This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 94 genes and 11 clinical features across 306 patients, 2 significant findings detected with Q value < 0.25.
-
TP53 mutation correlated to 'Time to Death'.
-
HLA-B mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
Table 1. Get Full Table Overview of the association between mutation status of 94 genes and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.
Clinical Features |
Time to Death |
AGE | GENDER |
PATHOLOGY T |
PATHOLOGY N |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
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 | t-test | Fisher's exact test | t-test | t-test | |
TP53 | 214 (70%) | 92 |
1.59e-05 (0.0158) |
0.769 (1.00) |
0.578 (1.00) |
0.00577 (1.00) |
0.0175 (1.00) |
0.0067 (1.00) |
0.152 (1.00) |
0.109 (1.00) |
0.387 (1.00) |
0.783 (1.00) |
0.0185 (1.00) |
HLA-B | 9 (3%) | 297 |
0.636 (1.00) |
0.701 (1.00) |
0.0676 (1.00) |
0.913 (1.00) |
0.0257 (1.00) |
0.311 (1.00) |
0.118 (1.00) |
0.828 (1.00) |
0.0922 (1.00) |
0.0829 (1.00) |
4.64e-08 (4.63e-05) |
NOTCH1 | 57 (19%) | 249 |
0.595 (1.00) |
0.129 (1.00) |
0.323 (1.00) |
0.753 (1.00) |
0.866 (1.00) |
0.948 (1.00) |
0.501 (1.00) |
0.00872 (1.00) |
0.588 (1.00) |
0.813 (1.00) |
0.211 (1.00) |
CDKN2A | 65 (21%) | 241 |
0.459 (1.00) |
0.697 (1.00) |
0.64 (1.00) |
0.664 (1.00) |
0.98 (1.00) |
0.264 (1.00) |
0.108 (1.00) |
0.0709 (1.00) |
0.183 (1.00) |
0.394 (1.00) |
0.92 (1.00) |
HRAS | 10 (3%) | 296 |
0.0791 (1.00) |
0.227 (1.00) |
1 (1.00) |
0.241 (1.00) |
0.0538 (1.00) |
0.0885 (1.00) |
0.461 (1.00) |
0.157 (1.00) |
0.157 (1.00) |
0.217 (1.00) |
0.219 (1.00) |
NFE2L2 | 17 (6%) | 289 |
0.038 (1.00) |
0.00698 (1.00) |
0.576 (1.00) |
0.772 (1.00) |
0.884 (1.00) |
0.502 (1.00) |
0.256 (1.00) |
0.906 (1.00) |
0.426 (1.00) |
0.309 (1.00) |
0.696 (1.00) |
PIK3CA | 64 (21%) | 242 |
0.272 (1.00) |
0.832 (1.00) |
0.207 (1.00) |
0.742 (1.00) |
0.477 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.699 (1.00) |
0.898 (1.00) |
0.357 (1.00) |
CASP8 | 27 (9%) | 279 |
0.549 (1.00) |
0.000303 (0.3) |
0.00127 (1.00) |
0.559 (1.00) |
0.103 (1.00) |
0.168 (1.00) |
0.491 (1.00) |
0.223 (1.00) |
0.0114 (1.00) |
0.131 (1.00) |
0.102 (1.00) |
FAT1 | 72 (24%) | 234 |
0.794 (1.00) |
0.00051 (0.506) |
0.131 (1.00) |
0.537 (1.00) |
0.76 (1.00) |
0.499 (1.00) |
0.877 (1.00) |
0.53 (1.00) |
0.0245 (1.00) |
0.133 (1.00) |
0.917 (1.00) |
JUB | 18 (6%) | 288 |
0.0943 (1.00) |
0.0802 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.282 (1.00) |
0.64 (1.00) |
0.785 (1.00) |
0.538 (1.00) |
0.186 (1.00) |
0.0655 (1.00) |
0.96 (1.00) |
MLL2 | 56 (18%) | 250 |
0.928 (1.00) |
0.993 (1.00) |
0.869 (1.00) |
0.242 (1.00) |
0.881 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.165 (1.00) |
0.393 (1.00) |
0.0676 (1.00) |
FBXW7 | 15 (5%) | 291 |
0.898 (1.00) |
0.0958 (1.00) |
0.372 (1.00) |
0.635 (1.00) |
0.31 (1.00) |
0.668 (1.00) |
0.544 (1.00) |
0.415 (1.00) |
0.386 (1.00) |
0.373 (1.00) |
0.367 (1.00) |
NSD1 | 33 (11%) | 273 |
0.194 (1.00) |
0.0819 (1.00) |
0.301 (1.00) |
0.778 (1.00) |
0.000562 (0.556) |
0.0362 (1.00) |
0.399 (1.00) |
0.218 (1.00) |
0.297 (1.00) |
0.947 (1.00) |
0.000301 (0.299) |
BAGE2 | 11 (4%) | 295 |
0.0589 (1.00) |
0.26 (1.00) |
0.733 (1.00) |
0.678 (1.00) |
0.807 (1.00) |
0.609 (1.00) |
0.735 (1.00) |
0.966 (1.00) |
0.645 (1.00) |
0.728 (1.00) |
0.234 (1.00) |
POTEC | 15 (5%) | 291 |
0.229 (1.00) |
0.0491 (1.00) |
0.133 (1.00) |
0.212 (1.00) |
0.926 (1.00) |
0.636 (1.00) |
0.544 (1.00) |
0.232 (1.00) |
0.00819 (1.00) |
0.872 (1.00) |
0.651 (1.00) |
ZNF750 | 13 (4%) | 293 |
0.571 (1.00) |
0.845 (1.00) |
0.123 (1.00) |
0.0594 (1.00) |
0.745 (1.00) |
0.67 (1.00) |
0.527 (1.00) |
0.9 (1.00) |
0.431 (1.00) |
0.162 (1.00) |
0.749 (1.00) |
EP300 | 25 (8%) | 281 |
0.642 (1.00) |
0.536 (1.00) |
0.641 (1.00) |
0.951 (1.00) |
0.586 (1.00) |
0.549 (1.00) |
0.636 (1.00) |
0.113 (1.00) |
0.374 (1.00) |
0.73 (1.00) |
0.569 (1.00) |
POM121L12 | 14 (5%) | 292 |
0.649 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.0736 (1.00) |
0.343 (1.00) |
0.444 (1.00) |
0.759 (1.00) |
0.427 (1.00) |
0.245 (1.00) |
0.773 (1.00) |
0.685 (1.00) |
RHOA | 4 (1%) | 302 |
0.288 (1.00) |
0.916 (1.00) |
0.303 (1.00) |
0.224 (1.00) |
0.182 (1.00) |
0.6 (1.00) |
0.575 (1.00) |
0.00186 (1.00) |
0.169 (1.00) |
0.547 (1.00) |
0.156 (1.00) |
B2M | 7 (2%) | 299 |
0.233 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.79 (1.00) |
0.683 (1.00) |
0.011 (1.00) |
||||
RAC1 | 9 (3%) | 297 |
0.676 (1.00) |
0.00682 (1.00) |
0.0676 (1.00) |
0.412 (1.00) |
0.215 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.721 (1.00) |
0.279 (1.00) |
0.00481 (1.00) |
0.0314 (1.00) |
ZNF804B | 21 (7%) | 285 |
0.356 (1.00) |
0.054 (1.00) |
0.805 (1.00) |
0.952 (1.00) |
0.743 (1.00) |
0.662 (1.00) |
0.117 (1.00) |
0.0266 (1.00) |
0.336 (1.00) |
0.873 (1.00) |
0.0429 (1.00) |
KCNT2 | 17 (6%) | 289 |
0.409 (1.00) |
0.663 (1.00) |
0.787 (1.00) |
0.238 (1.00) |
0.817 (1.00) |
0.816 (1.00) |
0.256 (1.00) |
0.17 (1.00) |
0.0804 (1.00) |
0.107 (1.00) |
0.561 (1.00) |
RASA1 | 14 (5%) | 292 |
0.466 (1.00) |
0.783 (1.00) |
0.364 (1.00) |
0.521 (1.00) |
0.895 (1.00) |
0.843 (1.00) |
0.204 (1.00) |
0.968 (1.00) |
0.855 (1.00) |
0.437 (1.00) |
0.925 (1.00) |
PRIM2 | 9 (3%) | 297 |
0.652 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.461 (1.00) |
0.229 (1.00) |
0.342 (1.00) |
0.457 (1.00) |
0.116 (1.00) |
0.0677 (1.00) |
0.907 (1.00) |
0.521 (1.00) |
CDH10 | 23 (8%) | 283 |
0.171 (1.00) |
0.0362 (1.00) |
0.336 (1.00) |
0.113 (1.00) |
0.797 (1.00) |
0.0701 (1.00) |
0.214 (1.00) |
0.098 (1.00) |
0.828 (1.00) |
0.153 (1.00) |
0.304 (1.00) |
CNTNAP5 | 15 (5%) | 291 |
0.173 (1.00) |
0.589 (1.00) |
0.0769 (1.00) |
0.0291 (1.00) |
0.379 (1.00) |
0.0492 (1.00) |
0.768 (1.00) |
0.139 (1.00) |
0.173 (1.00) |
0.234 (1.00) |
0.127 (1.00) |
POTEG | 10 (3%) | 296 |
0.432 (1.00) |
0.0789 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.89 (1.00) |
0.0959 (1.00) |
0.719 (1.00) |
0.31 (1.00) |
0.446 (1.00) |
0.0187 (1.00) |
0.428 (1.00) |
ZNF99 | 22 (7%) | 284 |
0.284 (1.00) |
0.876 (1.00) |
0.145 (1.00) |
0.124 (1.00) |
0.717 (1.00) |
0.433 (1.00) |
0.803 (1.00) |
0.327 (1.00) |
0.196 (1.00) |
0.623 (1.00) |
0.801 (1.00) |
OR2T12 | 11 (4%) | 295 |
0.876 (1.00) |
0.0516 (1.00) |
1 (1.00) |
0.0325 (1.00) |
0.134 (1.00) |
0.00529 (1.00) |
0.301 (1.00) |
0.0379 (1.00) |
0.0598 (1.00) |
0.201 (1.00) |
0.0674 (1.00) |
REG1A | 8 (3%) | 298 |
0.458 (1.00) |
0.573 (1.00) |
1 (1.00) |
0.636 (1.00) |
1 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.136 (1.00) |
0.236 (1.00) |
0.581 (1.00) |
0.465 (1.00) |
PABPC5 | 9 (3%) | 297 |
0.723 (1.00) |
0.717 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.686 (1.00) |
0.199 (1.00) |
0.698 (1.00) |
0.294 (1.00) |
0.32 (1.00) |
0.174 (1.00) |
0.933 (1.00) |
IL32 | 4 (1%) | 302 |
0.127 (1.00) |
0.932 (1.00) |
0.303 (1.00) |
0.878 (1.00) |
0.0875 (1.00) |
0.464 (1.00) |
0.575 (1.00) |
0.651 (1.00) |
0.791 (1.00) |
||
PRAMEF11 | 10 (3%) | 296 |
0.289 (1.00) |
0.0402 (1.00) |
0.145 (1.00) |
0.71 (1.00) |
0.686 (1.00) |
1 (1.00) |
0.719 (1.00) |
0.11 (1.00) |
0.872 (1.00) |
0.0976 (1.00) |
0.901 (1.00) |
EPHA2 | 14 (5%) | 292 |
0.0195 (1.00) |
0.891 (1.00) |
0.221 (1.00) |
0.932 (1.00) |
0.184 (1.00) |
0.805 (1.00) |
1 (1.00) |
0.00747 (1.00) |
0.349 (1.00) |
0.0793 (1.00) |
0.33 (1.00) |
FCRL4 | 13 (4%) | 293 |
0.368 (1.00) |
0.223 (1.00) |
0.526 (1.00) |
0.254 (1.00) |
0.555 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.711 (1.00) |
0.0883 (1.00) |
0.908 (1.00) |
LCP1 | 12 (4%) | 294 |
0.654 (1.00) |
0.847 (1.00) |
0.522 (1.00) |
0.0309 (1.00) |
1 (1.00) |
0.0394 (1.00) |
0.51 (1.00) |
0.915 (1.00) |
0.457 (1.00) |
0.7 (1.00) |
0.756 (1.00) |
LRFN5 | 13 (4%) | 293 |
0.893 (1.00) |
0.862 (1.00) |
1 (1.00) |
0.627 (1.00) |
0.0377 (1.00) |
0.878 (1.00) |
1 (1.00) |
0.719 (1.00) |
0.0655 (1.00) |
0.457 (1.00) |
0.477 (1.00) |
MAPK1 | 4 (1%) | 302 |
0.452 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.682 (1.00) |
0.712 (1.00) |
0.575 (1.00) |
0.885 (1.00) |
0.976 (1.00) |
||
PEG3 | 23 (8%) | 283 |
0.563 (1.00) |
0.983 (1.00) |
0.467 (1.00) |
0.956 (1.00) |
0.642 (1.00) |
0.718 (1.00) |
0.321 (1.00) |
0.14 (1.00) |
0.076 (1.00) |
0.801 (1.00) |
0.259 (1.00) |
PRSS1 | 8 (3%) | 298 |
0.287 (1.00) |
0.751 (1.00) |
0.000603 (0.597) |
0.869 (1.00) |
0.125 (1.00) |
1 (1.00) |
0.21 (1.00) |
0.0487 (1.00) |
0.67 (1.00) |
0.502 (1.00) |
|
DOK6 | 8 (3%) | 298 |
0.695 (1.00) |
0.348 (1.00) |
0.00634 (1.00) |
0.835 (1.00) |
0.125 (1.00) |
0.497 (1.00) |
0.685 (1.00) |
0.0744 (1.00) |
0.0219 (1.00) |
0.822 (1.00) |
0.86 (1.00) |
GABRB3 | 11 (4%) | 295 |
0.128 (1.00) |
0.621 (1.00) |
0.0389 (1.00) |
0.284 (1.00) |
0.089 (1.00) |
0.247 (1.00) |
0.735 (1.00) |
0.238 (1.00) |
0.973 (1.00) |
0.000266 (0.264) |
0.173 (1.00) |
STEAP4 | 10 (3%) | 296 |
0.634 (1.00) |
0.981 (1.00) |
0.295 (1.00) |
0.13 (1.00) |
1 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.038 (1.00) |
0.808 (1.00) |
0.363 (1.00) |
0.661 (1.00) |
ASXL3 | 21 (7%) | 285 |
0.494 (1.00) |
0.572 (1.00) |
0.456 (1.00) |
0.727 (1.00) |
0.459 (1.00) |
0.473 (1.00) |
0.303 (1.00) |
0.669 (1.00) |
0.289 (1.00) |
0.609 (1.00) |
0.803 (1.00) |
NTM | 7 (2%) | 299 |
0.847 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.098 (1.00) |
0.197 (1.00) |
0.823 (1.00) |
0.173 (1.00) |
0.721 (1.00) |
0.746 (1.00) |
FAM155A | 11 (4%) | 295 |
0.667 (1.00) |
0.497 (1.00) |
0.3 (1.00) |
0.502 (1.00) |
0.269 (1.00) |
0.202 (1.00) |
0.48 (1.00) |
0.455 (1.00) |
0.198 (1.00) |
0.454 (1.00) |
0.0429 (1.00) |
HLA-A | 9 (3%) | 297 |
0.498 (1.00) |
0.262 (1.00) |
1 (1.00) |
0.62 (1.00) |
0.336 (1.00) |
0.274 (1.00) |
0.24 (1.00) |
0.709 (1.00) |
0.00554 (1.00) |
0.273 (1.00) |
0.0104 (1.00) |
KRTAP1-5 | 3 (1%) | 303 |
0.258 (1.00) |
0.528 (1.00) |
0.564 (1.00) |
0.573 (1.00) |
0.475 (1.00) |
||||||
CTCF | 11 (4%) | 295 |
0.239 (1.00) |
0.0444 (1.00) |
0.181 (1.00) |
0.935 (1.00) |
0.606 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.0319 (1.00) |
0.192 (1.00) |
0.239 (1.00) |
BRWD3 | 16 (5%) | 290 |
0.222 (1.00) |
0.683 (1.00) |
0.000486 (0.482) |
0.731 (1.00) |
0.386 (1.00) |
0.93 (1.00) |
0.769 (1.00) |
0.838 (1.00) |
0.9 (1.00) |
0.989 (1.00) |
0.565 (1.00) |
CNPY3 | 3 (1%) | 303 |
0.0807 (1.00) |
0.564 (1.00) |
0.84 (1.00) |
0.773 (1.00) |
1 (1.00) |
1 (1.00) |
0.557 (1.00) |
||||
FAM101A | 4 (1%) | 302 |
0.806 (1.00) |
0.937 (1.00) |
1 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.79 (1.00) |
1 (1.00) |
0.33 (1.00) |
0.99 (1.00) |
||
PSG8 | 9 (3%) | 297 |
0.983 (1.00) |
0.074 (1.00) |
0.121 (1.00) |
0.956 (1.00) |
0.251 (1.00) |
0.382 (1.00) |
1 (1.00) |
0.0223 (1.00) |
0.928 (1.00) |
0.909 (1.00) |
0.00724 (1.00) |
OR56A1 | 8 (3%) | 298 |
0.866 (1.00) |
0.882 (1.00) |
0.689 (1.00) |
0.13 (1.00) |
0.89 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.274 (1.00) |
0.917 (1.00) |
0.271 (1.00) |
OR2M2 | 8 (3%) | 298 |
0.633 (1.00) |
0.384 (1.00) |
1 (1.00) |
0.521 (1.00) |
0.389 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.0479 (1.00) |
0.389 (1.00) |
0.801 (1.00) |
0.0211 (1.00) |
OR4M2 | 8 (3%) | 298 |
0.375 (1.00) |
0.608 (1.00) |
0.689 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.738 (1.00) |
0.685 (1.00) |
0.383 (1.00) |
0.741 (1.00) |
0.979 (1.00) |
0.0909 (1.00) |
CPXCR1 | 7 (2%) | 299 |
0.535 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.807 (1.00) |
0.671 (1.00) |
0.0728 (1.00) |
0.276 (1.00) |
0.98 (1.00) |
||
EYA1 | 10 (3%) | 296 |
0.811 (1.00) |
0.215 (1.00) |
0.145 (1.00) |
0.107 (1.00) |
0.408 (1.00) |
0.927 (1.00) |
0.719 (1.00) |
0.149 (1.00) |
0.97 (1.00) |
0.432 (1.00) |
0.901 (1.00) |
LINGO2 | 10 (3%) | 296 |
0.412 (1.00) |
0.308 (1.00) |
0.295 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.554 (1.00) |
0.131 (1.00) |
0.793 (1.00) |
0.63 (1.00) |
0.729 (1.00) |
0.567 (1.00) |
SEMA5A | 19 (6%) | 287 |
0.636 (1.00) |
0.386 (1.00) |
0.606 (1.00) |
0.932 (1.00) |
0.248 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.037 (1.00) |
0.0318 (1.00) |
0.559 (1.00) |
0.897 (1.00) |
TGFBR2 | 10 (3%) | 296 |
0.668 (1.00) |
0.0292 (1.00) |
1 (1.00) |
0.71 (1.00) |
0.336 (1.00) |
0.833 (1.00) |
0.07 (1.00) |
0.287 (1.00) |
0.331 (1.00) |
0.00839 (1.00) |
0.0498 (1.00) |
PLSCR1 | 5 (2%) | 301 |
0.0669 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.834 (1.00) |
0.362 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.817 (1.00) |
0.304 (1.00) |
0.933 (1.00) |
|
LIN28B | 6 (2%) | 300 |
0.466 (1.00) |
0.928 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.647 (1.00) |
0.585 (1.00) |
0.671 (1.00) |
0.635 (1.00) |
0.557 (1.00) |
|
AGTR1 | 8 (3%) | 298 |
0.324 (1.00) |
0.0224 (1.00) |
0.453 (1.00) |
0.898 (1.00) |
0.408 (1.00) |
0.671 (1.00) |
0.685 (1.00) |
0.0866 (1.00) |
0.389 (1.00) |
0.0329 (1.00) |
0.318 (1.00) |
C6 | 12 (4%) | 294 |
0.727 (1.00) |
0.516 (1.00) |
0.321 (1.00) |
0.848 (1.00) |
1 (1.00) |
0.817 (1.00) |
0.51 (1.00) |
0.172 (1.00) |
0.877 (1.00) |
0.21 (1.00) |
0.504 (1.00) |
MS4A14 | 9 (3%) | 297 |
0.998 (1.00) |
0.407 (1.00) |
0.0676 (1.00) |
0.382 (1.00) |
0.498 (1.00) |
0.364 (1.00) |
0.457 (1.00) |
0.795 (1.00) |
0.624 (1.00) |
0.815 (1.00) |
0.503 (1.00) |
HIST1H4E | 5 (2%) | 301 |
0.851 (1.00) |
0.549 (1.00) |
0.618 (1.00) |
0.878 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.334 (1.00) |
0.725 (1.00) |
|||
LBP | 7 (2%) | 299 |
0.98 (1.00) |
0.436 (1.00) |
0.678 (1.00) |
0.84 (1.00) |
0.255 (1.00) |
1 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.152 (1.00) |
0.828 (1.00) |
0.246 (1.00) |
RGS17 | 5 (2%) | 301 |
0.529 (1.00) |
0.483 (1.00) |
0.618 (1.00) |
0.84 (1.00) |
0.79 (1.00) |
0.334 (1.00) |
0.946 (1.00) |
0.644 (1.00) |
|||
LILRB1 | 12 (4%) | 294 |
0.885 (1.00) |
0.907 (1.00) |
0.522 (1.00) |
0.292 (1.00) |
0.52 (1.00) |
0.638 (1.00) |
1 (1.00) |
0.118 (1.00) |
0.602 (1.00) |
0.57 (1.00) |
0.506 (1.00) |
MAGEL2 | 12 (4%) | 294 |
0.477 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.0997 (1.00) |
0.0533 (1.00) |
0.308 (1.00) |
0.417 (1.00) |
0.225 (1.00) |
0.554 (1.00) |
0.483 (1.00) |
OR8D4 | 6 (2%) | 300 |
0.224 (1.00) |
0.132 (1.00) |
0.193 (1.00) |
0.762 (1.00) |
0.428 (1.00) |
0.2 (1.00) |
1 (1.00) |
0.804 (1.00) |
0.237 (1.00) |
0.263 (1.00) |
0.161 (1.00) |
HIST1H1B | 7 (2%) | 299 |
0.204 (1.00) |
0.0857 (1.00) |
0.398 (1.00) |
0.898 (1.00) |
0.15 (1.00) |
0.908 (1.00) |
0.683 (1.00) |
0.0554 (1.00) |
0.494 (1.00) |
||
C3ORF59 | 8 (3%) | 298 |
0.887 (1.00) |
0.831 (1.00) |
0.689 (1.00) |
0.554 (1.00) |
0.122 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.537 (1.00) |
0.429 (1.00) |
0.0498 (1.00) |
C8ORF34 | 7 (2%) | 299 |
0.223 (1.00) |
0.404 (1.00) |
0.678 (1.00) |
0.853 (1.00) |
0.887 (1.00) |
0.392 (1.00) |
0.377 (1.00) |
0.328 (1.00) |
0.443 (1.00) |
0.0396 (1.00) |
0.897 (1.00) |
OR8J1 | 9 (3%) | 297 |
0.706 (1.00) |
0.32 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.927 (1.00) |
0.24 (1.00) |
0.0166 (1.00) |
0.374 (1.00) |
0.426 (1.00) |
0.594 (1.00) |
RAB32 | 3 (1%) | 303 |
0.97 (1.00) |
0.352 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.301 (1.00) |
0.381 (1.00) |
||||
TMEM195 | 8 (3%) | 298 |
0.669 (1.00) |
0.0323 (1.00) |
1 (1.00) |
0.853 (1.00) |
1 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.496 (1.00) |
0.204 (1.00) |
0.28 (1.00) |
0.899 (1.00) |
PCDH11X | 21 (7%) | 285 |
0.724 (1.00) |
0.716 (1.00) |
0.00379 (1.00) |
0.134 (1.00) |
0.797 (1.00) |
0.971 (1.00) |
0.034 (1.00) |
0.125 (1.00) |
0.403 (1.00) |
0.531 (1.00) |
0.0236 (1.00) |
SLITRK4 | 12 (4%) | 294 |
0.115 (1.00) |
0.0417 (1.00) |
0.522 (1.00) |
0.767 (1.00) |
0.378 (1.00) |
0.951 (1.00) |
0.51 (1.00) |
0.211 (1.00) |
0.859 (1.00) |
0.564 (1.00) |
0.0818 (1.00) |
FRG2B | 6 (2%) | 300 |
0.899 (1.00) |
0.378 (1.00) |
0.0503 (1.00) |
0.762 (1.00) |
0.887 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.228 (1.00) |
0.249 (1.00) |
0.448 (1.00) |
OR2L13 | 7 (2%) | 299 |
0.382 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.137 (1.00) |
0.328 (1.00) |
0.216 (1.00) |
0.683 (1.00) |
0.652 (1.00) |
0.554 (1.00) |
0.341 (1.00) |
0.214 (1.00) |
CUL3 | 10 (3%) | 296 |
0.77 (1.00) |
0.467 (1.00) |
0.733 (1.00) |
0.0875 (1.00) |
0.554 (1.00) |
0.289 (1.00) |
0.131 (1.00) |
0.527 (1.00) |
0.195 (1.00) |
0.197 (1.00) |
0.971 (1.00) |
FOSL2 | 7 (2%) | 299 |
0.00662 (1.00) |
0.761 (1.00) |
0.398 (1.00) |
0.706 (1.00) |
0.682 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.412 (1.00) |
0.911 (1.00) |
0.986 (1.00) |
0.151 (1.00) |
GPR158 | 12 (4%) | 294 |
0.764 (1.00) |
0.779 (1.00) |
0.321 (1.00) |
0.453 (1.00) |
0.257 (1.00) |
0.137 (1.00) |
0.737 (1.00) |
0.706 (1.00) |
0.333 (1.00) |
0.359 (1.00) |
0.135 (1.00) |
PTPRT | 19 (6%) | 287 |
0.798 (1.00) |
0.509 (1.00) |
0.606 (1.00) |
0.134 (1.00) |
0.294 (1.00) |
0.251 (1.00) |
0.277 (1.00) |
0.471 (1.00) |
0.604 (1.00) |
0.671 (1.00) |
0.12 (1.00) |
POTEH | 7 (2%) | 299 |
0.502 (1.00) |
0.0775 (1.00) |
0.678 (1.00) |
0.464 (1.00) |
0.033 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.81 (1.00) |
0.271 (1.00) |
0.141 (1.00) |
0.539 (1.00) |
OR5D13 | 7 (2%) | 299 |
0.285 (1.00) |
0.209 (1.00) |
0.0183 (1.00) |
0.651 (1.00) |
1 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.575 (1.00) |
0.375 (1.00) |
0.952 (1.00) |
PRB1 | 7 (2%) | 299 |
0.558 (1.00) |
0.528 (1.00) |
0.196 (1.00) |
0.618 (1.00) |
0.408 (1.00) |
0.531 (1.00) |
0.377 (1.00) |
0.26 (1.00) |
0.366 (1.00) |
0.868 (1.00) |
0.993 (1.00) |
NEUROD6 | 7 (2%) | 299 |
0.685 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.636 (1.00) |
1 (1.00) |
1 (1.00) |
0.0728 (1.00) |
0.394 (1.00) |
0.911 (1.00) |
0.81 (1.00) |
0.0411 (1.00) |
DPP10 | 16 (5%) | 290 |
0.453 (1.00) |
0.111 (1.00) |
0.775 (1.00) |
0.973 (1.00) |
0.761 (1.00) |
0.569 (1.00) |
0.769 (1.00) |
0.886 (1.00) |
0.798 (1.00) |
0.0528 (1.00) |
0.084 (1.00) |
DPPA4 | 7 (2%) | 299 |
0.529 (1.00) |
0.692 (1.00) |
1 (1.00) |
1 (1.00) |
0.138 (1.00) |
0.738 (1.00) |
0.377 (1.00) |
0.849 (1.00) |
0.911 (1.00) |
0.661 (1.00) |
0.849 (1.00) |
EPDR1 | 6 (2%) | 300 |
0.946 (1.00) |
0.805 (1.00) |
0.668 (1.00) |
0.587 (1.00) |
0.234 (1.00) |
0.81 (1.00) |
0.647 (1.00) |
0.898 (1.00) |
0.32 (1.00) |
0.166 (1.00) |
0.325 (1.00) |
P value = 1.59e-05 (logrank test), Q value = 0.016
Table S1. Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 303 | 120 | 0.1 - 210.9 (14.8) |
TP53 MUTATED | 212 | 96 | 0.1 - 142.5 (13.2) |
TP53 WILD-TYPE | 91 | 24 | 0.8 - 210.9 (22.0) |
Figure S1. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D6V1.png)
P value = 4.64e-08 (t-test), Q value = 4.6e-05
Table S2. Gene #53: 'HLA-B MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 231 | 2.7 (5.3) |
HLA-B MUTATED | 5 | 0.2 (0.4) |
HLA-B WILD-TYPE | 226 | 2.8 (5.4) |
Figure S2. Get High-res Image Gene #53: 'HLA-B MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'
![](D53V11.png)
-
Mutation data file = HNSC-TP.mutsig.cluster.txt
-
Clinical data file = HNSC-TP.clin.merged.picked.txt
-
Number of patients = 306
-
Number of significantly mutated genes = 94
-
Number of selected clinical features = 11
-
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.