(primary solid tumor cohort)
This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 120 genes and 10 clinical features across 155 patients, 23 significant findings detected with Q value < 0.25.
-
BRAF mutation correlated to 'HISTOLOGICAL.TYPE'.
-
NRXN1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ACVR2A mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
CNBD1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
BTNL8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
GGT1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
GRIK3 mutation correlated to 'AGE'.
-
CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ERBB4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
IFT80 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
OR8J1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ZFHX4 mutation correlated to 'Time to Death'.
-
ZNF429 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
DKK4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
NALCN mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
SULT1C4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
UMOD mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
USP17L2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
FAM5C mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
OR6T1 mutation correlated to 'AGE'.
-
CYTL1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
NAALAD2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
TNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
BRAF | 20 (13%) | 135 |
0.82 (1.00) |
0.0257 (1.00) |
0.0586 (1.00) |
1.07e-05 (0.0126) |
0.149 (1.00) |
0.755 (1.00) |
0.401 (1.00) |
0.536 (1.00) |
0.59 (1.00) |
0.822 (1.00) |
NRXN1 | 17 (11%) | 138 |
0.734 (1.00) |
0.592 (1.00) |
0.609 (1.00) |
1 (1.00) |
0.059 (1.00) |
0.0423 (1.00) |
0.732 (1.00) |
0.0599 (1.00) |
0.757 (1.00) |
5.76e-05 (0.0672) |
ACVR2A | 8 (5%) | 147 |
0.242 (1.00) |
0.703 (1.00) |
0.0337 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.369 (1.00) |
1 (1.00) |
0.55 (1.00) |
1 (1.00) |
1.69e-06 (0.00198) |
CNBD1 | 6 (4%) | 149 |
0.582 (1.00) |
0.736 (1.00) |
0.442 (1.00) |
1 (1.00) |
0.689 (1.00) |
0.16 (1.00) |
0.612 (1.00) |
0.13 (1.00) |
1 (1.00) |
5.86e-09 (6.94e-06) |
BTNL8 | 3 (2%) | 152 |
0.0121 (1.00) |
0.62 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.561 (1.00) |
1 (1.00) |
6.1e-09 (7.2e-06) |
|
GGT1 | 3 (2%) | 152 |
0.865 (1.00) |
0.62 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.561 (1.00) |
1 (1.00) |
6.1e-09 (7.2e-06) |
|
GRIK3 | 14 (9%) | 141 |
0.536 (1.00) |
3.04e-05 (0.0356) |
0.402 (1.00) |
0.465 (1.00) |
0.876 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.707 (1.00) |
0.00185 (1.00) |
CASP8 | 10 (6%) | 145 |
0.417 (1.00) |
0.0469 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.147 (1.00) |
0.125 (1.00) |
0.401 (1.00) |
0.156 (1.00) |
0.444 (1.00) |
2.26e-06 (0.00266) |
ERBB4 | 14 (9%) | 141 |
0.0025 (1.00) |
0.989 (1.00) |
0.101 (1.00) |
0.433 (1.00) |
0.0143 (1.00) |
0.0514 (1.00) |
0.283 (1.00) |
0.108 (1.00) |
0.463 (1.00) |
6.48e-06 (0.00759) |
IFT80 | 7 (5%) | 148 |
0.911 (1.00) |
0.852 (1.00) |
1 (1.00) |
0.305 (1.00) |
0.867 (1.00) |
0.321 (1.00) |
0.613 (1.00) |
0.552 (1.00) |
1 (1.00) |
3.01e-07 (0.000355) |
OR8J1 | 4 (3%) | 151 |
0.355 (1.00) |
0.273 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.356 (1.00) |
1 (1.00) |
6.02e-09 (7.12e-06) |
ZFHX4 | 17 (11%) | 138 |
2.48e-05 (0.029) |
0.778 (1.00) |
0.453 (1.00) |
0.284 (1.00) |
0.0148 (1.00) |
0.4 (1.00) |
0.725 (1.00) |
0.452 (1.00) |
0.752 (1.00) |
0.038 (1.00) |
ZNF429 | 7 (5%) | 148 |
0.623 (1.00) |
0.22 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.0625 (1.00) |
0.321 (1.00) |
0.612 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.00011 (0.128) |
DKK4 | 4 (3%) | 151 |
0.0582 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.118 (1.00) |
0.312 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.401 (1.00) |
1 (1.00) |
6.02e-09 (7.12e-06) |
NALCN | 14 (9%) | 141 |
0.302 (1.00) |
0.68 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.774 (1.00) |
0.147 (1.00) |
0.281 (1.00) |
0.00959 (1.00) |
1 (1.00) |
6.79e-05 (0.0792) |
SULT1C4 | 3 (2%) | 152 |
0.03 (1.00) |
0.931 (1.00) |
1 (1.00) |
0.0651 (1.00) |
0.199 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.561 (1.00) |
1 (1.00) |
6.1e-09 (7.2e-06) |
UMOD | 7 (5%) | 148 |
0.493 (1.00) |
0.556 (1.00) |
1 (1.00) |
0.305 (1.00) |
0.313 (1.00) |
0.321 (1.00) |
0.613 (1.00) |
0.412 (1.00) |
0.633 (1.00) |
0.00011 (0.128) |
USP17L2 | 7 (5%) | 148 |
0.302 (1.00) |
0.805 (1.00) |
1 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.0961 (1.00) |
0.613 (1.00) |
0.125 (1.00) |
0.633 (1.00) |
5.78e-09 (6.85e-06) |
FAM5C | 10 (6%) | 145 |
0.0122 (1.00) |
0.845 (1.00) |
0.21 (1.00) |
0.195 (1.00) |
0.147 (1.00) |
0.125 (1.00) |
0.4 (1.00) |
0.127 (1.00) |
0.639 (1.00) |
5.21e-08 (6.13e-05) |
OR6T1 | 6 (4%) | 149 |
0.502 (1.00) |
0.000122 (0.142) |
0.681 (1.00) |
1 (1.00) |
0.689 (1.00) |
0.624 (1.00) |
0.548 (1.00) |
0.148 (1.00) |
0.535 (1.00) |
0.646 (1.00) |
CYTL1 | 4 (3%) | 151 |
0.248 (1.00) |
1 (1.00) |
1 (1.00) |
0.0483 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.401 (1.00) |
1 (1.00) |
6.02e-09 (7.12e-06) |
|
NAALAD2 | 11 (7%) | 144 |
0.884 (1.00) |
0.544 (1.00) |
0.13 (1.00) |
0.0156 (1.00) |
0.00551 (1.00) |
0.139 (1.00) |
1 (1.00) |
0.286 (1.00) |
1 (1.00) |
3.34e-05 (0.039) |
TNR | 15 (10%) | 140 |
0.444 (1.00) |
0.493 (1.00) |
0.588 (1.00) |
0.465 (1.00) |
0.163 (1.00) |
0.00835 (1.00) |
0.722 (1.00) |
0.0146 (1.00) |
1 (1.00) |
1.39e-06 (0.00163) |
APC | 103 (66%) | 52 |
0.291 (1.00) |
0.627 (1.00) |
0.042 (1.00) |
0.645 (1.00) |
0.797 (1.00) |
0.944 (1.00) |
0.165 (1.00) |
0.272 (1.00) |
0.0378 (1.00) |
0.561 (1.00) |
FBXW7 | 29 (19%) | 126 |
0.841 (1.00) |
0.0362 (1.00) |
0.154 (1.00) |
0.00324 (1.00) |
0.112 (1.00) |
0.604 (1.00) |
0.0169 (1.00) |
0.00243 (1.00) |
0.0795 (1.00) |
0.774 (1.00) |
KRAS | 58 (37%) | 97 |
0.226 (1.00) |
0.00304 (1.00) |
0.246 (1.00) |
0.648 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.317 (1.00) |
0.606 (1.00) |
0.315 (1.00) |
0.4 (1.00) |
NRAS | 15 (10%) | 140 |
0.281 (1.00) |
0.168 (1.00) |
0.0269 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.083 (1.00) |
0.469 (1.00) |
0.732 (1.00) |
0.276 (1.00) |
0.134 (1.00) |
PIK3CA | 26 (17%) | 129 |
0.661 (1.00) |
0.198 (1.00) |
0.83 (1.00) |
0.134 (1.00) |
0.554 (1.00) |
0.0107 (1.00) |
0.333 (1.00) |
0.028 (1.00) |
0.445 (1.00) |
0.000236 (0.274) |
TP53 | 75 (48%) | 80 |
0.696 (1.00) |
0.0728 (1.00) |
0.336 (1.00) |
0.00383 (1.00) |
0.557 (1.00) |
0.254 (1.00) |
0.558 (1.00) |
0.102 (1.00) |
0.803 (1.00) |
0.122 (1.00) |
SMAD4 | 18 (12%) | 137 |
0.587 (1.00) |
0.833 (1.00) |
0.625 (1.00) |
0.149 (1.00) |
0.949 (1.00) |
0.834 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.772 (1.00) |
0.414 (1.00) |
FAM123B | 19 (12%) | 136 |
0.717 (1.00) |
0.527 (1.00) |
0.811 (1.00) |
0.489 (1.00) |
0.675 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.655 (1.00) |
TTN | 69 (45%) | 86 |
0.625 (1.00) |
0.267 (1.00) |
0.421 (1.00) |
0.0237 (1.00) |
0.281 (1.00) |
0.166 (1.00) |
0.288 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.966 (1.00) |
WBSCR17 | 17 (11%) | 138 |
0.39 (1.00) |
0.0641 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.777 (1.00) |
0.938 (1.00) |
0.732 (1.00) |
0.0503 (1.00) |
0.212 (1.00) |
0.321 (1.00) |
ACVR1B | 13 (8%) | 142 |
0.759 (1.00) |
0.75 (1.00) |
0.78 (1.00) |
0.0345 (1.00) |
0.0242 (1.00) |
1 (1.00) |
0.721 (1.00) |
0.635 (1.00) |
1 (1.00) |
0.512 (1.00) |
TNFRSF10C | 6 (4%) | 149 |
0.978 (1.00) |
0.681 (1.00) |
0.59 (1.00) |
0.0968 (1.00) |
0.244 (1.00) |
0.0736 (1.00) |
0.0117 (1.00) |
0.105 (1.00) |
0.178 (1.00) |
|
SMAD2 | 10 (6%) | 145 |
0.617 (1.00) |
0.805 (1.00) |
0.327 (1.00) |
0.195 (1.00) |
0.401 (1.00) |
0.744 (1.00) |
0.636 (1.00) |
0.453 (1.00) |
0.404 (1.00) |
0.281 (1.00) |
MAP2K4 | 9 (6%) | 146 |
0.0181 (1.00) |
0.243 (1.00) |
0.746 (1.00) |
0.613 (1.00) |
0.504 (1.00) |
0.637 (1.00) |
0.4 (1.00) |
0.382 (1.00) |
0.639 (1.00) |
0.187 (1.00) |
PCBP1 | 4 (3%) | 151 |
0.00453 (1.00) |
1 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.641 (1.00) |
0.0347 (1.00) |
0.448 (1.00) |
1 (1.00) |
0.135 (1.00) |
|
FAT4 | 29 (19%) | 126 |
0.529 (1.00) |
0.0955 (1.00) |
0.543 (1.00) |
0.155 (1.00) |
0.672 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.111 (1.00) |
0.118 (1.00) |
0.409 (1.00) |
LRP1B | 30 (19%) | 125 |
0.805 (1.00) |
0.144 (1.00) |
0.228 (1.00) |
0.00324 (1.00) |
0.662 (1.00) |
0.407 (1.00) |
0.809 (1.00) |
0.406 (1.00) |
0.683 (1.00) |
0.185 (1.00) |
GRIA1 | 14 (9%) | 141 |
0.435 (1.00) |
0.84 (1.00) |
0.101 (1.00) |
1 (1.00) |
0.524 (1.00) |
0.929 (1.00) |
0.0757 (1.00) |
0.552 (1.00) |
0.728 (1.00) |
0.313 (1.00) |
SDK1 | 25 (16%) | 130 |
0.6 (1.00) |
0.248 (1.00) |
0.52 (1.00) |
0.0663 (1.00) |
0.781 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.671 (1.00) |
0.497 (1.00) |
0.718 (1.00) |
SOX9 | 9 (6%) | 146 |
0.28 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.231 (1.00) |
0.899 (1.00) |
1 (1.00) |
0.255 (1.00) |
1 (1.00) |
0.334 (1.00) |
|
DMD | 27 (17%) | 128 |
0.763 (1.00) |
0.517 (1.00) |
0.143 (1.00) |
0.0159 (1.00) |
0.127 (1.00) |
0.616 (1.00) |
0.0297 (1.00) |
0.00022 (0.255) |
0.139 (1.00) |
0.133 (1.00) |
CNTN6 | 15 (10%) | 140 |
0.493 (1.00) |
0.223 (1.00) |
0.0619 (1.00) |
0.708 (1.00) |
0.171 (1.00) |
0.21 (1.00) |
0.217 (1.00) |
0.216 (1.00) |
0.0482 (1.00) |
0.000761 (0.882) |
GABRA5 | 8 (5%) | 147 |
0.165 (1.00) |
0.518 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.416 (1.00) |
0.886 (1.00) |
1 (1.00) |
0.915 (1.00) |
1 (1.00) |
0.236 (1.00) |
OR2M4 | 8 (5%) | 147 |
0.587 (1.00) |
0.592 (1.00) |
0.495 (1.00) |
0.357 (1.00) |
0.884 (1.00) |
1 (1.00) |
1 (1.00) |
0.915 (1.00) |
0.639 (1.00) |
0.609 (1.00) |
OR6N1 | 8 (5%) | 147 |
0.914 (1.00) |
0.986 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.886 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.663 (1.00) |
PCDH9 | 16 (10%) | 139 |
0.222 (1.00) |
0.678 (1.00) |
0.429 (1.00) |
0.72 (1.00) |
0.73 (1.00) |
0.764 (1.00) |
0.725 (1.00) |
0.0456 (1.00) |
1 (1.00) |
0.0201 (1.00) |
TXNDC3 | 10 (6%) | 145 |
0.33 (1.00) |
0.517 (1.00) |
0.534 (1.00) |
0.659 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.401 (1.00) |
0.697 (1.00) |
0.651 (1.00) |
0.342 (1.00) |
MGC26647 | 7 (5%) | 148 |
0.863 (1.00) |
0.883 (1.00) |
0.276 (1.00) |
0.305 (1.00) |
0.216 (1.00) |
0.495 (1.00) |
0.613 (1.00) |
0.552 (1.00) |
0.633 (1.00) |
0.0798 (1.00) |
FAM22F | 8 (5%) | 147 |
0.0582 (1.00) |
0.633 (1.00) |
0.00647 (1.00) |
1 (1.00) |
0.0187 (1.00) |
0.687 (1.00) |
0.1 (1.00) |
0.0887 (1.00) |
0.133 (1.00) |
0.523 (1.00) |
TCF7L2 | 11 (7%) | 144 |
0.347 (1.00) |
0.343 (1.00) |
0.368 (1.00) |
0.214 (1.00) |
0.446 (1.00) |
1 (1.00) |
1 (1.00) |
0.884 (1.00) |
1 (1.00) |
0.319 (1.00) |
AFF2 | 15 (10%) | 140 |
0.808 (1.00) |
0.291 (1.00) |
0.588 (1.00) |
0.0639 (1.00) |
0.476 (1.00) |
0.752 (1.00) |
0.217 (1.00) |
0.115 (1.00) |
0.35 (1.00) |
0.127 (1.00) |
OTOL1 | 7 (5%) | 148 |
0.353 (1.00) |
0.17 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.0625 (1.00) |
0.267 (1.00) |
0.613 (1.00) |
0.507 (1.00) |
0.633 (1.00) |
0.313 (1.00) |
KCNA4 | 10 (6%) | 145 |
0.944 (1.00) |
0.155 (1.00) |
0.534 (1.00) |
0.0525 (1.00) |
0.823 (1.00) |
0.744 (1.00) |
0.401 (1.00) |
0.403 (1.00) |
0.651 (1.00) |
0.527 (1.00) |
ISL1 | 8 (5%) | 147 |
0.548 (1.00) |
0.975 (1.00) |
0.719 (1.00) |
0.357 (1.00) |
0.884 (1.00) |
0.1 (1.00) |
1 (1.00) |
0.424 (1.00) |
1 (1.00) |
0.77 (1.00) |
MGC42105 | 10 (6%) | 145 |
0.597 (1.00) |
0.975 (1.00) |
0.534 (1.00) |
0.659 (1.00) |
0.251 (1.00) |
0.477 (1.00) |
0.621 (1.00) |
0.59 (1.00) |
1 (1.00) |
0.05 (1.00) |
ACOT4 | 3 (2%) | 152 |
0.0294 (1.00) |
1 (1.00) |
0.405 (1.00) |
0.0332 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.477 (1.00) |
0.366 (1.00) |
0.647 (1.00) |
|
CDH11 | 13 (8%) | 142 |
0.545 (1.00) |
0.982 (1.00) |
0.564 (1.00) |
1 (1.00) |
1 (1.00) |
0.483 (1.00) |
0.7 (1.00) |
0.635 (1.00) |
0.707 (1.00) |
0.362 (1.00) |
ATM | 21 (14%) | 134 |
0.749 (1.00) |
0.891 (1.00) |
0.106 (1.00) |
0.331 (1.00) |
0.781 (1.00) |
0.421 (1.00) |
0.401 (1.00) |
0.183 (1.00) |
0.59 (1.00) |
0.181 (1.00) |
TPTE | 11 (7%) | 144 |
0.623 (1.00) |
0.785 (1.00) |
0.368 (1.00) |
0.0736 (1.00) |
0.649 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.832 (1.00) |
1 (1.00) |
0.63 (1.00) |
KLHL4 | 12 (8%) | 143 |
0.2 (1.00) |
0.12 (1.00) |
0.246 (1.00) |
0.0985 (1.00) |
0.0738 (1.00) |
1 (1.00) |
0.281 (1.00) |
0.0836 (1.00) |
0.067 (1.00) |
0.867 (1.00) |
ROBO1 | 14 (9%) | 141 |
0.67 (1.00) |
0.388 (1.00) |
0.78 (1.00) |
0.00676 (1.00) |
0.208 (1.00) |
0.737 (1.00) |
0.722 (1.00) |
0.0418 (1.00) |
1 (1.00) |
0.0402 (1.00) |
FLG | 26 (17%) | 129 |
0.242 (1.00) |
0.605 (1.00) |
0.673 (1.00) |
0.0274 (1.00) |
0.136 (1.00) |
0.123 (1.00) |
0.326 (1.00) |
0.196 (1.00) |
0.135 (1.00) |
0.0739 (1.00) |
PCDHB2 | 13 (8%) | 142 |
0.307 (1.00) |
0.847 (1.00) |
0.402 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.568 (1.00) |
0.7 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.457 (1.00) |
POSTN | 11 (7%) | 144 |
0.0656 (1.00) |
0.929 (1.00) |
1 (1.00) |
0.0736 (1.00) |
1 (1.00) |
0.231 (1.00) |
0.401 (1.00) |
0.248 (1.00) |
0.651 (1.00) |
0.377 (1.00) |
OR51V1 | 9 (6%) | 146 |
0.392 (1.00) |
0.849 (1.00) |
0.327 (1.00) |
0.00536 (1.00) |
0.0471 (1.00) |
0.224 (1.00) |
0.4 (1.00) |
0.0203 (1.00) |
0.651 (1.00) |
0.252 (1.00) |
LRRN3 | 9 (6%) | 146 |
0.997 (1.00) |
0.573 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.25 (1.00) |
0.0802 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.268 (1.00) |
PRDM9 | 11 (7%) | 144 |
0.413 (1.00) |
0.645 (1.00) |
0.368 (1.00) |
0.659 (1.00) |
0.183 (1.00) |
0.625 (1.00) |
0.0339 (1.00) |
0.445 (1.00) |
0.451 (1.00) |
0.399 (1.00) |
ADAM29 | 9 (6%) | 146 |
0.222 (1.00) |
0.651 (1.00) |
0.098 (1.00) |
1 (1.00) |
0.0452 (1.00) |
0.281 (1.00) |
0.0656 (1.00) |
0.0361 (1.00) |
1 (1.00) |
0.000673 (0.781) |
KIAA1486 | 9 (6%) | 146 |
0.137 (1.00) |
0.8 (1.00) |
0.746 (1.00) |
0.152 (1.00) |
0.169 (1.00) |
0.563 (1.00) |
0.4 (1.00) |
0.155 (1.00) |
0.072 (1.00) |
0.555 (1.00) |
PSG8 | 8 (5%) | 147 |
0.287 (1.00) |
0.794 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.339 (1.00) |
0.886 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.0577 (1.00) |
0.21 (1.00) |
NCKAP5 | 13 (8%) | 142 |
0.694 (1.00) |
0.918 (1.00) |
0.78 (1.00) |
0.433 (1.00) |
0.266 (1.00) |
0.568 (1.00) |
0.7 (1.00) |
0.817 (1.00) |
0.686 (1.00) |
0.889 (1.00) |
C8B | 9 (6%) | 146 |
0.285 (1.00) |
0.159 (1.00) |
0.098 (1.00) |
0.152 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.999 (1.00) |
DNAH5 | 28 (18%) | 127 |
0.812 (1.00) |
0.839 (1.00) |
0.411 (1.00) |
0.771 (1.00) |
0.537 (1.00) |
0.37 (1.00) |
0.809 (1.00) |
0.23 (1.00) |
0.683 (1.00) |
0.0919 (1.00) |
CCDC160 | 5 (3%) | 150 |
0.777 (1.00) |
0.21 (1.00) |
1 (1.00) |
0.144 (1.00) |
0.295 (1.00) |
0.548 (1.00) |
0.602 (1.00) |
0.535 (1.00) |
0.278 (1.00) |
|
DCAF4L2 | 9 (6%) | 146 |
0.951 (1.00) |
0.959 (1.00) |
1 (1.00) |
0.022 (1.00) |
0.0668 (1.00) |
0.799 (1.00) |
0.621 (1.00) |
0.812 (1.00) |
0.639 (1.00) |
0.453 (1.00) |
DKK2 | 5 (3%) | 150 |
0.727 (1.00) |
0.681 (1.00) |
0.582 (1.00) |
0.741 (1.00) |
0.295 (1.00) |
1 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.278 (1.00) |
|
EPHA3 | 13 (8%) | 142 |
0.455 (1.00) |
0.429 (1.00) |
0.402 (1.00) |
0.405 (1.00) |
0.468 (1.00) |
1 (1.00) |
1 (1.00) |
0.572 (1.00) |
0.686 (1.00) |
0.766 (1.00) |
GUCY1A3 | 10 (6%) | 145 |
0.11 (1.00) |
0.0668 (1.00) |
1 (1.00) |
0.0525 (1.00) |
0.17 (1.00) |
0.671 (1.00) |
0.4 (1.00) |
0.198 (1.00) |
0.651 (1.00) |
0.677 (1.00) |
INHBA | 7 (5%) | 148 |
0.884 (1.00) |
0.474 (1.00) |
0.442 (1.00) |
0.00112 (1.00) |
0.169 (1.00) |
0.645 (1.00) |
0.613 (1.00) |
0.275 (1.00) |
0.633 (1.00) |
0.586 (1.00) |
KLK2 | 3 (2%) | 152 |
0.229 (1.00) |
1 (1.00) |
0.405 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.869 (1.00) |
1 (1.00) |
0.572 (1.00) |
|
LPPR4 | 11 (7%) | 144 |
0.592 (1.00) |
0.236 (1.00) |
0.765 (1.00) |
0.685 (1.00) |
0.411 (1.00) |
0.0266 (1.00) |
1 (1.00) |
0.832 (1.00) |
1 (1.00) |
0.0669 (1.00) |
OR7C1 | 6 (4%) | 149 |
0.218 (1.00) |
0.442 (1.00) |
0.177 (1.00) |
0.274 (1.00) |
1 (1.00) |
1 (1.00) |
0.833 (1.00) |
1 (1.00) |
0.656 (1.00) |
|
SCN7A | 12 (8%) | 143 |
0.6 (1.00) |
0.772 (1.00) |
0.564 (1.00) |
0.381 (1.00) |
0.0445 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.0171 (1.00) |
1 (1.00) |
0.951 (1.00) |
TGFBR2 | 7 (5%) | 148 |
0.768 (1.00) |
0.412 (1.00) |
0.719 (1.00) |
0.0791 (1.00) |
0.737 (1.00) |
0.565 (1.00) |
0.613 (1.00) |
0.753 (1.00) |
0.633 (1.00) |
0.789 (1.00) |
TRPS1 | 13 (8%) | 142 |
0.675 (1.00) |
0.153 (1.00) |
0.564 (1.00) |
0.127 (1.00) |
0.0628 (1.00) |
0.198 (1.00) |
0.281 (1.00) |
0.178 (1.00) |
0.463 (1.00) |
0.074 (1.00) |
RIMS2 | 12 (8%) | 143 |
0.228 (1.00) |
0.996 (1.00) |
0.564 (1.00) |
0.0985 (1.00) |
0.276 (1.00) |
0.919 (1.00) |
0.677 (1.00) |
0.576 (1.00) |
0.686 (1.00) |
0.504 (1.00) |
SFMBT2 | 12 (8%) | 143 |
0.379 (1.00) |
0.591 (1.00) |
0.765 (1.00) |
0.405 (1.00) |
0.241 (1.00) |
0.839 (1.00) |
0.677 (1.00) |
0.942 (1.00) |
0.686 (1.00) |
0.576 (1.00) |
IL18R1 | 8 (5%) | 147 |
0.497 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.113 (1.00) |
0.0803 (1.00) |
0.286 (1.00) |
0.621 (1.00) |
0.268 (1.00) |
0.633 (1.00) |
0.775 (1.00) |
PCDH17 | 14 (9%) | 141 |
0.181 (1.00) |
0.323 (1.00) |
1 (1.00) |
0.699 (1.00) |
0.821 (1.00) |
0.147 (1.00) |
0.283 (1.00) |
0.104 (1.00) |
0.35 (1.00) |
0.0299 (1.00) |
FLRT2 | 11 (7%) | 144 |
0.64 (1.00) |
0.769 (1.00) |
0.368 (1.00) |
0.659 (1.00) |
0.0626 (1.00) |
0.691 (1.00) |
0.41 (1.00) |
0.274 (1.00) |
0.451 (1.00) |
0.14 (1.00) |
ZC3H13 | 17 (11%) | 138 |
0.841 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.0224 (1.00) |
0.209 (1.00) |
0.938 (1.00) |
0.221 (1.00) |
0.25 (1.00) |
0.368 (1.00) |
0.372 (1.00) |
PTEN | 4 (3%) | 151 |
0.123 (1.00) |
1 (1.00) |
0.501 (1.00) |
0.312 (1.00) |
0.819 (1.00) |
0.377 (1.00) |
0.415 (1.00) |
0.366 (1.00) |
0.492 (1.00) |
|
NRXN3 | 15 (10%) | 140 |
0.842 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.259 (1.00) |
0.883 (1.00) |
0.288 (1.00) |
0.291 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.0644 (1.00) |
LIFR | 13 (8%) | 142 |
0.114 (1.00) |
0.666 (1.00) |
0.564 (1.00) |
0.433 (1.00) |
0.103 (1.00) |
0.786 (1.00) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.0389 (1.00) |
OR2M2 | 6 (4%) | 149 |
0.219 (1.00) |
0.428 (1.00) |
0.117 (1.00) |
0.0282 (1.00) |
0.0381 (1.00) |
1 (1.00) |
0.171 (1.00) |
0.204 (1.00) |
0.181 (1.00) |
0.198 (1.00) |
TMEM132D | 15 (10%) | 140 |
0.91 (1.00) |
0.69 (1.00) |
0.186 (1.00) |
0.0639 (1.00) |
0.789 (1.00) |
0.56 (1.00) |
0.291 (1.00) |
0.0685 (1.00) |
0.35 (1.00) |
0.826 (1.00) |
SAT1 | 4 (3%) | 151 |
0.265 (1.00) |
0.0585 (1.00) |
0.501 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.869 (1.00) |
|
CDH18 | 10 (6%) | 145 |
0.179 (1.00) |
0.651 (1.00) |
0.0562 (1.00) |
0.659 (1.00) |
0.17 (1.00) |
0.477 (1.00) |
1 (1.00) |
0.644 (1.00) |
1 (1.00) |
0.0115 (1.00) |
P2RY10 | 6 (4%) | 149 |
0.387 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.689 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.0113 (1.00) |
SYT16 | 6 (4%) | 149 |
0.507 (1.00) |
0.587 (1.00) |
0.681 (1.00) |
0.24 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.612 (1.00) |
0.634 (1.00) |
1 (1.00) |
0.646 (1.00) |
CPXCR1 | 6 (4%) | 149 |
0.327 (1.00) |
0.643 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.482 (1.00) |
0.0178 (1.00) |
0.612 (1.00) |
0.232 (1.00) |
0.081 (1.00) |
0.0246 (1.00) |
PDZRN4 | 12 (8%) | 143 |
0.801 (1.00) |
0.159 (1.00) |
0.246 (1.00) |
0.00408 (1.00) |
0.276 (1.00) |
0.544 (1.00) |
1 (1.00) |
0.858 (1.00) |
1 (1.00) |
0.337 (1.00) |
ESR1 | 11 (7%) | 144 |
0.439 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.0296 (1.00) |
0.514 (1.00) |
0.401 (1.00) |
0.555 (1.00) |
0.651 (1.00) |
0.0575 (1.00) |
MIER3 | 10 (6%) | 145 |
0.463 (1.00) |
0.739 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.555 (1.00) |
0.202 (1.00) |
0.4 (1.00) |
0.382 (1.00) |
0.651 (1.00) |
0.00232 (1.00) |
NLRP5 | 10 (6%) | 145 |
0.64 (1.00) |
0.794 (1.00) |
0.746 (1.00) |
0.634 (1.00) |
0.555 (1.00) |
0.283 (1.00) |
1 (1.00) |
0.414 (1.00) |
0.444 (1.00) |
0.42 (1.00) |
PCDH10 | 14 (9%) | 141 |
0.218 (1.00) |
0.327 (1.00) |
0.101 (1.00) |
0.239 (1.00) |
0.468 (1.00) |
0.63 (1.00) |
0.722 (1.00) |
0.502 (1.00) |
1 (1.00) |
0.447 (1.00) |
PCDHB5 | 12 (8%) | 143 |
0.0482 (1.00) |
0.831 (1.00) |
0.0788 (1.00) |
1 (1.00) |
0.204 (1.00) |
0.499 (1.00) |
1 (1.00) |
0.0415 (1.00) |
0.463 (1.00) |
0.00645 (1.00) |
TRPC6 | 8 (5%) | 147 |
0.283 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.458 (1.00) |
0.523 (1.00) |
0.621 (1.00) |
0.153 (1.00) |
0.633 (1.00) |
0.87 (1.00) |
RHOA | 4 (3%) | 151 |
0.918 (1.00) |
1 (1.00) |
0.405 (1.00) |
0.741 (1.00) |
0.125 (1.00) |
0.469 (1.00) |
0.552 (1.00) |
0.457 (1.00) |
0.64 (1.00) |
|
SYNE1 | 37 (24%) | 118 |
0.773 (1.00) |
0.113 (1.00) |
0.576 (1.00) |
0.035 (1.00) |
0.591 (1.00) |
0.157 (1.00) |
0.544 (1.00) |
0.283 (1.00) |
0.741 (1.00) |
0.0154 (1.00) |
CHRM2 | 8 (5%) | 147 |
0.323 (1.00) |
0.778 (1.00) |
0.495 (1.00) |
0.613 (1.00) |
0.00611 (1.00) |
1 (1.00) |
0.131 (1.00) |
0.0187 (1.00) |
0.164 (1.00) |
0.939 (1.00) |
GALNT14 | 9 (6%) | 146 |
0.517 (1.00) |
0.996 (1.00) |
0.746 (1.00) |
0.634 (1.00) |
0.0103 (1.00) |
0.224 (1.00) |
0.4 (1.00) |
0.0203 (1.00) |
0.651 (1.00) |
0.339 (1.00) |
LRRIQ3 | 7 (5%) | 148 |
0.582 (1.00) |
0.495 (1.00) |
0.0633 (1.00) |
1 (1.00) |
0.313 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.903 (1.00) |
0.602 (1.00) |
0.59 (1.00) |
PCDH11X | 11 (7%) | 144 |
0.0128 (1.00) |
0.561 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.183 (1.00) |
0.231 (1.00) |
0.401 (1.00) |
0.248 (1.00) |
0.444 (1.00) |
0.0694 (1.00) |
TFAP2D | 5 (3%) | 150 |
0.0281 (1.00) |
0.21 (1.00) |
0.582 (1.00) |
0.784 (1.00) |
1 (1.00) |
1 (1.00) |
0.559 (1.00) |
1 (1.00) |
0.87 (1.00) |
|
CNTNAP4 | 10 (6%) | 145 |
0.353 (1.00) |
0.936 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.17 (1.00) |
0.141 (1.00) |
0.4 (1.00) |
0.0203 (1.00) |
0.651 (1.00) |
0.752 (1.00) |
DOCK2 | 16 (10%) | 139 |
0.922 (1.00) |
0.382 (1.00) |
1 (1.00) |
0.259 (1.00) |
0.162 (1.00) |
0.212 (1.00) |
0.217 (1.00) |
0.0962 (1.00) |
0.357 (1.00) |
0.087 (1.00) |
P value = 1.07e-05 (Fisher's exact test), Q value = 0.013
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 128 | 24 |
BRAF MUTATED | 9 | 11 |
BRAF WILD-TYPE | 119 | 13 |
P value = 5.76e-05 (t-test), Q value = 0.067
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
NRXN1 MUTATED | 17 | 0.4 (1.2) |
NRXN1 WILD-TYPE | 137 | 2.5 (4.7) |
P value = 1.69e-06 (t-test), Q value = 0.002
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
ACVR2A MUTATED | 8 | 0.2 (0.5) |
ACVR2A WILD-TYPE | 146 | 2.3 (4.6) |
P value = 5.86e-09 (t-test), Q value = 6.9e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
CNBD1 MUTATED | 6 | 0.0 (0.0) |
CNBD1 WILD-TYPE | 148 | 2.3 (4.5) |
P value = 6.1e-09 (t-test), Q value = 7.2e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
BTNL8 MUTATED | 3 | 0.0 (0.0) |
BTNL8 WILD-TYPE | 151 | 2.3 (4.5) |
P value = 6.1e-09 (t-test), Q value = 7.2e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
GGT1 MUTATED | 3 | 0.0 (0.0) |
GGT1 WILD-TYPE | 151 | 2.3 (4.5) |
P value = 3.04e-05 (t-test), Q value = 0.036
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 155 | 70.3 (12.0) |
GRIK3 MUTATED | 14 | 78.9 (5.8) |
GRIK3 WILD-TYPE | 141 | 69.5 (12.1) |
P value = 2.26e-06 (t-test), Q value = 0.0027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
CASP8 MUTATED | 10 | 0.2 (0.6) |
CASP8 WILD-TYPE | 144 | 2.4 (4.6) |
P value = 6.48e-06 (t-test), Q value = 0.0076
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
ERBB4 MUTATED | 14 | 0.3 (0.8) |
ERBB4 WILD-TYPE | 140 | 2.4 (4.6) |
P value = 3.01e-07 (t-test), Q value = 0.00035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
IFT80 MUTATED | 7 | 0.1 (0.4) |
IFT80 WILD-TYPE | 147 | 2.3 (4.6) |
P value = 6.02e-09 (t-test), Q value = 7.1e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
OR8J1 MUTATED | 4 | 0.0 (0.0) |
OR8J1 WILD-TYPE | 150 | 2.3 (4.5) |
P value = 2.48e-05 (logrank test), Q value = 0.029
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 11 | 0.9 - 52.0 (12.0) |
ZFHX4 MUTATED | 11 | 4 | 0.9 - 21.0 (1.0) |
ZFHX4 WILD-TYPE | 68 | 7 | 0.9 - 52.0 (13.9) |
P value = 0.00011 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
ZNF429 MUTATED | 7 | 0.3 (0.8) |
ZNF429 WILD-TYPE | 147 | 2.3 (4.6) |
P value = 6.02e-09 (t-test), Q value = 7.1e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
DKK4 MUTATED | 4 | 0.0 (0.0) |
DKK4 WILD-TYPE | 150 | 2.3 (4.5) |
P value = 6.79e-05 (t-test), Q value = 0.079
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
NALCN MUTATED | 14 | 0.4 (1.1) |
NALCN WILD-TYPE | 140 | 2.4 (4.6) |
P value = 6.1e-09 (t-test), Q value = 7.2e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
SULT1C4 MUTATED | 3 | 0.0 (0.0) |
SULT1C4 WILD-TYPE | 151 | 2.3 (4.5) |
P value = 0.00011 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
UMOD MUTATED | 7 | 0.3 (0.8) |
UMOD WILD-TYPE | 147 | 2.3 (4.6) |
P value = 5.78e-09 (t-test), Q value = 6.9e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
USP17L2 MUTATED | 7 | 0.0 (0.0) |
USP17L2 WILD-TYPE | 147 | 2.3 (4.6) |
P value = 5.21e-08 (t-test), Q value = 6.1e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
FAM5C MUTATED | 10 | 0.1 (0.3) |
FAM5C WILD-TYPE | 144 | 2.4 (4.6) |
P value = 0.000122 (t-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 155 | 70.3 (12.0) |
OR6T1 MUTATED | 6 | 63.7 (2.5) |
OR6T1 WILD-TYPE | 149 | 70.6 (12.2) |
P value = 6.02e-09 (t-test), Q value = 7.1e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
CYTL1 MUTATED | 4 | 0.0 (0.0) |
CYTL1 WILD-TYPE | 150 | 2.3 (4.5) |
P value = 3.34e-05 (t-test), Q value = 0.039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
NAALAD2 MUTATED | 11 | 0.4 (0.8) |
NAALAD2 WILD-TYPE | 143 | 2.4 (4.6) |
P value = 1.39e-06 (t-test), Q value = 0.0016
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 154 | 2.2 (4.5) |
TNR MUTATED | 15 | 0.2 (0.8) |
TNR WILD-TYPE | 139 | 2.4 (4.7) |
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Mutation data file = COAD-TP.mutsig.cluster.txt
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Clinical data file = COAD-TP.clin.merged.picked.txt
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Number of patients = 155
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Number of significantly mutated genes = 120
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Number of selected clinical features = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.