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'.
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NRXN1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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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'.
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SULT1C4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
UMOD mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
USP17L2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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FAM5C mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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OR6T1 mutation correlated to 'AGE'.
-
CYTL1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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NAALAD2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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TNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
Table 1. Get Full Table Overview of the association between mutation status of 120 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.
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
Table S1. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 128 | 24 |
BRAF MUTATED | 9 | 11 |
BRAF WILD-TYPE | 119 | 13 |
Figure S1. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 5.76e-05 (t-test), Q value = 0.067
Table S2. Gene #19: 'NRXN1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S2. Get High-res Image Gene #19: 'NRXN1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-06 (t-test), Q value = 0.002
Table S3. Gene #32: 'ACVR2A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S3. Get High-res Image Gene #32: 'ACVR2A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 5.86e-09 (t-test), Q value = 6.9e-06
Table S4. Gene #35: 'CNBD1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S4. Get High-res Image Gene #35: 'CNBD1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06
Table S5. Gene #44: 'BTNL8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S5. Get High-res Image Gene #44: 'BTNL8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06
Table S6. Gene #47: 'GGT1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S6. Get High-res Image Gene #47: 'GGT1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 3.04e-05 (t-test), Q value = 0.036
Table S7. Gene #52: 'GRIK3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
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) |
Figure S7. Get High-res Image Gene #52: 'GRIK3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

P value = 2.26e-06 (t-test), Q value = 0.0027
Table S8. Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S8. Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.48e-06 (t-test), Q value = 0.0076
Table S9. Gene #66: 'ERBB4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S9. Get High-res Image Gene #66: 'ERBB4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 3.01e-07 (t-test), Q value = 0.00035
Table S10. Gene #68: 'IFT80 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S10. Get High-res Image Gene #68: 'IFT80 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.02e-09 (t-test), Q value = 7.1e-06
Table S11. Gene #76: 'OR8J1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S11. Get High-res Image Gene #76: 'OR8J1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 2.48e-05 (logrank test), Q value = 0.029
Table S12. Gene #84: 'ZFHX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S12. Get High-res Image Gene #84: 'ZFHX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

P value = 0.00011 (t-test), Q value = 0.13
Table S13. Gene #87: 'ZNF429 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S13. Get High-res Image Gene #87: 'ZNF429 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.02e-09 (t-test), Q value = 7.1e-06
Table S14. Gene #94: 'DKK4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S14. Get High-res Image Gene #94: 'DKK4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.79e-05 (t-test), Q value = 0.079
Table S15. Gene #95: 'NALCN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S15. Get High-res Image Gene #95: 'NALCN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06
Table S16. Gene #96: 'SULT1C4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S16. Get High-res Image Gene #96: 'SULT1C4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 0.00011 (t-test), Q value = 0.13
Table S17. Gene #97: 'UMOD MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S17. Get High-res Image Gene #97: 'UMOD MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 5.78e-09 (t-test), Q value = 6.9e-06
Table S18. Gene #100: 'USP17L2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S18. Get High-res Image Gene #100: 'USP17L2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 5.21e-08 (t-test), Q value = 6.1e-05
Table S19. Gene #102: 'FAM5C MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S19. Get High-res Image Gene #102: 'FAM5C MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 0.000122 (t-test), Q value = 0.14
Table S20. Gene #105: 'OR6T1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
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) |
Figure S20. Get High-res Image Gene #105: 'OR6T1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

P value = 6.02e-09 (t-test), Q value = 7.1e-06
Table S21. Gene #111: 'CYTL1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S21. Get High-res Image Gene #111: 'CYTL1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 3.34e-05 (t-test), Q value = 0.039
Table S22. Gene #115: 'NAALAD2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S22. Get High-res Image Gene #115: 'NAALAD2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

P value = 1.39e-06 (t-test), Q value = 0.0016
Table S23. Gene #118: 'TNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
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) |
Figure S23. Get High-res Image Gene #118: 'TNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

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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
-
Number of patients = 155
-
Number of significantly mutated genes = 120
-
Number of selected clinical features = 10
-
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.