This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 79 arm-level results and 12 clinical features across 321 patients, one significant finding detected with Q value < 0.25.
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18p gain cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
AGE | GENDER |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
NUMBER OF LYMPH NODES |
||
nCNV (%) | 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 | t-test | Fisher's exact test | t-test | t-test | |
18p gain | 0 (0%) | 269 |
0.235 (1.00) |
0.391 (1.00) |
0.000163 (0.154) |
0.0111 (1.00) |
0.467 (1.00) |
0.51 (1.00) |
0.0417 (1.00) |
0.287 (1.00) |
0.272 (1.00) |
0.268 (1.00) |
0.866 (1.00) |
0.504 (1.00) |
1p gain | 0 (0%) | 311 |
0.604 (1.00) |
0.324 (1.00) |
0.0322 (1.00) |
0.538 (1.00) |
0.574 (1.00) |
0.875 (1.00) |
0.462 (1.00) |
0.476 (1.00) |
0.0395 (1.00) |
0.53 (1.00) |
0.0297 (1.00) |
|
1q gain | 0 (0%) | 282 |
0.828 (1.00) |
0.916 (1.00) |
0.705 (1.00) |
0.107 (1.00) |
0.00949 (1.00) |
0.394 (1.00) |
0.0862 (1.00) |
0.158 (1.00) |
0.963 (1.00) |
0.333 (1.00) |
0.884 (1.00) |
0.123 (1.00) |
2p gain | 0 (0%) | 290 |
0.719 (1.00) |
0.91 (1.00) |
0.299 (1.00) |
0.869 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.0211 (1.00) |
0.151 (1.00) |
0.869 (1.00) |
0.5 (1.00) |
2q gain | 0 (0%) | 300 |
0.775 (1.00) |
0.906 (1.00) |
0.455 (1.00) |
0.861 (1.00) |
0.908 (1.00) |
1 (1.00) |
0.976 (1.00) |
0.598 (1.00) |
0.0762 (1.00) |
0.0845 (1.00) |
0.879 (1.00) |
0.416 (1.00) |
3p gain | 0 (0%) | 293 |
0.314 (1.00) |
0.457 (1.00) |
0.273 (1.00) |
0.876 (1.00) |
0.574 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.493 (1.00) |
0.0777 (1.00) |
0.0919 (1.00) |
0.402 (1.00) |
0.207 (1.00) |
3q gain | 0 (0%) | 215 |
0.427 (1.00) |
0.42 (1.00) |
0.0476 (1.00) |
0.761 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.0729 (1.00) |
0.00325 (1.00) |
0.149 (1.00) |
0.847 (1.00) |
0.712 (1.00) |
0.466 (1.00) |
4p gain | 0 (0%) | 308 |
0.697 (1.00) |
0.108 (1.00) |
0.762 (1.00) |
0.804 (1.00) |
0.476 (1.00) |
0.344 (1.00) |
0.197 (1.00) |
0.517 (1.00) |
0.797 (1.00) |
0.896 (1.00) |
0.418 (1.00) |
|
4q gain | 0 (0%) | 312 |
0.529 (1.00) |
0.814 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.586 (1.00) |
0.399 (1.00) |
1 (1.00) |
0.579 (1.00) |
0.331 (1.00) |
0.456 (1.00) |
0.404 (1.00) |
|
5p gain | 0 (0%) | 239 |
0.751 (1.00) |
0.544 (1.00) |
0.117 (1.00) |
0.913 (1.00) |
0.832 (1.00) |
0.0167 (1.00) |
0.333 (1.00) |
0.454 (1.00) |
0.18 (1.00) |
0.484 (1.00) |
0.22 (1.00) |
0.0958 (1.00) |
5q gain | 0 (0%) | 293 |
0.459 (1.00) |
0.902 (1.00) |
0.828 (1.00) |
0.569 (1.00) |
0.627 (1.00) |
0.328 (1.00) |
0.0662 (1.00) |
0.35 (1.00) |
0.0634 (1.00) |
0.82 (1.00) |
0.715 (1.00) |
0.0637 (1.00) |
6p gain | 0 (0%) | 295 |
0.514 (1.00) |
0.0951 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.558 (1.00) |
0.053 (1.00) |
0.644 (1.00) |
0.785 (1.00) |
0.657 (1.00) |
0.827 (1.00) |
6q gain | 0 (0%) | 302 |
0.626 (1.00) |
0.391 (1.00) |
0.793 (1.00) |
0.289 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.149 (1.00) |
0.0537 (1.00) |
0.834 (1.00) |
0.944 (1.00) |
0.428 (1.00) |
0.827 (1.00) |
7p gain | 0 (0%) | 248 |
0.495 (1.00) |
0.0903 (1.00) |
0.554 (1.00) |
0.922 (1.00) |
0.861 (1.00) |
0.305 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.868 (1.00) |
0.604 (1.00) |
0.699 (1.00) |
7q gain | 0 (0%) | 276 |
0.451 (1.00) |
0.606 (1.00) |
0.474 (1.00) |
0.312 (1.00) |
0.616 (1.00) |
0.394 (1.00) |
0.381 (1.00) |
0.852 (1.00) |
0.164 (1.00) |
0.613 (1.00) |
0.526 (1.00) |
0.631 (1.00) |
8p gain | 0 (0%) | 272 |
0.0189 (1.00) |
0.553 (1.00) |
0.121 (1.00) |
0.233 (1.00) |
0.408 (1.00) |
0.561 (1.00) |
0.36 (1.00) |
0.715 (1.00) |
0.725 (1.00) |
0.0231 (1.00) |
0.975 (1.00) |
0.522 (1.00) |
8q gain | 0 (0%) | 188 |
0.174 (1.00) |
0.065 (1.00) |
0.801 (1.00) |
0.235 (1.00) |
0.202 (1.00) |
0.168 (1.00) |
0.359 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.145 (1.00) |
0.328 (1.00) |
0.43 (1.00) |
9p gain | 0 (0%) | 283 |
0.273 (1.00) |
0.259 (1.00) |
0.123 (1.00) |
0.914 (1.00) |
0.208 (1.00) |
1 (1.00) |
0.577 (1.00) |
0.84 (1.00) |
0.0595 (1.00) |
0.135 (1.00) |
0.589 (1.00) |
0.445 (1.00) |
9q gain | 0 (0%) | 271 |
0.435 (1.00) |
0.13 (1.00) |
0.734 (1.00) |
0.326 (1.00) |
0.954 (1.00) |
1 (1.00) |
0.41 (1.00) |
0.718 (1.00) |
0.987 (1.00) |
0.0925 (1.00) |
0.49 (1.00) |
0.487 (1.00) |
10p gain | 0 (0%) | 309 |
0.965 (1.00) |
0.666 (1.00) |
0.521 (1.00) |
0.566 (1.00) |
0.409 (1.00) |
1 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.406 (1.00) |
0.303 (1.00) |
0.203 (1.00) |
0.0216 (1.00) |
10q gain | 0 (0%) | 315 |
0.0676 (1.00) |
0.463 (1.00) |
1 (1.00) |
0.393 (1.00) |
0.865 (1.00) |
1 (1.00) |
0.779 (1.00) |
0.0297 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.256 (1.00) |
0.832 (1.00) |
11p gain | 0 (0%) | 305 |
0.7 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.545 (1.00) |
0.924 (1.00) |
0.355 (1.00) |
0.798 (1.00) |
0.4 (1.00) |
11q gain | 0 (0%) | 304 |
0.873 (1.00) |
0.163 (1.00) |
0.579 (1.00) |
0.815 (1.00) |
0.942 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.249 (1.00) |
0.864 (1.00) |
0.102 (1.00) |
0.901 (1.00) |
0.565 (1.00) |
12p gain | 0 (0%) | 260 |
0.232 (1.00) |
0.283 (1.00) |
0.116 (1.00) |
0.533 (1.00) |
0.59 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.504 (1.00) |
0.382 (1.00) |
0.453 (1.00) |
0.905 (1.00) |
0.755 (1.00) |
12q gain | 0 (0%) | 297 |
0.293 (1.00) |
0.907 (1.00) |
0.0983 (1.00) |
0.817 (1.00) |
0.789 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.316 (1.00) |
0.23 (1.00) |
0.125 (1.00) |
0.203 (1.00) |
0.616 (1.00) |
13q gain | 0 (0%) | 304 |
0.749 (1.00) |
0.962 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.0844 (1.00) |
1 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.472 (1.00) |
0.728 (1.00) |
0.897 (1.00) |
0.479 (1.00) |
14q gain | 0 (0%) | 269 |
0.814 (1.00) |
0.933 (1.00) |
0.405 (1.00) |
0.99 (1.00) |
0.312 (1.00) |
0.561 (1.00) |
0.652 (1.00) |
0.287 (1.00) |
0.209 (1.00) |
0.398 (1.00) |
0.777 (1.00) |
0.554 (1.00) |
15q gain | 0 (0%) | 309 |
0.808 (1.00) |
0.826 (1.00) |
0.745 (1.00) |
0.228 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.307 (1.00) |
0.182 (1.00) |
0.253 (1.00) |
0.11 (1.00) |
0.501 (1.00) |
16p gain | 0 (0%) | 300 |
0.875 (1.00) |
0.0012 (1.00) |
0.804 (1.00) |
1 (1.00) |
0.015 (1.00) |
1 (1.00) |
0.368 (1.00) |
0.792 (1.00) |
0.568 (1.00) |
0.765 (1.00) |
0.105 (1.00) |
0.0184 (1.00) |
16q gain | 0 (0%) | 293 |
0.786 (1.00) |
0.0966 (1.00) |
0.828 (1.00) |
0.444 (1.00) |
0.0871 (1.00) |
1 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.277 (1.00) |
0.744 (1.00) |
0.949 (1.00) |
0.773 (1.00) |
17p gain | 0 (0%) | 302 |
0.653 (1.00) |
0.887 (1.00) |
0.112 (1.00) |
0.123 (1.00) |
0.698 (1.00) |
0.328 (1.00) |
0.181 (1.00) |
0.783 (1.00) |
0.79 (1.00) |
0.395 (1.00) |
0.331 (1.00) |
0.44 (1.00) |
17q gain | 0 (0%) | 298 |
0.941 (1.00) |
0.98 (1.00) |
0.146 (1.00) |
0.0116 (1.00) |
0.141 (1.00) |
0.122 (1.00) |
0.181 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.00905 (1.00) |
0.844 (1.00) |
0.414 (1.00) |
18q gain | 0 (0%) | 301 |
0.0508 (1.00) |
0.693 (1.00) |
0.0736 (1.00) |
0.667 (1.00) |
0.651 (1.00) |
1 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.396 (1.00) |
0.236 (1.00) |
0.382 (1.00) |
0.679 (1.00) |
19p gain | 0 (0%) | 309 |
0.0282 (1.00) |
0.0823 (1.00) |
1 (1.00) |
0.842 (1.00) |
0.429 (1.00) |
0.256 (1.00) |
0.347 (1.00) |
1 (1.00) |
0.792 (1.00) |
0.423 (1.00) |
0.502 (1.00) |
0.369 (1.00) |
19q gain | 0 (0%) | 300 |
0.258 (1.00) |
0.625 (1.00) |
0.804 (1.00) |
0.108 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.353 (1.00) |
0.792 (1.00) |
0.695 (1.00) |
0.263 (1.00) |
0.964 (1.00) |
0.803 (1.00) |
20p gain | 0 (0%) | 256 |
0.154 (1.00) |
0.129 (1.00) |
0.357 (1.00) |
0.432 (1.00) |
0.24 (1.00) |
0.335 (1.00) |
0.31 (1.00) |
0.00835 (1.00) |
0.359 (1.00) |
0.293 (1.00) |
0.953 (1.00) |
0.356 (1.00) |
20q gain | 0 (0%) | 252 |
0.756 (1.00) |
0.0148 (1.00) |
0.0689 (1.00) |
0.395 (1.00) |
0.404 (1.00) |
0.579 (1.00) |
0.69 (1.00) |
0.00366 (1.00) |
0.344 (1.00) |
0.215 (1.00) |
0.511 (1.00) |
0.838 (1.00) |
21q gain | 0 (0%) | 312 |
0.95 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.915 (1.00) |
1 (1.00) |
1 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.962 (1.00) |
0.0144 (1.00) |
0.401 (1.00) |
0.479 (1.00) |
22q gain | 0 (0%) | 282 |
0.432 (1.00) |
0.124 (1.00) |
0.342 (1.00) |
0.95 (1.00) |
0.134 (1.00) |
0.561 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.0945 (1.00) |
0.387 (1.00) |
0.238 (1.00) |
0.644 (1.00) |
Xq gain | 0 (0%) | 301 |
0.0177 (1.00) |
0.536 (1.00) |
0.21 (1.00) |
0.387 (1.00) |
0.0813 (1.00) |
1 (1.00) |
0.924 (1.00) |
0.793 (1.00) |
0.173 (1.00) |
0.729 (1.00) |
0.978 (1.00) |
0.135 (1.00) |
1p loss | 0 (0%) | 305 |
0.209 (1.00) |
0.114 (1.00) |
0.57 (1.00) |
0.0117 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.225 (1.00) |
0.00653 (1.00) |
0.0636 (1.00) |
0.425 (1.00) |
0.335 (1.00) |
2p loss | 0 (0%) | 315 |
0.216 (1.00) |
0.993 (1.00) |
0.674 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.699 (1.00) |
0.63 (1.00) |
0.872 (1.00) |
0.221 (1.00) |
0.83 (1.00) |
0.0285 (1.00) |
|
2q loss | 0 (0%) | 311 |
0.183 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.162 (1.00) |
0.462 (1.00) |
0.0927 (1.00) |
0.419 (1.00) |
0.766 (1.00) |
0.54 (1.00) |
3p loss | 0 (0%) | 200 |
0.0174 (1.00) |
0.741 (1.00) |
0.0146 (1.00) |
0.358 (1.00) |
0.0833 (1.00) |
0.0712 (1.00) |
0.721 (1.00) |
1 (1.00) |
0.088 (1.00) |
0.132 (1.00) |
0.0808 (1.00) |
0.257 (1.00) |
3q loss | 0 (0%) | 300 |
0.241 (1.00) |
0.363 (1.00) |
0.209 (1.00) |
0.325 (1.00) |
0.111 (1.00) |
1 (1.00) |
0.244 (1.00) |
0.598 (1.00) |
0.782 (1.00) |
0.428 (1.00) |
0.285 (1.00) |
0.0807 (1.00) |
4p loss | 0 (0%) | 244 |
0.0765 (1.00) |
0.365 (1.00) |
0.112 (1.00) |
0.166 (1.00) |
0.432 (1.00) |
0.266 (1.00) |
0.0914 (1.00) |
0.76 (1.00) |
0.159 (1.00) |
0.000876 (0.824) |
0.605 (1.00) |
0.0899 (1.00) |
4q loss | 0 (0%) | 271 |
0.909 (1.00) |
0.527 (1.00) |
0.864 (1.00) |
0.182 (1.00) |
0.576 (1.00) |
0.394 (1.00) |
0.379 (1.00) |
0.718 (1.00) |
0.266 (1.00) |
0.361 (1.00) |
0.482 (1.00) |
0.196 (1.00) |
5p loss | 0 (0%) | 313 |
0.944 (1.00) |
0.0651 (1.00) |
0.691 (1.00) |
0.917 (1.00) |
1 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.206 (1.00) |
0.772 (1.00) |
0.478 (1.00) |
0.321 (1.00) |
0.388 (1.00) |
5q loss | 0 (0%) | 260 |
0.353 (1.00) |
0.285 (1.00) |
0.209 (1.00) |
0.249 (1.00) |
0.518 (1.00) |
1 (1.00) |
0.133 (1.00) |
0.868 (1.00) |
0.0113 (1.00) |
0.055 (1.00) |
0.738 (1.00) |
0.55 (1.00) |
6p loss | 0 (0%) | 302 |
0.307 (1.00) |
0.64 (1.00) |
0.296 (1.00) |
0.00123 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.409 (1.00) |
0.268 (1.00) |
0.125 (1.00) |
0.808 (1.00) |
0.562 (1.00) |
6q loss | 0 (0%) | 300 |
0.847 (1.00) |
0.153 (1.00) |
0.455 (1.00) |
0.0125 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.174 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.627 (1.00) |
0.63 (1.00) |
0.187 (1.00) |
7p loss | 0 (0%) | 316 |
0.807 (1.00) |
0.509 (1.00) |
1 (1.00) |
0.722 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.0327 (1.00) |
0.765 (1.00) |
0.524 (1.00) |
|
7q loss | 0 (0%) | 313 |
0.779 (1.00) |
0.956 (1.00) |
1 (1.00) |
0.453 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.399 (1.00) |
0.686 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.878 (1.00) |
0.391 (1.00) |
8p loss | 0 (0%) | 253 |
0.0482 (1.00) |
0.76 (1.00) |
0.547 (1.00) |
0.0127 (1.00) |
0.67 (1.00) |
0.13 (1.00) |
0.0823 (1.00) |
0.751 (1.00) |
0.244 (1.00) |
0.674 (1.00) |
0.68 (1.00) |
0.287 (1.00) |
8q loss | 0 (0%) | 314 |
0.226 (1.00) |
0.691 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.699 (1.00) |
0.671 (1.00) |
0.0666 (1.00) |
0.459 (1.00) |
0.525 (1.00) |
0.883 (1.00) |
9p loss | 0 (0%) | 233 |
0.529 (1.00) |
0.501 (1.00) |
0.332 (1.00) |
0.714 (1.00) |
0.751 (1.00) |
0.266 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.0271 (1.00) |
0.0134 (1.00) |
0.817 (1.00) |
0.925 (1.00) |
9q loss | 0 (0%) | 290 |
0.385 (1.00) |
0.425 (1.00) |
0.674 (1.00) |
0.744 (1.00) |
0.725 (1.00) |
0.455 (1.00) |
0.327 (1.00) |
0.824 (1.00) |
0.113 (1.00) |
0.165 (1.00) |
0.655 (1.00) |
0.178 (1.00) |
10p loss | 0 (0%) | 273 |
0.241 (1.00) |
0.456 (1.00) |
0.296 (1.00) |
0.107 (1.00) |
0.706 (1.00) |
0.0633 (1.00) |
0.465 (1.00) |
0.854 (1.00) |
0.0519 (1.00) |
0.431 (1.00) |
0.777 (1.00) |
0.768 (1.00) |
10q loss | 0 (0%) | 294 |
0.454 (1.00) |
0.868 (1.00) |
0.0441 (1.00) |
0.291 (1.00) |
0.908 (1.00) |
0.394 (1.00) |
0.296 (1.00) |
0.814 (1.00) |
0.453 (1.00) |
0.325 (1.00) |
0.132 (1.00) |
0.112 (1.00) |
11p loss | 0 (0%) | 280 |
0.332 (1.00) |
0.856 (1.00) |
0.457 (1.00) |
0.621 (1.00) |
0.044 (1.00) |
0.561 (1.00) |
0.189 (1.00) |
0.694 (1.00) |
0.544 (1.00) |
0.0581 (1.00) |
0.49 (1.00) |
0.408 (1.00) |
11q loss | 0 (0%) | 261 |
0.481 (1.00) |
0.412 (1.00) |
0.0161 (1.00) |
0.99 (1.00) |
0.207 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.0635 (1.00) |
0.873 (1.00) |
0.808 (1.00) |
0.281 (1.00) |
0.827 (1.00) |
12p loss | 0 (0%) | 309 |
0.116 (1.00) |
0.0122 (1.00) |
0.19 (1.00) |
0.0606 (1.00) |
0.042 (1.00) |
0.289 (1.00) |
0.0396 (1.00) |
0.106 (1.00) |
0.672 (1.00) |
0.0105 (1.00) |
0.547 (1.00) |
|
12q loss | 0 (0%) | 313 |
0.667 (1.00) |
0.391 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.263 (1.00) |
1 (1.00) |
1 (1.00) |
0.399 (1.00) |
0.656 (1.00) |
0.492 (1.00) |
0.5 (1.00) |
0.601 (1.00) |
13q loss | 0 (0%) | 257 |
0.625 (1.00) |
0.302 (1.00) |
0.0863 (1.00) |
0.65 (1.00) |
0.952 (1.00) |
0.602 (1.00) |
0.665 (1.00) |
0.516 (1.00) |
0.187 (1.00) |
0.0486 (1.00) |
0.338 (1.00) |
0.874 (1.00) |
14q loss | 0 (0%) | 305 |
0.684 (1.00) |
0.846 (1.00) |
0.252 (1.00) |
0.105 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.545 (1.00) |
0.733 (1.00) |
0.691 (1.00) |
0.817 (1.00) |
0.0589 (1.00) |
15q loss | 0 (0%) | 297 |
0.331 (1.00) |
0.856 (1.00) |
0.818 (1.00) |
0.947 (1.00) |
0.0738 (1.00) |
1 (1.00) |
0.871 (1.00) |
0.808 (1.00) |
0.765 (1.00) |
0.542 (1.00) |
0.69 (1.00) |
0.285 (1.00) |
16p loss | 0 (0%) | 309 |
0.405 (1.00) |
0.293 (1.00) |
0.521 (1.00) |
0.12 (1.00) |
0.232 (1.00) |
0.177 (1.00) |
0.497 (1.00) |
0.738 (1.00) |
0.446 (1.00) |
0.143 (1.00) |
0.113 (1.00) |
0.61 (1.00) |
16q loss | 0 (0%) | 295 |
0.219 (1.00) |
0.549 (1.00) |
0.0666 (1.00) |
0.577 (1.00) |
0.72 (1.00) |
0.256 (1.00) |
0.418 (1.00) |
0.469 (1.00) |
0.728 (1.00) |
0.355 (1.00) |
0.243 (1.00) |
0.194 (1.00) |
17p loss | 0 (0%) | 276 |
0.491 (1.00) |
0.033 (1.00) |
0.11 (1.00) |
0.284 (1.00) |
0.801 (1.00) |
0.51 (1.00) |
0.0559 (1.00) |
0.352 (1.00) |
0.412 (1.00) |
0.259 (1.00) |
0.238 (1.00) |
0.567 (1.00) |
17q loss | 0 (0%) | 315 |
0.694 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.321 (1.00) |
0.0923 (1.00) |
0.178 (1.00) |
0.147 (1.00) |
0.401 (1.00) |
0.609 (1.00) |
0.453 (1.00) |
0.00121 (1.00) |
18p loss | 0 (0%) | 292 |
0.788 (1.00) |
0.379 (1.00) |
0.396 (1.00) |
0.763 (1.00) |
0.348 (1.00) |
1 (1.00) |
0.932 (1.00) |
0.648 (1.00) |
0.8 (1.00) |
0.704 (1.00) |
0.41 (1.00) |
0.346 (1.00) |
18q loss | 0 (0%) | 231 |
0.0931 (1.00) |
0.177 (1.00) |
0.27 (1.00) |
0.736 (1.00) |
0.301 (1.00) |
0.13 (1.00) |
0.712 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.0337 (1.00) |
0.181 (1.00) |
0.513 (1.00) |
19p loss | 0 (0%) | 294 |
0.00806 (1.00) |
0.596 (1.00) |
0.0124 (1.00) |
0.198 (1.00) |
0.111 (1.00) |
1 (1.00) |
0.0813 (1.00) |
0.639 (1.00) |
0.167 (1.00) |
0.335 (1.00) |
0.0895 (1.00) |
0.312 (1.00) |
19q loss | 0 (0%) | 301 |
0.0503 (1.00) |
0.319 (1.00) |
0.0736 (1.00) |
0.0212 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.0411 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.0161 (1.00) |
0.433 (1.00) |
0.446 (1.00) |
20p loss | 0 (0%) | 300 |
0.849 (1.00) |
0.364 (1.00) |
0.209 (1.00) |
0.444 (1.00) |
0.668 (1.00) |
0.328 (1.00) |
0.469 (1.00) |
0.792 (1.00) |
0.542 (1.00) |
0.275 (1.00) |
0.337 (1.00) |
0.424 (1.00) |
20q loss | 0 (0%) | 311 |
0.158 (1.00) |
0.778 (1.00) |
0.0674 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.516 (1.00) |
0.261 (1.00) |
0.454 (1.00) |
21q loss | 0 (0%) | 264 |
0.985 (1.00) |
0.293 (1.00) |
0.143 (1.00) |
0.196 (1.00) |
0.0176 (1.00) |
0.155 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.997 (1.00) |
0.626 (1.00) |
0.824 (1.00) |
22q loss | 0 (0%) | 296 |
0.157 (1.00) |
0.853 (1.00) |
0.245 (1.00) |
0.45 (1.00) |
0.19 (1.00) |
1 (1.00) |
0.206 (1.00) |
0.808 (1.00) |
0.391 (1.00) |
0.739 (1.00) |
0.377 (1.00) |
0.00361 (1.00) |
Xq loss | 0 (0%) | 314 |
0.356 (1.00) |
0.968 (1.00) |
0.0996 (1.00) |
0.877 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.671 (1.00) |
0.317 (1.00) |
0.713 (1.00) |
0.625 (1.00) |
0.0644 (1.00) |
P value = 0.000163 (Fisher's exact test), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 90 | 231 |
18P GAIN CNV | 4 | 48 |
18P GAIN WILD-TYPE | 86 | 183 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = HNSC-TP.clin.merged.picked.txt
-
Number of patients = 321
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 12
-
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.