This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 65 arm-level events and 10 molecular subtypes across 36 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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No arm-level cnvs related to molecular subtypes.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1p gain | 10 (28%) | 26 |
0.0704 (0.781) |
0.808 (1.00) |
0.648 (1.00) |
0.791 (1.00) |
0.325 (0.977) |
0.553 (1.00) |
0.169 (0.922) |
0.265 (0.945) |
0.757 (1.00) |
0.245 (0.945) |
1q gain | 22 (61%) | 14 |
0.812 (1.00) |
0.119 (0.895) |
0.726 (1.00) |
0.817 (1.00) |
0.269 (0.945) |
0.355 (0.981) |
0.097 (0.827) |
0.161 (0.921) |
0.102 (0.827) |
0.181 (0.929) |
2p gain | 5 (14%) | 31 |
0.0603 (0.729) |
0.595 (1.00) |
0.579 (1.00) |
0.204 (0.945) |
0.702 (1.00) |
0.775 (1.00) |
0.583 (1.00) |
0.644 (1.00) |
0.132 (0.895) |
0.889 (1.00) |
2q gain | 6 (17%) | 30 |
0.427 (0.995) |
0.533 (1.00) |
0.727 (1.00) |
0.716 (1.00) |
0.586 (1.00) |
0.503 (1.00) |
0.385 (0.981) |
0.397 (0.981) |
0.131 (0.895) |
0.855 (1.00) |
3q gain | 7 (19%) | 29 |
0.605 (1.00) |
0.0206 (0.567) |
0.475 (1.00) |
0.279 (0.945) |
0.057 (0.727) |
0.0545 (0.725) |
0.242 (0.945) |
0.495 (1.00) |
0.155 (0.895) |
0.678 (1.00) |
5p gain | 12 (33%) | 24 |
0.89 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.199 (0.942) |
0.849 (1.00) |
0.976 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.873 (1.00) |
5q gain | 11 (31%) | 25 |
0.884 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.329 (0.981) |
0.732 (1.00) |
0.947 (1.00) |
0.697 (1.00) |
0.95 (1.00) |
0.845 (1.00) |
0.863 (1.00) |
6p gain | 8 (22%) | 28 |
1 (1.00) |
0.608 (1.00) |
0.757 (1.00) |
0.792 (1.00) |
0.608 (1.00) |
0.801 (1.00) |
0.0612 (0.729) |
0.155 (0.895) |
0.0207 (0.567) |
0.312 (0.97) |
6q gain | 3 (8%) | 33 |
0.409 (0.988) |
0.0979 (0.827) |
0.336 (0.981) |
0.677 (1.00) |
0.332 (0.981) |
0.733 (1.00) |
0.231 (0.945) |
0.676 (1.00) |
0.0124 (0.567) |
0.263 (0.945) |
7p gain | 7 (19%) | 29 |
0.635 (1.00) |
1 (1.00) |
1 (1.00) |
0.303 (0.97) |
0.402 (0.981) |
0.391 (0.981) |
0.39 (0.981) |
0.567 (1.00) |
0.0928 (0.827) |
0.17 (0.922) |
7q gain | 6 (17%) | 30 |
0.86 (1.00) |
0.633 (1.00) |
0.528 (1.00) |
0.688 (1.00) |
0.222 (0.945) |
0.535 (1.00) |
0.766 (1.00) |
0.822 (1.00) |
0.32 (0.977) |
0.0348 (0.67) |
8p gain | 5 (14%) | 31 |
0.628 (1.00) |
0.404 (0.984) |
0.523 (1.00) |
0.691 (1.00) |
0.491 (1.00) |
0.26 (0.945) |
0.169 (0.922) |
0.67 (1.00) |
0.377 (0.981) |
0.578 (1.00) |
8q gain | 11 (31%) | 25 |
0.792 (1.00) |
0.287 (0.945) |
0.419 (0.995) |
0.488 (1.00) |
0.0439 (0.68) |
0.151 (0.895) |
0.0502 (0.703) |
0.0779 (0.794) |
0.00628 (0.408) |
0.0317 (0.67) |
10p gain | 5 (14%) | 31 |
0.909 (1.00) |
0.286 (0.945) |
0.393 (0.981) |
0.0421 (0.68) |
0.164 (0.922) |
0.0733 (0.781) |
0.787 (1.00) |
0.934 (1.00) |
0.485 (1.00) |
0.363 (0.981) |
11p gain | 4 (11%) | 32 |
0.814 (1.00) |
0.283 (0.945) |
0.601 (1.00) |
0.103 (0.827) |
0.0355 (0.67) |
0.00565 (0.408) |
0.9 (1.00) |
0.746 (1.00) |
0.672 (1.00) |
0.089 (0.827) |
11q gain | 4 (11%) | 32 |
0.813 (1.00) |
0.287 (0.945) |
0.599 (1.00) |
0.102 (0.827) |
0.0353 (0.67) |
0.00507 (0.408) |
0.899 (1.00) |
0.748 (1.00) |
0.671 (1.00) |
0.0883 (0.827) |
12p gain | 9 (25%) | 27 |
0.0928 (0.827) |
0.449 (1.00) |
0.0463 (0.687) |
0.238 (0.945) |
0.907 (1.00) |
0.905 (1.00) |
0.589 (1.00) |
0.843 (1.00) |
1 (1.00) |
0.52 (1.00) |
12q gain | 8 (22%) | 28 |
0.017 (0.567) |
0.468 (1.00) |
0.151 (0.895) |
0.533 (1.00) |
0.938 (1.00) |
0.983 (1.00) |
0.562 (1.00) |
0.827 (1.00) |
1 (1.00) |
0.422 (0.995) |
13q gain | 3 (8%) | 33 |
0.876 (1.00) |
0.0985 (0.827) |
0.0102 (0.551) |
0.0381 (0.67) |
0.607 (1.00) |
0.886 (1.00) |
0.308 (0.97) |
0.265 (0.945) |
||
15q gain | 6 (17%) | 30 |
0.486 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.665 (1.00) |
0.66 (1.00) |
0.14 (0.895) |
0.436 (1.00) |
0.156 (0.895) |
0.0159 (0.567) |
16p gain | 7 (19%) | 29 |
0.21 (0.945) |
0.373 (0.981) |
0.726 (1.00) |
0.634 (1.00) |
0.513 (1.00) |
0.64 (1.00) |
0.391 (0.981) |
0.914 (1.00) |
0.374 (0.981) |
0.876 (1.00) |
16q gain | 5 (14%) | 31 |
0.541 (1.00) |
1 (1.00) |
0.807 (1.00) |
0.0955 (0.827) |
0.329 (0.981) |
0.623 (1.00) |
1 (1.00) |
0.933 (1.00) |
0.891 (1.00) |
1 (1.00) |
17p gain | 3 (8%) | 33 |
0.761 (1.00) |
1 (1.00) |
0.599 (1.00) |
0.249 (0.945) |
0.224 (0.945) |
0.213 (0.945) |
0.608 (1.00) |
0.611 (1.00) |
0.872 (1.00) |
0.316 (0.973) |
17q gain | 7 (19%) | 29 |
0.933 (1.00) |
1 (1.00) |
0.153 (0.895) |
0.532 (1.00) |
0.318 (0.973) |
0.258 (0.945) |
0.935 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.341 (0.981) |
18p gain | 7 (19%) | 29 |
0.0711 (0.781) |
0.764 (1.00) |
0.0639 (0.741) |
0.305 (0.97) |
0.514 (1.00) |
0.761 (1.00) |
0.441 (1.00) |
0.882 (1.00) |
0.972 (1.00) |
0.424 (0.995) |
18q gain | 6 (17%) | 30 |
0.24 (0.945) |
0.238 (0.945) |
0.324 (0.977) |
0.678 (1.00) |
0.114 (0.882) |
0.568 (1.00) |
0.14 (0.895) |
0.436 (1.00) |
0.132 (0.895) |
0.256 (0.945) |
19p gain | 6 (17%) | 30 |
1 (1.00) |
0.862 (1.00) |
0.704 (1.00) |
0.725 (1.00) |
0.664 (1.00) |
0.659 (1.00) |
0.553 (1.00) |
0.439 (1.00) |
0.395 (0.981) |
0.929 (1.00) |
19q gain | 6 (17%) | 30 |
1 (1.00) |
0.862 (1.00) |
0.704 (1.00) |
0.724 (1.00) |
0.663 (1.00) |
0.66 (1.00) |
0.551 (1.00) |
0.435 (1.00) |
0.397 (0.981) |
0.93 (1.00) |
20p gain | 11 (31%) | 25 |
0.739 (1.00) |
0.603 (1.00) |
0.311 (0.97) |
0.482 (1.00) |
0.578 (1.00) |
0.423 (0.995) |
0.174 (0.927) |
0.281 (0.945) |
0.472 (1.00) |
0.186 (0.931) |
20q gain | 12 (33%) | 24 |
0.726 (1.00) |
0.609 (1.00) |
0.142 (0.895) |
0.267 (0.945) |
0.454 (1.00) |
0.282 (0.945) |
0.0997 (0.827) |
0.148 (0.895) |
0.637 (1.00) |
0.205 (0.945) |
22q gain | 5 (14%) | 31 |
0.429 (0.995) |
0.711 (1.00) |
0.809 (1.00) |
1 (1.00) |
0.487 (1.00) |
0.288 (0.945) |
1 (1.00) |
0.932 (1.00) |
0.485 (1.00) |
1 (1.00) |
1p loss | 3 (8%) | 33 |
0.0189 (0.567) |
1 (1.00) |
0.762 (1.00) |
0.4 (0.981) |
0.412 (0.989) |
0.396 (0.981) |
0.605 (1.00) |
0.888 (1.00) |
0.52 (1.00) |
0.929 (1.00) |
3p loss | 24 (67%) | 12 |
0.154 (0.895) |
0.609 (1.00) |
0.694 (1.00) |
0.144 (0.895) |
0.355 (0.981) |
0.039 (0.67) |
0.553 (1.00) |
0.933 (1.00) |
0.916 (1.00) |
0.593 (1.00) |
3q loss | 4 (11%) | 32 |
0.732 (1.00) |
0.812 (1.00) |
0.604 (1.00) |
0.521 (1.00) |
0.563 (1.00) |
0.122 (0.895) |
0.213 (0.945) |
0.489 (1.00) |
0.174 (0.927) |
0.151 (0.895) |
4p loss | 11 (31%) | 25 |
1 (1.00) |
0.0724 (0.781) |
0.884 (1.00) |
0.862 (1.00) |
0.201 (0.942) |
0.19 (0.933) |
0.864 (1.00) |
0.659 (1.00) |
0.616 (1.00) |
0.731 (1.00) |
4q loss | 13 (36%) | 23 |
0.197 (0.942) |
0.249 (0.945) |
0.617 (1.00) |
0.688 (1.00) |
0.228 (0.945) |
0.389 (0.981) |
0.352 (0.981) |
0.838 (1.00) |
0.408 (0.988) |
0.49 (1.00) |
5q loss | 3 (8%) | 33 |
0.76 (1.00) |
0.765 (1.00) |
0.601 (1.00) |
0.25 (0.945) |
0.126 (0.895) |
0.0781 (0.794) |
0.606 (1.00) |
0.251 (0.945) |
0.312 (0.97) |
0.485 (1.00) |
6p loss | 5 (14%) | 31 |
0.578 (1.00) |
0.0227 (0.569) |
0.705 (1.00) |
1 (1.00) |
0.832 (1.00) |
0.982 (1.00) |
0.393 (0.981) |
0.24 (0.945) |
0.0584 (0.729) |
0.578 (1.00) |
6q loss | 20 (56%) | 16 |
0.015 (0.567) |
0.0049 (0.408) |
0.0888 (0.827) |
0.0228 (0.569) |
0.0193 (0.567) |
0.146 (0.895) |
0.378 (0.981) |
0.257 (0.945) |
0.603 (1.00) |
0.306 (0.97) |
7p loss | 4 (11%) | 32 |
0.399 (0.981) |
0.223 (0.945) |
0.4 (0.981) |
0.283 (0.945) |
0.394 (0.981) |
0.905 (1.00) |
0.176 (0.928) |
0.658 (1.00) |
||
7q loss | 4 (11%) | 32 |
1 (1.00) |
0.814 (1.00) |
0.4 (0.981) |
0.284 (0.945) |
0.213 (0.945) |
0.278 (0.945) |
0.0968 (0.827) |
0.0402 (0.67) |
||
8p loss | 10 (28%) | 26 |
0.00344 (0.408) |
0.183 (0.93) |
1 (1.00) |
0.547 (1.00) |
0.0488 (0.703) |
0.0779 (0.794) |
0.117 (0.895) |
0.037 (0.67) |
0.648 (1.00) |
0.24 (0.945) |
8q loss | 5 (14%) | 31 |
0.541 (1.00) |
0.234 (0.945) |
1 (1.00) |
0.726 (1.00) |
0.0983 (0.827) |
0.201 (0.942) |
0.584 (1.00) |
0.0255 (0.591) |
0.89 (1.00) |
0.0616 (0.729) |
9p loss | 18 (50%) | 18 |
0.0252 (0.591) |
0.322 (0.977) |
0.267 (0.945) |
0.00614 (0.408) |
0.514 (1.00) |
0.294 (0.957) |
0.0978 (0.827) |
0.128 (0.895) |
0.299 (0.966) |
0.17 (0.922) |
9q loss | 19 (53%) | 17 |
0.00559 (0.408) |
0.759 (1.00) |
0.259 (0.945) |
0.0113 (0.566) |
0.152 (0.895) |
0.131 (0.895) |
0.551 (1.00) |
0.37 (0.981) |
0.397 (0.981) |
0.276 (0.945) |
10p loss | 6 (17%) | 30 |
0.858 (1.00) |
0.862 (1.00) |
0.209 (0.945) |
0.11 (0.876) |
0.112 (0.877) |
0.356 (0.981) |
0.551 (1.00) |
0.775 (1.00) |
0.363 (0.981) |
0.00153 (0.408) |
10q loss | 5 (14%) | 31 |
0.583 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.675 (1.00) |
0.933 (1.00) |
0.982 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.892 (1.00) |
0.364 (0.981) |
11p loss | 8 (22%) | 28 |
0.0563 (0.727) |
1 (1.00) |
0.066 (0.753) |
0.487 (1.00) |
0.39 (0.981) |
0.534 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.784 (1.00) |
0.452 (1.00) |
11q loss | 9 (25%) | 27 |
0.0465 (0.687) |
0.895 (1.00) |
0.268 (0.945) |
0.487 (1.00) |
0.0508 (0.703) |
0.472 (1.00) |
0.875 (1.00) |
0.584 (1.00) |
0.978 (1.00) |
0.443 (1.00) |
12q loss | 3 (8%) | 33 |
0.764 (1.00) |
0.483 (1.00) |
0.333 (0.981) |
0.154 (0.895) |
0.861 (1.00) |
1 (1.00) |
0.308 (0.97) |
0.561 (1.00) |
||
13q loss | 16 (44%) | 20 |
0.0151 (0.567) |
0.917 (1.00) |
0.27 (0.945) |
0.518 (1.00) |
0.133 (0.895) |
0.525 (1.00) |
0.909 (1.00) |
0.486 (1.00) |
0.94 (1.00) |
0.574 (1.00) |
14q loss | 13 (36%) | 23 |
0.0319 (0.67) |
0.313 (0.97) |
0.249 (0.945) |
0.00828 (0.489) |
0.126 (0.895) |
0.0438 (0.68) |
1 (1.00) |
0.91 (1.00) |
0.726 (1.00) |
0.37 (0.981) |
15q loss | 5 (14%) | 31 |
0.153 (0.895) |
0.71 (1.00) |
1 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.285 (0.945) |
0.582 (1.00) |
0.755 (1.00) |
0.514 (1.00) |
0.631 (1.00) |
16p loss | 4 (11%) | 32 |
0.728 (1.00) |
0.813 (1.00) |
0.401 (0.981) |
1 (1.00) |
0.899 (1.00) |
0.966 (1.00) |
0.532 (1.00) |
0.394 (0.981) |
||
16q loss | 7 (19%) | 29 |
0.181 (0.929) |
0.277 (0.945) |
0.394 (0.981) |
0.428 (0.995) |
0.189 (0.933) |
0.412 (0.989) |
0.592 (1.00) |
0.0183 (0.567) |
0.615 (1.00) |
0.7 (1.00) |
17p loss | 10 (28%) | 26 |
0.427 (0.995) |
0.186 (0.931) |
0.858 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.356 (0.981) |
0.462 (1.00) |
0.289 (0.945) |
0.62 (1.00) |
0.628 (1.00) |
18p loss | 6 (17%) | 30 |
1 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.482 (1.00) |
0.944 (1.00) |
0.601 (1.00) |
0.285 (0.945) |
0.569 (1.00) |
0.537 (1.00) |
0.621 (1.00) |
18q loss | 8 (22%) | 28 |
0.613 (1.00) |
0.88 (1.00) |
0.578 (1.00) |
0.841 (1.00) |
0.537 (1.00) |
0.614 (1.00) |
0.201 (0.942) |
0.254 (0.945) |
0.379 (0.981) |
0.34 (0.981) |
19p loss | 4 (11%) | 32 |
0.902 (1.00) |
0.354 (0.981) |
0.808 (1.00) |
1 (1.00) |
0.398 (0.981) |
0.685 (1.00) |
0.0546 (0.725) |
0.245 (0.945) |
0.0209 (0.567) |
0.09 (0.827) |
19q loss | 3 (8%) | 33 |
0.657 (1.00) |
0.482 (1.00) |
0.333 (0.981) |
0.731 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.705 (1.00) |
||
20p loss | 5 (14%) | 31 |
0.908 (1.00) |
0.71 (1.00) |
0.485 (1.00) |
0.522 (1.00) |
0.169 (0.922) |
0.415 (0.992) |
0.656 (1.00) |
0.363 (0.981) |
||
21q loss | 15 (42%) | 21 |
0.649 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.714 (1.00) |
0.724 (1.00) |
0.289 (0.945) |
0.342 (0.981) |
0.628 (1.00) |
0.846 (1.00) |
0.448 (1.00) |
22q loss | 5 (14%) | 31 |
0.787 (1.00) |
0.842 (1.00) |
0.705 (1.00) |
0.376 (0.981) |
0.282 (0.945) |
0.153 (0.895) |
0.786 (1.00) |
0.805 (1.00) |
0.657 (1.00) |
0.578 (1.00) |
xp loss | 15 (42%) | 21 |
0.04 (0.67) |
0.00538 (0.408) |
0.65 (1.00) |
0.848 (1.00) |
0.201 (0.942) |
0.265 (0.945) |
0.636 (1.00) |
0.962 (1.00) |
0.178 (0.929) |
0.72 (1.00) |
xq loss | 15 (42%) | 21 |
0.0396 (0.67) |
0.00488 (0.408) |
0.649 (1.00) |
0.849 (1.00) |
0.201 (0.942) |
0.267 (0.945) |
0.635 (1.00) |
0.962 (1.00) |
0.18 (0.929) |
0.719 (1.00) |
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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22519028/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/22541054/CHOL-TP.transferedmergedcluster.txt
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Number of patients = 36
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Number of significantly arm-level cnvs = 65
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
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.