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 11 clinical features across 325 patients, one significant finding detected with Q value < 0.25.
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18p gain cnv correlated to 'GENDER'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
Clinical Features |
Time to Death |
AGE | GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | Chi-square test | t-test | t-test | Chi-square test | |
18p gain | 0 (0%) | 271 |
0.201 (1.00) |
0.391 (1.00) |
9.89e-05 (0.0776) |
0.383 (1.00) |
0.245 (1.00) |
0.698 (1.00) |
0.477 (1.00) |
0.463 (1.00) |
0.476 (1.00) |
0.108 (1.00) |
|
1p gain | 0 (0%) | 314 |
0.826 (1.00) |
0.555 (1.00) |
0.0797 (1.00) |
1 (1.00) |
0.437 (1.00) |
0.953 (1.00) |
0.656 (1.00) |
0.667 (1.00) |
0.819 (1.00) |
||
1q gain | 0 (0%) | 286 |
0.829 (1.00) |
0.992 (1.00) |
0.705 (1.00) |
0.163 (1.00) |
0.975 (1.00) |
0.744 (1.00) |
0.366 (1.00) |
0.0659 (1.00) |
0.113 (1.00) |
0.126 (1.00) |
|
2p gain | 0 (0%) | 294 |
0.72 (1.00) |
0.986 (1.00) |
0.3 (1.00) |
1 (1.00) |
0.0217 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.354 (1.00) |
0.503 (1.00) |
0.818 (1.00) |
|
2q gain | 0 (0%) | 303 |
0.687 (1.00) |
0.694 (1.00) |
0.337 (1.00) |
0.437 (1.00) |
0.0407 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.417 (1.00) |
0.954 (1.00) |
|
3p gain | 0 (0%) | 298 |
0.2 (1.00) |
0.639 (1.00) |
0.37 (1.00) |
0.244 (1.00) |
0.138 (1.00) |
0.59 (1.00) |
1 (1.00) |
0.971 (1.00) |
0.283 (1.00) |
0.926 (1.00) |
|
3q gain | 0 (0%) | 218 |
0.289 (1.00) |
0.477 (1.00) |
0.0185 (1.00) |
0.000894 (0.7) |
0.175 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.834 (1.00) |
0.515 (1.00) |
0.198 (1.00) |
|
4p gain | 0 (0%) | 312 |
0.698 (1.00) |
0.116 (1.00) |
0.761 (1.00) |
0.316 (1.00) |
0.55 (1.00) |
0.82 (1.00) |
0.279 (1.00) |
0.411 (1.00) |
0.308 (1.00) |
||
4q gain | 0 (0%) | 316 |
0.528 (1.00) |
0.774 (1.00) |
1 (1.00) |
1 (1.00) |
0.609 (1.00) |
0.415 (1.00) |
0.55 (1.00) |
0.407 (1.00) |
0.279 (1.00) |
||
5p gain | 0 (0%) | 243 |
0.725 (1.00) |
0.312 (1.00) |
0.0638 (1.00) |
1 (1.00) |
0.139 (1.00) |
0.14 (1.00) |
0.0159 (1.00) |
0.695 (1.00) |
0.107 (1.00) |
0.473 (1.00) |
|
5q gain | 0 (0%) | 295 |
0.647 (1.00) |
0.97 (1.00) |
0.672 (1.00) |
0.26 (1.00) |
0.049 (1.00) |
0.683 (1.00) |
0.303 (1.00) |
0.0935 (1.00) |
0.0393 (1.00) |
0.113 (1.00) |
|
6p gain | 0 (0%) | 299 |
0.515 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.0531 (1.00) |
0.599 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.39 (1.00) |
0.833 (1.00) |
0.612 (1.00) |
|
6q gain | 0 (0%) | 306 |
0.625 (1.00) |
0.423 (1.00) |
0.793 (1.00) |
0.0531 (1.00) |
0.8 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.821 (1.00) |
0.174 (1.00) |
|
7p gain | 0 (0%) | 252 |
0.497 (1.00) |
0.119 (1.00) |
0.554 (1.00) |
0.877 (1.00) |
0.572 (1.00) |
0.741 (1.00) |
0.301 (1.00) |
0.224 (1.00) |
0.632 (1.00) |
0.921 (1.00) |
|
7q gain | 0 (0%) | 280 |
0.453 (1.00) |
0.535 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.447 (1.00) |
0.366 (1.00) |
0.68 (1.00) |
0.591 (1.00) |
0.54 (1.00) |
|
8p gain | 0 (0%) | 276 |
0.0192 (1.00) |
0.481 (1.00) |
0.121 (1.00) |
0.858 (1.00) |
0.788 (1.00) |
0.832 (1.00) |
0.526 (1.00) |
0.307 (1.00) |
0.526 (1.00) |
0.274 (1.00) |
|
8q gain | 0 (0%) | 191 |
0.241 (1.00) |
0.0436 (1.00) |
0.802 (1.00) |
0.793 (1.00) |
0.501 (1.00) |
0.281 (1.00) |
0.175 (1.00) |
0.48 (1.00) |
0.512 (1.00) |
0.608 (1.00) |
|
9p gain | 0 (0%) | 286 |
0.273 (1.00) |
0.284 (1.00) |
0.0593 (1.00) |
0.427 (1.00) |
0.0393 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.472 (1.00) |
0.449 (1.00) |
0.264 (1.00) |
|
9q gain | 0 (0%) | 275 |
0.459 (1.00) |
0.252 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.796 (1.00) |
0.732 (1.00) |
1 (1.00) |
0.907 (1.00) |
0.492 (1.00) |
0.669 (1.00) |
|
10p gain | 0 (0%) | 313 |
0.963 (1.00) |
0.712 (1.00) |
0.521 (1.00) |
0.491 (1.00) |
0.384 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.821 (1.00) |
0.0211 (1.00) |
0.864 (1.00) |
|
10q gain | 0 (0%) | 319 |
0.0669 (1.00) |
0.49 (1.00) |
1 (1.00) |
0.0312 (1.00) |
0.509 (1.00) |
0.316 (1.00) |
1 (1.00) |
0.975 (1.00) |
0.827 (1.00) |
0.727 (1.00) |
|
11p gain | 0 (0%) | 309 |
0.701 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.548 (1.00) |
0.955 (1.00) |
0.862 (1.00) |
1 (1.00) |
0.774 (1.00) |
0.368 (1.00) |
0.322 (1.00) |
|
11q gain | 0 (0%) | 309 |
0.699 (1.00) |
0.221 (1.00) |
0.398 (1.00) |
1 (1.00) |
0.9 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.968 (1.00) |
0.0623 (1.00) |
0.787 (1.00) |
|
12p gain | 0 (0%) | 263 |
0.233 (1.00) |
0.204 (1.00) |
0.0584 (1.00) |
0.621 (1.00) |
0.413 (1.00) |
0.711 (1.00) |
1 (1.00) |
0.565 (1.00) |
0.775 (1.00) |
0.89 (1.00) |
|
12q gain | 0 (0%) | 301 |
0.294 (1.00) |
0.861 (1.00) |
0.0985 (1.00) |
0.134 (1.00) |
0.214 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.609 (1.00) |
0.799 (1.00) |
|
13q gain | 0 (0%) | 307 |
0.75 (1.00) |
0.696 (1.00) |
1 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.205 (1.00) |
0.488 (1.00) |
0.457 (1.00) |
|
14q gain | 0 (0%) | 271 |
0.819 (1.00) |
0.848 (1.00) |
0.512 (1.00) |
0.221 (1.00) |
0.233 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.644 (1.00) |
0.597 (1.00) |
0.141 (1.00) |
|
15q gain | 0 (0%) | 313 |
0.803 (1.00) |
0.797 (1.00) |
0.745 (1.00) |
0.306 (1.00) |
0.177 (1.00) |
0.0968 (1.00) |
1 (1.00) |
0.0417 (1.00) |
0.503 (1.00) |
0.944 (1.00) |
|
16p gain | 0 (0%) | 303 |
0.726 (1.00) |
0.00268 (1.00) |
0.806 (1.00) |
0.613 (1.00) |
0.808 (1.00) |
0.346 (1.00) |
1 (1.00) |
0.0543 (1.00) |
0.0177 (1.00) |
0.0423 (1.00) |
|
16q gain | 0 (0%) | 296 |
0.777 (1.00) |
0.0571 (1.00) |
0.829 (1.00) |
0.821 (1.00) |
0.219 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.168 (1.00) |
0.8 (1.00) |
0.13 (1.00) |
|
17p gain | 0 (0%) | 307 |
0.479 (1.00) |
0.629 (1.00) |
0.113 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.545 (1.00) |
0.303 (1.00) |
0.23 (1.00) |
0.496 (1.00) |
0.252 (1.00) |
|
17q gain | 0 (0%) | 303 |
0.732 (1.00) |
0.863 (1.00) |
0.145 (1.00) |
0.613 (1.00) |
0.397 (1.00) |
0.9 (1.00) |
0.104 (1.00) |
0.0831 (1.00) |
0.47 (1.00) |
0.206 (1.00) |
|
18q gain | 0 (0%) | 305 |
0.052 (1.00) |
0.756 (1.00) |
0.0185 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.614 (1.00) |
0.67 (1.00) |
0.743 (1.00) |
|
19p gain | 0 (0%) | 313 |
0.0282 (1.00) |
0.0751 (1.00) |
1 (1.00) |
1 (1.00) |
0.822 (1.00) |
0.452 (1.00) |
0.236 (1.00) |
0.842 (1.00) |
0.37 (1.00) |
0.675 (1.00) |
|
19q gain | 0 (0%) | 304 |
0.258 (1.00) |
0.681 (1.00) |
0.804 (1.00) |
1 (1.00) |
0.731 (1.00) |
0.918 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.794 (1.00) |
0.255 (1.00) |
|
20p gain | 0 (0%) | 259 |
0.154 (1.00) |
0.163 (1.00) |
0.357 (1.00) |
0.00558 (1.00) |
0.328 (1.00) |
0.848 (1.00) |
0.591 (1.00) |
0.41 (1.00) |
0.408 (1.00) |
0.398 (1.00) |
|
20q gain | 0 (0%) | 255 |
0.633 (1.00) |
0.0217 (1.00) |
0.1 (1.00) |
0.00673 (1.00) |
0.415 (1.00) |
0.677 (1.00) |
0.581 (1.00) |
0.493 (1.00) |
0.888 (1.00) |
0.629 (1.00) |
|
21q gain | 0 (0%) | 316 |
0.951 (1.00) |
0.111 (1.00) |
1 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.96 (1.00) |
0.481 (1.00) |
0.235 (1.00) |
|
22q gain | 0 (0%) | 285 |
0.432 (1.00) |
0.279 (1.00) |
0.264 (1.00) |
0.558 (1.00) |
0.106 (1.00) |
0.416 (1.00) |
0.571 (1.00) |
0.109 (1.00) |
0.673 (1.00) |
0.695 (1.00) |
|
Xq gain | 0 (0%) | 305 |
0.0176 (1.00) |
0.584 (1.00) |
0.21 (1.00) |
0.792 (1.00) |
0.197 (1.00) |
0.939 (1.00) |
1 (1.00) |
0.0589 (1.00) |
0.136 (1.00) |
0.72 (1.00) |
|
1p loss | 0 (0%) | 309 |
0.208 (1.00) |
0.0967 (1.00) |
0.57 (1.00) |
1 (1.00) |
0.00602 (1.00) |
0.356 (1.00) |
1 (1.00) |
0.52 (1.00) |
0.336 (1.00) |
0.398 (1.00) |
|
2p loss | 0 (0%) | 321 |
0.329 (1.00) |
0.809 (1.00) |
0.313 (1.00) |
0.244 (1.00) |
0.552 (1.00) |
0.81 (1.00) |
0.936 (1.00) |
0.0153 (1.00) |
0.957 (1.00) |
||
2q loss | 0 (0%) | 316 |
0.254 (1.00) |
0.707 (1.00) |
0.714 (1.00) |
0.692 (1.00) |
0.138 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.494 (1.00) |
0.135 (1.00) |
|
3p loss | 0 (0%) | 202 |
0.00766 (1.00) |
0.557 (1.00) |
0.00347 (1.00) |
0.592 (1.00) |
0.0613 (1.00) |
0.0641 (1.00) |
0.104 (1.00) |
0.263 (1.00) |
0.215 (1.00) |
0.24 (1.00) |
|
3q loss | 0 (0%) | 306 |
0.451 (1.00) |
0.436 (1.00) |
0.297 (1.00) |
0.58 (1.00) |
0.732 (1.00) |
0.352 (1.00) |
1 (1.00) |
0.208 (1.00) |
0.128 (1.00) |
0.368 (1.00) |
|
4p loss | 0 (0%) | 247 |
0.113 (1.00) |
0.336 (1.00) |
0.0596 (1.00) |
0.45 (1.00) |
0.137 (1.00) |
0.477 (1.00) |
0.231 (1.00) |
0.394 (1.00) |
0.0954 (1.00) |
0.208 (1.00) |
|
4q loss | 0 (0%) | 275 |
0.758 (1.00) |
0.382 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.457 (1.00) |
0.366 (1.00) |
0.73 (1.00) |
0.212 (1.00) |
0.483 (1.00) |
|
5p loss | 0 (0%) | 317 |
0.944 (1.00) |
0.0596 (1.00) |
0.691 (1.00) |
0.206 (1.00) |
0.762 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.389 (1.00) |
0.568 (1.00) |
|
5q loss | 0 (0%) | 262 |
0.444 (1.00) |
0.267 (1.00) |
0.0867 (1.00) |
0.745 (1.00) |
0.00626 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.409 (1.00) |
0.628 (1.00) |
0.19 (1.00) |
|
6p loss | 0 (0%) | 306 |
0.306 (1.00) |
0.69 (1.00) |
0.297 (1.00) |
0.414 (1.00) |
0.246 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.553 (1.00) |
0.18 (1.00) |
|
6q loss | 0 (0%) | 304 |
0.848 (1.00) |
0.174 (1.00) |
0.455 (1.00) |
0.602 (1.00) |
0.816 (1.00) |
0.502 (1.00) |
1 (1.00) |
0.239 (1.00) |
0.183 (1.00) |
0.193 (1.00) |
|
7p loss | 0 (0%) | 320 |
0.807 (1.00) |
0.49 (1.00) |
1 (1.00) |
1 (1.00) |
0.233 (1.00) |
0.712 (1.00) |
0.732 (1.00) |
0.521 (1.00) |
0.827 (1.00) |
||
7q loss | 0 (0%) | 316 |
0.809 (1.00) |
0.816 (1.00) |
0.714 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.82 (1.00) |
1 (1.00) |
0.787 (1.00) |
0.324 (1.00) |
0.514 (1.00) |
|
8p loss | 0 (0%) | 254 |
0.0901 (1.00) |
0.961 (1.00) |
0.766 (1.00) |
0.755 (1.00) |
0.271 (1.00) |
0.487 (1.00) |
0.144 (1.00) |
0.68 (1.00) |
0.271 (1.00) |
0.102 (1.00) |
|
8q loss | 0 (0%) | 319 |
0.0567 (1.00) |
0.754 (1.00) |
0.191 (1.00) |
0.633 (1.00) |
0.204 (1.00) |
0.745 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.7 (1.00) |
0.561 (1.00) |
|
9p loss | 0 (0%) | 234 |
0.552 (1.00) |
0.565 (1.00) |
0.271 (1.00) |
0.885 (1.00) |
0.0275 (1.00) |
0.993 (1.00) |
0.6 (1.00) |
0.702 (1.00) |
0.953 (1.00) |
0.235 (1.00) |
|
9q loss | 0 (0%) | 294 |
0.386 (1.00) |
0.471 (1.00) |
0.674 (1.00) |
0.509 (1.00) |
0.104 (1.00) |
0.541 (1.00) |
0.423 (1.00) |
0.404 (1.00) |
0.174 (1.00) |
0.503 (1.00) |
|
10p loss | 0 (0%) | 277 |
0.223 (1.00) |
0.526 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.0591 (1.00) |
0.722 (1.00) |
0.0772 (1.00) |
0.737 (1.00) |
0.757 (1.00) |
0.288 (1.00) |
|
10q loss | 0 (0%) | 299 |
0.416 (1.00) |
0.943 (1.00) |
0.0667 (1.00) |
0.472 (1.00) |
0.509 (1.00) |
0.103 (1.00) |
0.366 (1.00) |
0.966 (1.00) |
0.157 (1.00) |
0.456 (1.00) |
|
11p loss | 0 (0%) | 282 |
0.336 (1.00) |
0.908 (1.00) |
0.362 (1.00) |
0.566 (1.00) |
0.551 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.0195 (1.00) |
0.496 (1.00) |
0.00951 (1.00) |
|
11q loss | 0 (0%) | 263 |
0.682 (1.00) |
0.342 (1.00) |
0.00761 (1.00) |
0.0484 (1.00) |
0.841 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.263 (1.00) |
0.166 (1.00) |
|
12p loss | 0 (0%) | 314 |
0.0984 (1.00) |
0.0128 (1.00) |
0.303 (1.00) |
0.142 (1.00) |
0.145 (1.00) |
0.0094 (1.00) |
0.0248 (1.00) |
0.7 (1.00) |
0.096 (1.00) |
||
12q loss | 0 (0%) | 318 |
0.706 (1.00) |
0.418 (1.00) |
0.678 (1.00) |
0.675 (1.00) |
0.615 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.866 (1.00) |
0.802 (1.00) |
0.74 (1.00) |
|
13q loss | 0 (0%) | 262 |
0.544 (1.00) |
0.146 (1.00) |
0.0423 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.197 (1.00) |
0.6 (1.00) |
0.71 (1.00) |
0.914 (1.00) |
0.932 (1.00) |
|
14q loss | 0 (0%) | 309 |
0.67 (1.00) |
0.89 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.535 (1.00) |
0.0572 (1.00) |
0.202 (1.00) |
|
15q loss | 0 (0%) | 301 |
0.337 (1.00) |
0.794 (1.00) |
0.818 (1.00) |
1 (1.00) |
0.83 (1.00) |
0.791 (1.00) |
1 (1.00) |
0.0932 (1.00) |
0.287 (1.00) |
0.109 (1.00) |
|
16p loss | 0 (0%) | 313 |
0.404 (1.00) |
0.273 (1.00) |
0.521 (1.00) |
0.738 (1.00) |
0.412 (1.00) |
0.0972 (1.00) |
0.163 (1.00) |
0.74 (1.00) |
0.746 (1.00) |
0.522 (1.00) |
|
16q loss | 0 (0%) | 300 |
0.276 (1.00) |
0.581 (1.00) |
0.0672 (1.00) |
1 (1.00) |
0.43 (1.00) |
0.305 (1.00) |
0.236 (1.00) |
0.213 (1.00) |
0.333 (1.00) |
0.63 (1.00) |
|
17p loss | 0 (0%) | 280 |
0.483 (1.00) |
0.0436 (1.00) |
0.11 (1.00) |
0.852 (1.00) |
0.363 (1.00) |
0.328 (1.00) |
0.477 (1.00) |
0.94 (1.00) |
0.572 (1.00) |
0.0948 (1.00) |
|
17q loss | 0 (0%) | 320 |
0.603 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.0916 (1.00) |
0.39 (1.00) |
0.493 (1.00) |
0.0845 (1.00) |
0.881 (1.00) |
0.00118 (0.924) |
0.849 (1.00) |
|
18p loss | 0 (0%) | 296 |
0.787 (1.00) |
0.43 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.47 (1.00) |
1 (1.00) |
0.75 (1.00) |
0.349 (1.00) |
0.894 (1.00) |
|
18q loss | 0 (0%) | 235 |
0.115 (1.00) |
0.103 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.113 (1.00) |
0.166 (1.00) |
0.363 (1.00) |
0.524 (1.00) |
0.67 (1.00) |
|
19p loss | 0 (0%) | 297 |
0.00787 (1.00) |
0.884 (1.00) |
0.0451 (1.00) |
0.497 (1.00) |
0.157 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.126 (1.00) |
0.764 (1.00) |
0.024 (1.00) |
|
19q loss | 0 (0%) | 304 |
0.0458 (1.00) |
0.735 (1.00) |
0.209 (1.00) |
0.428 (1.00) |
0.205 (1.00) |
0.502 (1.00) |
1 (1.00) |
0.0679 (1.00) |
0.641 (1.00) |
0.00214 (1.00) |
|
20p loss | 0 (0%) | 304 |
0.847 (1.00) |
0.395 (1.00) |
0.209 (1.00) |
0.793 (1.00) |
0.509 (1.00) |
0.387 (1.00) |
0.303 (1.00) |
0.804 (1.00) |
0.405 (1.00) |
0.434 (1.00) |
|
20q loss | 0 (0%) | 315 |
0.158 (1.00) |
0.748 (1.00) |
0.0674 (1.00) |
1 (1.00) |
0.362 (1.00) |
0.231 (1.00) |
0.163 (1.00) |
0.702 (1.00) |
0.455 (1.00) |
0.561 (1.00) |
|
21q loss | 0 (0%) | 267 |
0.996 (1.00) |
0.277 (1.00) |
0.0524 (1.00) |
0.397 (1.00) |
0.15 (1.00) |
0.659 (1.00) |
0.164 (1.00) |
0.0394 (1.00) |
0.864 (1.00) |
0.0334 (1.00) |
|
22q loss | 0 (0%) | 300 |
0.156 (1.00) |
0.918 (1.00) |
0.245 (1.00) |
0.465 (1.00) |
0.369 (1.00) |
0.456 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.00343 (1.00) |
0.308 (1.00) |
|
Xq loss | 0 (0%) | 318 |
0.355 (1.00) |
0.987 (1.00) |
0.0992 (1.00) |
0.675 (1.00) |
0.301 (1.00) |
0.595 (1.00) |
1 (1.00) |
0.409 (1.00) |
0.0633 (1.00) |
0.62 (1.00) |
P value = 9.89e-05 (Fisher's exact test), Q value = 0.078
Table S1. Gene #32: '18p gain' versus Clinical Feature #3: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 91 | 234 |
18P GAIN CNV | 4 | 50 |
18P GAIN WILD-TYPE | 87 | 184 |
Figure S1. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'GENDER'
![](D32V3.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = HNSC-TP.clin.merged.picked.txt
-
Number of patients = 325
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 11
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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.