This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level results and 14 clinical features across 389 patients, 2 significant findings detected with Q value < 0.25.
-
1q loss cnv correlated to 'Time to Death'.
-
18p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 14 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 |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Chi-square 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 | Fisher's exact test | |
1q loss | 0 (0%) | 379 |
3.02e-05 (0.0323) |
0.684 (1.00) |
1 (1.00) |
0.0269 (1.00) |
0.792 (1.00) |
0.0653 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.0882 (1.00) |
0.37 (1.00) |
0.516 (1.00) |
1 (1.00) |
||
18p loss | 0 (0%) | 322 |
0.493 (1.00) |
0.096 (1.00) |
0.14 (1.00) |
0.00533 (1.00) |
0.317 (1.00) |
0.273 (1.00) |
0.451 (1.00) |
0.0481 (1.00) |
0.00756 (1.00) |
0.221 (1.00) |
9.54e-05 (0.102) |
0.579 (1.00) |
0.0345 (1.00) |
0.23 (1.00) |
1p gain | 0 (0%) | 340 |
0.839 (1.00) |
0.000928 (0.987) |
1 (1.00) |
0.475 (1.00) |
0.911 (1.00) |
0.662 (1.00) |
0.0036 (1.00) |
0.626 (1.00) |
0.00241 (1.00) |
0.49 (1.00) |
0.849 (1.00) |
0.866 (1.00) |
0.902 (1.00) |
0.308 (1.00) |
1q gain | 0 (0%) | 238 |
0.768 (1.00) |
0.172 (1.00) |
0.465 (1.00) |
0.557 (1.00) |
0.325 (1.00) |
0.426 (1.00) |
0.0263 (1.00) |
0.185 (1.00) |
0.0258 (1.00) |
0.242 (1.00) |
0.537 (1.00) |
0.405 (1.00) |
0.454 (1.00) |
0.145 (1.00) |
2p gain | 0 (0%) | 343 |
0.0933 (1.00) |
0.0304 (1.00) |
0.0822 (1.00) |
0.558 (1.00) |
0.828 (1.00) |
0.132 (1.00) |
0.775 (1.00) |
0.0927 (1.00) |
0.151 (1.00) |
1 (1.00) |
0.851 (1.00) |
0.136 (1.00) |
0.778 (1.00) |
0.437 (1.00) |
2q gain | 0 (0%) | 351 |
0.204 (1.00) |
0.145 (1.00) |
0.395 (1.00) |
0.889 (1.00) |
0.27 (1.00) |
0.962 (1.00) |
0.0969 (1.00) |
0.228 (1.00) |
0.707 (1.00) |
0.659 (1.00) |
0.236 (1.00) |
0.893 (1.00) |
1 (1.00) |
|
3p gain | 0 (0%) | 379 |
0.0991 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.982 (1.00) |
0.0854 (1.00) |
0.623 (1.00) |
0.545 (1.00) |
0.426 (1.00) |
0.414 (1.00) |
0.844 (1.00) |
0.362 (1.00) |
0.262 (1.00) |
0.386 (1.00) |
|
3q gain | 0 (0%) | 366 |
0.132 (1.00) |
0.943 (1.00) |
0.527 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.155 (1.00) |
0.91 (1.00) |
0.383 (1.00) |
0.334 (1.00) |
0.569 (1.00) |
0.592 (1.00) |
0.388 (1.00) |
0.64 (1.00) |
|
4p gain | 0 (0%) | 362 |
0.615 (1.00) |
0.0149 (1.00) |
0.321 (1.00) |
0.517 (1.00) |
0.221 (1.00) |
0.896 (1.00) |
0.0902 (1.00) |
0.271 (1.00) |
1 (1.00) |
0.042 (1.00) |
0.125 (1.00) |
0.905 (1.00) |
0.679 (1.00) |
|
4q gain | 0 (0%) | 380 |
0.592 (1.00) |
0.702 (1.00) |
0.311 (1.00) |
0.182 (1.00) |
0.0825 (1.00) |
0.364 (1.00) |
0.505 (1.00) |
0.644 (1.00) |
0.381 (1.00) |
0.0195 (1.00) |
0.448 (1.00) |
0.171 (1.00) |
1 (1.00) |
|
5p gain | 0 (0%) | 244 |
0.302 (1.00) |
0.089 (1.00) |
0.6 (1.00) |
0.83 (1.00) |
0.194 (1.00) |
0.494 (1.00) |
0.78 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.101 (1.00) |
0.0448 (1.00) |
0.567 (1.00) |
0.619 (1.00) |
0.113 (1.00) |
5q gain | 0 (0%) | 344 |
0.685 (1.00) |
0.962 (1.00) |
0.637 (1.00) |
0.852 (1.00) |
0.551 (1.00) |
0.686 (1.00) |
0.546 (1.00) |
0.803 (1.00) |
0.0677 (1.00) |
0.52 (1.00) |
0.159 (1.00) |
0.702 (1.00) |
0.77 (1.00) |
|
6p gain | 0 (0%) | 330 |
0.62 (1.00) |
0.971 (1.00) |
0.779 (1.00) |
0.738 (1.00) |
0.326 (1.00) |
0.479 (1.00) |
0.193 (1.00) |
0.792 (1.00) |
0.762 (1.00) |
0.751 (1.00) |
0.64 (1.00) |
0.104 (1.00) |
0.249 (1.00) |
0.939 (1.00) |
6q gain | 0 (0%) | 374 |
0.618 (1.00) |
0.262 (1.00) |
0.0147 (1.00) |
0.987 (1.00) |
0.845 (1.00) |
0.504 (1.00) |
0.53 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.55 (1.00) |
0.00542 (1.00) |
0.435 (1.00) |
0.633 (1.00) |
|
7p gain | 0 (0%) | 257 |
0.293 (1.00) |
0.0461 (1.00) |
0.83 (1.00) |
0.23 (1.00) |
0.431 (1.00) |
0.2 (1.00) |
0.00916 (1.00) |
0.088 (1.00) |
0.0298 (1.00) |
0.473 (1.00) |
0.565 (1.00) |
0.57 (1.00) |
0.64 (1.00) |
0.528 (1.00) |
7q gain | 0 (0%) | 295 |
0.678 (1.00) |
0.0143 (1.00) |
0.479 (1.00) |
0.915 (1.00) |
0.337 (1.00) |
0.393 (1.00) |
0.191 (1.00) |
0.0467 (1.00) |
0.0318 (1.00) |
0.592 (1.00) |
0.983 (1.00) |
0.784 (1.00) |
0.85 (1.00) |
0.338 (1.00) |
8p gain | 0 (0%) | 340 |
0.902 (1.00) |
0.00444 (1.00) |
0.287 (1.00) |
0.55 (1.00) |
0.706 (1.00) |
0.869 (1.00) |
0.108 (1.00) |
0.767 (1.00) |
0.728 (1.00) |
0.195 (1.00) |
0.0992 (1.00) |
0.0391 (1.00) |
0.732 (1.00) |
|
8q gain | 0 (0%) | 266 |
0.666 (1.00) |
0.00236 (1.00) |
0.326 (1.00) |
0.309 (1.00) |
0.256 (1.00) |
0.524 (1.00) |
0.391 (1.00) |
0.168 (1.00) |
0.23 (1.00) |
0.626 (1.00) |
0.472 (1.00) |
0.178 (1.00) |
0.0382 (1.00) |
0.833 (1.00) |
9p gain | 0 (0%) | 377 |
0.19 (1.00) |
0.217 (1.00) |
0.777 (1.00) |
0.86 (1.00) |
0.251 (1.00) |
0.731 (1.00) |
0.741 (1.00) |
0.899 (1.00) |
1 (1.00) |
0.297 (1.00) |
0.181 (1.00) |
0.661 (1.00) |
0.633 (1.00) |
|
9q gain | 0 (0%) | 384 |
0.0586 (1.00) |
0.16 (1.00) |
0.664 (1.00) |
0.999 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.75 (1.00) |
0.796 (1.00) |
1 (1.00) |
|
10p gain | 0 (0%) | 346 |
0.871 (1.00) |
0.67 (1.00) |
0.0509 (1.00) |
0.842 (1.00) |
0.862 (1.00) |
0.634 (1.00) |
0.173 (1.00) |
0.891 (1.00) |
0.522 (1.00) |
0.711 (1.00) |
0.0302 (1.00) |
0.0108 (1.00) |
0.447 (1.00) |
0.199 (1.00) |
10q gain | 0 (0%) | 366 |
0.717 (1.00) |
0.717 (1.00) |
0.0823 (1.00) |
0.47 (1.00) |
0.398 (1.00) |
0.227 (1.00) |
0.551 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.122 (1.00) |
0.0949 (1.00) |
0.261 (1.00) |
0.0946 (1.00) |
|
11p gain | 0 (0%) | 357 |
0.44 (1.00) |
0.0826 (1.00) |
0.46 (1.00) |
0.503 (1.00) |
0.824 (1.00) |
0.712 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.441 (1.00) |
0.675 (1.00) |
0.223 (1.00) |
0.794 (1.00) |
0.835 (1.00) |
0.523 (1.00) |
11q gain | 0 (0%) | 345 |
0.22 (1.00) |
0.000304 (0.325) |
0.148 (1.00) |
0.586 (1.00) |
0.81 (1.00) |
0.618 (1.00) |
0.579 (1.00) |
0.519 (1.00) |
0.155 (1.00) |
0.264 (1.00) |
0.123 (1.00) |
0.0659 (1.00) |
0.132 (1.00) |
0.84 (1.00) |
12p gain | 0 (0%) | 340 |
0.74 (1.00) |
0.00842 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.147 (1.00) |
0.065 (1.00) |
1 (1.00) |
0.0281 (1.00) |
1 (1.00) |
0.484 (1.00) |
0.0247 (1.00) |
0.131 (1.00) |
0.768 (1.00) |
|
12q gain | 0 (0%) | 349 |
0.955 (1.00) |
0.0582 (1.00) |
1 (1.00) |
0.448 (1.00) |
0.145 (1.00) |
0.0801 (1.00) |
0.683 (1.00) |
0.0414 (1.00) |
0.708 (1.00) |
0.0189 (1.00) |
0.0518 (1.00) |
0.0556 (1.00) |
0.6 (1.00) |
|
13q gain | 0 (0%) | 375 |
0.827 (1.00) |
0.496 (1.00) |
0.79 (1.00) |
0.976 (1.00) |
0.131 (1.00) |
0.468 (1.00) |
0.136 (1.00) |
0.422 (1.00) |
0.529 (1.00) |
0.715 (1.00) |
0.458 (1.00) |
0.904 (1.00) |
1 (1.00) |
|
14q gain | 0 (0%) | 348 |
0.43 (1.00) |
0.424 (1.00) |
0.409 (1.00) |
0.637 (1.00) |
0.516 (1.00) |
0.412 (1.00) |
0.321 (1.00) |
0.47 (1.00) |
0.644 (1.00) |
0.249 (1.00) |
0.583 (1.00) |
0.71 (1.00) |
0.583 (1.00) |
0.728 (1.00) |
15q gain | 0 (0%) | 379 |
0.303 (1.00) |
0.411 (1.00) |
0.76 (1.00) |
0.177 (1.00) |
0.678 (1.00) |
0.351 (1.00) |
0.442 (1.00) |
0.209 (1.00) |
1 (1.00) |
0.864 (1.00) |
0.0993 (1.00) |
0.842 (1.00) |
0.589 (1.00) |
|
16p gain | 0 (0%) | 336 |
0.464 (1.00) |
0.164 (1.00) |
0.882 (1.00) |
0.356 (1.00) |
0.52 (1.00) |
0.459 (1.00) |
0.511 (1.00) |
0.626 (1.00) |
0.513 (1.00) |
0.744 (1.00) |
0.586 (1.00) |
0.141 (1.00) |
0.781 (1.00) |
0.249 (1.00) |
16q gain | 0 (0%) | 354 |
0.616 (1.00) |
0.067 (1.00) |
0.293 (1.00) |
0.319 (1.00) |
0.166 (1.00) |
0.344 (1.00) |
0.517 (1.00) |
0.418 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.0871 (1.00) |
0.462 (1.00) |
0.597 (1.00) |
1 (1.00) |
17p gain | 0 (0%) | 366 |
0.762 (1.00) |
0.56 (1.00) |
0.195 (1.00) |
0.284 (1.00) |
0.46 (1.00) |
0.966 (1.00) |
0.506 (1.00) |
0.394 (1.00) |
0.34 (1.00) |
0.0239 (1.00) |
0.0495 (1.00) |
0.648 (1.00) |
0.895 (1.00) |
0.516 (1.00) |
17q gain | 0 (0%) | 322 |
0.24 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.336 (1.00) |
0.0301 (1.00) |
0.332 (1.00) |
0.0198 (1.00) |
0.0184 (1.00) |
0.0598 (1.00) |
0.0666 (1.00) |
0.543 (1.00) |
0.651 (1.00) |
0.0106 (1.00) |
18p gain | 0 (0%) | 351 |
0.775 (1.00) |
0.0871 (1.00) |
0.0605 (1.00) |
0.613 (1.00) |
0.203 (1.00) |
0.947 (1.00) |
0.644 (1.00) |
0.837 (1.00) |
0.98 (1.00) |
0.707 (1.00) |
0.104 (1.00) |
0.755 (1.00) |
0.827 (1.00) |
0.83 (1.00) |
18q gain | 0 (0%) | 366 |
0.526 (1.00) |
0.0441 (1.00) |
0.195 (1.00) |
0.613 (1.00) |
0.847 (1.00) |
0.889 (1.00) |
0.797 (1.00) |
0.891 (1.00) |
0.867 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.732 (1.00) |
0.113 (1.00) |
0.425 (1.00) |
19p gain | 0 (0%) | 383 |
0.337 (1.00) |
0.0498 (1.00) |
1 (1.00) |
1 (1.00) |
0.335 (1.00) |
0.336 (1.00) |
0.244 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.821 (1.00) |
0.431 (1.00) |
0.425 (1.00) |
|
19q gain | 0 (0%) | 370 |
0.991 (1.00) |
0.897 (1.00) |
0.639 (1.00) |
0.568 (1.00) |
0.46 (1.00) |
0.49 (1.00) |
0.333 (1.00) |
0.703 (1.00) |
0.613 (1.00) |
0.335 (1.00) |
0.235 (1.00) |
0.277 (1.00) |
0.74 (1.00) |
|
20p gain | 0 (0%) | 337 |
0.896 (1.00) |
0.663 (1.00) |
0.882 (1.00) |
0.548 (1.00) |
0.806 (1.00) |
0.424 (1.00) |
0.629 (1.00) |
0.9 (1.00) |
0.148 (1.00) |
0.74 (1.00) |
0.907 (1.00) |
0.149 (1.00) |
0.463 (1.00) |
0.553 (1.00) |
20q gain | 0 (0%) | 322 |
0.725 (1.00) |
0.224 (1.00) |
0.419 (1.00) |
0.138 (1.00) |
0.706 (1.00) |
0.139 (1.00) |
0.873 (1.00) |
0.678 (1.00) |
0.823 (1.00) |
0.221 (1.00) |
0.0305 (1.00) |
0.0902 (1.00) |
0.659 (1.00) |
0.901 (1.00) |
21q gain | 0 (0%) | 355 |
0.8 (1.00) |
0.844 (1.00) |
0.213 (1.00) |
0.794 (1.00) |
0.626 (1.00) |
0.557 (1.00) |
0.418 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.885 (1.00) |
0.0151 (1.00) |
0.593 (1.00) |
1 (1.00) |
|
22q gain | 0 (0%) | 374 |
0.34 (1.00) |
0.354 (1.00) |
0.793 (1.00) |
0.328 (1.00) |
0.2 (1.00) |
0.0324 (1.00) |
0.465 (1.00) |
0.287 (1.00) |
0.554 (1.00) |
0.268 (1.00) |
0.463 (1.00) |
0.454 (1.00) |
0.74 (1.00) |
|
Xq gain | 0 (0%) | 371 |
0.355 (1.00) |
0.471 (1.00) |
0.228 (1.00) |
0.81 (1.00) |
0.649 (1.00) |
0.593 (1.00) |
0.724 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.316 (1.00) |
0.509 (1.00) |
0.74 (1.00) |
|
1p loss | 0 (0%) | 363 |
0.192 (1.00) |
0.707 (1.00) |
0.226 (1.00) |
0.586 (1.00) |
0.907 (1.00) |
0.692 (1.00) |
0.387 (1.00) |
0.0861 (1.00) |
0.141 (1.00) |
0.214 (1.00) |
0.0823 (1.00) |
0.945 (1.00) |
0.271 (1.00) |
|
2p loss | 0 (0%) | 384 |
0.237 (1.00) |
0.146 (1.00) |
1 (1.00) |
0.953 (1.00) |
1 (1.00) |
1 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.0769 (1.00) |
1 (1.00) |
||
2q loss | 0 (0%) | 386 |
1 (1.00) |
0.443 (1.00) |
1 (1.00) |
|||||||||||
3p loss | 0 (0%) | 312 |
0.446 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.0141 (1.00) |
0.789 (1.00) |
0.617 (1.00) |
0.504 (1.00) |
0.169 (1.00) |
0.00483 (1.00) |
1 (1.00) |
0.424 (1.00) |
0.036 (1.00) |
0.165 (1.00) |
0.78 (1.00) |
3q loss | 0 (0%) | 342 |
0.42 (1.00) |
0.724 (1.00) |
0.644 (1.00) |
0.0171 (1.00) |
0.464 (1.00) |
0.465 (1.00) |
0.8 (1.00) |
0.458 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.0647 (1.00) |
0.365 (1.00) |
0.591 (1.00) |
0.851 (1.00) |
4p loss | 0 (0%) | 354 |
0.465 (1.00) |
0.012 (1.00) |
0.484 (1.00) |
0.625 (1.00) |
0.528 (1.00) |
0.32 (1.00) |
0.265 (1.00) |
0.65 (1.00) |
0.479 (1.00) |
0.409 (1.00) |
0.795 (1.00) |
0.138 (1.00) |
0.283 (1.00) |
0.78 (1.00) |
4q loss | 0 (0%) | 347 |
0.578 (1.00) |
0.0473 (1.00) |
0.14 (1.00) |
0.851 (1.00) |
0.892 (1.00) |
0.155 (1.00) |
0.00814 (1.00) |
0.514 (1.00) |
0.0645 (1.00) |
0.254 (1.00) |
0.6 (1.00) |
0.125 (1.00) |
0.907 (1.00) |
0.628 (1.00) |
5p loss | 0 (0%) | 377 |
0.737 (1.00) |
0.918 (1.00) |
0.154 (1.00) |
0.0604 (1.00) |
0.937 (1.00) |
0.733 (1.00) |
0.0966 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.778 (1.00) |
0.446 (1.00) |
0.492 (1.00) |
0.342 (1.00) |
|
5q loss | 0 (0%) | 339 |
0.642 (1.00) |
0.0227 (1.00) |
0.0691 (1.00) |
0.705 (1.00) |
0.0648 (1.00) |
0.884 (1.00) |
0.0709 (1.00) |
0.501 (1.00) |
0.263 (1.00) |
0.492 (1.00) |
0.244 (1.00) |
0.0906 (1.00) |
0.504 (1.00) |
0.214 (1.00) |
6p loss | 0 (0%) | 357 |
0.661 (1.00) |
0.0805 (1.00) |
0.138 (1.00) |
0.12 (1.00) |
0.707 (1.00) |
0.478 (1.00) |
0.614 (1.00) |
0.173 (1.00) |
0.632 (1.00) |
0.221 (1.00) |
0.283 (1.00) |
0.568 (1.00) |
0.308 (1.00) |
0.271 (1.00) |
6q loss | 0 (0%) | 303 |
0.665 (1.00) |
0.136 (1.00) |
0.541 (1.00) |
0.0285 (1.00) |
0.565 (1.00) |
0.2 (1.00) |
0.246 (1.00) |
0.638 (1.00) |
0.49 (1.00) |
0.407 (1.00) |
0.16 (1.00) |
0.859 (1.00) |
0.312 (1.00) |
0.779 (1.00) |
7p loss | 0 (0%) | 378 |
0.848 (1.00) |
0.249 (1.00) |
1 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.282 (1.00) |
0.442 (1.00) |
0.254 (1.00) |
0.445 (1.00) |
0.507 (1.00) |
0.299 (1.00) |
0.297 (1.00) |
0.296 (1.00) |
|
7q loss | 0 (0%) | 377 |
0.682 (1.00) |
0.204 (1.00) |
0.558 (1.00) |
0.000297 (0.317) |
0.894 (1.00) |
0.691 (1.00) |
1 (1.00) |
0.677 (1.00) |
0.474 (1.00) |
0.158 (1.00) |
0.172 (1.00) |
0.249 (1.00) |
||
8p loss | 0 (0%) | 291 |
0.758 (1.00) |
0.844 (1.00) |
0.558 (1.00) |
0.254 (1.00) |
0.187 (1.00) |
0.069 (1.00) |
0.675 (1.00) |
0.678 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.546 (1.00) |
0.0551 (1.00) |
0.68 (1.00) |
0.62 (1.00) |
8q loss | 0 (0%) | 377 |
0.185 (1.00) |
0.633 (1.00) |
0.395 (1.00) |
0.0425 (1.00) |
0.512 (1.00) |
0.801 (1.00) |
0.284 (1.00) |
1 (1.00) |
1 (1.00) |
0.167 (1.00) |
0.21 (1.00) |
1 (1.00) |
||
9p loss | 0 (0%) | 272 |
0.0149 (1.00) |
0.419 (1.00) |
0.0456 (1.00) |
0.87 (1.00) |
0.58 (1.00) |
0.154 (1.00) |
0.0129 (1.00) |
0.762 (1.00) |
0.0227 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.104 (1.00) |
0.815 (1.00) |
0.504 (1.00) |
9q loss | 0 (0%) | 290 |
0.396 (1.00) |
0.582 (1.00) |
0.727 (1.00) |
0.99 (1.00) |
0.694 (1.00) |
0.314 (1.00) |
0.147 (1.00) |
0.513 (1.00) |
0.187 (1.00) |
0.428 (1.00) |
0.405 (1.00) |
0.0569 (1.00) |
0.999 (1.00) |
0.273 (1.00) |
10p loss | 0 (0%) | 362 |
0.285 (1.00) |
0.716 (1.00) |
0.108 (1.00) |
0.106 (1.00) |
0.898 (1.00) |
0.483 (1.00) |
0.424 (1.00) |
0.892 (1.00) |
0.382 (1.00) |
0.633 (1.00) |
0.0877 (1.00) |
0.815 (1.00) |
0.636 (1.00) |
|
10q loss | 0 (0%) | 356 |
0.337 (1.00) |
0.201 (1.00) |
0.719 (1.00) |
0.000308 (0.328) |
0.321 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.397 (1.00) |
0.0649 (1.00) |
0.287 (1.00) |
0.856 (1.00) |
0.81 (1.00) |
|
11p loss | 0 (0%) | 362 |
0.289 (1.00) |
0.0115 (1.00) |
0.843 (1.00) |
0.611 (1.00) |
0.907 (1.00) |
0.135 (1.00) |
0.128 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.000842 (0.897) |
0.0199 (1.00) |
0.883 (1.00) |
|
11q loss | 0 (0%) | 365 |
0.347 (1.00) |
0.966 (1.00) |
0.407 (1.00) |
0.705 (1.00) |
0.297 (1.00) |
0.968 (1.00) |
0.599 (1.00) |
0.0324 (1.00) |
0.819 (1.00) |
0.354 (1.00) |
0.0372 (1.00) |
0.281 (1.00) |
0.383 (1.00) |
0.743 (1.00) |
12p loss | 0 (0%) | 355 |
0.336 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.533 (1.00) |
0.797 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.544 (1.00) |
0.69 (1.00) |
0.688 (1.00) |
0.0348 (1.00) |
0.0247 (1.00) |
0.77 (1.00) |
12q loss | 0 (0%) | 368 |
0.0612 (1.00) |
0.947 (1.00) |
0.654 (1.00) |
0.847 (1.00) |
0.481 (1.00) |
0.375 (1.00) |
0.365 (1.00) |
0.293 (1.00) |
0.615 (1.00) |
0.995 (1.00) |
0.166 (1.00) |
0.261 (1.00) |
1 (1.00) |
|
13q loss | 0 (0%) | 301 |
0.194 (1.00) |
0.166 (1.00) |
0.467 (1.00) |
0.562 (1.00) |
0.172 (1.00) |
0.952 (1.00) |
0.156 (1.00) |
0.439 (1.00) |
0.211 (1.00) |
0.786 (1.00) |
0.903 (1.00) |
0.487 (1.00) |
0.0981 (1.00) |
0.473 (1.00) |
14q loss | 0 (0%) | 347 |
0.671 (1.00) |
0.436 (1.00) |
0.87 (1.00) |
0.798 (1.00) |
0.531 (1.00) |
0.509 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.941 (1.00) |
0.465 (1.00) |
0.392 (1.00) |
0.405 (1.00) |
0.355 (1.00) |
0.475 (1.00) |
15q loss | 0 (0%) | 308 |
0.834 (1.00) |
0.0563 (1.00) |
0.319 (1.00) |
0.773 (1.00) |
0.204 (1.00) |
0.775 (1.00) |
0.979 (1.00) |
0.934 (1.00) |
0.891 (1.00) |
0.581 (1.00) |
0.23 (1.00) |
0.215 (1.00) |
0.752 (1.00) |
0.313 (1.00) |
16p loss | 0 (0%) | 358 |
0.619 (1.00) |
0.219 (1.00) |
0.189 (1.00) |
0.336 (1.00) |
0.939 (1.00) |
0.953 (1.00) |
0.00845 (1.00) |
0.0615 (1.00) |
0.207 (1.00) |
0.815 (1.00) |
0.125 (1.00) |
0.687 (1.00) |
0.366 (1.00) |
|
16q loss | 0 (0%) | 338 |
0.24 (1.00) |
0.299 (1.00) |
0.653 (1.00) |
0.724 (1.00) |
0.0193 (1.00) |
0.187 (1.00) |
0.531 (1.00) |
0.127 (1.00) |
0.176 (1.00) |
0.735 (1.00) |
0.986 (1.00) |
0.451 (1.00) |
0.543 (1.00) |
0.536 (1.00) |
17p loss | 0 (0%) | 292 |
0.998 (1.00) |
0.245 (1.00) |
0.638 (1.00) |
0.107 (1.00) |
0.731 (1.00) |
0.688 (1.00) |
0.771 (1.00) |
0.661 (1.00) |
0.503 (1.00) |
0.427 (1.00) |
0.365 (1.00) |
0.00391 (1.00) |
0.0442 (1.00) |
0.184 (1.00) |
17q loss | 0 (0%) | 373 |
0.181 (1.00) |
0.371 (1.00) |
0.308 (1.00) |
0.646 (1.00) |
0.531 (1.00) |
0.593 (1.00) |
0.75 (1.00) |
0.457 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.131 (1.00) |
0.0566 (1.00) |
0.708 (1.00) |
|
18q loss | 0 (0%) | 294 |
0.031 (1.00) |
0.41 (1.00) |
0.477 (1.00) |
0.486 (1.00) |
0.291 (1.00) |
0.107 (1.00) |
0.294 (1.00) |
0.229 (1.00) |
0.00304 (1.00) |
0.18 (1.00) |
0.115 (1.00) |
0.698 (1.00) |
0.383 (1.00) |
0.0198 (1.00) |
19p loss | 0 (0%) | 288 |
0.0341 (1.00) |
0.28 (1.00) |
0.0818 (1.00) |
0.562 (1.00) |
0.708 (1.00) |
0.151 (1.00) |
0.032 (1.00) |
0.0985 (1.00) |
0.281 (1.00) |
1 (1.00) |
0.495 (1.00) |
0.0725 (1.00) |
0.408 (1.00) |
0.137 (1.00) |
19q loss | 0 (0%) | 331 |
0.0757 (1.00) |
0.495 (1.00) |
0.775 (1.00) |
0.00559 (1.00) |
0.45 (1.00) |
0.287 (1.00) |
0.276 (1.00) |
0.0602 (1.00) |
0.345 (1.00) |
0.518 (1.00) |
0.325 (1.00) |
0.242 (1.00) |
0.533 (1.00) |
0.034 (1.00) |
20p loss | 0 (0%) | 337 |
0.151 (1.00) |
0.852 (1.00) |
0.766 (1.00) |
0.0151 (1.00) |
0.681 (1.00) |
0.201 (1.00) |
0.1 (1.00) |
0.205 (1.00) |
0.119 (1.00) |
0.74 (1.00) |
0.51 (1.00) |
0.852 (1.00) |
0.0777 (1.00) |
1 (1.00) |
20q loss | 0 (0%) | 368 |
0.305 (1.00) |
0.346 (1.00) |
0.826 (1.00) |
0.344 (1.00) |
0.872 (1.00) |
0.714 (1.00) |
0.212 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.843 (1.00) |
0.432 (1.00) |
0.268 (1.00) |
0.516 (1.00) |
|
21q loss | 0 (0%) | 335 |
0.838 (1.00) |
0.285 (1.00) |
0.0182 (1.00) |
0.124 (1.00) |
0.529 (1.00) |
0.877 (1.00) |
0.728 (1.00) |
0.831 (1.00) |
0.768 (1.00) |
0.501 (1.00) |
0.407 (1.00) |
0.0213 (1.00) |
0.703 (1.00) |
0.629 (1.00) |
22q loss | 0 (0%) | 310 |
0.805 (1.00) |
0.0263 (1.00) |
0.0575 (1.00) |
0.657 (1.00) |
0.795 (1.00) |
0.831 (1.00) |
0.979 (1.00) |
0.16 (1.00) |
0.991 (1.00) |
0.147 (1.00) |
0.136 (1.00) |
0.00651 (1.00) |
0.0513 (1.00) |
0.21 (1.00) |
Xq loss | 0 (0%) | 379 |
0.283 (1.00) |
0.0652 (1.00) |
0.0486 (1.00) |
0.0253 (1.00) |
0.349 (1.00) |
1 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.0882 (1.00) |
0.295 (1.00) |
0.633 (1.00) |
0.928 (1.00) |
1 (1.00) |
P value = 3.02e-05 (logrank test), Q value = 0.032
Table S1. Gene #42: '1q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 349 | 85 | 0.0 - 224.0 (8.1) |
1Q LOSS CNV | 8 | 4 | 0.1 - 21.5 (7.0) |
1Q LOSS WILD-TYPE | 341 | 81 | 0.0 - 224.0 (8.1) |
Figure S1. Get High-res Image Gene #42: '1q loss' versus Clinical Feature #1: 'Time to Death'
![](D42V1.png)
P value = 9.54e-05 (t-test), Q value = 0.1
Table S2. Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 274 | 41.3 (27.0) |
18P LOSS CNV | 47 | 30.8 (17.0) |
18P LOSS WILD-TYPE | 227 | 43.4 (28.2) |
Figure S2. Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
![](D72V11.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 389
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 14
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.