellExperiment` object](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). +All files in that folder will be prefixed by the library ID. + +The files containing the suffixes `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` contain the quantified gene expression data as a [`SingleCellExperiment` object](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). + +the files containing the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_processed_rna.hdf5` contain the quantified gene expression data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). +If your data contains libraries with ADT tags, three additional files with the suffixes `_unfiltered_adt.hdf5`, `_filtered_adt.hdf5`, and `_processed_adt.hdf5`will be provided. +These files contain the quantified ADT tag data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). + For more information on the contents of these files, see the [ScPCA portal docs section on single cell gene expression file contents](https://scpca.readthedocs.io/en/latest/sce_file_contents.html). See below for the expected structure of the `results` folder: @@ -419,11 +425,14 @@ See below for the expected structure of the `results` folder: ``` results └── sample_id + ├── library_id_unfiltered.rds ├── library_id_filtered.rds - ├── library_id_metadata.json ├── library_id_processed.rds - ├── library_id_qc.html - └── library_id_unfiltered.rds + ├── library_id_unfiltered_rna.hdf5 + ├── library_id_filtered_rna.hdf5 + ├── library_id_processed_rna.hdf5 + ├── library_id_metadata.json + └── library_id_qc.html ``` If bulk libraries were processed, a `bulk_quant.tsv` and `bulk_metadata.tsv` summarizing the counts data and metadata across all libraries will also be present in the `results` directory. @@ -435,7 +444,7 @@ The `rad` folder (nested inside the `checkpoints` folder) contains the output fr If bulk libraries are processed, there will be an additional `salmon` folder that contains the output from running [`salmon quant`](https://salmon.readthedocs.io/en/latest/file_formats.html) on each library processed. All files pertaining to a specific library will be nested within a folder labeled with the library ID. -Additionally, for each run, all files related to that run will be inside a folder labeled with the run ID followed by the type of run (i.e. `rna` or `features` for CITE-seq) and nested within the library ID folder. +Additionally, for each run, all files related to that run will be inside a folder labeled with the run ID followed by the type of run (i.e. `rna` or `features` for libraries with ADT tags) and nested within the library ID folder. See below for the expected structure of the `checkpoints` folder: From 46ebb253319f699c3d65e10f1edf9008118f747b Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 20 Sep 2023 11:31:21 -0500 Subject: [PATCH 233/268] a little rewording --- external-instructions.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/external-instructions.md b/external-instructions.md index 76246f25..6d857ea6 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -412,10 +412,10 @@ The `results` folder will contain the final output files produced by the workflo Within the `results` folder, all files pertaining to a specific sample will be nested within a folder labeled with the sample ID. All files in that folder will be prefixed by the library ID. -The files containing the suffixes `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` contain the quantified gene expression data as a [`SingleCellExperiment` object](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). +The files with the suffixes `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` contain the quantified gene expression data as a [`SingleCellExperiment` object](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). -the files containing the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_processed_rna.hdf5` contain the quantified gene expression data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). -If your data contains libraries with ADT tags, three additional files with the suffixes `_unfiltered_adt.hdf5`, `_filtered_adt.hdf5`, and `_processed_adt.hdf5`will be provided. +The files with the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_processed_rna.hdf5` contain the quantified gene expression data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). +If the input data contains libraries with ADT tags, three additional files with the suffixes `_unfiltered_adt.hdf5`, `_filtered_adt.hdf5`, and `_processed_adt.hdf5`will be provided for each library. These files contain the quantified ADT tag data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). For more information on the contents of these files, see the [ScPCA portal docs section on single cell gene expression file contents](https://scpca.readthedocs.io/en/latest/sce_file_contents.html). From 0a4f3472adfd0d987531af72c402877f9eca7061 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Wed, 20 Sep 2023 11:40:22 -0500 Subject: [PATCH 234/268] doctoc --- external-instructions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external-instructions.md b/external-instructions.md index 6d857ea6..3b077267 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -15,7 +15,7 @@ - [Downloading container images](#downloading-container-images) - [Repeating mapping steps](#repeating-mapping-steps) - [Special considerations for specific data types](#special-considerations-for-specific-data-types) - - [Libraries with additional feature data (ADT tags or cellhash)](#libraries-with-additional-feature-data-adt-tags-or-cellhash) + - [Libraries with additional feature data (ADT or cellhash)](#libraries-with-additional-feature-data-adt-or-cellhash) - [Multiplexed (cellhash) libraries](#multiplexed-cellhash-libraries) - [Spatial transcriptomics libraries](#spatial-transcriptomics-libraries) - [Output files](#output-files) From 49416eb7a7dcf965a53f1fefb2900a0f0af200b4 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 20 Sep 2023 16:30:50 -0500 Subject: [PATCH 235/268] add sample metadata to external docs --- README.md | 5 +++-- external-instructions.md | 47 ++++++++++++++++++++++++++++++---------- 2 files changed, 39 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 494fc533..c9da2852 100644 --- a/README.md +++ b/README.md @@ -26,8 +26,9 @@ For all other users, `scpca-nf` can be set up for your computing environment wit To run `scpca-nf` on your own samples, you will need to complete the following steps: 1. [Organize your files](external-instructions.md#file-organization) so that each folder contains fastq files relevant to a single sequencing run. -2. [Prepare a metadata file](external-instructions.md#prepare-the-metadata-file) with one row per library containing all information needed to process your samples. -3. Set up a [configuration file](external-instructions.md#configuration-files), including the [definition of a profile](external-instructions.md#setting-up-a-profile-in-the-configuration-file), dictating where nextflow should execute the workflow. +2. [Prepare a run metadata file](external-instructions.md#prepare-the-run-metadata-file) with one row per library containing all information needed to process your samples. +3. [Prepare a sample metadata file]() with one row per sample containing any relevant metadata about each sample (e.g., diagnosis, age, sex, cell line). +4. Set up a [configuration file](external-instructions.md#configuration-files), including the [definition of a profile](external-instructions.md#setting-up-a-profile-in-the-configuration-file), dictating where nextflow should execute the workflow. You may also [test your configuration file using example data](examples/README.md). diff --git a/external-instructions.md b/external-instructions.md index 3b077267..701ad7b7 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -45,9 +45,9 @@ You will need to make sure you have the following software installed on your HPC You will need to have your files organized in a particular manner so that each folder contains only the FASTQ files that pertain to a single library. See the [section below on file organization](#file-organization) for more information on how to set up your files. -3. **Create a [metadata file](#prepare-the-metadata-file).** -Create a TSV (tab-separated values) file with one sequencing library per row and pertinent information related to that sequencing run in each column. -See the [section below on preparing a metadata file](#prepare-the-metadata-file) for more information on creating a metadata file for your samples. +3. **Create a [run metadata file](#prepare-the-run-metadata-file) and [sample metadata file](#prepare-the-sample-metadata-file).** +Create two TSV (tab-separated values) files - one file with one sequencing library per row and pertinent information related to that sequencing run in each column (run metadata) and the other file with one sample per row and any relevant sample metadata (e.g., daignosis, age, sex, cell line) (sample metadata). +See the sections below on preparing a [run metadata file](#prepare-the-run-metadata-file) and [sample metadata file](#prepare-the-sample-metadata-file) for more information on creating a metadata file for your samples. 4. **Create a [configuration file](#configuration-files) and [define a profile](#setting-up-a-profile-in-the-configuration-file).** Create a configuration file that stores user defined parameters and a profile indicating the system and other system related settings to use for executing the workflow. @@ -65,13 +65,14 @@ nextflow run AlexsLemonade/scpca-nf \ ``` Where `` is the **relative** path to the [configuration file](#configuration-files) that you have setup and `` is the name of the profile that you chose when [creating a profile](#setting-up-a-profile-in-the-configuration-file). -This command will pull the `scpca-nf` workflow directly from Github, using the `v0.5.4` version, and run it based on the settings in the configuration file that you have defined. +This command will pull the `scpca-nf` workflow directly from Github, and run it based on the settings in the configuration file that you have defined. **Note:** `scpca-nf` is under active development. Using the above command will run the workflow from the `main` branch of the workflow repository. To update to the latest released version you can run `nextflow pull AlexsLemonade/scpca-nf` before the `nextflow run` command. To be sure that you are using a consistent version, you can specify use of a release tagged version of the workflow, set below with the `-r` flag. +The command below will pull the `scpca-nf` workflow directly from Github using the `v0.5.4` version. Released versions can be found on the [`scpca-nf` repository releases page](https://github.com/AlexsLemonade/scpca-nf/releases). ```sh @@ -92,9 +93,9 @@ Any sequencing runs that contain multiple libraries must be demultiplexed and FA If the same sequencing library was sequenced across multiple flow cells (e.g., to increase coverage), all FASTQ files should be combined into the same folder. If a library has a corresponding ADT library and therefore a separate set of FASTQ files, the FASTQ files corresponding to the ADT library should be in their own folder, with a unique run ID. -## Prepare the metadata file +## Prepare the run metadata file -Using `scpca-nf` requires a metadata file as a TSV (tab separated values) file, where each sequencing run to be processed is a row and columns contain associated information about that run. +Using `scpca-nf` requires a run metadata file as a TSV (tab separated values) file, where each sequencing run to be processed is a row and columns contain associated information about that run. For each sequencing run, you will need to provide a Run ID (`scpca_run_id`), library ID (`scpca_library_id`), and sample ID (`scpca_sample_id`). The run ID will correspond to the name of the folder that contains the FASTQ files associated with the sequencing run. @@ -134,14 +135,37 @@ The following columns may be necessary for running other data modalities (CITE-s | `slide_section` | The slide section for spatial transcriptomics samples (only required for spatial transcriptomics) | | `slide_serial_number`| The slide serial number for spatial transcriptomics samples (only required for spatial transcriptomics) | -We have provided an example metadata file for reference that can be found in [`examples/example_metadata.tsv`](examples/example_metadata.tsv). +We have provided an example run metadata file for reference. + +| [View example run metadata](examples/example_run_metadata.tsv) | +| ------------------------------------------------------------------| + +## Prepare the sample metadata file + +Using `scpca-nf` requires a sample metadata file as a TSV (tab separated values) file, where each unique sample that is present in the `scpca_sample_id` column of the run metadata file is a row, and columns contain any relevant sample metadata (e.g., diagnosis, age, sex, cell line). +For each library that is processed, the corresponding sample metadata will be added to the `SingleCellExperiment` and `AnnData` objects output by the workflow (see the section on [Output files](#output-files)). + +At a minimum, all sample metadata tables must contain a column with `scpca_sample_id` as the header. +The contents of this column should contain all unique sample ids that are present in the `scpca_sample_id` column of the run metadata file. + +We encourage you to use standard terminology, such as ontology terms, to describe samples when possible. +There is no limit to the number of columns allowed for the sample metadata, and you may include as many metadata fields as you please. + +We have provided an example run metadata file for reference. + +| [View example sample metadata](examples/example_sample_metadata.tsv) | +| ---------------------------------------------------------------------| + +**Before using the workflow with data that you might plan to submit to ScPCA, please be sure to look at the [guidelines for sample metadata](https://scpca.alexslemonade.org/contribute).** ## Configuring `scpca-nf` for your environment -Two workflow parameters are required for running `scpca-nf` on your own data: +Three workflow parameters are required for running `scpca-nf` on your own data: -- `run_metafile`: the metadata file with sample information, prepared according to the directions above. +- `run_metafile`: the metadata file with **library** information, prepared according to the directions [above](#prepare-the-run-metadata-file). - This has a default value of `run_metadata.tsv`, but you will likely want to set your own file path. +- `sample_metafile`: the metadata file with **sample** information, prepared according to the directions [above](#prepare-the-sample-metadata-file). + - This has a default value of `sample_metadata.tsv`, but you will likely want to set your own file path. - `outdir`: the output directory where results will be stored. - The default output is `scpca_out`, but again, you will likely want to customize this. @@ -159,13 +183,14 @@ Note that all parameters can be overridden with a user config file or at the com ### Configuration files -Workflow parameters can also be set in a [configuration file](https://www.nextflow.io/docs/latest/config.html#configuration-file) by setting the values `params.run_metafile` and `params.outdir` as follows. +Workflow parameters can also be set in a [configuration file](https://www.nextflow.io/docs/latest/config.html#configuration-file) by setting the values `params.run_metafile`, `params.sample_metafile`, and `params.outdir` as follows. We could first create a file `my_config.config` (or a filename of your choice) with the following contents: ```groovy // my_config.config params.run_metafile = '' +params.sample_metafile = '' params.outdir = '' params.max_cpus = 24 params.max_memory = 96.GB @@ -317,7 +342,7 @@ nextflow run AlexsLemonade/scpca-nf \ ### Libraries with additional feature data (ADT or cellhash) Libraries processed using multiple modalities, such as those that include runs with ADT or cellhash tags, will require a file containing the barcode IDs and sequences. -The file location should be specified in the `feature_barcode_file` for each library as listed in the [metadata file](#prepare-the-metadata-file); multiple libraries can and should use the same `feature_barcode_file` if the same feature barcode sequences are expected. +The file location should be specified in the `feature_barcode_file` for each library as listed in the [run metadata file](#prepare-the-run-metadata-file); multiple libraries can and should use the same `feature_barcode_file` if the same feature barcode sequences are expected. The `feature_barcode_file` itself is a tab separated file with one line per barcode and no header. The first column will contain the barcode or antibody ID and the second column the barcode nucleotide sequence. From 226b96c193a86f80e273bdde6deb9b301ef55f39 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 20 Sep 2023 16:31:04 -0500 Subject: [PATCH 236/268] add sample metadata to example files and readme --- examples/README.md | 16 +++++++++++----- ...ple_metadata.tsv => example_run_metadata.tsv} | 0 examples/example_sample_metadata.tsv | 7 +++++++ examples/user_template.config | 3 ++- 4 files changed, 20 insertions(+), 6 deletions(-) rename examples/{example_metadata.tsv => example_run_metadata.tsv} (100%) create mode 100644 examples/example_sample_metadata.tsv diff --git a/examples/README.md b/examples/README.md index 08e00c0d..559f2857 100644 --- a/examples/README.md +++ b/examples/README.md @@ -16,14 +16,20 @@ We recommend using the example 10X dataset from a [human glioblastoma donor that The fastq files for this example data can be downloaded from the following link (**note:** These files will take approximately 10 GB of disk space upon download and expanding the tar file): [Brain_Tumor_3p_fastqs.tar](https://cf.10xgenomics.com/samples/cell-exp/6.0.0/Brain_Tumor_3p/Brain_Tumor_3p_fastqs.tar). -Following download and unzipping of the fastq files, you will need to create a tab-separated values metadata file that looks like the following: +Following download and unzipping of the fastq files, you will need to create a tab-separated values **run** metadata file that looks like the following: -| scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | seq_unit | sample_reference | files_directory | submitter_cell_types_file | -| ------------ | ---------------- | --------------- | ---------------- | ---------- | -------- | ---------------- | --------------- | ------------------------ | -| run01 | library01 | sample01 | project01 | 10Xv3.1 | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_file +| scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | assay_ontology_term_id | seq_unit | sample_reference | files_directory | submitter_cell_types_file | +| ------------ | ---------------- | --------------- | ---------------- | ---------- | -----------------------|-------- | ---------------- | --------------- | ------------------------ | +| run01 | library01 | sample01 | project01 | 10Xv3.1 | EFO:XXX | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_file Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column, and similarly the full path for the `submitter_cell_types_file` column. +You will also need to create a tab-separated values **sample** metadata file that looks like the following: + +| scpca_sample_id | +| --------------- | +| sample01 | + The following command can then be used to test your configuration setup with the example data: ``` @@ -35,7 +41,7 @@ nextflow run AlexsLemonade/scpca-nf \ Where `` is the **relative** path to the configuration file that you have setup after following the instructions on [creating a configuration file](../external-data-instructions.md#configuration-files), `` is the name of the profile that you chose when creating a profile, and `` is the **full** path to the metadata TSV you created. For the [example configuration file that we provided](./user_template.config), we used the profile name `cluster` and would indicate that we would like to use that profile at the command line with `-profile cluster`. -For more detailed information on setting up the metadata file for your own data, see instructions on [preparing the metadata file](../external-data-instructions.md#prepare-the-metadata-file). +For more detailed information on setting up the metadata file for your own data, see instructions on [preparing the run metadata file](../external-data-instructions.md#prepare-the-run-metadata-file). ## Example output diff --git a/examples/example_metadata.tsv b/examples/example_run_metadata.tsv similarity index 100% rename from examples/example_metadata.tsv rename to examples/example_run_metadata.tsv diff --git a/examples/example_sample_metadata.tsv b/examples/example_sample_metadata.tsv new file mode 100644 index 00000000..6c2da390 --- /dev/null +++ b/examples/example_sample_metadata.tsv @@ -0,0 +1,7 @@ +scpca_sample_id optional_column_1 optional_column_2 +sample01 diagnosis1 age1 +sample02 diagnosis2 age2 +sample03 diagnosis3 age3 +sample04 diagnosis4 age4 +sample05 diagnosis5 age5 +sample06 diagnosis6 age6 diff --git a/examples/user_template.config b/examples/user_template.config index 89e3d10e..8c1dda30 100644 --- a/examples/user_template.config +++ b/examples/user_template.config @@ -9,7 +9,8 @@ The values presented here are examples, and should be replaced with the correct paths to any indicated files or other values that need to be set. */ -params.run_metafile = 'example_metadata.tsv' // Input data table +params.run_metafile = 'example_run_metadata.tsv' // Input run metadata table +params.sample_metafile = 'example_sample_metadata.tsv' // Input sample metadata table params.outdir = "scpca_out" // Output base directory for results From 8e23bf7960b85a2c87eeff5785492bb4a20f61cc Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 21 Sep 2023 08:50:10 -0500 Subject: [PATCH 237/268] output rds files from sce report --- main.nf | 6 +----- modules/qc-report.nf | 3 ++- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index fbdfefb0..eaf764b9 100644 --- a/main.nf +++ b/main.nf @@ -225,11 +225,7 @@ workflow { sce_qc_report(cluster_sce.out, report_template_tuple) // convert SCE object to anndata - anndata_ch = cluster_sce.out - // join clustering output with qc report data - // we need to be able to grab the number of cells for each object from the metadata json (output from sce_qc_report) - // tuple of [meta, unfiltered, filtered, processed, qc report, metadata json] - .join(sce_qc_report.out, by: 0, failOnDuplicate: true, failOnMismatch: true) + anndata_ch = sce_qc_report.out // skip multiplexed libraries .filter{!(it[0]["library_id"] in multiplex_libs.getVal())} sce_to_anndata(anndata_ch) diff --git a/modules/qc-report.nf b/modules/qc-report.nf index 6f649203..ee18bf96 100644 --- a/modules/qc-report.nf +++ b/modules/qc-report.nf @@ -10,7 +10,8 @@ process sce_qc_report{ tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) tuple path(template_dir), val(template_file) output: - tuple val(meta), path(qc_report), path(metadata_json) + tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds), + path(qc_report), path(metadata_json) script: qc_report = "${meta.library_id}_qc.html" template_path = "${template_dir}/${template_file}" From 4857a02c5647672cc7852674333d612c460914cc Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 21 Sep 2023 08:50:23 -0500 Subject: [PATCH 238/268] add comment --- modules/export-anndata.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 479d4232..db581970 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -54,9 +54,11 @@ process move_normalized_counts{ workflow sce_to_anndata{ take: + // tuple of [meta, unfiltered rds, filtered rds, processed rds, qc report, metadata json] sce_files_ch main: sce_ch = sce_files_ch + // remove qc report and spread files so only one type of file gets passed through to the process // make tuple of [meta, sce_file, type of file, metadata.json] .flatMap{[[it[0], it[1], "unfiltered", it[5]], [it[0], it[2], "filtered", it[5]], From a26cf6c9a40232fbc4e94c604813c68b6bcbb662 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 09:44:22 -0500 Subject: [PATCH 239/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- modules/qc-report.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/qc-report.nf b/modules/qc-report.nf index ee18bf96..de9aa8a6 100644 --- a/modules/qc-report.nf +++ b/modules/qc-report.nf @@ -10,8 +10,8 @@ process sce_qc_report{ tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) tuple path(template_dir), val(template_file) output: - tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds), - path(qc_report), path(metadata_json) + tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds), path(metadata_json), emit: data + path qc_report, emit: report script: qc_report = "${meta.library_id}_qc.html" template_path = "${template_dir}/${template_file}" From e6f932abc06afa8a9950d24c4a2edaee9f19bf00 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 21 Sep 2023 09:51:19 -0500 Subject: [PATCH 240/268] separate qc report from output --- main.nf | 2 +- modules/export-anndata.nf | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index eaf764b9..1e22fcc6 100644 --- a/main.nf +++ b/main.nf @@ -225,7 +225,7 @@ workflow { sce_qc_report(cluster_sce.out, report_template_tuple) // convert SCE object to anndata - anndata_ch = sce_qc_report.out + anndata_ch = sce_qc_report.out.data // skip multiplexed libraries .filter{!(it[0]["library_id"] in multiplex_libs.getVal())} sce_to_anndata(anndata_ch) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index db581970..e6e85e6a 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -54,15 +54,15 @@ process move_normalized_counts{ workflow sce_to_anndata{ take: - // tuple of [meta, unfiltered rds, filtered rds, processed rds, qc report, metadata json] + // tuple of [meta, unfiltered rds, filtered rds, processed rds, metadata json] sce_files_ch main: sce_ch = sce_files_ch - // remove qc report and spread files so only one type of file gets passed through to the process + // spread files so only one type of file gets passed through to the process at a time // make tuple of [meta, sce_file, type of file, metadata.json] - .flatMap{[[it[0], it[1], "unfiltered", it[5]], - [it[0], it[2], "filtered", it[5]], - [it[0], it[3], "processed", it[5]] + .flatMap{[[it[0], it[1], "unfiltered", it[4]], + [it[0], it[2], "filtered", it[4]], + [it[0], it[3], "processed", it[4]] ]} // remove any sce files that don't have enough cells in the sce object // number of cells are stored in each metadata.json file From 6a033520661baba92b1673f2f8e4c76802c3a22d Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 21 Sep 2023 09:51:28 -0500 Subject: [PATCH 241/268] remove cluster publishDir --- modules/cluster-sce.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/cluster-sce.nf b/modules/cluster-sce.nf index ae0db5ca..a79fc907 100644 --- a/modules/cluster-sce.nf +++ b/modules/cluster-sce.nf @@ -6,7 +6,6 @@ process cluster_sce{ container params.SCPCATOOLS_CONTAINER label 'mem_8' tag "${meta.library_id}" - publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) output: From 4741dfcc3ad4ab625e1179f49ed5808a421f9d8d Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 13:41:00 -0500 Subject: [PATCH 242/268] Apply suggestions from code review Co-authored-by: Joshua Shapiro --- README.md | 2 +- examples/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c9da2852..6b92a3a5 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ To run `scpca-nf` on your own samples, you will need to complete the following s 1. [Organize your files](external-instructions.md#file-organization) so that each folder contains fastq files relevant to a single sequencing run. 2. [Prepare a run metadata file](external-instructions.md#prepare-the-run-metadata-file) with one row per library containing all information needed to process your samples. -3. [Prepare a sample metadata file]() with one row per sample containing any relevant metadata about each sample (e.g., diagnosis, age, sex, cell line). +3. [Prepare a sample metadata file](external-instructions.md#prepare-the-sample-metadata-file) with one row per sample containing any relevant metadata about each sample (e.g., diagnosis, age, sex, cell line). 4. Set up a [configuration file](external-instructions.md#configuration-files), including the [definition of a profile](external-instructions.md#setting-up-a-profile-in-the-configuration-file), dictating where nextflow should execute the workflow. You may also [test your configuration file using example data](examples/README.md). diff --git a/examples/README.md b/examples/README.md index 559f2857..6d53b0cb 100644 --- a/examples/README.md +++ b/examples/README.md @@ -19,7 +19,7 @@ The fastq files for this example data can be downloaded from the following link Following download and unzipping of the fastq files, you will need to create a tab-separated values **run** metadata file that looks like the following: | scpca_run_id | scpca_library_id | scpca_sample_id | scpca_project_id | technology | assay_ontology_term_id | seq_unit | sample_reference | files_directory | submitter_cell_types_file | -| ------------ | ---------------- | --------------- | ---------------- | ---------- | -----------------------|-------- | ---------------- | --------------- | ------------------------ | +| ------------ | ---------------- | --------------- | ---------------- | ---------- | ---------------------- | -------- | ---------------- | --------------- | ------------------------ | | run01 | library01 | sample01 | project01 | 10Xv3.1 | EFO:XXX | cell | Homo_sapiens.GRCh38.104 | /path/to/example_fastq_files | /path/to/annotated_cell_types_file Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column, and similarly the full path for the `submitter_cell_types_file` column. From 503c0f6119792b886361e510c77582202324a715 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 14:07:28 -0500 Subject: [PATCH 243/268] document assay ontology and handle null values --- bin/generate_unfiltered_sce.R | 1 + external-instructions.md | 4 +++- main.nf | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 5a89247f..a7b5d716 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -51,6 +51,7 @@ option_list <- list( make_option( opt_str = c("--assay_ontology_term_id"), type = "character", + default = NULL, help = "Experimental Factor Ontology term associated with provided tech_version" ), make_option( diff --git a/external-instructions.md b/external-instructions.md index 701ad7b7..f8b5fbdd 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -5,7 +5,8 @@ - [Overview](#overview) - [File organization](#file-organization) -- [Prepare the metadata file](#prepare-the-metadata-file) +- [Prepare the run metadata file](#prepare-the-run-metadata-file) +- [Prepare the sample metadata file](#prepare-the-sample-metadata-file) - [Configuring `scpca-nf` for your environment](#configuring-scpca-nf-for-your-environment) - [Configuration files](#configuration-files) - [Setting up a profile in the configuration file](#setting-up-a-profile-in-the-configuration-file) @@ -122,6 +123,7 @@ To run the workflow, you will need to create a tab separated values (TSV) metada | `scpca_sample_id` | A unique sample ID for each tissue or unique source.
    For multiplexed libraries, separate multiple samples with semicolons (`;`) | | `scpca_project_id` | A unique ID for each group of related samples. All results for samples with the same project ID will be returned in the same folder labeled with the project ID. | | `technology` | Sequencing/library technology used
    For single-cell/single-nuclei libraries use either `10Xv2`, `10Xv2_5prime`, `10Xv3`, or `10Xv31`.
    For ADT or CITE-seq libraries use either `CITEseq_10Xv2`, `CITEseq_10Xv3`, or `CITEseq_10Xv3.1`
    For cellhash libraries use either `cellhash_10Xv2`, `cellhash_10Xv3`, or `cellhash_10Xv3.1`
    For bulk RNA-seq use either `single_end` or `paired_end`.
    For spatial transcriptomics use `visium` | +| `assay_ontology_term_id` | [Experimental Factor Ontology](https://www.ebi.ac.uk/ols/ontologies/efo) term id associated with the `tech_version` | | `seq_unit` | Sequencing unit (one of: `cell`, `nucleus`, `bulk`, or `spot`)| | `sample_reference`| The name of the reference to use for mapping, available references include: `Homo_sapiens.GRCh38.104` and `Mus_musculus.GRCm39.104` | | `files_directory` | path/uri to directory containing fastq files (unique per run) | diff --git a/main.nf b/main.nf index 1e22fcc6..684f972d 100644 --- a/main.nf +++ b/main.nf @@ -95,7 +95,7 @@ workflow { project_id: Utils.parseNA(it.scpca_project_id)?: "no_project", submitter: it.submitter, technology: it.technology, - assay_ontology_term_id: it.assay_ontology_term_id, + assay_ontology_term_id: Utils.parseNA(it.assay_ontology_term_id), seq_unit: it.seq_unit, submitter_cell_types_file: Utils.parseNA(it.submitter_cell_types_file), feature_barcode_file: Utils.parseNA(it.feature_barcode_file), From c7022684241f059ef7d7aff120d6d58e6c771b2c Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 14:21:41 -0500 Subject: [PATCH 244/268] add example columns and fix some missing run metadatas --- examples/README.md | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/examples/README.md b/examples/README.md index 6d53b0cb..b37d340f 100644 --- a/examples/README.md +++ b/examples/README.md @@ -24,11 +24,18 @@ Following download and unzipping of the fastq files, you will need to create a t Be sure to enter the **full** path to the directory containing the fastq files in the `files_directory` column, and similarly the full path for the `submitter_cell_types_file` column. -You will also need to create a tab-separated values **sample** metadata file that looks like the following: +You will also need to create a tab-separated values **sample** metadata file. +At a minimum, the sample metadata file must contain a column with `scpca_sample_id` as the header_. +The contents of this column should contain all unique sample ids that are present in the `scpca_sample_id` column of the run metadata file. -| scpca_sample_id | -| --------------- | -| sample01 | +Below is an example of a sample metadata file: + +| scpca_sample_id | diagnosis | age | +| --------------- | --------- | --- | +| sample01 | glioblastoma | 71 | + +**Note that the `diagnosis` and `age` columns are shown as example sample metadata one might include in the sample metadata file. +The metadata file that you create does not need to match this exacly, but it must contain the required `scpca_sample_id` column.** The following command can then be used to test your configuration setup with the example data: @@ -36,12 +43,13 @@ The following command can then be used to test your configuration setup with the nextflow run AlexsLemonade/scpca-nf \ -config \ -profile \ - --run_metafile + --run_metafile \ + --sample_metafile ``` -Where `` is the **relative** path to the configuration file that you have setup after following the instructions on [creating a configuration file](../external-data-instructions.md#configuration-files), `` is the name of the profile that you chose when creating a profile, and `` is the **full** path to the metadata TSV you created. +Where `` is the **relative** path to the configuration file that you have setup after following the instructions on [creating a configuration file](../external-data-instructions.md#configuration-files), `` is the name of the profile that you chose when creating a profile, `` is the **full** path to the run metadata TSV you created, and `` is the **full** path to the sample metadata TSV you created. For the [example configuration file that we provided](./user_template.config), we used the profile name `cluster` and would indicate that we would like to use that profile at the command line with `-profile cluster`. -For more detailed information on setting up the metadata file for your own data, see instructions on [preparing the run metadata file](../external-data-instructions.md#prepare-the-run-metadata-file). +For more detailed information on setting up the metadata file for your own data, see instructions on [preparing the run metadata file](../external-data-instructions.md#prepare-the-run-metadata-file) and [preparing the sample metadata file](../external-instructions.md/#prepare-the-sample-metadata-file). ## Example output From 1dc2fdc6445ec235d440f880f36d4dc664bae993 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 14:21:55 -0500 Subject: [PATCH 245/268] emphasize the required column and suggest some additional columns --- external-instructions.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/external-instructions.md b/external-instructions.md index f8b5fbdd..e9a6b219 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -147,11 +147,12 @@ We have provided an example run metadata file for reference. Using `scpca-nf` requires a sample metadata file as a TSV (tab separated values) file, where each unique sample that is present in the `scpca_sample_id` column of the run metadata file is a row, and columns contain any relevant sample metadata (e.g., diagnosis, age, sex, cell line). For each library that is processed, the corresponding sample metadata will be added to the `SingleCellExperiment` and `AnnData` objects output by the workflow (see the section on [Output files](#output-files)). -At a minimum, all sample metadata tables must contain a column with `scpca_sample_id` as the header. +_At a minimum, all sample metadata tables must contain a column with `scpca_sample_id` as the header_. The contents of this column should contain all unique sample ids that are present in the `scpca_sample_id` column of the run metadata file. We encourage you to use standard terminology, such as ontology terms, to describe samples when possible. There is no limit to the number of columns allowed for the sample metadata, and you may include as many metadata fields as you please. +Some suggested columns include diagnosis, tissue, age, sex, stage of disease, cell line. We have provided an example run metadata file for reference. From 98b1d6c4aaaeeddd111184e375fb2d70e28b1eec Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 14:33:11 -0500 Subject: [PATCH 246/268] add assay ontology to example run metadata --- examples/example_run_metadata.tsv | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/examples/example_run_metadata.tsv b/examples/example_run_metadata.tsv index 40743932..15b8af38 100644 --- a/examples/example_run_metadata.tsv +++ b/examples/example_run_metadata.tsv @@ -1,8 +1,7 @@ -scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number submitter_cell_types_file -run01 library01 sample01 project01 10Xv3.1 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 NA NA NA NA NA -run02 library01 sample01 project01 CITEseq_10Xv3 cell Homo_sapiens.GRCh38.104 example_fastqs/run02 example_barcode_files/cite_barcodes.tsv 2[1-15] NA NA NA -run03 library02 sample02 project01 visium spot Homo_sapiens.GRCh38.104 example_fastqs/run03 NA NA A1 VXXXX-XXX NA -run04 library03 sample03;sample04 project01 10Xv3.1 cell Mus_musculus.GRCm39.104 example_fastqs/run04 NA NA NA NA NA -run05 library03 sample03;sample04 project01 cellhash cell Mus_musculus.GRCm39.104 example_fastqs/run05 example_barcode_files/cellhash_barcodes.tsv 2[1-10] NA NA NA -run06 library04 sample05 project01 paired_end bulk Mus_musculus.GRCm39.104 example_fastqs/run06 NA NA NA NA NA -run07 library05 sample06 project01 10Xv3.1 cell Homo_sapiens.GRCh38.104 example_fastqs/run07 NA NA NA NA example_metadata_files/submitter_celltypes.tsv +scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology assay_ontology_term_id seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number submitter_cell_types_file +run01 library01 sample01 project01 10Xv3.1 EFO:0009922 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 NA NA NA NA example_metadata_files/submitter_celltypes.tsv +run02 library01 sample01 project01 CITEseq_10Xv3 EFO:0030011 cell Homo_sapiens.GRCh38.104 example_fastqs/run02 example_barcode_files/cite_barcodes.tsv 2[1-15] NA NA NA +run03 library02 sample02 project01 visium EFO:0010961 spot Homo_sapiens.GRCh38.104 example_fastqs/run03 NA NA A1 VXXXX-XXX NA +run04 library03 sample03;sample04 project01 10Xv3.1 EFO:0009922 cell Mus_musculus.GRCm39.104 example_fastqs/run04 NA NA NA NA NA +run05 library03 sample03;sample04 project01 cellhash_10Xv3.1 EFO:0030012 cell Mus_musculus.GRCm39.104 example_fastqs/run05 example_barcode_files/cellhash_barcodes.tsv 2[1-10] NA NA NA +run06 library04 sample05 project01 paired_end EFO:0003747 bulk Mus_musculus.GRCm39.104 example_fastqs/run06 NA NA NA NA NA From 00479a27bb1ad8b5a1c1555855f8512359e854be Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 15:27:25 -0500 Subject: [PATCH 247/268] add run07 back in --- examples/example_run_metadata.tsv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/examples/example_run_metadata.tsv b/examples/example_run_metadata.tsv index 15b8af38..340baafa 100644 --- a/examples/example_run_metadata.tsv +++ b/examples/example_run_metadata.tsv @@ -1,7 +1,8 @@ scpca_run_id scpca_library_id scpca_sample_id scpca_project_id technology assay_ontology_term_id seq_unit sample_reference files_directory feature_barcode_file feature_barcode_geom slide_section slide_serial_number submitter_cell_types_file -run01 library01 sample01 project01 10Xv3.1 EFO:0009922 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 NA NA NA NA example_metadata_files/submitter_celltypes.tsv +run01 library01 sample01 project01 10Xv3.1 EFO:0009922 cell Homo_sapiens.GRCh38.104 example_fastqs/run01 NA NA NA NA NA run02 library01 sample01 project01 CITEseq_10Xv3 EFO:0030011 cell Homo_sapiens.GRCh38.104 example_fastqs/run02 example_barcode_files/cite_barcodes.tsv 2[1-15] NA NA NA run03 library02 sample02 project01 visium EFO:0010961 spot Homo_sapiens.GRCh38.104 example_fastqs/run03 NA NA A1 VXXXX-XXX NA run04 library03 sample03;sample04 project01 10Xv3.1 EFO:0009922 cell Mus_musculus.GRCm39.104 example_fastqs/run04 NA NA NA NA NA run05 library03 sample03;sample04 project01 cellhash_10Xv3.1 EFO:0030012 cell Mus_musculus.GRCm39.104 example_fastqs/run05 example_barcode_files/cellhash_barcodes.tsv 2[1-10] NA NA NA run06 library04 sample05 project01 paired_end EFO:0003747 bulk Mus_musculus.GRCm39.104 example_fastqs/run06 NA NA NA NA NA +run07 library05 sample06 project01 10Xv3.1 EFO:0009922 cell Homo_sapiens.GRCh38.104 example_fastqs/run07 NA NA NA NA example_metadata_files/submitter_celltypes.tsv From 3347c246542cf18143c84e16530fb06dcb59f494 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 15:29:22 -0500 Subject: [PATCH 248/268] make assay ontology argument optional --- modules/sce-processing.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 0ef4bf7a..0417111e 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -20,12 +20,12 @@ process make_unfiltered_sce{ --mito_file ${mito_file} \ --gtf_file ${ref_gtf} \ --technology ${meta.technology} \ - --assay_ontology_term_id ${meta.assay_ontology_term_id} \ --seq_unit ${meta.seq_unit} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ + ${meta.assay_ontology_term_id? "--assay_ontology_term_id ${meta.assay_ontology_term_id}" : ""} \ ${params.spliced_only ? '--spliced_only' : ''} @@ -77,12 +77,12 @@ process make_merged_unfiltered_sce{ --mito_file ${mito_file} \ --gtf_file ${ref_gtf} \ --technology ${meta.technology} \ - --assay_ontology_term_id ${meta.assay_ontology_term_id} \ --seq_unit ${meta.seq_unit} \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ --project_id "${meta.project_id}" \ --sample_metadata_file ${sample_metafile} \ + ${meta.assay_ontology_term_id? "--assay_ontology_term_id ${meta.assay_ontology_term_id}" : ""} \ ${params.spliced_only ? '--spliced_only' : ''} # Only run script if annotations are available: From a9658b1731dc4ec4cecd747d69111c1f4166d8e0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 21 Sep 2023 15:33:17 -0500 Subject: [PATCH 249/268] update internal instructions for running example data --- internal-instructions.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/internal-instructions.md b/internal-instructions.md index 67c3e6e7..299cfdb5 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -47,7 +47,8 @@ The following command should be used to run the workflow and process the example nextflow run AlexsLemonade/scpca-nf \ -profile ccdl,batch \ --run_ids run01 \ - --run_metafile s3://scpca-references/example-data/example_metadata.tsv \ + --run_metafile s3://scpca-references/example-data/example_run_metadata.tsv \ + --sample_metafile s3://scpca-references/example-data/example_sample_metadata.tsv \ --outdir s3://scpca-references/example-data/scpca_out ``` From 1b411e13be6354abac514d18638d99d76a0567c9 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 22 Sep 2023 09:20:50 -0500 Subject: [PATCH 250/268] Apply suggestions from code review Co-authored-by: Stephanie Spielman --- README.md | 2 +- external-instructions.md | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 494fc533..d4c3c779 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ All dependencies for the workflow outside of the Nextflow workflow engine itself Nextflow will also handle parallelizing sample processing as allowed by your environment, minimizing total run time. The workflow processes fastq files from single-cell and single-nuclei RNA-seq samples using [alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) to create gene by cell matrices. -The workflow outputs gene expression data stored as both [`SingleCellExperiment` objects](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) and [`AnnData` objects](https://anndata.readthedocs.io/en/latest/). +The workflow outputs gene expression data in two formats: as [`SingleCellExperiment` objects](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) and as [`AnnData` objects](https://anndata.readthedocs.io/en/latest/). Reads from samples are aligned using selective alignment, to an index with transcripts corresponding to spliced cDNA and to intronic regions, denoted by alevin-fry as `splici`. These matrices are filtered and additional processing is performed to calculate quality control statistics, create reduced-dimension transformations, and create output reports. `scpca-nf` can also process libraries with ADT tags (e.g., CITE-seq), bulk RNA-seq, and spatial transcriptomics samples. diff --git a/external-instructions.md b/external-instructions.md index 3b077267..1e7585ee 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -120,7 +120,7 @@ To run the workflow, you will need to create a tab separated values (TSV) metada | `scpca_library_id`| A unique library ID for each unique set of cells | | `scpca_sample_id` | A unique sample ID for each tissue or unique source.
    For multiplexed libraries, separate multiple samples with semicolons (`;`) | | `scpca_project_id` | A unique ID for each group of related samples. All results for samples with the same project ID will be returned in the same folder labeled with the project ID. | -| `technology` | Sequencing/library technology used
    For single-cell/single-nuclei libraries use either `10Xv2`, `10Xv2_5prime`, `10Xv3`, or `10Xv31`.
    For ADT or CITE-seq libraries use either `CITEseq_10Xv2`, `CITEseq_10Xv3`, or `CITEseq_10Xv3.1`
    For cellhash libraries use either `cellhash_10Xv2`, `cellhash_10Xv3`, or `cellhash_10Xv3.1`
    For bulk RNA-seq use either `single_end` or `paired_end`.
    For spatial transcriptomics use `visium` | +| `technology` | Sequencing/library technology used
    For single-cell/single-nuclei libraries use either `10Xv2`, `10Xv2_5prime`, `10Xv3`, or `10Xv31`.
    For ADT (CITE-seq) libraries use either `CITEseq_10Xv2`, `CITEseq_10Xv3`, or `CITEseq_10Xv3.1`
    For cellhash libraries use either `cellhash_10Xv2`, `cellhash_10Xv3`, or `cellhash_10Xv3.1`
    For bulk RNA-seq use either `single_end` or `paired_end`.
    For spatial transcriptomics use `visium` | | `seq_unit` | Sequencing unit (one of: `cell`, `nucleus`, `bulk`, or `spot`)| | `sample_reference`| The name of the reference to use for mapping, available references include: `Homo_sapiens.GRCh38.104` and `Mus_musculus.GRCm39.104` | | `files_directory` | path/uri to directory containing fastq files (unique per run) | @@ -412,9 +412,9 @@ The `results` folder will contain the final output files produced by the workflo Within the `results` folder, all files pertaining to a specific sample will be nested within a folder labeled with the sample ID. All files in that folder will be prefixed by the library ID. -The files with the suffixes `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` contain the quantified gene expression data as a [`SingleCellExperiment` object](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). +The files with the suffixes `_unfiltered.rds`, `_filtered.rds`, and `_processed.rds` provide quantified gene expression data as [`SingleCellExperiment` objects](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html). -The files with the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_processed_rna.hdf5` contain the quantified gene expression data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). +The files with the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_processed_rna.hdf5` provide the quantified gene expression data as [`AnnData` objects](https://anndata.readthedocs.io/en/latest/). If the input data contains libraries with ADT tags, three additional files with the suffixes `_unfiltered_adt.hdf5`, `_filtered_adt.hdf5`, and `_processed_adt.hdf5`will be provided for each library. These files contain the quantified ADT tag data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). From c68c2095e819087163aafa7fa7f42875fe6c220f Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 09:25:30 -0500 Subject: [PATCH 251/268] mention cell hash --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d4c3c779..ca5e432f 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ The workflow processes fastq files from single-cell and single-nuclei RNA-seq sa The workflow outputs gene expression data in two formats: as [`SingleCellExperiment` objects](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) and as [`AnnData` objects](https://anndata.readthedocs.io/en/latest/). Reads from samples are aligned using selective alignment, to an index with transcripts corresponding to spliced cDNA and to intronic regions, denoted by alevin-fry as `splici`. These matrices are filtered and additional processing is performed to calculate quality control statistics, create reduced-dimension transformations, and create output reports. -`scpca-nf` can also process libraries with ADT tags (e.g., CITE-seq), bulk RNA-seq, and spatial transcriptomics samples. +`scpca-nf` can also process libraries with ADT tags (e.g., CITE-seq), multiplexed libraries (e.g., cell hashing), bulk RNA-seq, and spatial transcriptomics samples. For more information on the contents of the output files and the processing of all modalities, please see the [ScPCA Portal docs](https://scpca.readthedocs.io/en/latest/). From 3e9358f0763c8db7826645d3b0a842cc0ffe256a Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 09:31:05 -0500 Subject: [PATCH 252/268] add a note about not supporting cell hashing with AnnData --- external-instructions.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/external-instructions.md b/external-instructions.md index 1e7585ee..6661ba8e 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -418,6 +418,9 @@ The files with the suffixes `_unfiltered_rna.hdf5`, `_filtered_rna.hdf5`, and `_ If the input data contains libraries with ADT tags, three additional files with the suffixes `_unfiltered_adt.hdf5`, `_filtered_adt.hdf5`, and `_processed_adt.hdf5`will be provided for each library. These files contain the quantified ADT tag data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). +**Note: We currently do not output `AnnData` objects (`.hdf5` files) for any multiplexed libraries. +The output for multiplexed libraries will only contain `SingleCellExperiment` objects (`.rds` files).** + For more information on the contents of these files, see the [ScPCA portal docs section on single cell gene expression file contents](https://scpca.readthedocs.io/en/latest/sce_file_contents.html). See below for the expected structure of the `results` folder: From ecf77934c04d13a15ad5082c354e2b6f33ee8069 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 09:57:34 -0500 Subject: [PATCH 253/268] describe metadata files for creating output --- internal-instructions.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/internal-instructions.md b/internal-instructions.md index 299cfdb5..00532608 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -41,7 +41,13 @@ nextflow run AlexsLemonade/scpca-nf -r v0.5.4 -profile ccdl,batch --project SCPC We provide an [example of the expected outputs](./examples/README.md#example-output) after running `scpca-nf` available for external users. If there have been major updates to the directory structure or the contents of the output, the example data should be re-processed such that the example output we provide mimics the current expected output from `scpca-nf`. -The following command should be used to run the workflow and process the example data: +First, please check the metadata files present in `s3://scpca-references/example-data` are up to date with changes in the workflow. +There should be both an `example_run_metadata.tsv` and `example_sample_metadata.tsv`. +The columns of these files should match the expected input columns of the workflow (see the section on preparing the [run metadata](./external-instructions.md#prepare-the-run-metadata-file) and [sample metadata](./external-instructions.md#prepare-the-sample-metadata-file)). + +Additionally, the `example_run_metadata.tsv` should contain at least 1 row with `run01` in the `scpca_run_id` column and `s3://scpca-references/example-data/example_fastqs/run01` in the `files_directory` column. + +Once you have confirmed that the metadata looks correct, the following command should be used to run the workflow and process the example data: ```sh nextflow run AlexsLemonade/scpca-nf \ From 67abb1d6dca57f336d80d414c44ce0c21232ff7b Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 10:04:00 -0500 Subject: [PATCH 254/268] account for columns that we don't require not being present --- bin/generate_unfiltered_sce.R | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index a7b5d716..9f1ad643 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -161,11 +161,19 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> dplyr::rename("sample_id" = "scpca_sample_id") |> # add library ID as column in sample metadata # we need this so we are able to merge sample metadata with colData later - dplyr::mutate(library_id = opt$library_id) |> - # remove upload date as we don't provide this on the portal - dplyr::select(-upload_date) |> - # rename to donor id for czi compliance - dplyr::rename("donor_id" = "participant_id") + dplyr::mutate(library_id = opt$library_id) + +if("upload_date" %in% colnames(sample_metadata_df)){ + sample_metadata_df -> sample_metadata_df |> + # remove upload date as we don't provide this on the portal + dplyr::select(-upload_date) +} + +if("participant_id" %in% colnames(sample_metadata_df)){ + sample_metadata_df -> sample_metadata_df |> + # rename to donor id for czi compliance + dplyr::rename("donor_id" = "participant_id") +} # add per cell and per gene statistics to colData and rowData unfiltered_sce <- unfiltered_sce |> From d6d38b7515e392aa57613bd34c15ec7d688406cf Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 10:04:15 -0500 Subject: [PATCH 255/268] add a nextflow pull and use development --- internal-instructions.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/internal-instructions.md b/internal-instructions.md index 00532608..3d330e88 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -47,10 +47,12 @@ The columns of these files should match the expected input columns of the workfl Additionally, the `example_run_metadata.tsv` should contain at least 1 row with `run01` in the `scpca_run_id` column and `s3://scpca-references/example-data/example_fastqs/run01` in the `files_directory` column. -Once you have confirmed that the metadata looks correct, the following command should be used to run the workflow and process the example data: +Once you have confirmed that the metadata looks correct, the following commands should be used to run the workflow and process the example data: ```sh -nextflow run AlexsLemonade/scpca-nf \ +nextflow pull AlexsLemonade/scpca-nf -r development + +nextflow run AlexsLemonade/scpca-nf -r development \ -profile ccdl,batch \ --run_ids run01 \ --run_metafile s3://scpca-references/example-data/example_run_metadata.tsv \ From 467b51af7f40a023a8c1b9cf970a21667a64807e Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 22 Sep 2023 10:04:54 -0500 Subject: [PATCH 256/268] rewording per review suggestion Co-authored-by: Stephanie Spielman --- external-instructions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external-instructions.md b/external-instructions.md index 6661ba8e..a2f1b0b0 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -419,7 +419,7 @@ If the input data contains libraries with ADT tags, three additional files with These files contain the quantified ADT tag data as an [`AnnData` object](https://anndata.readthedocs.io/en/latest/). **Note: We currently do not output `AnnData` objects (`.hdf5` files) for any multiplexed libraries. -The output for multiplexed libraries will only contain `SingleCellExperiment` objects (`.rds` files).** +Only `SingleCellExperiment` objects (`.rds` files) will be provided for multiplexed libraries.** For more information on the contents of these files, see the [ScPCA portal docs section on single cell gene expression file contents](https://scpca.readthedocs.io/en/latest/sce_file_contents.html). From 7eaea9d2556c042700669b0d4825649b1e553699 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 10:19:45 -0500 Subject: [PATCH 257/268] spell diagnosis --- external-instructions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external-instructions.md b/external-instructions.md index f7c1d1c5..5518186c 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -47,7 +47,7 @@ You will need to have your files organized in a particular manner so that each f See the [section below on file organization](#file-organization) for more information on how to set up your files. 3. **Create a [run metadata file](#prepare-the-run-metadata-file) and [sample metadata file](#prepare-the-sample-metadata-file).** -Create two TSV (tab-separated values) files - one file with one sequencing library per row and pertinent information related to that sequencing run in each column (run metadata) and the other file with one sample per row and any relevant sample metadata (e.g., daignosis, age, sex, cell line) (sample metadata). +Create two TSV (tab-separated values) files - one file with one sequencing library per row and pertinent information related to that sequencing run in each column (run metadata) and the other file with one sample per row and any relevant sample metadata (e.g., diagnosis, age, sex, cell line) (sample metadata). See the sections below on preparing a [run metadata file](#prepare-the-run-metadata-file) and [sample metadata file](#prepare-the-sample-metadata-file) for more information on creating a metadata file for your samples. 4. **Create a [configuration file](#configuration-files) and [define a profile](#setting-up-a-profile-in-the-configuration-file).** From ce57e0d2fda0ceb1debd1b2c2153cd41d3529d42 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 22 Sep 2023 10:26:49 -0500 Subject: [PATCH 258/268] finally found the readme file spell check was talking about --- components/dictionary.txt | 1 + examples/README.md | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/components/dictionary.txt b/components/dictionary.txt index bbfb9fe8..36a10573 100644 --- a/components/dictionary.txt +++ b/components/dictionary.txt @@ -13,6 +13,7 @@ data's demultiplexed demultiplexing Dockerfile +EFO embeddings Ensembl et diff --git a/examples/README.md b/examples/README.md index b37d340f..732a03e7 100644 --- a/examples/README.md +++ b/examples/README.md @@ -35,7 +35,7 @@ Below is an example of a sample metadata file: | sample01 | glioblastoma | 71 | **Note that the `diagnosis` and `age` columns are shown as example sample metadata one might include in the sample metadata file. -The metadata file that you create does not need to match this exacly, but it must contain the required `scpca_sample_id` column.** +The metadata file that you create does not need to match this exactly, but it must contain the required `scpca_sample_id` column.** The following command can then be used to test your configuration setup with the example data: From 2783c0aee12af3deefeb178e9a46bfee994a5712 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 22 Sep 2023 13:30:54 -0500 Subject: [PATCH 259/268] Apply suggestions from code review Co-authored-by: Stephanie Spielman --- bin/generate_unfiltered_sce.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 9f1ad643..db97096d 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -164,13 +164,13 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> dplyr::mutate(library_id = opt$library_id) if("upload_date" %in% colnames(sample_metadata_df)){ - sample_metadata_df -> sample_metadata_df |> + sample_metadata_df <- sample_metadata_df |> # remove upload date as we don't provide this on the portal dplyr::select(-upload_date) } if("participant_id" %in% colnames(sample_metadata_df)){ - sample_metadata_df -> sample_metadata_df |> + sample_metadata_df <- sample_metadata_df |> # rename to donor id for czi compliance dplyr::rename("donor_id" = "participant_id") } From 0bd7ae7825355f39ef1798175d02d4f829112afe Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Fri, 22 Sep 2023 13:31:06 -0500 Subject: [PATCH 260/268] remove quotes Co-authored-by: Stephanie Spielman --- bin/generate_unfiltered_sce.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index db97096d..1dbbbacd 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -172,7 +172,7 @@ if("upload_date" %in% colnames(sample_metadata_df)){ if("participant_id" %in% colnames(sample_metadata_df)){ sample_metadata_df <- sample_metadata_df |> # rename to donor id for czi compliance - dplyr::rename("donor_id" = "participant_id") + dplyr::rename(donor_id = participant_id) } # add per cell and per gene statistics to colData and rowData From ba776ebd0b7b0a4ef01fadd41995e8f83643f339 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 28 Sep 2023 10:40:12 -0500 Subject: [PATCH 261/268] remove renaming donor id --- bin/generate_unfiltered_sce.R | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R index 1dbbbacd..7a99837d 100755 --- a/bin/generate_unfiltered_sce.R +++ b/bin/generate_unfiltered_sce.R @@ -161,7 +161,7 @@ sample_metadata_df <- readr::read_tsv(opt$sample_metadata_file) |> dplyr::rename("sample_id" = "scpca_sample_id") |> # add library ID as column in sample metadata # we need this so we are able to merge sample metadata with colData later - dplyr::mutate(library_id = opt$library_id) + dplyr::mutate(library_id = opt$library_id) if("upload_date" %in% colnames(sample_metadata_df)){ sample_metadata_df <- sample_metadata_df |> @@ -169,12 +169,6 @@ if("upload_date" %in% colnames(sample_metadata_df)){ dplyr::select(-upload_date) } -if("participant_id" %in% colnames(sample_metadata_df)){ - sample_metadata_df <- sample_metadata_df |> - # rename to donor id for czi compliance - dplyr::rename(donor_id = participant_id) -} - # add per cell and per gene statistics to colData and rowData unfiltered_sce <- unfiltered_sce |> add_cell_mito_qc(mito = mito_genes) |> From 8a46fe5123df2844cc3525cca91af41a4fcb8f9c Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Thu, 28 Sep 2023 15:38:10 -0500 Subject: [PATCH 262/268] remove title and move schema --- bin/sce_to_anndata.R | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 19b912ec..869cc5f0 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -71,12 +71,8 @@ format_czi <- function(sce) { # create columns for assay and suspension ontology terms assay_ontology_term_id = metadata(sce)$assay_ontology_term_id, suspension_type = metadata(sce)$seq_unit, - # move project id to title slot in metadata list - title = metadata(sce)$project_id, # add is_primary_data column; only needed for anndata objects - is_primary_data = FALSE, - # add schema version - schema_version = "3.0.0" + is_primary_data = FALSE ) # add colData back to sce object @@ -88,6 +84,9 @@ format_czi <- function(sce) { # remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] + # add schema version + metadata(sce)$schema_version = "3.0.0" + # modify rowData # we don't do any gene filtering between normalized and raw counts matrix # so everything gets set to false From 6f1cd4928ee118aa5e8a7fc97141e96f9d01561a Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 9 Oct 2023 09:21:29 -0500 Subject: [PATCH 263/268] move schema version to first step --- bin/sce_to_anndata.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/bin/sce_to_anndata.R b/bin/sce_to_anndata.R index 869cc5f0..cb6c9f48 100755 --- a/bin/sce_to_anndata.R +++ b/bin/sce_to_anndata.R @@ -55,6 +55,10 @@ if (!(stringr::str_ends(opt$output_rna_h5, ".hdf5|.h5"))) { # sure that the sce that is getting converted to AnnData is compliant with CZI # CZI 3.0.0 requirements: https://github.com/chanzuckerberg/single-cell-curation/blob/b641130fe53b8163e50c39af09ee3fcaa14c5ea7/schema/3.0.0/schema.md format_czi <- function(sce) { + + # add schema version + metadata(sce)$schema_version = "3.0.0" + # add library_id as an sce colData column # need this column to join in the sample metadata with the colData sce$library_id <- metadata(sce)$library_id @@ -84,9 +88,6 @@ format_czi <- function(sce) { # remove sample metadata from sce metadata, otherwise conflicts with converting object metadata(sce) <- metadata(sce)[names(metadata(sce)) != "sample_metadata"] - # add schema version - metadata(sce)$schema_version = "3.0.0" - # modify rowData # we don't do any gene filtering between normalized and raw counts matrix # so everything gets set to false From 612546f8c24f29abebf3974aee24e36331dc8632 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 10 Oct 2023 12:55:00 -0400 Subject: [PATCH 264/268] Don't stub anndata if no feature --- modules/export-anndata.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index e6e85e6a..9d65ece5 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -8,7 +8,7 @@ process export_anndata{ input: tuple val(meta), path(sce_file), val(file_type) output: - tuple val(meta), path("${meta.library_id}_${file_type}*.hdf5"), val(file_type) + tuple val(meta), path("${meta.library_id}_${file_type}_*.hdf5"), val(file_type) script: rna_hdf5_file = "${meta.library_id}_${file_type}_rna.hdf5" feature_hdf5_file = "${meta.library_id}_${file_type}_${meta.feature_type}.hdf5" @@ -23,9 +23,10 @@ process export_anndata{ stub: rna_hdf5_file = "${meta.library_id}_${file_type}_rna.hdf5" feature_hdf5_file = "${meta.library_id}_${file_type}_${meta.feature_type}.hdf5" + feature_present = meta.feature_type in ["adt", "cellhash"] """ touch ${rna_hdf5_file} - touch ${feature_hdf5_file} + ${feature_present ? "touch ${feature_hdf5_file}" : ''} """ } From a8e8d87bd81d03d33216fd92de0f509b9829c144 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 10 Oct 2023 14:24:56 -0500 Subject: [PATCH 265/268] Merge pull request #487 from AlexsLemonade/jashapiro/try-no-null2 Try to solve intermittent workflow failures --- bin/add_submitter_annotations.R | 0 bin/classify_SingleR.R | 0 bin/classify_cellassign.R | 0 bin/cluster_sce.R | 0 bin/{filter_sce_rds.R => filter_sce.R} | 0 bin/generate_cellassign_refs.R | 0 bin/integrate_sce.R | 0 bin/merge_sces.R | 0 bin/predict_cellassign.py | 0 bin/train_SingleR.R | 0 lib/Utils.groovy | 10 ++++---- main.nf | 2 +- modules/af-features.nf | 1 + modules/bulk-salmon.nf | 1 + modules/classify-celltypes.nf | 3 +++ modules/export-anndata.nf | 5 +++- modules/qc-report.nf | 32 ++++++++++++++++++++++---- modules/samtools.nf | 1 + modules/sce-processing.nf | 18 +++++++-------- modules/spaceranger.nf | 1 + 20 files changed, 54 insertions(+), 20 deletions(-) mode change 100644 => 100755 bin/add_submitter_annotations.R mode change 100644 => 100755 bin/classify_SingleR.R mode change 100644 => 100755 bin/classify_cellassign.R mode change 100644 => 100755 bin/cluster_sce.R rename bin/{filter_sce_rds.R => filter_sce.R} (100%) mode change 100644 => 100755 bin/generate_cellassign_refs.R mode change 100644 => 100755 bin/integrate_sce.R mode change 100644 => 100755 bin/merge_sces.R mode change 100644 => 100755 bin/predict_cellassign.py mode change 100644 => 100755 bin/train_SingleR.R diff --git a/bin/add_submitter_annotations.R b/bin/add_submitter_annotations.R old mode 100644 new mode 100755 diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R old mode 100644 new mode 100755 diff --git a/bin/classify_cellassign.R b/bin/classify_cellassign.R old mode 100644 new mode 100755 diff --git a/bin/cluster_sce.R b/bin/cluster_sce.R old mode 100644 new mode 100755 diff --git a/bin/filter_sce_rds.R b/bin/filter_sce.R similarity index 100% rename from bin/filter_sce_rds.R rename to bin/filter_sce.R diff --git a/bin/generate_cellassign_refs.R b/bin/generate_cellassign_refs.R old mode 100644 new mode 100755 diff --git a/bin/integrate_sce.R b/bin/integrate_sce.R old mode 100644 new mode 100755 diff --git a/bin/merge_sces.R b/bin/merge_sces.R old mode 100644 new mode 100755 diff --git a/bin/predict_cellassign.py b/bin/predict_cellassign.py old mode 100644 new mode 100755 diff --git a/bin/train_SingleR.R b/bin/train_SingleR.R old mode 100644 new mode 100755 diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 944a1db0..fa61a6af 100644 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -38,21 +38,23 @@ class Utils { */ static def getMetaVal(file, key){ def obj = new JsonSlurper().parse(file) + return(obj[key]) } /** - * Replace a string with an NA value with null + * Replace a string with an NA value with "" + * (which evaluates as false in boolean contexts) * * @param str A string - * @return The input string unless it was NA or a variant thereof, in which case returns null + * @return The input string unless it was NA or a variant thereof, in which case returns "" */ static def parseNA(str) { if (str){ - str.toLowerCase() in ["na","n/a","nan"]? null : str + str.toLowerCase() in ['na','n/a','nan']? '' : str } else { - null + '' } } } diff --git a/main.nf b/main.nf index 684f972d..b21540dd 100644 --- a/main.nf +++ b/main.nf @@ -93,7 +93,7 @@ workflow { library_id: it.scpca_library_id, sample_id: it.scpca_sample_id.split(";").sort().join(","), project_id: Utils.parseNA(it.scpca_project_id)?: "no_project", - submitter: it.submitter, + submitter: Utils.parseNA(it.submitter), technology: it.technology, assay_ontology_term_id: Utils.parseNA(it.assay_ontology_term_id), seq_unit: it.seq_unit, diff --git a/modules/af-features.nf b/modules/af-features.nf index 8f371fe0..56c33517 100644 --- a/modules/af-features.nf +++ b/modules/af-features.nf @@ -2,6 +2,7 @@ //index a feature barcode file process index_feature{ container params.SALMON_CONTAINER + tag "${id}" input: tuple val(id), path(feature_file) diff --git a/modules/bulk-salmon.nf b/modules/bulk-salmon.nf index c8956b19..c7d6d438 100644 --- a/modules/bulk-salmon.nf +++ b/modules/bulk-salmon.nf @@ -70,6 +70,7 @@ process merge_bulk_quants { container params.SCPCATOOLS_CONTAINER label 'mem_8' publishDir "${params.results_dir}/${meta.project_id}", mode: 'copy' + tag "${meta.project_id}" input: tuple val(meta), path(salmon_directories), path(t2g_bulk) path(library_metadata) diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf index 6c6217ed..d404928f 100644 --- a/modules/classify-celltypes.nf +++ b/modules/classify-celltypes.nf @@ -3,6 +3,7 @@ process classify_singleR { container params.SCPCATOOLS_CONTAINER label 'mem_8' label 'cpus_4' + tag "${meta.library_id}" input: tuple val(meta), path(processed_rds), path(singler_model_file) output: @@ -30,6 +31,7 @@ process predict_cellassign { publishDir "${params.checkpoints_dir}/celltype/${meta.library_id}", mode: 'copy' label 'mem_32' label 'cpus_12' + tag "${meta.library_id}" input: tuple val(meta), path(processed_hdf5), path(cellassign_reference_mtx), val(ref_name) output: @@ -56,6 +58,7 @@ process classify_cellassign { publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' label 'mem_4' label 'cpus_2' + tag "${meta.library_id}" input: tuple val(meta), path(input_rds), path(cellassign_predictions), val(ref_name) output: diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 9d65ece5..94c5f79a 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -67,7 +67,10 @@ workflow sce_to_anndata{ ]} // remove any sce files that don't have enough cells in the sce object // number of cells are stored in each metadata.json file - .filter{ Utils.getMetaVal(file(it[3]), "${it[2]}_cells") > 1 } + .filter{ + cells = Utils.getMetaVal(file(it[3]), "${it[2]}_cells"); + cells ? cells > 1 : true // if no cell count, keep file (for testing) + } // remove metadata.json file from tuple .map{it.dropRight(1)} diff --git a/modules/qc-report.nf b/modules/qc-report.nf index de9aa8a6..bd9e6f5f 100644 --- a/modules/qc-report.nf +++ b/modules/qc-report.nf @@ -10,7 +10,7 @@ process sce_qc_report{ tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) tuple path(template_dir), val(template_file) output: - tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds), path(metadata_json), emit: data + tuple val(meta), path(unfiltered_out), path(filtered_out), path(processed_out), path(metadata_json), emit: data path qc_report, emit: report script: qc_report = "${meta.library_id}_qc.html" @@ -18,14 +18,30 @@ process sce_qc_report{ metadata_json = "${meta.library_id}_metadata.json" workflow_url = workflow.repository ?: workflow.manifest.homePage workflow_version = workflow.revision ?: workflow.manifest.version + // names for final output files + unfiltered_out = "${meta.library_id}_unfiltered.rds" + filtered_out = "${meta.library_id}_filtered.rds" + processed_out = "${meta.library_id}_processed.rds" """ + # move files for output + if [ "${unfiltered_rds}" != "${unfiltered_out}" ]; then + mv "${unfiltered_rds}" "${unfiltered_out}" + fi + if [ "${filtered_rds}" != "${filtered_out}" ]; then + mv "${filtered_rds}" "${filtered_out}" + fi + if [ "${processed_rds}" != "${processed_out}" ]; then + mv "${processed_rds}" "${processed_out}" + fi + + # generate report sce_qc_report.R \ --report_template "${template_path}" \ --library_id "${meta.library_id}" \ --sample_id "${meta.sample_id}" \ - --unfiltered_sce ${unfiltered_rds} \ - --filtered_sce ${filtered_rds} \ - --processed_sce ${processed_rds} \ + --unfiltered_sce ${unfiltered_out} \ + --filtered_sce ${filtered_out} \ + --processed_sce ${processed_out} \ --qc_report_file ${qc_report} \ --metadata_json ${metadata_json} \ --technology "${meta.technology}" \ @@ -37,10 +53,16 @@ process sce_qc_report{ --seed "${params.seed}" """ stub: + unfiltered_out = "${meta.library_id}_unfiltered.rds" + filtered_out = "${meta.library_id}_filtered.rds" + processed_out = "${meta.library_id}_processed.rds" qc_report = "${meta.library_id}_qc.html" metadata_json = "${meta.library_id}_metadata.json" """ + touch ${unfiltered_out} + touch ${filtered_out} + touch ${processed_out} touch ${qc_report} - echo '{}' > ${metadata_json} + echo '{"unfiltered_cells": 10, "filtered_cells": 10, "processed_cells": 10}' > ${metadata_json} """ } diff --git a/modules/samtools.nf b/modules/samtools.nf index a58d75a1..02c3e93c 100644 --- a/modules/samtools.nf +++ b/modules/samtools.nf @@ -1,6 +1,7 @@ process index_bam{ container params.SAMTOOLS_CONTAINER + tag "${meta.run_id}" input: tuple val(meta), path(bamfile) output: diff --git a/modules/sce-processing.nf b/modules/sce-processing.nf index 0417111e..ea16bf24 100644 --- a/modules/sce-processing.nf +++ b/modules/sce-processing.nf @@ -12,7 +12,6 @@ process make_unfiltered_sce{ tuple val(meta), path(unfiltered_rds) script: unfiltered_rds = "${meta.library_id}_unfiltered.rds" - """ generate_unfiltered_sce.R \ --alevin_dir ${alevin_dir} \ @@ -48,18 +47,18 @@ process make_unfiltered_sce{ // channels with RNA and feature data process make_merged_unfiltered_sce{ label 'mem_8' - tag "${meta.library_id}" + tag "${rna_meta.library_id}" container params.SCPCATOOLS_CONTAINER input: tuple val(feature_meta), path(feature_alevin_dir), - val (meta), path(alevin_dir), + val(rna_meta), path(alevin_dir), path(mito_file), path(ref_gtf), path(submitter_cell_types_file) path sample_metafile output: tuple val(meta), path(unfiltered_rds) script: - unfiltered_rds = "${meta.library_id}_unfiltered.rds" - // add feature metadata as an element of the main meta object + // add feature metadata as elements of the main meta object + meta = rna_meta.clone() meta['feature_type'] = feature_meta.technology.split('_')[0] meta['feature_meta'] = feature_meta @@ -68,6 +67,7 @@ process make_merged_unfiltered_sce{ meta['feature_type'] = "adt" } + unfiltered_rds = "${meta.library_id}_unfiltered.rds" """ generate_unfiltered_sce.R \ --alevin_dir ${alevin_dir} \ @@ -92,12 +92,13 @@ process make_merged_unfiltered_sce{ --library_id "${meta.library_id}" \ --submitter_cell_types_file "${submitter_cell_types_file}" fi - """ stub: - unfiltered_rds = "${meta.library_id}_unfiltered.rds" + meta = rna_meta.clone() meta['feature_type'] = feature_meta.technology.split('_')[0] meta['feature_meta'] = feature_meta + + unfiltered_rds = "${meta.library_id}_unfiltered.rds" """ touch "${meta.library_id}_unfiltered.rds" """ @@ -121,7 +122,7 @@ process filter_sce{ feature_barcode_file.name != "NO_FILE.txt" """ - filter_sce_rds.R \ + filter_sce.R \ --unfiltered_file ${unfiltered_rds} \ --filtered_file ${filtered_rds} \ ${adt_present ? "--adt_name ${meta.feature_type}":""} \ @@ -200,7 +201,6 @@ process post_process_sce{ tuple val(meta), path(unfiltered_rds), path(filtered_rds), path(processed_rds) script: processed_rds = "${meta.library_id}_processed.rds" - """ post_process_sce.R \ --filtered_sce_file ${filtered_rds} \ diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf index 54318a09..70ef72a2 100644 --- a/modules/spaceranger.nf +++ b/modules/spaceranger.nf @@ -44,6 +44,7 @@ process spaceranger{ process spaceranger_publish{ container params.SCPCATOOLS_CONTAINER + tag "${meta.library_id}" publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy' input: tuple val(meta), path(spatial_out) From 01d83b88d6a2e8f08e513907378da18587bdb2e3 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 11 Oct 2023 10:03:03 -0500 Subject: [PATCH 266/268] update version numbers --- config/containers.config | 2 +- external-instructions.md | 6 +++--- internal-instructions.md | 2 +- nextflow.config | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/config/containers.config b/config/containers.config index e01373a3..af1c0aa5 100644 --- a/config/containers.config +++ b/config/containers.config @@ -1,5 +1,5 @@ // Docker container images -SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:edge' +SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:v0.3.0' ALEVINFRY_CONTAINER = 'quay.io/biocontainers/alevin-fry:0.7.0--h9f5acd7_1' BCFTOOLS_CONTAINER = 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' diff --git a/external-instructions.md b/external-instructions.md index 5518186c..12031ac4 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -73,12 +73,12 @@ Using the above command will run the workflow from the `main` branch of the work To update to the latest released version you can run `nextflow pull AlexsLemonade/scpca-nf` before the `nextflow run` command. To be sure that you are using a consistent version, you can specify use of a release tagged version of the workflow, set below with the `-r` flag. -The command below will pull the `scpca-nf` workflow directly from Github using the `v0.5.4` version. +The command below will pull the `scpca-nf` workflow directly from Github using the `v0.6.0` version. Released versions can be found on the [`scpca-nf` repository releases page](https://github.com/AlexsLemonade/scpca-nf/releases). ```sh nextflow run AlexsLemonade/scpca-nf \ - -r v0.5.4 \ + -r v0.6.0 \ -config \ -profile ``` @@ -308,7 +308,7 @@ If you will be analyzing spatial expression data, you will also need the Cell Ra If your compute nodes do not have internet access, you will likely have to pre-pull the required container images as well. When doing this, it is important to be sure that you also specify the revision (version tag) of the `scpca-nf` workflow that you are using. -For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.5.4`, then you will want to set `-r v0.5.4` for `get_refs.py` as well to be sure you have the correct containers. +For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.6.0`, then you will want to set `-r v0.6.0` for `get_refs.py` as well to be sure you have the correct containers. By default, `get_refs.py` will download files and images associated with the latest release. If your system uses Docker, you can add the `--docker` flag: diff --git a/internal-instructions.md b/internal-instructions.md index 3d330e88..38275825 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -33,7 +33,7 @@ nextflow run AlexsLemonade/scpca-nf -profile ccdl,batch When running the workflow for a project or group of samples that is ready to be released on ScPCA portal, please use the tag for the latest release: ``` -nextflow run AlexsLemonade/scpca-nf -r v0.5.4 -profile ccdl,batch --project SCPCP000000 +nextflow run AlexsLemonade/scpca-nf -r v0.6.0 -profile ccdl,batch --project SCPCP000000 ``` ### Processing example data diff --git a/nextflow.config b/nextflow.config index c126a1b3..eaee44a9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest{ homePage = 'https://github.com/AlexsLemonade/scpca-nf' mainScript = 'main.nf' defaultBranch = 'main' - version = 'v0.5.4' + version = 'v0.6.0' } // global parameters for workflows From 6963e5bb25826e406636537f7c97a81c26de8eab Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:07:25 -0500 Subject: [PATCH 267/268] remove multiplexed if statement Co-authored-by: Joshua Shapiro --- bin/sce_qc_report.R | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R index 69e6b56b..f60b1c9c 100755 --- a/bin/sce_qc_report.R +++ b/bin/sce_qc_report.R @@ -146,11 +146,7 @@ processed_sce_meta <- metadata(processed_sce) sample_ids <- unlist(stringr::str_split(opt$sample_id, ",|;")) |> sort() # check for multiplexing -multiplexed <- if (length(sample_ids) > 1) { - TRUE -} else { - FALSE -} +multiplexed <- length(sample_ids) > 1 # sanity check ids if (!is.null(sce_meta$sample_id)) { From 6a7301d929eeb2ec99ae37ee53b4f2c90e230c5f Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:10:05 -0500 Subject: [PATCH 268/268] minor comment and formatting fixes Co-authored-by: Joshua Shapiro --- main.nf | 4 ++-- modules/export-anndata.nf | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index b21540dd..8e22ee6c 100644 --- a/main.nf +++ b/main.nf @@ -218,10 +218,10 @@ workflow { all_sce_ch = sce_ch.no_genetic.mix(genetic_demux_sce.out) post_process_sce(all_sce_ch) - // Cluster SCE and export RDS files to publishDir + // Cluster SCE cluster_sce(post_process_sce.out) - // generate QC reports + // generate QC reports and publish .rds files with SCEs. sce_qc_report(cluster_sce.out, report_template_tuple) // convert SCE object to anndata diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 94c5f79a..0a69a016 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -46,10 +46,10 @@ process move_normalized_counts{ --anndata_file \${file} done """ - stub: - """ - # nothing to do since files don't move - """ + stub: + """ + # nothing to do since files don't move + """ }