This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 81 genes and 13 clinical features across 395 patients, no significant finding detected with Q value < 0.25.
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No gene mutations related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-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 | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 196 (50%) | 199 |
0.927 (1.00) |
0.505 (1.00) |
0.11 (0.937) |
0.578 (1.00) |
0.0164 (0.797) |
0.531 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.298 (1.00) |
0.68 (1.00) |
0.102 (0.936) |
0.0015 (0.614) |
1 (1.00) |
RB1 | 70 (18%) | 325 |
0.165 (1.00) |
0.0892 (0.917) |
0.811 (1.00) |
0.443 (1.00) |
0.0649 (0.9) |
0.639 (1.00) |
0.452 (1.00) |
0.548 (1.00) |
0.0767 (0.907) |
0.0744 (0.9) |
0.29 (1.00) |
0.453 (1.00) |
1 (1.00) |
ELF3 | 46 (12%) | 349 |
0.486 (1.00) |
0.00399 (0.797) |
0.954 (1.00) |
0.415 (1.00) |
0.987 (1.00) |
1 (1.00) |
0.283 (1.00) |
1 (1.00) |
0.718 (1.00) |
0.821 (1.00) |
0.925 (1.00) |
1 (1.00) |
0.603 (1.00) |
TSC1 | 33 (8%) | 362 |
0.464 (1.00) |
0.281 (1.00) |
0.65 (1.00) |
0.321 (1.00) |
0.674 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.39 (1.00) |
0.542 (1.00) |
0.259 (1.00) |
0.487 (1.00) |
0.801 (1.00) |
0.502 (1.00) |
PIK3CA | 86 (22%) | 309 |
0.524 (1.00) |
0.629 (1.00) |
0.646 (1.00) |
0.206 (1.00) |
0.243 (1.00) |
0.463 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.495 (1.00) |
0.183 (1.00) |
0.0177 (0.797) |
0.196 (1.00) |
0.679 (1.00) |
RHOB | 26 (7%) | 369 |
0.838 (1.00) |
0.0611 (0.9) |
0.71 (1.00) |
1 (1.00) |
0.257 (1.00) |
0.559 (1.00) |
1 (1.00) |
1 (1.00) |
0.321 (1.00) |
0.451 (1.00) |
0.772 (1.00) |
0.289 (1.00) |
1 (1.00) |
KDM6A | 103 (26%) | 292 |
0.508 (1.00) |
0.71 (1.00) |
0.459 (1.00) |
0.707 (1.00) |
0.248 (1.00) |
0.744 (1.00) |
0.897 (1.00) |
0.302 (1.00) |
0.353 (1.00) |
0.148 (1.00) |
0.0251 (0.797) |
0.971 (1.00) |
0.686 (1.00) |
CDKN2A | 26 (7%) | 369 |
0.715 (1.00) |
0.735 (1.00) |
0.374 (1.00) |
0.713 (1.00) |
1 (1.00) |
0.503 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.861 (1.00) |
0.143 (1.00) |
0.545 (1.00) |
0.913 (1.00) |
1 (1.00) |
ARID1A | 97 (25%) | 298 |
0.435 (1.00) |
0.388 (1.00) |
0.595 (1.00) |
0.563 (1.00) |
0.172 (1.00) |
0.733 (1.00) |
0.229 (1.00) |
0.426 (1.00) |
0.334 (1.00) |
0.351 (1.00) |
0.7 (1.00) |
0.00175 (0.614) |
0.432 (1.00) |
STAG2 | 56 (14%) | 339 |
0.202 (1.00) |
0.376 (1.00) |
0.104 (0.936) |
0.391 (1.00) |
0.303 (1.00) |
0.0229 (0.797) |
0.51 (1.00) |
0.503 (1.00) |
0.209 (1.00) |
0.225 (1.00) |
0.167 (1.00) |
0.0482 (0.852) |
0.608 (1.00) |
ZFP36L1 | 25 (6%) | 370 |
0.296 (1.00) |
0.178 (1.00) |
0.134 (1.00) |
0.48 (1.00) |
0.248 (1.00) |
0.0393 (0.797) |
1 (1.00) |
0.358 (1.00) |
0.194 (1.00) |
0.815 (1.00) |
0.00886 (0.797) |
1 (1.00) |
1 (1.00) |
CDKN1A | 35 (9%) | 360 |
0.554 (1.00) |
0.952 (1.00) |
0.751 (1.00) |
0.193 (1.00) |
0.567 (1.00) |
1 (1.00) |
0.311 (1.00) |
0.688 (1.00) |
0.00941 (0.797) |
0.689 (1.00) |
0.477 (1.00) |
0.0247 (0.797) |
0.526 (1.00) |
EP300 | 61 (15%) | 334 |
0.0731 (0.9) |
0.251 (1.00) |
0.877 (1.00) |
0.444 (1.00) |
0.259 (1.00) |
0.694 (1.00) |
0.875 (1.00) |
0.221 (1.00) |
0.866 (1.00) |
0.288 (1.00) |
0.659 (1.00) |
0.189 (1.00) |
1 (1.00) |
MLL2 | 114 (29%) | 281 |
0.39 (1.00) |
0.0894 (0.917) |
0.511 (1.00) |
0.924 (1.00) |
0.165 (1.00) |
0.306 (1.00) |
0.8 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.584 (1.00) |
0.0686 (0.9) |
0.349 (1.00) |
1 (1.00) |
FGFR3 | 56 (14%) | 339 |
0.16 (1.00) |
0.101 (0.936) |
0.0197 (0.797) |
0.00287 (0.756) |
0.0965 (0.927) |
0.248 (1.00) |
0.0329 (0.797) |
0.196 (1.00) |
0.0514 (0.852) |
0.123 (0.958) |
0.541 (1.00) |
0.0245 (0.797) |
0.607 (1.00) |
ERCC2 | 38 (10%) | 357 |
0.0884 (0.917) |
0.0201 (0.797) |
0.506 (1.00) |
0.946 (1.00) |
1 (1.00) |
1 (1.00) |
0.562 (1.00) |
0.237 (1.00) |
0.0192 (0.797) |
0.225 (1.00) |
0.392 (1.00) |
0.726 (1.00) |
0.175 (1.00) |
CREBBP | 48 (12%) | 347 |
0.477 (1.00) |
0.891 (1.00) |
0.956 (1.00) |
0.385 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.159 (1.00) |
0.491 (1.00) |
0.974 (1.00) |
0.83 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.604 (1.00) |
HRAS | 17 (4%) | 378 |
0.352 (1.00) |
0.324 (1.00) |
0.386 (1.00) |
0.108 (0.936) |
0.676 (1.00) |
0.44 (1.00) |
0.158 (1.00) |
0.573 (1.00) |
0.352 (1.00) |
0.423 (1.00) |
0.873 (1.00) |
0.0444 (0.85) |
1 (1.00) |
FOXA1 | 14 (4%) | 381 |
0.617 (1.00) |
0.839 (1.00) |
0.124 (0.959) |
0.368 (1.00) |
0.0909 (0.917) |
0.0802 (0.915) |
0.762 (1.00) |
0.547 (1.00) |
0.0715 (0.9) |
0.0305 (0.797) |
0.0205 (0.797) |
0.698 (1.00) |
1 (1.00) |
KRAS | 13 (3%) | 382 |
0.000833 (0.614) |
0.489 (1.00) |
0.417 (1.00) |
0.345 (1.00) |
0.0123 (0.797) |
1 (1.00) |
0.198 (1.00) |
0.492 (1.00) |
0.546 (1.00) |
0.118 (0.947) |
0.32 (1.00) |
0.294 (1.00) |
1 (1.00) |
RHOA | 18 (5%) | 377 |
0.502 (1.00) |
0.457 (1.00) |
0.139 (1.00) |
0.479 (1.00) |
0.437 (1.00) |
0.0643 (0.9) |
0.422 (1.00) |
0.613 (1.00) |
0.00562 (0.797) |
0.805 (1.00) |
0.887 (1.00) |
0.289 (1.00) |
|
KIAA1267 | 24 (6%) | 371 |
0.176 (1.00) |
0.13 (0.989) |
0.671 (1.00) |
0.479 (1.00) |
0.908 (1.00) |
0.559 (1.00) |
0.346 (1.00) |
0.358 (1.00) |
0.966 (1.00) |
0.336 (1.00) |
0.82 (1.00) |
0.333 (1.00) |
0.397 (1.00) |
MLL | 44 (11%) | 351 |
0.879 (1.00) |
0.0132 (0.797) |
0.545 (1.00) |
0.504 (1.00) |
0.83 (1.00) |
0.604 (1.00) |
0.467 (1.00) |
0.711 (1.00) |
0.232 (1.00) |
0.669 (1.00) |
0.277 (1.00) |
0.838 (1.00) |
0.606 (1.00) |
FAT1 | 50 (13%) | 345 |
0.527 (1.00) |
0.0206 (0.797) |
0.193 (1.00) |
0.654 (1.00) |
0.202 (1.00) |
0.324 (1.00) |
0.0394 (0.797) |
0.733 (1.00) |
0.115 (0.941) |
0.0478 (0.852) |
0.0243 (0.797) |
0.76 (1.00) |
0.295 (1.00) |
KLF5 | 23 (6%) | 372 |
0.511 (1.00) |
0.606 (1.00) |
0.933 (1.00) |
0.168 (1.00) |
0.69 (1.00) |
1 (1.00) |
0.329 (1.00) |
0.316 (1.00) |
0.0933 (0.919) |
0.339 (1.00) |
0.771 (1.00) |
0.174 (1.00) |
1 (1.00) |
PTEN | 14 (4%) | 381 |
0.587 (1.00) |
0.677 (1.00) |
0.899 (1.00) |
0.201 (1.00) |
0.555 (1.00) |
1 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.91 (1.00) |
0.345 (1.00) |
0.605 (1.00) |
1 (1.00) |
1 (1.00) |
C3ORF70 | 17 (4%) | 378 |
0.0757 (0.906) |
0.0777 (0.909) |
0.402 (1.00) |
0.228 (1.00) |
0.316 (1.00) |
0.44 (1.00) |
1 (1.00) |
1 (1.00) |
0.321 (1.00) |
0.552 (1.00) |
0.0147 (0.797) |
0.371 (1.00) |
1 (1.00) |
PSIP1 | 20 (5%) | 375 |
0.632 (1.00) |
0.122 (0.958) |
0.27 (1.00) |
0.115 (0.941) |
0.263 (1.00) |
0.532 (1.00) |
0.307 (1.00) |
0.253 (1.00) |
0.603 (1.00) |
0.222 (1.00) |
0.193 (1.00) |
0.198 (1.00) |
1 (1.00) |
MLL3 | 74 (19%) | 321 |
0.539 (1.00) |
0.867 (1.00) |
0.464 (1.00) |
0.337 (1.00) |
0.95 (1.00) |
0.255 (1.00) |
0.0392 (0.797) |
0.777 (1.00) |
0.13 (0.989) |
0.427 (1.00) |
0.801 (1.00) |
0.463 (1.00) |
0.361 (1.00) |
ASXL2 | 36 (9%) | 359 |
0.587 (1.00) |
0.579 (1.00) |
0.714 (1.00) |
0.642 (1.00) |
0.319 (1.00) |
1 (1.00) |
1 (1.00) |
0.395 (1.00) |
0.633 (1.00) |
0.63 (1.00) |
0.435 (1.00) |
0.703 (1.00) |
1 (1.00) |
ZBTB7B | 11 (3%) | 384 |
0.149 (1.00) |
0.38 (1.00) |
0.813 (1.00) |
0.746 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.38 (1.00) |
0.64 (1.00) |
0.135 (1.00) |
0.0282 (0.797) |
1 (1.00) |
RXRA | 24 (6%) | 371 |
0.954 (1.00) |
0.105 (0.936) |
0.438 (1.00) |
0.4 (1.00) |
0.753 (1.00) |
0.532 (1.00) |
0.81 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.501 (1.00) |
0.514 (1.00) |
0.257 (1.00) |
0.382 (1.00) |
FBXW7 | 30 (8%) | 365 |
0.323 (1.00) |
0.088 (0.917) |
0.315 (1.00) |
0.348 (1.00) |
0.244 (1.00) |
0.324 (1.00) |
0.192 (1.00) |
0.656 (1.00) |
0.725 (1.00) |
0.952 (1.00) |
0.275 (1.00) |
0.64 (1.00) |
1 (1.00) |
RBM10 | 22 (6%) | 373 |
0.722 (1.00) |
0.523 (1.00) |
0.47 (1.00) |
0.583 (1.00) |
0.108 (0.936) |
1 (1.00) |
1 (1.00) |
0.614 (1.00) |
0.94 (1.00) |
0.473 (1.00) |
0.138 (1.00) |
0.887 (1.00) |
1 (1.00) |
NFE2L2 | 24 (6%) | 371 |
0.316 (1.00) |
0.723 (1.00) |
0.149 (1.00) |
0.0623 (0.9) |
0.823 (1.00) |
0.115 (0.941) |
0.0292 (0.797) |
1 (1.00) |
0.686 (1.00) |
0.677 (1.00) |
0.466 (1.00) |
0.0713 (0.9) |
1 (1.00) |
CUL1 | 19 (5%) | 376 |
0.844 (1.00) |
0.579 (1.00) |
0.731 (1.00) |
0.782 (1.00) |
0.333 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.613 (1.00) |
0.418 (1.00) |
0.17 (1.00) |
0.48 (1.00) |
0.878 (1.00) |
0.337 (1.00) |
HLA-A | 5 (1%) | 390 |
0.472 (1.00) |
0.877 (1.00) |
0.398 (1.00) |
0.036 (0.797) |
0.683 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.877 (1.00) |
1 (1.00) |
1 (1.00) |
||
GNA13 | 12 (3%) | 383 |
0.696 (1.00) |
0.614 (1.00) |
0.639 (1.00) |
0.637 (1.00) |
0.708 (1.00) |
1 (1.00) |
0.311 (1.00) |
1 (1.00) |
0.0715 (0.9) |
0.717 (1.00) |
0.195 (1.00) |
0.557 (1.00) |
0.22 (1.00) |
NUDT11 | 7 (2%) | 388 |
0.809 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.51 (1.00) |
0.731 (1.00) |
1 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.985 (1.00) |
1 (1.00) |
1 (1.00) |
||
MBD1 | 12 (3%) | 383 |
0.47 (1.00) |
0.599 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.311 (1.00) |
0.492 (1.00) |
0.0409 (0.797) |
0.437 (1.00) |
0.0924 (0.917) |
0.401 (1.00) |
1 (1.00) |
SCARF2 | 8 (2%) | 387 |
0.279 (1.00) |
0.144 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.646 (1.00) |
0.444 (1.00) |
0.758 (1.00) |
1 (1.00) |
FOXQ1 | 14 (4%) | 381 |
0.288 (1.00) |
0.385 (1.00) |
0.648 (1.00) |
1 (1.00) |
0.327 (1.00) |
1 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.0704 (0.9) |
0.635 (1.00) |
0.718 (1.00) |
1 (1.00) |
|
FAM47C | 21 (5%) | 374 |
0.0834 (0.915) |
0.774 (1.00) |
0.398 (1.00) |
0.95 (1.00) |
0.0392 (0.797) |
1 (1.00) |
0.0362 (0.797) |
0.614 (1.00) |
0.846 (1.00) |
0.989 (1.00) |
0.0724 (0.9) |
0.89 (1.00) |
0.382 (1.00) |
METTL3 | 17 (4%) | 378 |
0.0727 (0.9) |
0.892 (1.00) |
0.373 (1.00) |
0.358 (1.00) |
0.947 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.597 (1.00) |
0.0964 (0.927) |
0.248 (1.00) |
0.145 (1.00) |
0.314 (1.00) |
1 (1.00) |
ZNF185 | 5 (1%) | 390 |
0.965 (1.00) |
0.38 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.463 (1.00) |
1 (1.00) |
0.334 (1.00) |
1 (1.00) |
0.107 (0.936) |
1 (1.00) |
1 (1.00) |
||
ERBB2 | 48 (12%) | 347 |
0.0313 (0.797) |
0.267 (1.00) |
0.626 (1.00) |
0.932 (1.00) |
0.468 (1.00) |
0.607 (1.00) |
0.726 (1.00) |
0.489 (1.00) |
0.68 (1.00) |
0.915 (1.00) |
0.191 (1.00) |
0.724 (1.00) |
1 (1.00) |
ATM | 53 (13%) | 342 |
0.324 (1.00) |
0.663 (1.00) |
0.748 (1.00) |
0.798 (1.00) |
0.362 (1.00) |
0.368 (1.00) |
0.241 (1.00) |
1 (1.00) |
0.0834 (0.915) |
0.216 (1.00) |
0.216 (1.00) |
0.349 (1.00) |
0.313 (1.00) |
UNC93B1 | 7 (2%) | 388 |
0.305 (1.00) |
0.536 (1.00) |
0.591 (1.00) |
0.537 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.301 (1.00) |
1 (1.00) |
1 (1.00) |
||
SF1 | 10 (3%) | 385 |
0.511 (1.00) |
0.0879 (0.917) |
0.115 (0.941) |
1 (1.00) |
0.0143 (0.797) |
1 (1.00) |
0.0701 (0.9) |
1 (1.00) |
0.701 (1.00) |
0.334 (1.00) |
0.0575 (0.89) |
0.62 (1.00) |
1 (1.00) |
BCL2L1 | 4 (1%) | 391 |
0.0275 (0.797) |
0.746 (1.00) |
0.346 (1.00) |
0.289 (1.00) |
1 (1.00) |
1 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.941 (1.00) |
1 (1.00) |
1 (1.00) |
||
DNAH6 | 16 (4%) | 379 |
0.957 (1.00) |
0.944 (1.00) |
0.213 (1.00) |
0.159 (1.00) |
0.636 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.547 (1.00) |
0.747 (1.00) |
0.762 (1.00) |
0.0723 (0.9) |
0.874 (1.00) |
0.289 (1.00) |
HES1 | 11 (3%) | 384 |
0.375 (1.00) |
0.0519 (0.852) |
0.933 (1.00) |
1 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.736 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.559 (1.00) |
0.402 (1.00) |
1 (1.00) |
|
ERBB3 | 41 (10%) | 354 |
0.437 (1.00) |
0.741 (1.00) |
0.525 (1.00) |
0.769 (1.00) |
0.506 (1.00) |
0.607 (1.00) |
0.193 (1.00) |
0.707 (1.00) |
0.074 (0.9) |
0.742 (1.00) |
0.532 (1.00) |
0.0592 (0.895) |
0.191 (1.00) |
TXNIP | 17 (4%) | 378 |
0.926 (1.00) |
0.21 (1.00) |
0.768 (1.00) |
0.23 (1.00) |
0.827 (1.00) |
1 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.195 (1.00) |
0.933 (1.00) |
0.674 (1.00) |
0.063 (0.9) |
0.272 (1.00) |
THRAP3 | 14 (4%) | 381 |
0.442 (1.00) |
0.0914 (0.917) |
0.204 (1.00) |
0.801 (1.00) |
0.487 (1.00) |
1 (1.00) |
0.762 (1.00) |
0.547 (1.00) |
0.686 (1.00) |
0.257 (1.00) |
0.0384 (0.797) |
0.417 (1.00) |
0.0339 (0.797) |
SPTAN1 | 45 (11%) | 350 |
0.0496 (0.852) |
0.0526 (0.852) |
0.417 (1.00) |
0.219 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.105 (0.936) |
1 (1.00) |
0.963 (1.00) |
0.387 (1.00) |
0.323 (1.00) |
0.597 (1.00) |
0.225 (1.00) |
ARID1B | 23 (6%) | 372 |
0.852 (1.00) |
0.359 (1.00) |
0.433 (1.00) |
0.409 (1.00) |
0.274 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.686 (1.00) |
0.0518 (0.852) |
0.105 (0.936) |
0.384 (1.00) |
1 (1.00) |
NRAS | 7 (2%) | 388 |
0.207 (1.00) |
0.37 (1.00) |
0.334 (1.00) |
0.455 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.193 (1.00) |
0.362 (1.00) |
0.0812 (0.915) |
1 (1.00) |
|
RPTN | 15 (4%) | 380 |
0.949 (1.00) |
0.991 (1.00) |
0.265 (1.00) |
0.853 (1.00) |
0.0889 (0.917) |
1 (1.00) |
0.768 (1.00) |
0.573 (1.00) |
0.895 (1.00) |
0.046 (0.852) |
0.145 (1.00) |
0.516 (1.00) |
1 (1.00) |
RAI1 | 21 (5%) | 374 |
0.101 (0.936) |
0.769 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.122 (0.958) |
0.115 (0.941) |
0.306 (1.00) |
0.617 (1.00) |
0.665 (1.00) |
0.814 (1.00) |
0.141 (1.00) |
1 (1.00) |
0.321 (1.00) |
TMCO4 | 12 (3%) | 383 |
0.93 (1.00) |
0.855 (1.00) |
0.683 (1.00) |
0.496 (1.00) |
0.708 (1.00) |
0.472 (1.00) |
0.739 (1.00) |
1 (1.00) |
0.418 (1.00) |
0.636 (1.00) |
0.725 (1.00) |
0.0333 (0.797) |
1 (1.00) |
CNOT1 | 21 (5%) | 374 |
0.0118 (0.797) |
0.392 (1.00) |
0.194 (1.00) |
0.483 (1.00) |
0.755 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.617 (1.00) |
0.0269 (0.797) |
0.0177 (0.797) |
0.214 (1.00) |
0.629 (1.00) |
0.00674 (0.797) |
PARD3 | 22 (6%) | 373 |
0.294 (1.00) |
0.706 (1.00) |
0.586 (1.00) |
0.237 (1.00) |
0.277 (1.00) |
1 (1.00) |
0.0211 (0.797) |
0.617 (1.00) |
0.00945 (0.797) |
0.571 (1.00) |
0.349 (1.00) |
0.283 (1.00) |
0.0787 (0.91) |
EZR | 12 (3%) | 383 |
0.0155 (0.797) |
0.432 (1.00) |
0.345 (1.00) |
0.34 (1.00) |
0.513 (1.00) |
0.291 (1.00) |
0.516 (1.00) |
0.492 (1.00) |
0.321 (1.00) |
0.154 (1.00) |
0.135 (1.00) |
0.205 (1.00) |
1 (1.00) |
MOAP1 | 7 (2%) | 388 |
0.0408 (0.797) |
0.107 (0.936) |
0.809 (1.00) |
0.861 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.285 (1.00) |
0.246 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.712 (1.00) |
1 (1.00) |
SF3B1 | 24 (6%) | 371 |
0.521 (1.00) |
0.035 (0.797) |
0.186 (1.00) |
0.519 (1.00) |
0.72 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.625 (1.00) |
0.00968 (0.797) |
0.941 (1.00) |
0.839 (1.00) |
0.395 (1.00) |
1 (1.00) |
RUNX1 | 13 (3%) | 382 |
0.554 (1.00) |
0.729 (1.00) |
0.445 (1.00) |
0.239 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.462 (1.00) |
0.687 (1.00) |
0.947 (1.00) |
0.0922 (0.917) |
0.483 (1.00) |
1 (1.00) |
MEGF8 | 20 (5%) | 375 |
0.32 (1.00) |
0.755 (1.00) |
0.498 (1.00) |
0.623 (1.00) |
0.432 (1.00) |
1 (1.00) |
0.119 (0.947) |
0.613 (1.00) |
0.829 (1.00) |
0.0285 (0.797) |
0.242 (1.00) |
0.537 (1.00) |
0.305 (1.00) |
CASP8 | 14 (4%) | 381 |
0.231 (1.00) |
0.791 (1.00) |
0.303 (1.00) |
0.719 (1.00) |
0.59 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.895 (1.00) |
0.568 (1.00) |
0.563 (1.00) |
0.838 (1.00) |
1 (1.00) |
DAZAP1 | 6 (2%) | 389 |
0.357 (1.00) |
0.914 (1.00) |
0.0518 (0.852) |
0.215 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.321 (1.00) |
0.206 (1.00) |
0.712 (1.00) |
1 (1.00) |
1 (1.00) |
USP28 | 13 (3%) | 382 |
0.471 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.927 (1.00) |
0.42 (1.00) |
0.369 (1.00) |
1 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.535 (1.00) |
0.478 (1.00) |
0.837 (1.00) |
1 (1.00) |
SETD2 | 27 (7%) | 368 |
0.615 (1.00) |
0.838 (1.00) |
0.529 (1.00) |
0.807 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.821 (1.00) |
1 (1.00) |
0.0499 (0.852) |
0.0321 (0.797) |
0.7 (1.00) |
0.765 (1.00) |
1 (1.00) |
EME1 | 5 (1%) | 390 |
0.658 (1.00) |
0.0554 (0.871) |
0.467 (1.00) |
0.575 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.332 (1.00) |
1 (1.00) |
|||
ADC | 5 (1%) | 390 |
0.481 (1.00) |
0.214 (1.00) |
0.468 (1.00) |
0.577 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.925 (1.00) |
0.331 (1.00) |
1 (1.00) |
|
CNOT3 | 10 (3%) | 385 |
0.108 (0.936) |
0.497 (1.00) |
0.929 (1.00) |
1 (1.00) |
0.684 (1.00) |
0.369 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.721 (1.00) |
0.883 (1.00) |
0.246 (1.00) |
1 (1.00) |
|
SSH3 | 15 (4%) | 380 |
0.0969 (0.927) |
0.287 (1.00) |
0.43 (1.00) |
0.157 (1.00) |
0.221 (1.00) |
1 (1.00) |
0.768 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.2 (1.00) |
0.598 (1.00) |
1 (1.00) |
|
AHR | 22 (6%) | 373 |
0.318 (1.00) |
0.958 (1.00) |
0.205 (1.00) |
0.362 (1.00) |
0.435 (1.00) |
0.472 (1.00) |
0.616 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.885 (1.00) |
0.971 (1.00) |
1 (1.00) |
0.367 (1.00) |
EIF4A2 | 11 (3%) | 384 |
0.501 (1.00) |
0.931 (1.00) |
0.618 (1.00) |
0.202 (1.00) |
0.521 (1.00) |
0.331 (1.00) |
0.302 (1.00) |
1 (1.00) |
0.567 (1.00) |
0.792 (1.00) |
0.669 (1.00) |
0.768 (1.00) |
1 (1.00) |
EPHA2 | 19 (5%) | 376 |
0.579 (1.00) |
0.11 (0.937) |
0.52 (1.00) |
0.361 (1.00) |
0.0145 (0.797) |
0.369 (1.00) |
0.0552 (0.871) |
0.612 (1.00) |
0.533 (1.00) |
0.194 (1.00) |
0.999 (1.00) |
0.118 (0.947) |
1 (1.00) |
OGDH | 19 (5%) | 376 |
0.23 (1.00) |
0.341 (1.00) |
0.887 (1.00) |
0.941 (1.00) |
1 (1.00) |
1 (1.00) |
0.424 (1.00) |
1 (1.00) |
0.476 (1.00) |
0.29 (1.00) |
0.545 (1.00) |
0.278 (1.00) |
0.337 (1.00) |
POU3F1 | 3 (1%) | 392 |
0.334 (1.00) |
0.693 (1.00) |
0.0832 (0.915) |
0.576 (1.00) |
0.0595 (0.895) |
1 (1.00) |
1 (1.00) |
0.0275 (0.797) |
1 (1.00) |
1 (1.00) |
-
Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
-
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22811975/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt
-
Number of patients = 395
-
Number of significantly mutated genes = 81
-
Number of selected clinical features = 13
-
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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.