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variables.R
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variables.R
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# set shared snRNA processing parameters ----------------------------------
num_pc <- 30
num_features <- 3000
resolution_findclusters <- 0.5
# gene lists --------------------------------------------------------------
## SMG source 1: Sato et al, Nature Genetics, 2013
## SMG source 1: TCGA, Nature, 2013
ccRCC_SMGs <- c("VHL", "PBRM1", "BAP1", "TCEB1", "SETD2", "TP53", "PIK3CA", "MTOR", "KDM5C", "PTEN","TSC1",
"CCNB2",
"MSR1", "TXNIP", "BTNL3", "SLITRK6", "RHEB", "ARID1A", "NPNT",
"FPGT", "MUDENG", "TET2", "MUC4", "MLLT10", "MSGN1", "KRT32", "M6PR", "RPL14", "GRB7", "CSMD3", "DNHD1", "NLRP12", "VMO1", "OR4C13", "KCNMA1", "LMAN2L", "ZNF536", "YIPF3")
ccRCC_drivers <- c("VHL", "PBRM1", "BAP1", "TCEB1", "SETD2", "TP53", "PIK3CA", "MTOR", "KDM5C", "PTEN","TSC1")
# Two examples
# of cullin–RING ubiquitin ligase system molecular assemblies using CUL2 or CUL5 (left) and CUL3 (right) that interact with the BC-box protein–
# Elongin C–Elongin B complex and BTB protein, respectively, to recruit substrate for ubiquitination and subsequent degradation. VHL and KEAP1 are examples of BC-box and BTB proteins, respectively, that recruit HIF and NRF2 proteins for ubiquitin-mediated degradation.
vhl_complex_genes <- c("VHL",
"TCEB1", "TCEB2",
"ELOC", "ELOB",
"RBX1", "RNF7",
"CUL2", "CUL5")
keap1_nrf2_complex_genes <- c("NFE2L2", "KEAP1", "CUL3", "RBX1")
ubiquitin_proteasome_genes <- c(vhl_complex_genes,
keap1_nrf2_complex_genes,
"USP24", "NEDD4", "WWP2", "URB1", "USP34")
swisnf_genes <- c("PBRM1", "ARID1A", "ARID1B", "ARID2", "SMARCA2", "SMARCA4", "SMARCB1", "SMARCC1", "SMARCC2", "SMARCD2", "SMARCD2")
other_epigeneticregulator_genes <- c("SETD2",
"BAP1",
"KDM5C", "KDM6A",
"TET2")
pi3k_mtor_genes <- c("EGFR", "ERBB3", "FGFR3", "FGFR4", "IGF1R", "PIK3CA", "PIK3CB", "PIK3CG","PTEN", "AKT1", "AKT2", "AKT3", "MTOR", "TSC1", "TSC2", "RPS6KA2", "RPS6KA3", "RPS6KA6", "RHEB",
"SRC", "PKT2")
p53_cellcycle_genes <- c("ATM", "CHECK2", "TP53", "MDM2", "CDKN2A", "CCND1", "E2F3", "CCNB2",
"MYC")
fat_cadherins_genes <- c("FAT1", "FAT2", "FAT3", "FAT4")
## genes mutated in ccRCC
genes_pathogenicpathways_in_ccRCC <- c(ubiquitin_proteasome_genes,
swisnf_genes,
other_epigeneticregulator_genes,
pi3k_mtor_genes,
p53_cellcycle_genes,
fat_cadherins_genes)
genes_pathogenicpathways_in_ccRCC <- unique(genes_pathogenicpathways_in_ccRCC)
## PBAF gens
### reference: https://www.nature.com/articles/onc20094/figures/1
### reference: https://www.nature.com/articles/onc20094/tables/1
pbaf_genes <- c("PBRM1", "ARID2", "SMARCE1", "SMARCC2", "ACTL6A", "ACTL6B", "SMARCC1", "SMARCD1", "SMARCB1")
# sample annotation -------------------------------------------------------
snatacsample_anno_df <- data.frame(case = c("C3L-00088", "C3N-01200",
"C3L-01313", "C3N-01200", "C3L-01287", "C3L-00416",
"C3L-00610", "C3N-00733", "C3L-00079", "C3L-00416",
"C3L-00088", "C3L-00088", "C3L-00448", "C3L-00917"),
easyid = c("C3L-00088-N", "C3N-01200-N",
"C3L-01313-T1", "C3N-01200-T1", "C3L-01287-T1", "C3L-00416-T2",
"C3L-00610-T1", "C3N-00733-T1", "C3L-00079-T1", "C3L-00416-T2",
"C3L-00088-T1", "C3L-00088-T2", "C3L-00448-T1", "C3L-00917-T1"),
sample_group = c(rep("NAT", 2),
rep("BAP1-mutant tumor", 4),
rep("PBRM1-mutant tumor", 4),
rep("non-mutant tumor", 4)))