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rdmorin authored Dec 4, 2024
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## The lists

### DLBCL, FL and BL combined list

|Gene|DLBCL Tier|FL Tier|BL Tier|
|:-:|:-:|:-:|
|ARID1A|1|1|1|
|BCL6|1|1|1|
|BCL7A|1|1|1|
|CCND3|1|1|1|
|CREBBP|1|1|1|
|EZH2|1|1|1|
|FOXO1|1|1|1|
|GNA13|1|1|1|
|GNAI2|1|1|1|
|HIST1H1E|1|1|1|
|IGLL5|1|1|1|
|KMT2D|1|1|1|
|MYC|1|1|1|
|SMARCA4|1|1|1|
|TP53|1|1|1|
|B2M|1|1|2|
|BCL2|1|1|2|
|CARD11|1|1|2|
|CD83|1|1|2|
|EBF1|1|1|2|
|HIST1H1B|1|1|2|
|IRF8|1|1|2|
|PIM1|1|1|2|
|TBL1XR1|1|1|2|
|TNFRSF14|1|1|2|
|HIST1H1C|1|1|3|
|HIST1H2AM|1|1|3|
|ACTB|1|1||
|BCL10|1|1||
|BTK|1|1||
|EEF1A1|1|1||
|EP300|1|1||
|FAS|1|1||
|HIST1H1D|1|1||
|HIST1H2AC|1|1||
|HIST1H2BC|1|1||
|HVCN1|1|1||
|KLHL6|1|1||
|MEF2B|1|1||
|POU2AF1|1|1||
|POU2F2|1|1||
|RRAGC|1|1||
|SGK1|1|1||
|SOCS1|1|1||
|STAT6|1|1||
|TMSB4X|1|1||
|TNFAIP3|1|1||
|DDX3X|1|2|1|
|P2RY8|1|2|1|
|RHOA|1|2|1|
|BTG1|1|2|2|
|CXCR4|1|2|2|
|S1PR2|1|2|2|
|BTG2|1|2|3|
|CD79B|1|2|3|
|ACTG1|1|2||
|CD70|1|2||
|DUSP2|1|2||
|IRF4|1|2||
|ITPKB|1|2||
|KLF2|1|2||
|LTB|1|2||
|MEF2C|1|2||
|MYD88|1|2||
|NFKBIA|1|2||
|TMEM30A|1|2||
|ZNF608|1|2||
|FBXO11|1||1|
|HNRNPU|1||1|
|PTEN|1||1|
|RFX7|1||1|
|SIN3A|1||1|
|CDKN2A|1||2|
|IKZF3|1||2|
|KMT2C|1||2|
|PRDM1|1||2|
|TET2|1||2|
|ZFP36L1|1||2|
|BRAF|1||3|
|DTX1|1||3|
|ETS1|1||3|
|HIST1H2BK|1||3|
|MTOR|1||3|
|NOTCH1|1||3|
|SF3B1|1||3|
|ATM|1|||
|BIRC6|1|||
|CD58|1|||
|CIITA|1|||
|ETV6|1|||
|FBXW7|1|||
|GRB2|1|||
|GRHPR|1|||
|HIST1H3B|1|||
|HIST2H2BE|1|||
|HLA-A|1|||
|HLA-B|1|||
|HLA-C|1|||
|HLA-DMB|1|||
|IL4R|1|||
|JUNB|1|||
|KLHL14|1|||
|KRAS|1|||
|LCOR|1|||
|LRRN3|1|||
|MGA|1|||
|MPEG1|1|||
|MS4A1|1|||
|NFKBIE|1|||
|NFKBIZ|1|||
|NOL9|1|||
|NOTCH2|1|||
|OSBPL10|1|||
|PIM2|1|||
|PTPN6|1|||
|RB1|1|||
|SETD1B|1|||
|SPEN|1|||
|STAT3|1|||
|TAF1|1|||
|TOX|1|||
|UBE2A|1|||
|WEE1|1|||
|XPO1|1|||
|ZC3H12A|1|||
|ZNF292|1|||
|HIST1H2AG|2|1|3|
|MAP2K1|2|1||
|ID3|2||1|
|TCL1A|2||1|
|USP7|2||1|
|WNK1|2||1|
|PHF6|3||1|
|ATP6AP1||1||
|ATP6V1B2||1||
|CTSS||1||
|HIST1H2BG||1||
|VMA21||1||
|BACH2|||1|
|BMP7|||1|
|CHD8|||1|
|PCBP1|||1|
|TCF3|||1|
|TFAP4|||1|

### DLBCL

The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The second column (Tier) refers to our confidence in the gene. Each gene is assigned to one of three based on the extent of data supporting its role in that entity, with Tier 1 and Tier 2 respectively representing the high- and moderate-confidence genes. Genes of particularly low confidence can also be assigned to a third tier, though not all lists contain Tier 3 genes. The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL.
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