From 1e23ea6f1dafaa12c41ffdd5db553f6a5df1c86a Mon Sep 17 00:00:00 2001 From: Ryan Morin Date: Fri, 9 Aug 2024 11:08:18 -0700 Subject: [PATCH] fill in missing references --- resources/curated/dlbcl_genes.tsv | 50 ++++++++++++++++++++++--------- 1 file changed, 36 insertions(+), 14 deletions(-) diff --git a/resources/curated/dlbcl_genes.tsv b/resources/curated/dlbcl_genes.tsv index 2d4a3cf8..1dc2ab77 100644 --- a/resources/curated/dlbcl_genes.tsv +++ b/resources/curated/dlbcl_genes.tsv @@ -124,6 +124,13 @@ ZC3H12A 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 LOF 19747 ZFP36L1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 ZNF292 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 ZNF608 1 FALSE NA NA morinMutationalStructuralAnalysis2013 FALSE 23292937 +ADAMTSL3 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +AKAP8 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +ANKLE2 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +BCL2L10 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +BRSK1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +C12orf35 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +CAMTA1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 ABI3BP 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 ADAMTS1 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 AICDA 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 @@ -133,16 +140,17 @@ ARID5B 2 FALSE PASS 4 reddyGeneticFunctionalDrivers2017 FALSE 28985567 ASXL3 2 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 ATR 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 BCL11A 2 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -BCOR 2 FALSE NA NA NA FALSE NA BCR 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 BIRC3 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 BLK 2 TRUE NA NA NA FALSE NA BRINP3 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 BTBD3 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 CADPS2 2 FALSE PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 +CYTS5B 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 CASP8 2 FALSE NA 4 reddyGeneticFunctionalDrivers2017 FALSE 28985567 CD22 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 CD274 2 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 +DCHS1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 CD36 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 CD44 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 CD74 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 @@ -153,7 +161,7 @@ CNTNAP5 2 FALSE PASS 4 morinMutationalStructuralAnalysis2013 FALSE 23699601 COQ7 2 FALSE PASS 3 chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 CPS1 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 CRIP1 2 FALSE PASS 3 chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -CXCR5 2 FALSE NA FALSE 29641966 +CXCR5 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 DAZAP1 2 FALSE NA pararajalingamCodingNoncodingDrivers2020 FALSE 32160292 DDX10 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 DHX16 2 FALSE PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 @@ -162,7 +170,9 @@ DNM2 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 DNMT3B 2 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 DOCK1 2 FALSE PASS 3 chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 DSG4 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 -EIF2AK3 2 TRUE NA NA NA FALSE NA +DPYD 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +EIF2AK3 2 TRUE NA NA schmitzGeneticsPathogenesisDiffuse2018a FALSE NA +DSC3 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 ERAP2 2 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 EZR 2 TRUE NA NA NA FALSE NA FAM102A 2 TRUE NA NA NA FALSE NA @@ -171,6 +181,8 @@ FAT2 2 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 FAT4 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 FCRL3 2 TRUE NA NA NA FALSE NA FNBP1 2 TRUE NA NA NA FALSE NA +DUSP27 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +DUSP9 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 FOXC1 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 FOXP1 2 TRUE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 FUBP1 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 @@ -203,6 +215,7 @@ KCMF1 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 KLHL21 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 KRTAP5-5 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 LAMA5 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 +FBXO31 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 LAPTM5 2 TRUE PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 LCOR 2 FALSE NA FALSE 30275490 LPP 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 @@ -218,15 +231,11 @@ MIR155HG 2 TRUE NA NA NA FALSE NA MPDZ 2 FALSE PASS 4 morinMutationalStructuralAnalysis2013 FALSE 23699601 MSH6 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 MYBPC2 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 -MYO1E 2 TRUE NA NA NA FALSE NA MYOM2 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 NAV1 2 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 NCOA3 2 TRUE NA NA NA FALSE NA -NCOR2 2 FALSE NA NA NA FALSE NA NEAT1 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 NF1 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 28985567 -NFKB1 2 FALSE NA NA NA FALSE NA -NLRC5 2 FALSE NA NA NA FALSE NA NLRP5 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 ODZ3 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 OR6K3 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 @@ -235,7 +244,6 @@ PAPOLG 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 PASD1 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 PASK 2 FALSE PASS 4 morinMutationalStructuralAnalysis2013 FALSE 23699601 PAX5 2 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a FALSE 11460166 -PCBP1 2 FALSE NA NA NA FALSE NA PCDHB11 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 PCDHB6 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 PCLO 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 @@ -244,13 +252,10 @@ PDS5B 2 FALSE PASS 4 morinMutationalStructuralAnalysis2013 FALSE 23699601 PIK3CD 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 PIK3R1 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 PNPO 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 -PPP1R9B 2 FALSE NA NA NA FALSE NA PRKCB 2 FALSE PASS 4 morinMutationalStructuralAnalysis2013 FALSE 23699601 PRKDC 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 PRPS1 2 FALSE PASS 4 chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -PTMA 2 TRUE NA NA NA FALSE NA -PTPN1 2 TRUE NA NA NA FALSE NA -PTPRD 2 FALSE NA NA NA FALSE NA +PTPRD 2 FALSE NA NA drevalGeneticSubdivisionsFollicular2023 FALSE NA RAC2 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 RAPGEF1 2 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 RCC 2 TRUE NA NA NA FALSE NA @@ -261,7 +266,7 @@ RHOH 2 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a FALSE NA RUBCNL 2 TRUE NA NA NA FALSE NA S1PR1 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 SAMD9L 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 -SEL1L3 2 TRUE NA NA NA FALSE NA +SEL1L3 2 TRUE NA NA schmitzGeneticsPathogenesisDiffuse2018a FALSE NA SEPTIN9 2 TRUE NA NA NA FALSE NA SERPINA9 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 SETD2 2 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 @@ -275,6 +280,7 @@ SRPX 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 SRRM2 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 ST6GAL1 2 TRUE NA arthurGenomewideDiscoverySomatic2018 FALSE 30275490 STAT5B 2 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 +HMGB1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 SYN2 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 SYPL1 2 FALSE PASS 3 morinMutationalStructuralAnalysis2013 FALSE 23699601 TAP1 2 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE 29641966 @@ -288,7 +294,7 @@ TNF 2 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 TRAF3 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 TRAF6 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 TRIP12 2 FALSE NA NA NA FALSE NA -UBE2J1 2 TRUE NA NA FALSE NA +UBE2J1 2 TRUE NA schmitzGeneticsPathogenesisDiffuse2018a FALSE NA UBR5 2 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 23292937 UHRF1BP1 2 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 UNC5B 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 @@ -304,6 +310,22 @@ ZEB2 2 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 ZFX 2 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 ZNF217 2 FALSE PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE 33953289 ZNF423 2 FALSE PASS 3 chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 +KDM2B 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +MAGEC3 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +MED12L 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +MTMR8 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +MYO1G 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +OFD1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +PMS1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +PPP2R5A 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +RASGEF1A 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +RGAG1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +SERPINA1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +SMARCA1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +TLL2 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +TSC22D1 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +ZNF521 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 +ZWILCH 2 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 ABCA3 3 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 ABCA4 3 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 ABCB1 3 FALSE NA fanComprehensiveCharacterizationDriver2020b FALSE 32565964