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Merge branch 'main' of github.com:morinlab/LLMPP
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@rdmorin
rdmorin committed Apr 29, 2024
2 parents ca75208 + 398cdac commit 28910a6
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108 changes: 0 additions & 108 deletions resources/curated/PMBL_HL_MGZL.csv
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108 changes: 108 additions & 0 deletions resources/curated/PMBL_HL_MGZL.tsv
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Gene Curated PMBL_De_Leval MGZL_De_Leval CHL_De_Leval CHL_Wienand CHL_Gomez CHL_Alig CHL_Desch earliest_description freq_PMBCL_Mottok
ACTB TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE NA 27.08
ACTG1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 31431735 16.67
GPR126 FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE NA 3.12
AXDND1 FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE 37910143 2.08
ARID1A TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE NA 14.58
ARID5B TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 15.62
B2M TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA 48.96
BIRC6 TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE NA 20.83
BTG1 TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE NA 25
BCL7A FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE NA 15.62
CARD11 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA NA
CCND3 FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE NA 8.33
CD58 TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE NA 28.12
CD83 TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE NA 10.42
CDKN2A TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 1.04
CDH5 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 3.12
CHD8 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 5.21
CHD2 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 4.17
CIITA FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 31431735 26.04
CISH FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 7.29
CREBBP TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 8.33
CSF2RB TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE NA 20.83
DDX3X TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE NA 11.46
DNAH12 FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE NA 7.29
DTX1 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 5.21
DUSP2 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 13.54
EBF1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 6.25
EEF1A1 FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE NA 8.33
EP300 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 11.46
EGR1 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE NA 9.38
ETS1 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 3.12
EWSR1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA NA
EZH2 TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE NA 7.29
FAS TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 6.25
FAT1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 11.46
FAT4 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 22.92
GNA13 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA 41.67
HIST1H1C TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 18.75
HIST1H1D TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 10.42
HIST1H1D TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE NA 10.42
HIST1H1B TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE NA 11.46
HLA-A NA FALSE FALSE FALSE FALSE FALSE FALSE TRUE 31431735 10.42
HLA-B TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE NA 7.29
HLA-C FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE NA 8.33
IL4R TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE NA 32.29
IGLL5 FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE NA 31.25
IRF8 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 8.33
IRF4 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 9.38
IKBKB FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE NA 11.46
ITPKB TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE NA 41.67
ITGB2 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 2.08
JAK1 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 11.46
KLF2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 31431735 3.12
KMT2C TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE NA 9.38
KMT2D FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE NA 17.71
LTB TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE NA 17.71
LIMD2 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 4.17
MS4A1 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 4.17
MYB FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 31431735 1.04
NFKBIA TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE NA 7.29
NFKBIE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE NA 41.67
NFKB2 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 11.46
WHSC1 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 3.12
OR13C2 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 NA
OSBPL10 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 11.46
P2RY8 TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE NA NA
PCDH7 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 5.21
PCBP1 FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE NA 8.33
PCLO TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 29.17
PHIP TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 8.33
PIM1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 10.42
PIM2 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 1.04
PRKDC TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 4.17
PTPN1 TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE NA 16.67
PTPRD TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 11.46
RDH12 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 NA
RHOA TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 2.08
RBM38 FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE NA 5.21
S1PR2 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA NA
SCN9A FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 9.38
SGK1 TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE NA 10.42
SIN3A TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 2.08
SMAD3 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE NA 1.04
SMARCA2 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 5.21
SMARCA4 TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE NA 4.17
SOCS1 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA 62.5
SPEN TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE NA 7.29
STAT3 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA NA
STAT6 TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE NA 42.71
STRAP FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE 37910143 NA
TAP1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 6.25
TBL1XR1 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 5.21
TCF3 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 7.29
TET3 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 2.08
TMSB4X TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 27.08
TNFAIP3 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA 42.71
TNFRSF1B TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 1.04
TP53 TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE NA 10.42
TRAF3 TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE NA 8.33
UBE2A TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE NA 4.17
UBR5 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 5.21
UNC5C TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA NA
VPS13B TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE NA 11.46
WEE1 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 11.46
XPO1 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA 27.08
ZFP36L1 TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE NA 13.54
ZNF217 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA 29.17
5 changes: 3 additions & 2 deletions resources/curated/bl_genes.tsv
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Expand Up @@ -13,7 +13,7 @@ BCR 31558468 FALSE NA 6.4 10.9 7 6.9 FALSE TRUE 6.0046189376443415 aSHM target g
BIRC6 NA FALSE DLBCL 3.8 14.9 NA NA FALSE FALSE 6.0046189376443415 DLBCL gene with extremely low mutation rate in BL
BMP7 31558468 TRUE NA 8.9 5 9 8.9 TRUE FALSE 6.466512702078522 Confirmed by multiple studies
BTG2 31558468 FALSE NA 4.2 9.9 16 15.8 FALSE TRUE 4.849884526558891 aSHM target genes have elevated mutation rate but the mutations may not represent drivers. More evidence is needed.
C10orf12 NA FALSE DLBCL 0 NA NA NA FALSE FALSE 3.464203233256351 DLBCL gene with extremely low mutation rate in BL
LCOR NA FALSE DLBCL 0 NA NA NA FALSE FALSE 3.464203233256351 DLBCL gene with extremely low mutation rate in BL
CARD11 NA FALSE DLBCL 1.7 10.9 NA NA FALSE FALSE 4.157043879907621 DLBCL gene with extremely low mutation rate in BL
CCND3 22885699 TRUE BL 28 17.8 19 18.8 TRUE FALSE 27.48267898383372 Mutated at high frequency in both DLBCL and BL
CCNF 26468873 FALSE NA NA NA NA NA FALSE FALSE 1.6166281755196306 Hot spot reported in this study is a rare germline variant in African populations
Expand Down Expand Up @@ -72,6 +72,7 @@ KMT2D 30617194 TRUE DLBCL 14 15.8 13 12.9 TRUE FALSE 11.316397228637413 Mutated
LTB NA FALSE DLBCL 3 5.9 NA NA FALSE TRUE 3.0023094688221708 Borderline evidence to consider this also a BL gene
MCL1 31558468 FALSE NA 2.1 2 4 4 FALSE FALSE 1.8475750577367205 Low frequency of coding mutations in all cohorts including initial study after reanalysis of raw data. Mutations in this gene reported by Panea et al were not well supported by the data in that study.
MEF2B NA FALSE DLBCL 0.8 3 NA NA FALSE TRUE 1.3856812933025404 DLBCL gene with extremely low mutation rate in BL
MIR142 30617194 FALSE NA NA NA NA NA FALSE TRUE NA
MME 31558468 FALSE NA 0.8 5.9 2 2 FALSE FALSE 1.8475750577367205 Low frequency of coding mutations in all cohorts including initial study after reanalysis of raw data. Mutations in this gene reported by Panea et al were not well supported by the data in that study.
MTOR 31558468 FALSE NA 3.4 10.9 5 5 FALSE FALSE 4.618937644341801 Mutation frequencies are inconsistent between studies. Nominating study is an outlier.
MYC TBD TRUE BL 60.2 49.5 64 63.4 FALSE TRUE 61.89376443418014 Hot spots from aSHM can affect MYC protein stability
Expand Down Expand Up @@ -111,7 +112,7 @@ STAT6 NA FALSE DLBCL 1.7 2 NA NA FALSE FALSE 1.6166281755196306 DLBCL gene with
SYNCRIP 31558468 FALSE BL 2.5 5 NA NA FALSE FALSE 3.0023094688221708 Low frequency of coding mutations in all cohorts including initial study
TBL1XR1 NA FALSE DLBCL 4.7 7.9 NA NA FALSE TRUE 6.0046189376443415 DLBCL gene with extremely low mutation rate in BL
TCF3 22885699 TRUE BL 11 9.9 5 5 TRUE FALSE 11.547344110854503 Confirmed by multiple studies
TCL1A 30617194 FALSE BL 5.9 4 5 5 FALSE TRUE 4.157043879907621 aSHM target genes have elevated mutation rate but the mutations may not represent drivers. More evidence is needed.
TCL1A 30617194 TRUE BL 5.9 4 5 5 FALSE TRUE 4.157043879907621 aSHM target genes have elevated mutation rate but the mutations may not represent drivers. More evidence is needed.
TET2 31558468 FALSE DLBCL 5.1 10.9 NA NA FALSE FALSE 5.311778290993072 DLBCL gene with extremely low mutation rate in BL
TFAP4 30617194 TRUE BL 10.6 9.9 12 11.9 TRUE FALSE 10.161662817551964 Confirmed by multiple studies
TMEM30A NA FALSE DLBCL 1.3 5 NA NA FALSE FALSE 1.8475750577367205 DLBCL gene with extremely low mutation rate in BL
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