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Datasets:
nicolynnvila
/
splicing_epistasis_okgp_tcga_driver_recurrent

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Tags:
genomics
splicing
epistasis
1000-genomes
oncokb
tcga
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Datasets
pandas
Polars
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epistasis_id
stringlengths
37
49
arm
stringclasses
2 values
gene
stringclasses
55 values
chrom
int64
1
22
mut1
stringlengths
18
24
mut2
stringlengths
18
24
distance
int64
1
100
n_mut1
int64
3
254
n_mut2
int64
3
254
n_both
int64
0
204
NCOA4:10:46029051:G:C|NCOA4:10:46029056:G:A
observed
NCOA4
10
NCOA4:10:46029051:G:C
NCOA4:10:46029056:G:A
5
18
88
1
STIL:1:47314012:C:T|STIL:1:47314021:C:T
observed
STIL
1
STIL:1:47314012:C:T
STIL:1:47314021:C:T
9
34
238
5
STIL:1:47313951:A:C|STIL:1:47314021:C:T
observed
STIL
1
STIL:1:47313951:A:C
STIL:1:47314021:C:T
70
89
238
18
ACVR2A:2:147913576:C:A|ACVR2A:2:147913614:A:G
observed
ACVR2A
2
ACVR2A:2:147913576:C:A
ACVR2A:2:147913614:A:G
38
67
69
3
ERC1:12:1487531:C:T|ERC1:12:1487557:G:A
observed
ERC1
12
ERC1:12:1487531:C:T
ERC1:12:1487557:G:A
26
41
55
1
POLG:15:89325271:T:A|POLG:15:89325342:C:A
observed
POLG
15
POLG:15:89325271:T:A
POLG:15:89325342:C:A
71
242
4
1
ERC1:12:1486650:C:A|ERC1:12:1486677:G:A
observed
ERC1
12
ERC1:12:1486650:C:A
ERC1:12:1486677:G:A
27
210
45
43
ERC1:12:1485326:A:T|ERC1:12:1485357:A:G
observed
ERC1
12
ERC1:12:1485326:A:T
ERC1:12:1485357:A:G
31
68
81
1
POLG:15:89321383:G:A|POLG:15:89321459:G:C
observed
POLG
15
POLG:15:89321383:G:A
POLG:15:89321459:G:C
76
185
86
18
FANCI:15:89292723:C:T|FANCI:15:89292751:C:A
observed
FANCI
15
FANCI:15:89292723:C:T
FANCI:15:89292751:C:A
28
157
33
5
PTK7:6:43147192:T:C|PTK7:6:43147204:T:C
observed
PTK7
6
PTK7:6:43147192:T:C
PTK7:6:43147204:T:C
12
86
13
2
DNMT3A:2:25326110:G:A|DNMT3A:2:25326131:T:C
observed
DNMT3A
2
DNMT3A:2:25326110:G:A
DNMT3A:2:25326131:T:C
21
178
34
1
SLX4:16:3590783:G:A|SLX4:16:3590814:C:G
observed
SLX4
16
SLX4:16:3590783:G:A
SLX4:16:3590814:C:G
31
200
88
3
APOBEC3B:22:38989417:G:T|APOBEC3B:22:38989458:T:C
observed
APOBEC3B
22
APOBEC3B:22:38989417:G:T
APOBEC3B:22:38989458:T:C
41
13
12
2
ERC1:12:1486676:C:T|ERC1:12:1486677:G:A
observed
ERC1
12
ERC1:12:1486676:C:T
ERC1:12:1486677:G:A
1
219
45
1
MOB3B:9:27516585:G:A|MOB3B:9:27516622:C:T
observed
MOB3B
9
MOB3B:9:27516585:G:A
MOB3B:9:27516622:C:T
37
31
17
1
ACSL3:2:222918461:A:G|ACSL3:2:222918537:G:A
observed
ACSL3
2
ACSL3:2:222918461:A:G
ACSL3:2:222918537:G:A
76
6
228
6
FCGR2B:1:161672893:G:A|FCGR2B:1:161672906:A:G
observed
FCGR2B
1
FCGR2B:1:161672893:G:A
FCGR2B:1:161672906:A:G
13
41
8
1
ERC1:12:1484773:G:A|ERC1:12:1484778:C:T
observed
ERC1
12
ERC1:12:1484773:G:A
ERC1:12:1484778:C:T
5
46
4
1
MOB3B:9:27518751:G:A|MOB3B:9:27518774:G:A
observed
MOB3B
9
MOB3B:9:27518751:G:A
MOB3B:9:27518774:G:A
23
19
158
1
JAK1:1:64982737:A:G|JAK1:1:64982750:G:T
observed
JAK1
1
JAK1:1:64982737:A:G
JAK1:1:64982750:G:T
13
160
6
2
SLX4:16:3606746:T:C|SLX4:16:3606778:G:A
observed
SLX4
16
SLX4:16:3606746:T:C
SLX4:16:3606778:G:A
32
5
51
1
POLG:15:89311537:C:T|POLG:15:89311582:C:T
observed
POLG
15
POLG:15:89311537:C:T
POLG:15:89311582:C:T
45
175
69
10
POLG:15:89312713:G:T|POLG:15:89312792:C:T
observed
POLG
15
POLG:15:89312713:G:T
POLG:15:89312792:C:T
79
154
11
1
AXL:19:41256080:G:T|AXL:19:41256095:G:T
observed
AXL
19
AXL:19:41256080:G:T
AXL:19:41256095:G:T
15
54
178
2
EPHA7:6:93391994:T:C|EPHA7:6:93392013:T:A
observed
EPHA7
6
EPHA7:6:93391994:T:C
EPHA7:6:93392013:T:A
19
13
58
1
EPHA7:6:93387962:G:A|EPHA7:6:93387974:G:A
observed
EPHA7
6
EPHA7:6:93387962:G:A
EPHA7:6:93387974:G:A
12
135
7
6
CDKN2A:9:21975696:G:A|CDKN2A:9:21975703:G:T
observed
CDKN2A
9
CDKN2A:9:21975696:G:A
CDKN2A:9:21975703:G:T
7
232
5
1
ERC1:12:1485330:A:G|ERC1:12:1485357:A:G
observed
ERC1
12
ERC1:12:1485330:A:G
ERC1:12:1485357:A:G
27
65
81
1
ZBTB7A:19:4056490:G:A|ZBTB7A:19:4056534:G:A
observed
ZBTB7A
19
ZBTB7A:19:4056490:G:A
ZBTB7A:19:4056534:G:A
44
120
9
1
PTCH1:9:95507757:T:C|PTCH1:9:95507764:C:T
observed
PTCH1
9
PTCH1:9:95507757:T:C
PTCH1:9:95507764:C:T
7
31
35
1
SETD5:3:9443235:G:C|SETD5:3:9443266:A:T
observed
SETD5
3
SETD5:3:9443235:G:C
SETD5:3:9443266:A:T
31
3
57
1
CSF1:1:109927497:G:A|CSF1:1:109927551:C:T
observed
CSF1
1
CSF1:1:109927497:G:A
CSF1:1:109927551:C:T
54
4
85
1
ARID4B:1:235277636:G:T|ARID4B:1:235277640:G:T
observed
ARID4B
1
ARID4B:1:235277636:G:T
ARID4B:1:235277640:G:T
4
6
11
4
ERC1:12:1440397:G:A|ERC1:12:1440441:C:T
observed
ERC1
12
ERC1:12:1440397:G:A
ERC1:12:1440441:C:T
44
149
99
6
PRKCI:3:170227096:A:C|PRKCI:3:170227132:T:C
observed
PRKCI
3
PRKCI:3:170227096:A:C
PRKCI:3:170227132:T:C
36
137
4
1
WT1:11:32418810:G:A|WT1:11:32418830:C:A
observed
WT1
11
WT1:11:32418810:G:A
WT1:11:32418830:C:A
20
62
37
1
APOBEC3B:22:38989417:G:T|APOBEC3B:22:38989418:A:C
observed
APOBEC3B
22
APOBEC3B:22:38989417:G:T
APOBEC3B:22:38989418:A:C
1
13
13
13
NT5C2:10:103221861:G:T|NT5C2:10:103221879:G:A
observed
NT5C2
10
NT5C2:10:103221861:G:T
NT5C2:10:103221879:G:A
18
132
10
1
IKZF2:2:213146649:G:A|IKZF2:2:213146728:C:T
observed
IKZF2
2
IKZF2:2:213146649:G:A
IKZF2:2:213146728:C:T
79
81
8
1
FANCI:15:89279114:C:G|FANCI:15:89279163:T:C
observed
FANCI
15
FANCI:15:89279114:C:G
FANCI:15:89279163:T:C
49
6
252
1
STIL:1:47302512:G:A|STIL:1:47302563:A:G
observed
STIL
1
STIL:1:47302512:G:A
STIL:1:47302563:A:G
51
31
27
1
TEK:9:27206824:C:T|TEK:9:27206868:C:T
observed
TEK
9
TEK:9:27206824:C:T
TEK:9:27206868:C:T
44
27
39
1
CRBN:3:3161462:T:C|CRBN:3:3161474:C:T
observed
CRBN
3
CRBN:3:3161462:T:C
CRBN:3:3161474:C:T
12
15
86
15
TEK:9:27217311:A:G|TEK:9:27217409:G:A
observed
TEK
9
TEK:9:27217311:A:G
TEK:9:27217409:G:A
98
69
100
1
MGA:15:41715052:G:A|MGA:15:41715077:C:A
observed
MGA
15
MGA:15:41715052:G:A
MGA:15:41715077:C:A
25
67
41
1
MGA:15:41718287:G:A|MGA:15:41718307:A:G
observed
MGA
15
MGA:15:41718287:G:A
MGA:15:41718307:A:G
20
11
200
1
TFG:3:100717694:A:G|TFG:3:100717781:G:A
observed
TFG
3
TFG:3:100717694:A:G
TFG:3:100717781:G:A
87
4
143
4
PRKCI:3:170278373:C:T|PRKCI:3:170278422:C:T
observed
PRKCI
3
PRKCI:3:170278373:C:T
PRKCI:3:170278422:C:T
49
20
66
1
DNMT3A:2:25263562:T:C|DNMT3A:2:25263621:C:T
observed
DNMT3A
2
DNMT3A:2:25263562:T:C
DNMT3A:2:25263621:C:T
59
6
24
1
ERC1:12:1399028:C:G|ERC1:12:1399082:A:T
observed
ERC1
12
ERC1:12:1399028:C:G
ERC1:12:1399082:A:T
54
43
114
3
TEK:9:27172821:C:G|TEK:9:27172872:C:T
observed
TEK
9
TEK:9:27172821:C:G
TEK:9:27172872:C:T
51
52
20
17
CRBN:3:3149374:G:C|CRBN:3:3149466:G:T
observed
CRBN
3
CRBN:3:3149374:G:C
CRBN:3:3149466:G:T
92
228
16
3
TFG:3:100748556:G:A|TFG:3:100748569:A:G
observed
TFG
3
TFG:3:100748556:G:A
TFG:3:100748569:A:G
13
5
62
1
PTCH1:9:95483683:T:C|PTCH1:9:95483772:T:G
observed
PTCH1
9
PTCH1:9:95483683:T:C
PTCH1:9:95483772:T:G
89
9
177
1
DAZAP1:19:1416845:G:A|DAZAP1:19:1416904:G:A
observed
DAZAP1
19
DAZAP1:19:1416845:G:A
DAZAP1:19:1416904:G:A
59
5
232
1
TEK:9:27209471:A:C|TEK:9:27209559:C:T
observed
TEK
9
TEK:9:27209471:A:C
TEK:9:27209559:C:T
88
172
92
1
DNMT3A:2:25323539:G:A|DNMT3A:2:25323567:A:G
observed
DNMT3A
2
DNMT3A:2:25323539:G:A
DNMT3A:2:25323567:A:G
28
8
168
1
ACSL6:5:132000838:G:A|ACSL6:5:132000881:G:A
observed
ACSL6
5
ACSL6:5:132000838:G:A
ACSL6:5:132000881:G:A
43
62
40
1
APOBEC3B:22:38988744:T:G|APOBEC3B:22:38988841:G:A
observed
APOBEC3B
22
APOBEC3B:22:38988744:T:G
APOBEC3B:22:38988841:G:A
97
88
95
88
ACSL3:2:222936935:G:A|ACSL3:2:222936997:C:T
observed
ACSL3
2
ACSL3:2:222936935:G:A
ACSL3:2:222936997:C:T
62
17
51
1
DNMT3A:2:25307147:C:T|DNMT3A:2:25307211:T:C
observed
DNMT3A
2
DNMT3A:2:25307147:C:T
DNMT3A:2:25307211:T:C
64
34
48
1
GNA12:7:2812783:A:C|GNA12:7:2812847:G:A
observed
GNA12
7
GNA12:7:2812783:A:C
GNA12:7:2812847:G:A
64
118
43
2
FANCI:15:89288338:A:C|FANCI:15:89288376:A:C
observed
FANCI
15
FANCI:15:89288338:A:C
FANCI:15:89288376:A:C
38
156
24
2
DNMT3B:20:32804339:G:C|DNMT3B:20:32804358:G:A
observed
DNMT3B
20
DNMT3B:20:32804339:G:C
DNMT3B:20:32804358:G:A
19
115
3
2
ARID4B:1:235208044:T:C|ARID4B:1:235208111:G:A
observed
ARID4B
1
ARID4B:1:235208044:T:C
ARID4B:1:235208111:G:A
67
24
5
1
TEK:9:27221162:G:A|TEK:9:27221184:G:A
observed
TEK
9
TEK:9:27221162:G:A
TEK:9:27221184:G:A
22
16
158
2
JAK1:1:64840464:T:C|JAK1:1:64840518:G:A
observed
JAK1
1
JAK1:1:64840464:T:C
JAK1:1:64840518:G:A
54
14
107
2
DAZAP1:19:1407896:C:T|DAZAP1:19:1407915:C:T
observed
DAZAP1
19
DAZAP1:19:1407896:C:T
DAZAP1:19:1407915:C:T
19
20
43
2
PLAG1:8:56161240:T:G|PLAG1:8:56161250:A:G
observed
PLAG1
8
PLAG1:8:56161240:T:G
PLAG1:8:56161250:A:G
10
162
28
28
TLE1:9:81611358:T:C|TLE1:9:81611407:A:G
observed
TLE1
9
TLE1:9:81611358:T:C
TLE1:9:81611407:A:G
49
159
24
3
FANCI:15:89285089:C:A|FANCI:15:89285100:A:G
observed
FANCI
15
FANCI:15:89285089:C:A
FANCI:15:89285100:A:G
11
38
5
1
ACSL3:2:222874718:C:T|ACSL3:2:222874814:A:G
observed
ACSL3
2
ACSL3:2:222874718:C:T
ACSL3:2:222874814:A:G
96
8
194
3
PC:11:66886582:A:G|PC:11:66886646:T:C
observed
PC
11
PC:11:66886582:A:G
PC:11:66886646:T:C
64
232
3
1
ELN:7:74064146:T:C|ELN:7:74064212:A:G
observed
ELN
7
ELN:7:74064146:T:C
ELN:7:74064212:A:G
66
47
5
4
POLG:15:89309000:C:G|POLG:15:89309048:T:C
observed
POLG
15
POLG:15:89309000:C:G
POLG:15:89309048:T:C
48
15
5
1
MOB3B:9:27491746:G:A|MOB3B:9:27491793:A:G
observed
MOB3B
9
MOB3B:9:27491746:G:A
MOB3B:9:27491793:A:G
47
29
52
1
TEK:9:27117007:G:A|TEK:9:27117011:G:T
observed
TEK
9
TEK:9:27117007:G:A
TEK:9:27117011:G:T
4
80
23
4
POLG:15:89317700:T:G|POLG:15:89317779:T:C
observed
POLG
15
POLG:15:89317700:T:G
POLG:15:89317779:T:C
79
74
11
11
SETD5:3:9471435:G:C|SETD5:3:9471504:G:T
observed
SETD5
3
SETD5:3:9471435:G:C
SETD5:3:9471504:G:T
69
67
4
1
PRKCI:3:170248551:A:G|PRKCI:3:170248605:C:T
observed
PRKCI
3
PRKCI:3:170248551:A:G
PRKCI:3:170248605:C:T
54
3
122
3
SP140:2:230261848:A:C|SP140:2:230261934:C:T
observed
SP140
2
SP140:2:230261848:A:C
SP140:2:230261934:C:T
86
58
105
3
JAK1:1:64860422:T:G|JAK1:1:64860461:T:C
observed
JAK1
1
JAK1:1:64860422:T:G
JAK1:1:64860461:T:C
39
10
189
1
CDK8:13:26334462:C:G|CDK8:13:26334484:C:A
observed
CDK8
13
CDK8:13:26334462:C:G
CDK8:13:26334484:C:A
22
3
191
3
SLX4:16:3594325:G:C|SLX4:16:3594326:G:A
observed
SLX4
16
SLX4:16:3594325:G:C
SLX4:16:3594326:G:A
1
15
15
15
IKZF2:2:213142249:T:C|IKZF2:2:213142282:T:C
observed
IKZF2
2
IKZF2:2:213142249:T:C
IKZF2:2:213142282:T:C
33
6
106
1
QKI:6:163473389:A:C|QKI:6:163473485:C:T
observed
QKI
6
QKI:6:163473389:A:C
QKI:6:163473485:C:T
96
193
5
5
DNMT3B:20:32792009:A:G|DNMT3B:20:32792081:T:C
observed
DNMT3B
20
DNMT3B:20:32792009:A:G
DNMT3B:20:32792081:T:C
72
39
99
39
IKZF2:2:213142221:C:T|IKZF2:2:213142282:T:C
observed
IKZF2
2
IKZF2:2:213142221:C:T
IKZF2:2:213142282:T:C
61
10
106
1
FANCI:15:89272991:G:C|FANCI:15:89273043:T:C
observed
FANCI
15
FANCI:15:89272991:G:C
FANCI:15:89273043:T:C
52
157
21
3
PLAG1:8:56173063:C:T|PLAG1:8:56173103:C:A
observed
PLAG1
8
PLAG1:8:56173063:C:T
PLAG1:8:56173103:C:A
40
146
79
6
CRTC1:19:18701479:G:A|CRTC1:19:18701571:T:G
observed
CRTC1
19
CRTC1:19:18701479:G:A
CRTC1:19:18701571:T:G
92
5
59
5
GNA12:7:2783361:G:T|GNA12:7:2783403:C:T
observed
GNA12
7
GNA12:7:2783361:G:T
GNA12:7:2783403:C:T
42
21
87
1
JAK1:1:64972854:C:T|JAK1:1:64972924:G:A
observed
JAK1
1
JAK1:1:64972854:C:T
JAK1:1:64972924:G:A
70
108
20
20
NCOA4:10:46024436:T:C|NCOA4:10:46024534:G:A
observed
NCOA4
10
NCOA4:10:46024436:T:C
NCOA4:10:46024534:G:A
98
51
10
1
NT5C2:10:103227636:T:C|NT5C2:10:103227667:T:G
observed
NT5C2
10
NT5C2:10:103227636:T:C
NT5C2:10:103227667:T:G
31
17
21
17
IKZF2:2:213137784:T:C|IKZF2:2:213137864:C:T
observed
IKZF2
2
IKZF2:2:213137784:T:C
IKZF2:2:213137864:C:T
80
12
29
1
MOB3B:9:27454384:T:C|MOB3B:9:27454387:G:A
observed
MOB3B
9
MOB3B:9:27454384:T:C
MOB3B:9:27454387:G:A
3
61
114
4
CBLB:3:105689520:A:G|CBLB:3:105689610:A:G
observed
CBLB
3
CBLB:3:105689520:A:G
CBLB:3:105689610:A:G
90
7
30
1
EZR:6:158778147:T:A|EZR:6:158778162:A:C
observed
EZR
6
EZR:6:158778147:T:A
EZR:6:158778162:A:C
15
12
95
1
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Splicing epistasis — Driver+TCGA-recurrent panel (Panel A)

12,714 cis-double SNV pairs (6,357 observed + 6,357 unobserved-matched) in 1000 Genomes across 56 genes that satisfy:

  • listed in OncoKB cancerGeneList.tsv (any inclusion criterion), AND
  • carry ≥2 TCGA-clean double-mutation pairs each with ≥5 carriers (per tcga_de_novo_pairs_clean.csv from the original paper-2 code dump)

Built as the driver arm of a three-panel strict test that disentangles cancer-driver status from TCGA-recurrent-doublet status. Companion panels:

  • splicing_epistasis_okgp_tcga_nondriver_recurrent — 663 non-driver TCGA-recurrent genes
  • splicing_epistasis_okgp_tcga_silent_control — 719 random TCGA-silent genes

Methodology

Same as paper §2 ¶1-5:

  • ≤100 nt intra-gene window
  • ≥3 1KG carriers per constituent
  • TopLD r² ≥ 0.2 dropped
  • Greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt
  • seed=42

Files

  • inputs.parquet — 12,714 matched-arm pairs (observed + unobserved). Score with the same per_pair Modal pipeline used for paper-138 / non-cancer-1000.
  • gene_panel.txt — the 56-gene list
  • stats.json — enumeration / matching counts
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