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rdmorin committed May 24, 2024
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47 changes: 24 additions & 23 deletions resources/curated/fl_genes.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,19 @@ gene curated Dreval Hubschmann Crouch de_Leval Kalmbach Russler-Germain First_de
ABL2 FALSE FALSE FALSE FALSE FALSE TRUE FALSE 37563306 russler-germainMutationsAssociatedProgression2023a 0.6928406466512702 NA
ACTB TRUE TRUE TRUE FALSE FALSE FALSE FALSE NA 5.311778290993072 aSHM
ACTG1 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 3.0023094688221708 NA
ARID1A TRUE FALSE TRUE TRUE TRUE FALSE FALSE NA 12.471131639722863 NA
ATP6AP1 TRUE TRUE TRUE FALSE TRUE FALSE FALSE NA 4.849884526558891 NA
ARID1A TRUE FALSE TRUE TRUE TRUE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 12.471131639722863 NA
ATP6AP1 TRUE TRUE TRUE FALSE TRUE FALSE FALSE 26691987 okosunRecurrentMTORC1activatingRRAGC2016a 4.849884526558891 NA
ATP6V1A FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 1.1547344110854503 NA
ATP6V1B2 TRUE TRUE TRUE FALSE TRUE FALSE FALSE NA 7.390300230946882 NA
ATP6V1B2 TRUE TRUE TRUE FALSE TRUE FALSE FALSE 26691987 okosunRecurrentMTORC1activatingRRAGC2016a 7.390300230946882 NA
B2M TRUE TRUE TRUE FALSE TRUE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 8.545034642032332 NA
BCL10 FALSE FALSE FALSE FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 2.3094688221709005 NA
BCL2 TRUE TRUE TRUE TRUE TRUE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 50.34642032332564 NA
BCL6 TRUE FALSE FALSE FALSE FALSE FALSE TRUE 37084389 5.773672055427252 aSHM
BCL7A TRUE FALSE TRUE TRUE TRUE TRUE TRUE NA 13.856812933025404 aSHM
BCL7A TRUE FALSE TRUE TRUE TRUE TRUE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 13.856812933025404 aSHM
BIRC6 TRUE TRUE FALSE FALSE FALSE FALSE FALSE NA 3.695150115473441 NA
BTG1 TRUE TRUE FALSE TRUE TRUE FALSE FALSE NA 6.466512702078522 aSHM
BTG2 TRUE TRUE TRUE TRUE FALSE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 4.387990762124711 aSHM
BTK TRUE FALSE FALSE FALSE TRUE FALSE FALSE NA 6.928406466512702 NA
BTK TRUE FALSE FALSE FALSE TRUE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 6.928406466512702 NA
CARD11 TRUE FALSE FALSE FALSE TRUE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 14.780600461893764 NA
CCDC42BPB FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b NA NA
CCND3 TRUE TRUE FALSE FALSE FALSE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 3.233256351039261 NA
Expand All @@ -24,8 +24,8 @@ CD83 TRUE TRUE NA TRUE FALSE FALSE FALSE 37493986 russler-germainMutationsAssoci
CILP FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 0.4618937644341801 NA
CPNE8 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 2.0785219399538106 NA
CREBBP TRUE TRUE NA TRUE TRUE TRUE TRUE 21796119 65.1270207852194 NA
CTSS TRUE FALSE NA FALSE TRUE FALSE FALSE NA 3.9260969976905313 NA
CXCR4 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 khodabakhshiRecurrentTargetsAberrant2012 3.464203233256351 NA
CTSS TRUE FALSE NA FALSE TRUE FALSE FALSE 32330423 barariaCathepsinAlterationsInduce2020c 3.9260969976905313 NA
CXCR4 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 3.464203233256351 NA
CYP2A6 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 0.23094688221709006 NA
DDX3X FALSE TRUE NA FALSE FALSE FALSE FALSE 37084389 2.540415704387991 NA
DHX15 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 0.6928406466512702 NA
Expand All @@ -42,23 +42,23 @@ GBP7 FALSE FALSE NA FALSE FALSE TRUE FALSE 37563306 russler-germainMutationsAsso
GNA13 TRUE TRUE TRUE FALSE TRUE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 10.161662817551964 NA
GNAI2 TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 4.157043879907621 NA
GRM6 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 0.9237875288683602 NA
HIST1H1B TRUE TRUE NA TRUE FALSE FALSE FALSE NA 5.542725173210162 aSHM
HIST1H1B TRUE TRUE NA TRUE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 5.542725173210162 aSHM
HIST1H1C TRUE TRUE NA TRUE TRUE FALSE FALSE 21796119 morinFrequentMutationHistonemodifying2011 5.080831408775982 aSHM
HIST1H1D TRUE FALSE NA TRUE FALSE FALSE TRUE NA 3.233256351039261 aSHM
HIST1H1E TRUE TRUE NA TRUE TRUE FALSE TRUE NA 12.933025404157044 aSHM
HIST1H2AC TRUE FALSE NA TRUE FALSE FALSE TRUE NA 2.3094688221709005 aSHM
HIST1H2AG TRUE FALSE NA TRUE FALSE FALSE FALSE NA 2.0785219399538106 aSHM
HIST1H2AM TRUE FALSE NA TRUE FALSE FALSE TRUE NA 3.695150115473441 aSHM
HIST1H2BC TRUE FALSE NA TRUE FALSE FALSE FALSE NA 3.464203233256351 aSHM
HIST1H2BD TRUE FALSE NA TRUE FALSE FALSE FALSE NA 1.1547344110854503 aSHM
HIST1H2BG TRUE FALSE NA TRUE FALSE FALSE FALSE NA 2.0785219399538106 aSHM
HIST1H2BM FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 0.6928406466512702 aSHM
HIST1H1D TRUE FALSE NA TRUE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 3.233256351039261 aSHM
HIST1H1E TRUE TRUE NA TRUE TRUE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 12.933025404157044 aSHM
HIST1H2AC TRUE FALSE NA TRUE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 2.3094688221709005 aSHM
HIST1H2AG TRUE FALSE NA TRUE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 2.0785219399538106 aSHM
HIST1H2AM TRUE FALSE NA TRUE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 3.695150115473441 aSHM
HIST1H2BC TRUE FALSE NA TRUE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 3.464203233256351 aSHM
HIST1H2BD TRUE FALSE NA TRUE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 1.1547344110854503 aSHM
HIST1H2BG TRUE FALSE NA TRUE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 2.0785219399538106 aSHM
HIST1H2BM FALSE FALSE NA FALSE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 0.6928406466512702 aSHM
HIST1H3B TRUE FALSE NA TRUE FALSE FALSE FALSE NA 1.6166281755196306 aSHM
HIST1H3G TRUE FALSE NA TRUE FALSE FALSE TRUE NA 1.6166281755196306 aSHM
HIST1H3I FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 1.1547344110854503 aSHM
HIST1H3G TRUE FALSE NA TRUE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 1.6166281755196306 aSHM
HIST1H3I FALSE FALSE NA FALSE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 1.1547344110854503 aSHM
HLA-B FALSE TRUE NA FALSE FALSE FALSE FALSE NA 3.464203233256351 NA
HNRNPD FALSE TRUE NA FALSE FALSE FALSE FALSE NA NA NA
HVCN1 TRUE FALSE NA FALSE TRUE FALSE FALSE NA 6.466512702078522 NA
HVCN1 TRUE FALSE NA FALSE TRUE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b 6.466512702078522 NA
ID3 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 0.9237875288683602 NA
IGLL5 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 35.33487297921478 aSHM/SHM. Unclear if this should be considered a gene
IRF4 TRUE FALSE NA FALSE FALSE FALSE FALSE NA 1.1547344110854503 LBCL-IRF4
Expand All @@ -85,9 +85,8 @@ NFKBIA FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAs
OR8H2 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 1.1547344110854503 NA
P2RY8 FALSE TRUE NA FALSE FALSE FALSE FALSE NA 2.3094688221709005 NA
PCLO TRUE TRUE NA FALSE FALSE FALSE FALSE NA 9.237875288683602 NA
PDS5B FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 morinMutationalStructuralAnalysis2013 1.6166281755196306 NA
PIM1 TRUE TRUE NA TRUE TRUE FALSE TRUE NA 9.237875288683602 NA
POU2AF1 TRUE TRUE NA FALSE TRUE TRUE TRUE NA 12.240184757505773 NA
POU2AF1 TRUE TRUE NA FALSE TRUE TRUE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 12.240184757505773 NA
POU2F2 TRUE FALSE NA FALSE TRUE TRUE FALSE NA 6.235565819861431 NA
PPP4C FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 2.0785219399538106 NA
PRKDC FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 schmitzGeneticsPathogenesisDiffuse2018a 3.0023094688221708 NA
Expand All @@ -99,7 +98,7 @@ S1PR2 TRUE FALSE NA FALSE TRUE FALSE FALSE NA 6.235565819861431 NA
SESN1 FALSE FALSE NA FALSE FALSE FALSE FALSE 28659443 0.23094688221709006 NA
SGK1 TRUE TRUE TRUE TRUE TRUE FALSE TRUE 21796119 morinFrequentMutationHistonemodifying2011 6.0046189376443415 NA
SHROOM3 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 1.1547344110854503 NA
SMARCA4 TRUE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 4.157043879907621 NA
SMARCA4 TRUE FALSE NA FALSE FALSE FALSE TRUE 28064239 krysiakRecurrentSomaticMutations2017b 4.157043879907621 NA
SOCS1 TRUE TRUE TRUE TRUE TRUE FALSE TRUE NA 9.699769053117782 NA
SRRM2 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 1.3856812933025404 NA
STAB2 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 2.540415704387991 NA
Expand All @@ -114,3 +113,5 @@ TPP1 FALSE FALSE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMecha
VMA21 TRUE TRUE TRUE FALSE FALSE FALSE FALSE 33953289 hubschmannMutationalMechanismsShaping2021b 5.080831408775982 NA
XIRP2 FALSE FALSE NA FALSE FALSE FALSE TRUE 37493986 russler-germainMutationsAssociatedProgression2023a 3.9260969976905313 NA
ZC3H12A FALSE TRUE NA FALSE FALSE FALSE FALSE NA 0.4618937644341801 NA
EGR1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b
ZNF608 FALSE FALSE FALSE FALSE FALSE FALSE FALSE 28064239 krysiakRecurrentSomaticMutations2017b
1 change: 1 addition & 0 deletions resources/curated/fl_tiers.tsv
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Expand Up @@ -35,6 +35,7 @@ EBF1 1
EEF1A1 2
EP300 1
EZH2 1
EGR1 2
FAS 1
FOXO1 1
FZR1 2
Expand Down
27 changes: 14 additions & 13 deletions resources/curated/gene_history_first.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,9 @@ ARID5B 2017 reddyGeneticFunctionalDrivers2017 DLBCL 2
ATM 2013 beaLandscapeSomaticMutations2013 MCL 1
ATP11C 2014 zhangGenomicLandscapeMantle2014 MCL 2
ATP2C2 2012 loveGeneticLandscapeMutations2012 BL 2
ATP6AP1 NA Unknown FL 1
ATP6AP1 2016 okosunRecurrentMTORC1activatingRRAGC2016a FL 1
ATP6V1A 2021 hubschmannMutationalMechanismsShaping2021b FL 2
ATP6V1B2 NA Unknown FL 1
ATP6V1B2 2016 okosunRecurrentMTORC1activatingRRAGC2016a FL 1
ATR 2017 reddyGeneticFunctionalDrivers2017 DLBCL 2
B2M 2011 morinFrequentMutationHistonemodifying2011 DLBCL 1
BACH2 2019 grandeGenomewideDiscoverySomatic2019 BL 2
Expand All @@ -34,7 +34,7 @@ BCL11A NA Unknown DLBCL 1
BCL2 1992 tanakaFrequentIncidenceSomatic1992 DLBCL 1
BCL2L11 NA Unknown BL 2
BCL6 2011 morinFrequentMutationHistonemodifying2011 DLBCL 1
BCL7A 2018 arthurGenomewideDiscoverySomatic2018 DLBCL 1
BCL7A 2017 krysiakRecurrentSomaticMutations2017b FL 1
BCOR 2020 nadeuGenomicEpigenomicInsights2020a MCL 1
BCR NA Unknown DLBCL 1
BIRC3 2013 beaLandscapeSomaticMutations2013 MCL 1
Expand Down Expand Up @@ -98,7 +98,7 @@ CRIP1 2018 chapuyMolecularSubtypesDiffuse2018b DLBCL 2
CRYBG3 2013 beaLandscapeSomaticMutations2013 MCL 2
CTCF 2019 paneaWholeGenomeLandscape2019 BL 2
CTNNA2 2014 zhangGenomicLandscapeMantle2014 MCL 2
CTSS NA Unknown FL 1
CTSS 2020 barariaCathepsinAlterationsInduce2020c FL 1
CXCR4 2012 khodabakhshiRecurrentTargetsAberrant2012 DLBCL 1
CXCR5 2018 schmitzGeneticsPathogenesisDiffuse2018a DLBCL 1
CYB5D1 2012 loveGeneticLandscapeMutations2012 BL 2
Expand Down Expand Up @@ -130,6 +130,7 @@ E2F2 2022 burkhardtClinicalRelevanceMolecular2022b BL 2
EBF1 2013 bohleRoleEarlyBcell2013 DLBCL 1
EDNRB 2022 burkhardtClinicalRelevanceMolecular2022b BL 2
EEF1A1 2021 hubschmannMutationalMechanismsShaping2021b DLBCL 1
EGR1 2017 krysiakRecurrentSomaticMutations2017b FL 2
EHD1 NA Unknown BL 2
EIF2AK3 NA Unknown DLBCL 2
EIF2AK4 2014 zhangGenomicLandscapeMantle2014 MCL 2
Expand Down Expand Up @@ -189,23 +190,23 @@ GSG2 2018 schmitzGeneticsPathogenesisDiffuse2018a DLBCL 2
GTSE1 2012 schmitzBurkittLymphomaPathogenesis2012 BL 2
HDAC7 2013 morinMutationalStructuralAnalysis2013 DLBCL 2
HEPH 2014 zhangGenomicLandscapeMantle2014 MCL 2
HIST1H1B 2018 chapuyMolecularSubtypesDiffuse2018b DLBCL 1
HIST1H1B 2017 krysiakRecurrentSomaticMutations2017b FL 1
HIST1H1C 2011 morinFrequentMutationHistonemodifying2011 DLBCL 1
HIST1H1D 2013 morinMutationalStructuralAnalysis2013 DLBCL 1
HIST1H1E 2013 morinMutationalStructuralAnalysis2013 DLBCL 1
HIST1H2AC 2013 morinMutationalStructuralAnalysis2013 DLBCL 1
HIST1H2AG 2013 morinMutationalStructuralAnalysis2013 DLBCL 2
HIST1H2AM 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H2AM 2017 krysiakRecurrentSomaticMutations2017b FL 1
HIST1H2BC 2017 reddyGeneticFunctionalDrivers2017 DLBCL 1
HIST1H2BD NA Unknown FL 1
HIST1H2BG NA Unknown FL 1
HIST1H2BD 2017 krysiakRecurrentSomaticMutations2017b FL 1
HIST1H2BG 2017 krysiakRecurrentSomaticMutations2017b FL 1
HIST1H2BK 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H2BM 2023 russler-germainMutationsAssociatedProgression2023a FL 2
HIST1H2BM 2017 krysiakRecurrentSomaticMutations2017b FL 2
HIST1H3B 2013 zhangGeneticHeterogeneityDiffuse2013 DLBCL 1
HIST1H3D 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H3G NA Unknown FL 1
HIST1H3G 2017 krysiakRecurrentSomaticMutations2017b FL 1
HIST1H3H 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H3I 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H3I 2017 krysiakRecurrentSomaticMutations2017b FL 2
HIST1H3J 2019 paneaWholeGenomeLandscape2019 BL 2
HIST1H4J 2019 paneaWholeGenomeLandscape2019 BL 2
HIST2H2BE 2018 schmitzGeneticsPathogenesisDiffuse2018a DLBCL 1
Expand All @@ -221,7 +222,7 @@ HNRNPD NA Unknown DLBCL 1
HNRNPH1 2020 pararajalingamCodingNoncodingDrivers2020 DLBCL 1
HNRNPU 2017 reddyGeneticFunctionalDrivers2017 DLBCL 1
HRAS 2017 reddyGeneticFunctionalDrivers2017 DLBCL 2
HVCN1 NA Unknown DLBCL 1
HVCN1 2017 krysiakRecurrentSomaticMutations2017b FL 1
ICK 2012 loveGeneticLandscapeMutations2012 BL 2
ID3 2012 schmitzBurkittLymphomaPathogenesis2012 DLBCL 2
IER2 2013 morinMutationalStructuralAnalysis2013 DLBCL 2
Expand Down Expand Up @@ -365,7 +366,7 @@ POGZ 2013 morinMutationalStructuralAnalysis2013 DLBCL 2
POLRMT 2012 loveGeneticLandscapeMutations2012 BL 2
POR 2012 loveGeneticLandscapeMutations2012 BL 2
POT1 2014 zhangGenomicLandscapeMantle2014 MCL 1
POU2AF1 NA Unknown DLBCL 1
POU2AF1 2017 krysiakRecurrentSomaticMutations2017b FL 1
POU2F2 2013 zhangGeneticHeterogeneityDiffuse2013 DLBCL 1
PPP1R9B NA Unknown DLBCL 1
PPP4C 2021 hubschmannMutationalMechanismsShaping2021b FL 2
Expand Down
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