This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 71 focal events and 8 clinical features across 560 patients, 16 significant findings detected with Q value < 0.25.
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amp_7p11.2 cnv correlated to 'Time to Death' and 'AGE'.
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amp_7q11.21 cnv correlated to 'Time to Death' and 'AGE'.
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amp_7q21.2 cnv correlated to 'Time to Death' and 'AGE'.
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del_9p21.3 cnv correlated to 'AGE'.
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del_10p15.3 cnv correlated to 'Time to Death' and 'AGE'.
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del_10p13 cnv correlated to 'Time to Death' and 'AGE'.
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del_10p11.23 cnv correlated to 'Time to Death' and 'AGE'.
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del_10q23.31 cnv correlated to 'Time to Death' and 'AGE'.
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del_10q26.3 cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 7p11 2 | 492 (88%) | 68 |
4.09e-07 (0.00023) |
6.33e-12 (3.6e-09) |
0.427 (1.00) |
0.104 (1.00) |
0.0566 (1.00) |
0.0716 (1.00) |
0.476 (1.00) |
0.0584 (1.00) |
amp 7q11 21 | 450 (80%) | 110 |
3.31e-05 (0.0184) |
3.29e-07 (0.000185) |
0.327 (1.00) |
0.619 (1.00) |
0.00675 (1.00) |
0.137 (1.00) |
0.264 (1.00) |
0.14 (1.00) |
amp 7q21 2 | 465 (83%) | 95 |
0.000402 (0.223) |
1.21e-05 (0.00675) |
0.565 (1.00) |
0.507 (1.00) |
0.106 (1.00) |
0.148 (1.00) |
0.036 (1.00) |
0.0439 (1.00) |
del 10p15 3 | 454 (81%) | 106 |
2.81e-06 (0.00157) |
1.49e-08 (8.43e-06) |
0.185 (1.00) |
0.523 (1.00) |
0.00507 (1.00) |
0.73 (1.00) |
0.147 (1.00) |
0.278 (1.00) |
del 10p13 | 456 (81%) | 104 |
1.99e-06 (0.00112) |
7.92e-08 (4.48e-05) |
0.0756 (1.00) |
0.991 (1.00) |
0.00384 (1.00) |
0.817 (1.00) |
0.119 (1.00) |
0.27 (1.00) |
del 10p11 23 | 461 (82%) | 99 |
8.88e-08 (5.01e-05) |
3.16e-10 (1.79e-07) |
0.175 (1.00) |
0.178 (1.00) |
0.00214 (1.00) |
0.812 (1.00) |
0.136 (1.00) |
0.251 (1.00) |
del 10q23 31 | 497 (89%) | 63 |
1.42e-05 (0.00788) |
1.58e-07 (8.88e-05) |
0.785 (1.00) |
0.0823 (1.00) |
0.00518 (1.00) |
1 (1.00) |
0.299 (1.00) |
0.639 (1.00) |
del 9p21 3 | 409 (73%) | 151 |
0.0203 (1.00) |
4.81e-05 (0.0267) |
0.559 (1.00) |
0.126 (1.00) |
0.597 (1.00) |
0.357 (1.00) |
0.642 (1.00) |
0.745 (1.00) |
del 10q26 3 | 498 (89%) | 62 |
0.000945 (0.522) |
6.64e-06 (0.0037) |
0.68 (1.00) |
0.0838 (1.00) |
0.0139 (1.00) |
1 (1.00) |
0.0833 (1.00) |
0.636 (1.00) |
amp 1p36 21 | 91 (16%) | 469 |
0.064 (1.00) |
0.309 (1.00) |
0.482 (1.00) |
0.189 (1.00) |
0.0706 (1.00) |
0.902 (1.00) |
0.162 (1.00) |
0.404 (1.00) |
amp 1q32 1 | 155 (28%) | 405 |
0.451 (1.00) |
0.168 (1.00) |
1 (1.00) |
0.3 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.864 (1.00) |
0.526 (1.00) |
amp 1q44 | 97 (17%) | 463 |
0.347 (1.00) |
0.868 (1.00) |
0.304 (1.00) |
0.417 (1.00) |
0.153 (1.00) |
0.55 (1.00) |
0.771 (1.00) |
0.427 (1.00) |
amp 2p24 3 | 48 (9%) | 512 |
0.255 (1.00) |
0.34 (1.00) |
0.356 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.51 (1.00) |
0.612 (1.00) |
amp 3q26 33 | 108 (19%) | 452 |
0.283 (1.00) |
0.0395 (1.00) |
0.661 (1.00) |
0.714 (1.00) |
0.00467 (1.00) |
0.909 (1.00) |
0.261 (1.00) |
0.701 (1.00) |
amp 4p16 3 | 48 (9%) | 512 |
0.851 (1.00) |
0.806 (1.00) |
0.356 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.691 (1.00) |
1 (1.00) |
amp 4q12 | 105 (19%) | 455 |
0.349 (1.00) |
0.163 (1.00) |
0.376 (1.00) |
0.823 (1.00) |
0.332 (1.00) |
0.296 (1.00) |
0.684 (1.00) |
1 (1.00) |
amp 7q31 2 | 458 (82%) | 102 |
0.00652 (1.00) |
0.00225 (1.00) |
0.433 (1.00) |
0.861 (1.00) |
0.216 (1.00) |
0.0595 (1.00) |
0.047 (1.00) |
0.055 (1.00) |
amp 8q24 21 | 70 (12%) | 490 |
0.257 (1.00) |
0.4 (1.00) |
0.516 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.0597 (1.00) |
1 (1.00) |
amp 11p13 | 29 (5%) | 531 |
0.805 (1.00) |
0.374 (1.00) |
0.847 (1.00) |
0.59 (1.00) |
0.844 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.51 (1.00) |
amp 12p13 32 | 82 (15%) | 478 |
0.86 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.74 (1.00) |
0.521 (1.00) |
0.55 (1.00) |
0.685 (1.00) |
amp 12q14 1 | 131 (23%) | 429 |
0.326 (1.00) |
0.561 (1.00) |
0.359 (1.00) |
0.85 (1.00) |
0.487 (1.00) |
0.749 (1.00) |
0.753 (1.00) |
0.31 (1.00) |
amp 12q15 | 91 (16%) | 469 |
0.782 (1.00) |
0.481 (1.00) |
0.413 (1.00) |
0.902 (1.00) |
0.874 (1.00) |
0.462 (1.00) |
0.649 (1.00) |
0.23 (1.00) |
amp 13q34 | 32 (6%) | 528 |
0.826 (1.00) |
0.653 (1.00) |
0.36 (1.00) |
0.541 (1.00) |
0.461 (1.00) |
0.701 (1.00) |
0.771 (1.00) |
1 (1.00) |
amp 13q34 | 29 (5%) | 531 |
0.694 (1.00) |
0.536 (1.00) |
0.698 (1.00) |
0.395 (1.00) |
0.848 (1.00) |
0.687 (1.00) |
0.623 (1.00) |
1 (1.00) |
amp 14q32 33 | 36 (6%) | 524 |
0.475 (1.00) |
0.0061 (1.00) |
0.486 (1.00) |
0.311 (1.00) |
0.228 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
amp 17p13 2 | 50 (9%) | 510 |
0.583 (1.00) |
0.643 (1.00) |
0.175 (1.00) |
0.947 (1.00) |
0.344 (1.00) |
0.526 (1.00) |
0.683 (1.00) |
1 (1.00) |
amp 17q25 1 | 81 (14%) | 479 |
0.0231 (1.00) |
0.00884 (1.00) |
0.176 (1.00) |
0.452 (1.00) |
0.859 (1.00) |
0.606 (1.00) |
0.188 (1.00) |
0.689 (1.00) |
amp 19p13 3 | 236 (42%) | 324 |
0.24 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.13 (1.00) |
0.527 (1.00) |
0.927 (1.00) |
0.418 (1.00) |
0.572 (1.00) |
amp 19p13 2 | 241 (43%) | 319 |
0.161 (1.00) |
0.948 (1.00) |
0.931 (1.00) |
0.471 (1.00) |
0.472 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.77 (1.00) |
amp 19q12 | 209 (37%) | 351 |
0.411 (1.00) |
0.681 (1.00) |
0.655 (1.00) |
0.999 (1.00) |
0.573 (1.00) |
0.851 (1.00) |
0.756 (1.00) |
0.385 (1.00) |
amp 21q21 1 | 68 (12%) | 492 |
0.637 (1.00) |
0.016 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.0637 (1.00) |
0.404 (1.00) |
0.104 (1.00) |
0.378 (1.00) |
del 1p36 32 | 96 (17%) | 464 |
0.927 (1.00) |
0.68 (1.00) |
0.029 (1.00) |
0.652 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.143 (1.00) |
0.701 (1.00) |
del 1p36 23 | 130 (23%) | 430 |
0.534 (1.00) |
0.224 (1.00) |
0.00771 (1.00) |
0.0989 (1.00) |
0.197 (1.00) |
0.391 (1.00) |
0.158 (1.00) |
0.312 (1.00) |
del 1p32 3 | 60 (11%) | 500 |
0.591 (1.00) |
0.0637 (1.00) |
0.126 (1.00) |
0.628 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.304 (1.00) |
1 (1.00) |
del 1p22 1 | 47 (8%) | 513 |
0.515 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.113 (1.00) |
0.624 (1.00) |
0.747 (1.00) |
1 (1.00) |
del 1q42 11 | 48 (9%) | 512 |
0.111 (1.00) |
0.402 (1.00) |
0.878 (1.00) |
0.0444 (1.00) |
0.785 (1.00) |
0.144 (1.00) |
0.358 (1.00) |
0.249 (1.00) |
del 1q44 | 34 (6%) | 526 |
0.525 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.305 (1.00) |
0.415 (1.00) |
0.705 (1.00) |
0.649 (1.00) |
0.482 (1.00) |
del 2q22 1 | 45 (8%) | 515 |
0.334 (1.00) |
0.071 (1.00) |
0.34 (1.00) |
0.586 (1.00) |
0.152 (1.00) |
0.0665 (1.00) |
0.367 (1.00) |
0.612 (1.00) |
del 2q37 1 | 54 (10%) | 506 |
0.952 (1.00) |
0.707 (1.00) |
0.187 (1.00) |
0.64 (1.00) |
0.808 (1.00) |
0.282 (1.00) |
0.618 (1.00) |
1 (1.00) |
del 3p21 1 | 52 (9%) | 508 |
0.0184 (1.00) |
0.0219 (1.00) |
0.882 (1.00) |
0.792 (1.00) |
0.24 (1.00) |
0.0427 (1.00) |
0.446 (1.00) |
0.338 (1.00) |
del 3q13 31 | 58 (10%) | 502 |
0.62 (1.00) |
0.17 (1.00) |
0.395 (1.00) |
0.245 (1.00) |
0.499 (1.00) |
0.372 (1.00) |
0.196 (1.00) |
0.377 (1.00) |
del 3q22 1 | 58 (10%) | 502 |
0.623 (1.00) |
0.354 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.5 (1.00) |
0.766 (1.00) |
0.231 (1.00) |
0.377 (1.00) |
del 3q29 | 65 (12%) | 495 |
0.319 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.331 (1.00) |
0.575 (1.00) |
0.325 (1.00) |
0.93 (1.00) |
1 (1.00) |
del 4p16 3 | 76 (14%) | 484 |
0.454 (1.00) |
0.0775 (1.00) |
0.256 (1.00) |
0.365 (1.00) |
0.524 (1.00) |
0.113 (1.00) |
0.526 (1.00) |
0.662 (1.00) |
del 4q34 3 | 89 (16%) | 471 |
0.189 (1.00) |
0.173 (1.00) |
0.0339 (1.00) |
0.581 (1.00) |
0.936 (1.00) |
0.137 (1.00) |
0.248 (1.00) |
1 (1.00) |
del 5q35 3 | 52 (9%) | 508 |
0.0364 (1.00) |
0.228 (1.00) |
1 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.84 (1.00) |
0.0858 (1.00) |
del 6q22 31 | 156 (28%) | 404 |
0.0545 (1.00) |
0.245 (1.00) |
0.101 (1.00) |
0.487 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.193 (1.00) |
del 6q26 | 177 (32%) | 383 |
0.102 (1.00) |
0.959 (1.00) |
0.264 (1.00) |
0.919 (1.00) |
0.229 (1.00) |
0.846 (1.00) |
0.622 (1.00) |
0.353 (1.00) |
del 8p23 2 | 65 (12%) | 495 |
0.194 (1.00) |
0.0401 (1.00) |
0.348 (1.00) |
0.246 (1.00) |
0.836 (1.00) |
0.674 (1.00) |
0.0176 (1.00) |
0.376 (1.00) |
del 9q34 2 | 76 (14%) | 484 |
0.952 (1.00) |
0.995 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.101 (1.00) |
0.691 (1.00) |
0.451 (1.00) |
0.23 (1.00) |
del 11p15 5 | 127 (23%) | 433 |
0.0197 (1.00) |
0.00568 (1.00) |
0.216 (1.00) |
0.17 (1.00) |
0.474 (1.00) |
0.829 (1.00) |
1 (1.00) |
1 (1.00) |
del 11p11 2 | 103 (18%) | 457 |
0.0732 (1.00) |
0.693 (1.00) |
0.221 (1.00) |
0.549 (1.00) |
0.245 (1.00) |
0.815 (1.00) |
0.713 (1.00) |
1 (1.00) |
del 11q14 1 | 95 (17%) | 465 |
0.945 (1.00) |
0.627 (1.00) |
0.3 (1.00) |
0.871 (1.00) |
0.371 (1.00) |
0.116 (1.00) |
1 (1.00) |
0.7 (1.00) |
del 12p13 1 | 71 (13%) | 489 |
0.1 (1.00) |
0.962 (1.00) |
0.437 (1.00) |
0.412 (1.00) |
0.602 (1.00) |
0.413 (1.00) |
0.276 (1.00) |
1 (1.00) |
del 12q12 | 74 (13%) | 486 |
0.443 (1.00) |
0.664 (1.00) |
0.8 (1.00) |
0.989 (1.00) |
0.853 (1.00) |
0.505 (1.00) |
0.433 (1.00) |
0.655 (1.00) |
del 12q15 | 76 (14%) | 484 |
0.638 (1.00) |
0.601 (1.00) |
0.45 (1.00) |
0.353 (1.00) |
0.922 (1.00) |
0.354 (1.00) |
0.215 (1.00) |
0.205 (1.00) |
del 13q14 2 | 234 (42%) | 326 |
0.983 (1.00) |
0.681 (1.00) |
0.792 (1.00) |
0.836 (1.00) |
0.234 (1.00) |
0.646 (1.00) |
0.275 (1.00) |
1 (1.00) |
del 14q13 1 | 174 (31%) | 386 |
0.628 (1.00) |
0.553 (1.00) |
0.113 (1.00) |
0.544 (1.00) |
0.808 (1.00) |
0.695 (1.00) |
0.112 (1.00) |
0.117 (1.00) |
del 14q24 2 | 170 (30%) | 390 |
0.717 (1.00) |
0.525 (1.00) |
0.259 (1.00) |
0.852 (1.00) |
0.647 (1.00) |
0.622 (1.00) |
0.379 (1.00) |
1 (1.00) |
del 15q14 | 147 (26%) | 413 |
0.311 (1.00) |
0.0344 (1.00) |
0.768 (1.00) |
0.956 (1.00) |
0.79 (1.00) |
0.41 (1.00) |
0.168 (1.00) |
0.324 (1.00) |
del 16p12 2 | 92 (16%) | 468 |
0.0581 (1.00) |
0.235 (1.00) |
0.352 (1.00) |
0.709 (1.00) |
0.51 (1.00) |
0.392 (1.00) |
0.464 (1.00) |
1 (1.00) |
del 16q23 3 | 95 (17%) | 465 |
0.0285 (1.00) |
0.78 (1.00) |
0.565 (1.00) |
0.0836 (1.00) |
0.877 (1.00) |
0.011 (1.00) |
0.161 (1.00) |
0.701 (1.00) |
del 17p13 2 | 82 (15%) | 478 |
0.73 (1.00) |
0.457 (1.00) |
0.271 (1.00) |
0.405 (1.00) |
0.74 (1.00) |
0.799 (1.00) |
1 (1.00) |
0.702 (1.00) |
del 17p13 1 | 92 (16%) | 468 |
0.449 (1.00) |
0.132 (1.00) |
0.0796 (1.00) |
0.996 (1.00) |
0.583 (1.00) |
0.178 (1.00) |
0.948 (1.00) |
1 (1.00) |
del 17q11 2 | 68 (12%) | 492 |
0.264 (1.00) |
0.538 (1.00) |
0.895 (1.00) |
0.381 (1.00) |
0.916 (1.00) |
0.0948 (1.00) |
0.815 (1.00) |
1 (1.00) |
del 18q22 3 | 80 (14%) | 480 |
0.571 (1.00) |
0.497 (1.00) |
0.805 (1.00) |
0.114 (1.00) |
0.859 (1.00) |
0.698 (1.00) |
0.405 (1.00) |
0.398 (1.00) |
del 19q13 41 | 98 (18%) | 462 |
0.0179 (1.00) |
0.355 (1.00) |
0.91 (1.00) |
0.693 (1.00) |
0.727 (1.00) |
1 (1.00) |
0.378 (1.00) |
1 (1.00) |
del 21q22 11 | 46 (8%) | 514 |
0.882 (1.00) |
0.294 (1.00) |
0.756 (1.00) |
0.188 (1.00) |
0.689 (1.00) |
0.321 (1.00) |
0.454 (1.00) |
0.081 (1.00) |
del 22q13 32 | 210 (38%) | 350 |
0.97 (1.00) |
0.187 (1.00) |
0.789 (1.00) |
0.481 (1.00) |
0.623 (1.00) |
0.574 (1.00) |
0.362 (1.00) |
1 (1.00) |
del xp22 2 | 115 (21%) | 445 |
0.297 (1.00) |
0.655 (1.00) |
0.831 (1.00) |
0.285 (1.00) |
0.946 (1.00) |
1 (1.00) |
0.588 (1.00) |
0.474 (1.00) |
del xq23 | 106 (19%) | 454 |
0.204 (1.00) |
0.437 (1.00) |
0.659 (1.00) |
0.247 (1.00) |
0.788 (1.00) |
0.419 (1.00) |
0.341 (1.00) |
0.478 (1.00) |
P value = 4.09e-07 (logrank test), Q value = 0.00023
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
AMP PEAK 8(7P11.2) MUTATED | 492 | 414 | 0.1 - 127.6 (9.5) |
AMP PEAK 8(7P11.2) WILD-TYPE | 68 | 48 | 0.2 - 108.8 (15.1) |
P value = 6.33e-12 (Wilcoxon-test), Q value = 3.6e-09
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
AMP PEAK 8(7P11.2) MUTATED | 492 | 59.8 (12.5) |
AMP PEAK 8(7P11.2) WILD-TYPE | 68 | 43.6 (18.8) |
P value = 3.31e-05 (logrank test), Q value = 0.018
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
AMP PEAK 9(7Q11.21) MUTATED | 450 | 376 | 0.1 - 127.6 (9.4) |
AMP PEAK 9(7Q11.21) WILD-TYPE | 110 | 86 | 0.2 - 108.8 (13.8) |
P value = 3.29e-07 (Wilcoxon-test), Q value = 0.00018
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
AMP PEAK 9(7Q11.21) MUTATED | 450 | 59.9 (12.5) |
AMP PEAK 9(7Q11.21) WILD-TYPE | 110 | 49.5 (18.5) |
P value = 0.000402 (logrank test), Q value = 0.22
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
AMP PEAK 10(7Q21.2) MUTATED | 465 | 390 | 0.1 - 127.6 (9.7) |
AMP PEAK 10(7Q21.2) WILD-TYPE | 95 | 72 | 0.1 - 108.8 (12.4) |
P value = 1.21e-05 (Wilcoxon-test), Q value = 0.0068
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
AMP PEAK 10(7Q21.2) MUTATED | 465 | 59.5 (12.5) |
AMP PEAK 10(7Q21.2) WILD-TYPE | 95 | 49.7 (19.8) |
P value = 4.81e-05 (Wilcoxon-test), Q value = 0.027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 19(9P21.3) MUTATED | 409 | 59.3 (13.7) |
DEL PEAK 19(9P21.3) WILD-TYPE | 151 | 54.0 (15.7) |
P value = 2.81e-06 (logrank test), Q value = 0.0016
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
DEL PEAK 21(10P15.3) MUTATED | 454 | 383 | 0.1 - 92.7 (9.9) |
DEL PEAK 21(10P15.3) WILD-TYPE | 106 | 79 | 0.1 - 127.6 (11.7) |
P value = 1.49e-08 (Wilcoxon-test), Q value = 8.4e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 21(10P15.3) MUTATED | 454 | 59.9 (12.5) |
DEL PEAK 21(10P15.3) WILD-TYPE | 106 | 49.0 (18.5) |
P value = 1.99e-06 (logrank test), Q value = 0.0011
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
DEL PEAK 22(10P13) MUTATED | 456 | 384 | 0.1 - 92.7 (9.9) |
DEL PEAK 22(10P13) WILD-TYPE | 104 | 78 | 0.1 - 127.6 (11.5) |
P value = 7.92e-08 (Wilcoxon-test), Q value = 4.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 22(10P13) MUTATED | 456 | 59.8 (12.4) |
DEL PEAK 22(10P13) WILD-TYPE | 104 | 49.2 (19.0) |
P value = 8.88e-08 (logrank test), Q value = 5e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
DEL PEAK 23(10P11.23) MUTATED | 461 | 388 | 0.1 - 92.7 (9.7) |
DEL PEAK 23(10P11.23) WILD-TYPE | 99 | 74 | 0.1 - 127.6 (12.9) |
P value = 3.16e-10 (Wilcoxon-test), Q value = 1.8e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 23(10P11.23) MUTATED | 461 | 60.0 (12.3) |
DEL PEAK 23(10P11.23) WILD-TYPE | 99 | 47.7 (18.8) |
P value = 1.42e-05 (logrank test), Q value = 0.0079
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 560 | 462 | 0.1 - 127.6 (10.1) |
DEL PEAK 24(10Q23.31) MUTATED | 497 | 416 | 0.1 - 127.6 (9.9) |
DEL PEAK 24(10Q23.31) WILD-TYPE | 63 | 46 | 0.2 - 108.8 (12.7) |
P value = 1.58e-07 (Wilcoxon-test), Q value = 8.9e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 24(10Q23.31) MUTATED | 497 | 59.2 (13.3) |
DEL PEAK 24(10Q23.31) WILD-TYPE | 63 | 47.2 (18.6) |
P value = 6.64e-06 (Wilcoxon-test), Q value = 0.0037
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 560 | 57.9 (14.5) |
DEL PEAK 25(10Q26.3) MUTATED | 498 | 59.1 (13.4) |
DEL PEAK 25(10Q26.3) WILD-TYPE | 62 | 48.3 (18.7) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = GBM-TP.merged_data.txt
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Number of patients = 560
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Number of significantly focal cnvs = 71
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Number of selected clinical features = 8
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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 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.