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Datasets:
nicolynnvila
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splicing_epistasis_okgp_tcga_silent_control

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Tags:
genomics
splicing
epistasis
1000-genomes
control
tcga-silent
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pandas
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epistasis_id
stringlengths
35
57
arm
stringclasses
2 values
gene
stringclasses
599 values
chrom
int64
1
22
mut1
stringlengths
17
28
mut2
stringlengths
17
28
distance
int64
1
100
n_mut1
int64
3
254
n_mut2
int64
3
254
n_both
int64
0
254
C11orf58:11:16739863:G:C|C11orf58:11:16739887:C:T
observed
C11orf58
11
C11orf58:11:16739863:G:C
C11orf58:11:16739887:C:T
24
77
71
4
NOS2:17:27796372:C:T|NOS2:17:27796468:T:A
observed
NOS2
17
NOS2:17:27796372:C:T
NOS2:17:27796468:T:A
96
3
17
1
ELOVL6:4:110084361:G:A|ELOVL6:4:110084391:T:C
observed
ELOVL6
4
ELOVL6:4:110084361:G:A
ELOVL6:4:110084391:T:C
30
160
216
3
KLHL22:22:20481505:G:A|KLHL22:22:20481509:G:A
observed
KLHL22
22
KLHL22:22:20481505:G:A
KLHL22:22:20481509:G:A
4
4
180
4
PTPRG:3:61612463:G:A|PTPRG:3:61612531:C:T
observed
PTPRG
3
PTPRG:3:61612463:G:A
PTPRG:3:61612531:C:T
68
180
18
2
RPL28:19:55395505:G:A|RPL28:19:55395507:C:G
observed
RPL28
19
RPL28:19:55395505:G:A
RPL28:19:55395507:C:G
2
10
216
1
SS18L2:3:42595970:A:G|SS18L2:3:42596054:G:A
observed
SS18L2
3
SS18L2:3:42595970:A:G
SS18L2:3:42596054:G:A
84
97
67
3
CCND1:11:69654262:A:G|CCND1:11:69654301:A:G
observed
CCND1
11
CCND1:11:69654262:A:G
CCND1:11:69654301:A:G
39
112
9
1
SCLT1:4:128956544:C:T|SCLT1:4:128956626:T:C
observed
SCLT1
4
SCLT1:4:128956544:C:T
SCLT1:4:128956626:T:C
82
90
29
1
ICAM2:17:64016390:T:C|ICAM2:17:64016434:T:A
observed
ICAM2
17
ICAM2:17:64016390:T:C
ICAM2:17:64016434:T:A
44
89
14
2
EYA2:20:47140042:A:T|EYA2:20:47140133:G:A
observed
EYA2
20
EYA2:20:47140042:A:T
EYA2:20:47140133:G:A
91
91
87
3
DCDC2C:2:3813074:T:A|DCDC2C:2:3813076:T:A
observed
DCDC2C
2
DCDC2C:2:3813074:T:A
DCDC2C:2:3813076:T:A
2
38
48
17
FRYL:4:48753809:G:A|FRYL:4:48753816:G:A
observed
FRYL
4
FRYL:4:48753809:G:A
FRYL:4:48753816:G:A
7
94
8
8
SAMD5:6:147724139:A:G|SAMD5:6:147724159:A:G
observed
SAMD5
6
SAMD5:6:147724139:A:G
SAMD5:6:147724159:A:G
20
115
15
1
PTEN:10:87903688:C:T|PTEN:10:87903696:G:A
observed
PTEN
10
PTEN:10:87903688:C:T
PTEN:10:87903696:G:A
8
52
6
1
C12orf42:12:103405003:A:G|C12orf42:12:103405075:C:T
observed
C12orf42
12
C12orf42:12:103405003:A:G
C12orf42:12:103405075:C:T
72
3
102
1
MECR:1:29226244:T:C|MECR:1:29226309:C:T
observed
MECR
1
MECR:1:29226244:T:C
MECR:1:29226309:C:T
65
48
26
26
FRYL:4:48723311:T:C|FRYL:4:48723372:G:A
observed
FRYL
4
FRYL:4:48723311:T:C
FRYL:4:48723372:G:A
61
160
22
22
OR52M1:11:4545699:C:T|OR52M1:11:4545709:A:G
observed
OR52M1
11
OR52M1:11:4545699:C:T
OR52M1:11:4545709:A:G
10
5
90
1
GNB5:15:52164119:T:C|GNB5:15:52164205:G:A
observed
GNB5
15
GNB5:15:52164119:T:C
GNB5:15:52164205:G:A
86
24
6
1
CLDND2:19:51368785:C:T|CLDND2:19:51368840:C:G
observed
CLDND2
19
CLDND2:19:51368785:C:T
CLDND2:19:51368840:C:G
55
82
19
1
KRTAP5-1:11:1585172:G:A|KRTAP5-1:11:1585192:C:T
observed
KRTAP5-1
11
KRTAP5-1:11:1585172:G:A
KRTAP5-1:11:1585192:C:T
20
36
39
32
SALL3:18:78988356:T:C|SALL3:18:78988364:G:T
observed
SALL3
18
SALL3:18:78988356:T:C
SALL3:18:78988364:G:T
8
7
121
2
ANAPC15:11:72112561:G:C|ANAPC15:11:72112602:A:G
observed
ANAPC15
11
ANAPC15:11:72112561:G:C
ANAPC15:11:72112602:A:G
41
3
3
3
RPL4:15:66510778:A:G|RPL4:15:66510815:A:G
observed
RPL4
15
RPL4:15:66510778:A:G
RPL4:15:66510815:A:G
37
19
85
4
PCDHB15:5:141247150:G:T|PCDHB15:5:141247210:G:A
observed
PCDHB15
5
PCDHB15:5:141247150:G:T
PCDHB15:5:141247210:G:A
60
10
36
10
C2CD4C:19:406855:C:T|C2CD4C:19:406927:C:A
observed
C2CD4C
19
C2CD4C:19:406855:C:T
C2CD4C:19:406927:C:A
72
14
33
1
CHRM1:11:62909880:G:A|CHRM1:11:62909964:T:G
observed
CHRM1
11
CHRM1:11:62909880:G:A
CHRM1:11:62909964:T:G
84
121
7
1
ARRDC2:19:18002900:C:T|ARRDC2:19:18002976:G:A
observed
ARRDC2
19
ARRDC2:19:18002900:C:T
ARRDC2:19:18002976:G:A
76
203
7
1
LILRA4:19:54334988:T:A|LILRA4:19:54335048:A:T
observed
LILRA4
19
LILRA4:19:54334988:T:A
LILRA4:19:54335048:A:T
60
20
170
20
SKA2:17:59116760:T:A|SKA2:17:59116761:T:A
observed
SKA2
17
SKA2:17:59116760:T:A
SKA2:17:59116761:T:A
1
4
4
4
LARS1:5:146114833:C:T|LARS1:5:146114834:C:T
observed
LARS1
5
LARS1:5:146114833:C:T
LARS1:5:146114834:C:T
1
60
25
1
CNTNAP2:7:146470526:G:A|CNTNAP2:7:146470597:A:G
observed
CNTNAP2
7
CNTNAP2:7:146470526:G:A
CNTNAP2:7:146470597:A:G
71
5
16
1
RAB11B:19:8402107:C:T|RAB11B:19:8402206:C:A
observed
RAB11B
19
RAB11B:19:8402107:C:T
RAB11B:19:8402206:C:A
99
81
26
2
ZNF670:1:247068942:G:A|ZNF670:1:247069042:C:T
observed
ZNF670
1
ZNF670:1:247068942:G:A
ZNF670:1:247069042:C:T
100
50
13
3
CACNA1D:3:53361813:C:T|CACNA1D:3:53361887:C:T
observed
CACNA1D
3
CACNA1D:3:53361813:C:T
CACNA1D:3:53361887:C:T
74
12
54
2
PINX1:8:10798850:G:C|PINX1:8:10798879:C:A
observed
PINX1
8
PINX1:8:10798850:G:C
PINX1:8:10798879:C:A
29
60
116
1
TRPM6:9:74803210:G:T|TRPM6:9:74803262:A:C
observed
TRPM6
9
TRPM6:9:74803210:G:T
TRPM6:9:74803262:A:C
52
44
52
2
FOXF2:6:1394949:G:A|FOXF2:6:1394951:G:A
observed
FOXF2
6
FOXF2:6:1394949:G:A
FOXF2:6:1394951:G:A
2
33
5
1
STK11IP:2:219608417:G:C|STK11IP:2:219608435:G:A
observed
STK11IP
2
STK11IP:2:219608417:G:C
STK11IP:2:219608435:G:A
18
100
7
7
SPTBN1:2:54620130:C:T|SPTBN1:2:54620204:G:T
observed
SPTBN1
2
SPTBN1:2:54620130:C:T
SPTBN1:2:54620204:G:T
74
134
32
1
ILK:11:6604700:G:A|ILK:11:6604725:A:G
observed
ILK
11
ILK:11:6604700:G:A
ILK:11:6604725:A:G
25
237
3
1
TMEM266:15:76188658:T:C|TMEM266:15:76188754:G:A
observed
TMEM266
15
TMEM266:15:76188658:T:C
TMEM266:15:76188754:G:A
96
28
8
8
SERPINB7:18:63779863:T:A|SERPINB7:18:63779883:A:C
observed
SERPINB7
18
SERPINB7:18:63779863:T:A
SERPINB7:18:63779883:A:C
20
13
13
13
KLHL22:22:20460911:G:A|KLHL22:22:20460979:T:G
observed
KLHL22
22
KLHL22:22:20460911:G:A
KLHL22:22:20460979:T:G
68
4
178
4
ATP2C2:16:84416883:G:A|ATP2C2:16:84416884:G:T
observed
ATP2C2
16
ATP2C2:16:84416883:G:A
ATP2C2:16:84416884:G:T
1
14
211
14
SPAG16:2:214306917:A:C|SPAG16:2:214306944:G:A
observed
SPAG16
2
SPAG16:2:214306917:A:C
SPAG16:2:214306944:G:A
27
11
11
11
PTPN7:1:202152487:G:C|PTPN7:1:202152555:C:T
observed
PTPN7
1
PTPN7:1:202152487:G:C
PTPN7:1:202152555:C:T
68
74
12
1
ESR2:14:64225434:T:G|ESR2:14:64225435:C:A
observed
ESR2
14
ESR2:14:64225434:T:G
ESR2:14:64225435:C:A
1
3
3
3
HOATZ:11:111529491:G:A|HOATZ:11:111529583:C:T
observed
HOATZ
11
HOATZ:11:111529491:G:A
HOATZ:11:111529583:C:T
92
48
193
6
ARRDC2:19:18006918:C:T|ARRDC2:19:18006945:A:T
observed
ARRDC2
19
ARRDC2:19:18006918:C:T
ARRDC2:19:18006945:A:T
27
10
103
2
MED15:22:20572746:C:G|MED15:22:20572812:C:T
observed
MED15
22
MED15:22:20572746:C:G
MED15:22:20572812:C:T
66
18
40
1
ATP8A2:13:25641015:C:T|ATP8A2:13:25641037:G:A
observed
ATP8A2
13
ATP8A2:13:25641015:C:T
ATP8A2:13:25641037:G:A
22
73
27
2
SAMD5:6:147675750:A:C|SAMD5:6:147675826:G:A
observed
SAMD5
6
SAMD5:6:147675750:A:C
SAMD5:6:147675826:G:A
76
11
159
2
PPP1R26:9:135484687:T:C|PPP1R26:9:135484751:G:A
observed
PPP1R26
9
PPP1R26:9:135484687:T:C
PPP1R26:9:135484751:G:A
64
42
8
8
KLK7:19:50984037:C:A|KLK7:19:50984097:C:G
observed
KLK7
19
KLK7:19:50984037:C:A
KLK7:19:50984097:C:G
60
3
3
3
RAPGEF4:2:172913424:A:G|RAPGEF4:2:172913475:C:T
observed
RAPGEF4
2
RAPGEF4:2:172913424:A:G
RAPGEF4:2:172913475:C:T
51
223
7
7
FKBP8:19:18537575:C:T|FKBP8:19:18537588:C:T
observed
FKBP8
19
FKBP8:19:18537575:C:T
FKBP8:19:18537588:C:T
13
5
159
1
ABTB1:3:127673355:G:A|ABTB1:3:127673417:G:A
observed
ABTB1
3
ABTB1:3:127673355:G:A
ABTB1:3:127673417:G:A
62
53
3
1
POLD1:19:50397699:G:A|POLD1:19:50397768:T:G
observed
POLD1
19
POLD1:19:50397699:G:A
POLD1:19:50397768:T:G
69
20
152
3
CDA:1:20600303:G:T|CDA:1:20600358:G:C
observed
CDA
1
CDA:1:20600303:G:T
CDA:1:20600358:G:C
55
9
23
1
PLAAT1:3:193257297:A:G|PLAAT1:3:193257376:A:G
observed
PLAAT1
3
PLAAT1:3:193257297:A:G
PLAAT1:3:193257376:A:G
79
153
81
9
KPNA4:3:160500148:C:A|KPNA4:3:160500149:A:C
observed
KPNA4
3
KPNA4:3:160500148:C:A
KPNA4:3:160500149:A:C
1
12
12
12
TMPRSS12:12:50850776:C:T|TMPRSS12:12:50850817:C:T
observed
TMPRSS12
12
TMPRSS12:12:50850776:C:T
TMPRSS12:12:50850817:C:T
41
11
12
11
CCKBR:11:6266715:A:G|CCKBR:11:6266765:C:G
observed
CCKBR
11
CCKBR:11:6266715:A:G
CCKBR:11:6266765:C:G
50
4
4
4
TNNT1:19:55142092:C:T|TNNT1:19:55142151:T:C
observed
TNNT1
19
TNNT1:19:55142092:C:T
TNNT1:19:55142151:T:C
59
6
107
2
ANKRD33B:5:10653038:T:G|ANKRD33B:5:10653045:T:A
observed
ANKRD33B
5
ANKRD33B:5:10653038:T:G
ANKRD33B:5:10653045:T:A
7
53
24
2
ZNF626:19:20629064:G:C|ZNF626:19:20629101:G:A
observed
ZNF626
19
ZNF626:19:20629064:G:C
ZNF626:19:20629101:G:A
37
5
8
3
DNAH11:7:21607446:A:G|DNAH11:7:21607508:C:A
observed
DNAH11
7
DNAH11:7:21607446:A:G
DNAH11:7:21607508:C:A
62
143
88
10
STOX2:4:183892428:G:A|STOX2:4:183892439:C:T
observed
STOX2
4
STOX2:4:183892428:G:A
STOX2:4:183892439:C:T
11
4
4
1
ROS1:6:117373549:G:A|ROS1:6:117373572:G:A
observed
ROS1
6
ROS1:6:117373549:G:A
ROS1:6:117373572:G:A
23
58
24
1
MYEOV:11:69326750:T:C|MYEOV:11:69326840:T:C
observed
MYEOV
11
MYEOV:11:69326750:T:C
MYEOV:11:69326840:T:C
90
8
102
8
MAD2L2:1:11659234:A:G|MAD2L2:1:11659246:G:T
observed
MAD2L2
1
MAD2L2:1:11659234:A:G
MAD2L2:1:11659246:G:T
12
118
8
1
FURIN:15:90873642:G:T|FURIN:15:90873713:C:G
observed
FURIN
15
FURIN:15:90873642:G:T
FURIN:15:90873713:C:G
71
233
5
5
MIS18A:21:32270481:G:A|MIS18A:21:32270526:G:A
observed
MIS18A
21
MIS18A:21:32270481:G:A
MIS18A:21:32270526:G:A
45
39
87
5
SLC66A2:18:79913896:C:T|SLC66A2:18:79913972:G:A
observed
SLC66A2
18
SLC66A2:18:79913896:C:T
SLC66A2:18:79913972:G:A
76
109
7
1
CISD3:17:38735499:C:T|CISD3:17:38735552:G:A
observed
CISD3
17
CISD3:17:38735499:C:T
CISD3:17:38735552:G:A
53
12
5
1
EXTL3:8:28623343:G:C|EXTL3:8:28623414:G:A
observed
EXTL3
8
EXTL3:8:28623343:G:C
EXTL3:8:28623414:G:A
71
16
18
16
TMEM38A:19:16665290:G:A|TMEM38A:19:16665317:A:T
observed
TMEM38A
19
TMEM38A:19:16665290:G:A
TMEM38A:19:16665317:A:T
27
3
96
1
CEMIP2:9:71707620:G:A|CEMIP2:9:71707709:G:A
observed
CEMIP2
9
CEMIP2:9:71707620:G:A
CEMIP2:9:71707709:G:A
89
27
212
27
C1orf100:1:244388113:G:C|C1orf100:1:244388181:G:A
observed
C1orf100
1
C1orf100:1:244388113:G:C
C1orf100:1:244388181:G:A
68
18
3
1
CNTNAP2:7:146494587:G:A|CNTNAP2:7:146494686:G:C
observed
CNTNAP2
7
CNTNAP2:7:146494587:G:A
CNTNAP2:7:146494686:G:C
99
27
25
25
BMT2:7:112877585:A:G|BMT2:7:112877678:T:C
observed
BMT2
7
BMT2:7:112877585:A:G
BMT2:7:112877678:T:C
93
4
60
1
GPR78:4:8584386:C:T|GPR78:4:8584427:C:T
observed
GPR78
4
GPR78:4:8584386:C:T
GPR78:4:8584427:C:T
41
153
31
1
LRATD2:8:126552607:T:C|LRATD2:8:126552699:C:T
observed
LRATD2
8
LRATD2:8:126552607:T:C
LRATD2:8:126552699:C:T
92
8
17
1
SERPINH1:11:75566327:T:C|SERPINH1:11:75566331:C:T
observed
SERPINH1
11
SERPINH1:11:75566327:T:C
SERPINH1:11:75566331:C:T
4
16
133
1
MYO3B:2:170563064:T:A|MYO3B:2:170563089:T:C
observed
MYO3B
2
MYO3B:2:170563064:T:A
MYO3B:2:170563089:T:C
25
16
168
3
ZNF124:1:247150057:C:A|ZNF124:1:247150131:G:A
observed
ZNF124
1
ZNF124:1:247150057:C:A
ZNF124:1:247150131:G:A
74
35
16
1
WRN:8:31116120:C:T|WRN:8:31116126:C:T
observed
WRN
8
WRN:8:31116120:C:T
WRN:8:31116126:C:T
6
11
204
1
ZNF26:12:132996078:G:A|ZNF26:12:132996103:C:T
observed
ZNF26
12
ZNF26:12:132996078:G:A
ZNF26:12:132996103:C:T
25
12
86
1
FMOD:1:203340719:C:G|FMOD:1:203340744:T:C
observed
FMOD
1
FMOD:1:203340719:C:G
FMOD:1:203340744:T:C
25
43
8
8
SCD5:4:82670746:G:A|SCD5:4:82670756:A:G
observed
SCD5
4
SCD5:4:82670746:G:A
SCD5:4:82670756:A:G
10
185
8
1
CCND1:11:69650325:C:T|CCND1:11:69650326:G:A
observed
CCND1
11
CCND1:11:69650325:C:T
CCND1:11:69650326:G:A
1
93
43
4
POLR1F:7:19703866:T:C|POLR1F:7:19703887:G:C
observed
POLR1F
7
POLR1F:7:19703866:T:C
POLR1F:7:19703887:G:C
21
4
219
4
SLC66A2:18:79916286:C:T|SLC66A2:18:79916298:T:C
observed
SLC66A2
18
SLC66A2:18:79916286:C:T
SLC66A2:18:79916298:T:C
12
64
63
63
STOX2:4:183840380:C:T|STOX2:4:183840399:T:G
observed
STOX2
4
STOX2:4:183840380:C:T
STOX2:4:183840399:T:G
19
65
20
2
GPR78:4:8609131:C:T|GPR78:4:8609163:T:C
observed
GPR78
4
GPR78:4:8609131:C:T
GPR78:4:8609163:T:C
32
7
73
1
MYEOV:11:69329683:G:A|MYEOV:11:69329703:C:G
observed
MYEOV
11
MYEOV:11:69329683:G:A
MYEOV:11:69329703:C:G
20
116
102
11
ZNF676:19:22186055:T:G|ZNF676:19:22186078:G:A
observed
ZNF676
19
ZNF676:19:22186055:T:G
ZNF676:19:22186078:G:A
23
69
17
1
FBXL22:15:63601009:C:A|FBXL22:15:63601045:G:T
observed
FBXL22
15
FBXL22:15:63601009:C:A
FBXL22:15:63601045:G:T
36
7
193
1
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Splicing epistasis — TCGA-silent control panel (Panel C)

143,408 cis-double SNV pairs (71,704 observed + 71,704 unobserved-matched) in 1000 Genomes across 719 randomly sampled protein-coding genes that have zero TCGA double-mutation pairs in tcga_de_novo_pairs_clean_relaxed.csv (the broad TCGA pair pool).

Built as the null arm of a three-panel strict test. These genes show no evidence of recurrent doublet events in TCGA — the prediction is that they should show no 1KG depletion either.

Methodology

Same as paper §2 ¶1-5:

  • Sample 719 protein-coding MANE-select genes uniformly at random from the TCGA-silent universe
  • ≤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

Panel size (719) matches the combined size of Panel A (56 drivers) + Panel B (663 non-drivers).

Files

  • inputs.parquet — 143,408 matched-arm pairs
  • gene_panel.txt — the 719-gene list
  • stats.json — enumeration / matching counts
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Number of rows:
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Total file size:
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