This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 66 arm-level events and 10 molecular subtypes across 36 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
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6q loss cnv correlated to 'CN_CNMF'.
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 | |
6q loss | 20 (56%) | 16 |
0.000242 (0.16) |
0.0129 (0.569) |
0.0887 (1.00) |
0.022 (0.649) |
0.193 (1.00) |
0.146 (1.00) |
0.209 (1.00) |
0.256 (1.00) |
0.32 (1.00) |
0.409 (1.00) |
1p gain | 10 (28%) | 26 |
0.139 (1.00) |
0.649 (1.00) |
0.653 (1.00) |
0.793 (1.00) |
0.634 (1.00) |
0.55 (1.00) |
0.108 (1.00) |
0.264 (1.00) |
0.26 (1.00) |
0.688 (1.00) |
1q gain | 21 (58%) | 15 |
0.516 (1.00) |
0.0931 (1.00) |
1 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.235 (1.00) |
0.114 (1.00) |
0.177 (1.00) |
0.736 (1.00) |
0.592 (1.00) |
2p gain | 6 (17%) | 30 |
0.662 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.635 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.366 (1.00) |
0.546 (1.00) |
1 (1.00) |
0.599 (1.00) |
2q gain | 6 (17%) | 30 |
0.182 (1.00) |
0.628 (1.00) |
0.726 (1.00) |
0.719 (1.00) |
0.526 (1.00) |
0.503 (1.00) |
0.369 (1.00) |
0.397 (1.00) |
1 (1.00) |
0.601 (1.00) |
3p gain | 3 (8%) | 33 |
0.231 (1.00) |
0.0965 (1.00) |
0.325 (1.00) |
0.153 (1.00) |
0.338 (1.00) |
0.236 (1.00) |
0.0637 (1.00) |
0.577 (1.00) |
||
3q gain | 8 (22%) | 28 |
0.236 (1.00) |
0.0593 (1.00) |
0.185 (1.00) |
0.716 (1.00) |
0.101 (1.00) |
0.0994 (1.00) |
0.54 (1.00) |
0.667 (1.00) |
1 (1.00) |
0.398 (1.00) |
4p gain | 3 (8%) | 33 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.769 (1.00) |
0.423 (1.00) |
0.559 (1.00) |
1 (1.00) |
||
5p gain | 12 (33%) | 24 |
1 (1.00) |
0.822 (1.00) |
0.885 (1.00) |
0.2 (1.00) |
0.615 (1.00) |
0.977 (1.00) |
0.761 (1.00) |
1 (1.00) |
1 (1.00) |
0.761 (1.00) |
5q gain | 12 (33%) | 24 |
1 (1.00) |
0.824 (1.00) |
0.884 (1.00) |
0.199 (1.00) |
0.613 (1.00) |
0.978 (1.00) |
0.764 (1.00) |
1 (1.00) |
1 (1.00) |
0.762 (1.00) |
6p gain | 7 (19%) | 29 |
0.684 (1.00) |
1 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.893 (1.00) |
0.185 (1.00) |
0.317 (1.00) |
0.674 (1.00) |
0.239 (1.00) |
7p gain | 7 (19%) | 29 |
0.684 (1.00) |
1 (1.00) |
1 (1.00) |
0.3 (1.00) |
0.209 (1.00) |
0.388 (1.00) |
0.373 (1.00) |
0.566 (1.00) |
0.674 (1.00) |
0.0183 (0.636) |
7q gain | 6 (17%) | 30 |
1 (1.00) |
0.63 (1.00) |
0.525 (1.00) |
0.689 (1.00) |
0.448 (1.00) |
0.534 (1.00) |
0.687 (1.00) |
0.82 (1.00) |
1 (1.00) |
0.00678 (0.53) |
8p gain | 6 (17%) | 30 |
1 (1.00) |
0.239 (1.00) |
0.393 (1.00) |
0.67 (1.00) |
0.337 (1.00) |
0.167 (1.00) |
0.204 (1.00) |
0.364 (1.00) |
0.367 (1.00) |
0.116 (1.00) |
8q gain | 12 (33%) | 24 |
1 (1.00) |
0.205 (1.00) |
0.383 (1.00) |
0.57 (1.00) |
0.17 (1.00) |
0.537 (1.00) |
0.184 (1.00) |
0.166 (1.00) |
0.721 (1.00) |
0.132 (1.00) |
10p gain | 5 (14%) | 31 |
1 (1.00) |
0.397 (1.00) |
0.391 (1.00) |
0.0406 (0.884) |
0.835 (1.00) |
0.0738 (1.00) |
0.785 (1.00) |
0.934 (1.00) |
0.63 (1.00) |
0.863 (1.00) |
11p gain | 4 (11%) | 32 |
0.605 (1.00) |
0.177 (1.00) |
0.603 (1.00) |
0.103 (1.00) |
0.203 (1.00) |
0.00581 (0.53) |
0.74 (1.00) |
0.749 (1.00) |
0.287 (1.00) |
0.187 (1.00) |
11q gain | 4 (11%) | 32 |
0.605 (1.00) |
0.176 (1.00) |
0.597 (1.00) |
0.104 (1.00) |
0.202 (1.00) |
0.00554 (0.53) |
0.739 (1.00) |
0.748 (1.00) |
0.287 (1.00) |
0.185 (1.00) |
12p gain | 9 (25%) | 27 |
1 (1.00) |
0.558 (1.00) |
0.0454 (0.907) |
0.237 (1.00) |
1 (1.00) |
0.905 (1.00) |
0.463 (1.00) |
0.842 (1.00) |
0.443 (1.00) |
0.335 (1.00) |
12q gain | 8 (22%) | 28 |
1 (1.00) |
0.533 (1.00) |
0.154 (1.00) |
0.536 (1.00) |
0.88 (1.00) |
0.983 (1.00) |
0.437 (1.00) |
0.824 (1.00) |
0.236 (1.00) |
0.629 (1.00) |
13q gain | 3 (8%) | 33 |
0.231 (1.00) |
0.0967 (1.00) |
0.0415 (0.884) |
0.0396 (0.884) |
0.395 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.0249 (0.686) |
||
15q gain | 6 (17%) | 30 |
0.662 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.863 (1.00) |
0.656 (1.00) |
0.194 (1.00) |
0.439 (1.00) |
0.677 (1.00) |
0.00887 (0.532) |
16p gain | 7 (19%) | 29 |
0.0918 (1.00) |
0.573 (1.00) |
0.727 (1.00) |
0.633 (1.00) |
0.663 (1.00) |
0.64 (1.00) |
0.374 (1.00) |
0.914 (1.00) |
0.674 (1.00) |
0.298 (1.00) |
16q gain | 5 (14%) | 31 |
0.342 (1.00) |
1 (1.00) |
0.807 (1.00) |
0.095 (1.00) |
1 (1.00) |
0.625 (1.00) |
0.923 (1.00) |
0.932 (1.00) |
1 (1.00) |
0.927 (1.00) |
17p gain | 3 (8%) | 33 |
1 (1.00) |
1 (1.00) |
0.599 (1.00) |
0.249 (1.00) |
0.774 (1.00) |
0.213 (1.00) |
0.685 (1.00) |
0.611 (1.00) |
0.559 (1.00) |
0.579 (1.00) |
17q gain | 7 (19%) | 29 |
1 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.533 (1.00) |
0.495 (1.00) |
0.256 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.418 (1.00) |
0.524 (1.00) |
18p gain | 7 (19%) | 29 |
1 (1.00) |
0.759 (1.00) |
0.0659 (1.00) |
0.302 (1.00) |
0.665 (1.00) |
0.76 (1.00) |
0.485 (1.00) |
0.881 (1.00) |
0.418 (1.00) |
0.847 (1.00) |
18q gain | 6 (17%) | 30 |
0.391 (1.00) |
0.332 (1.00) |
0.321 (1.00) |
0.676 (1.00) |
0.0695 (1.00) |
0.57 (1.00) |
0.195 (1.00) |
0.438 (1.00) |
0.677 (1.00) |
0.393 (1.00) |
19p gain | 6 (17%) | 30 |
0.662 (1.00) |
0.858 (1.00) |
0.702 (1.00) |
0.722 (1.00) |
0.628 (1.00) |
0.657 (1.00) |
0.581 (1.00) |
0.435 (1.00) |
0.0628 (1.00) |
1 (1.00) |
19q gain | 6 (17%) | 30 |
0.662 (1.00) |
0.859 (1.00) |
0.706 (1.00) |
0.721 (1.00) |
0.626 (1.00) |
0.66 (1.00) |
0.581 (1.00) |
0.438 (1.00) |
0.0628 (1.00) |
1 (1.00) |
20p gain | 11 (31%) | 25 |
1 (1.00) |
0.607 (1.00) |
0.312 (1.00) |
0.478 (1.00) |
0.726 (1.00) |
0.423 (1.00) |
0.236 (1.00) |
0.282 (1.00) |
0.465 (1.00) |
0.34 (1.00) |
20q gain | 12 (33%) | 24 |
0.732 (1.00) |
0.615 (1.00) |
0.143 (1.00) |
0.266 (1.00) |
0.752 (1.00) |
0.283 (1.00) |
0.142 (1.00) |
0.149 (1.00) |
0.499 (1.00) |
0.224 (1.00) |
21q gain | 3 (8%) | 33 |
1 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.678 (1.00) |
0.458 (1.00) |
0.887 (1.00) |
0.185 (1.00) |
0.711 (1.00) |
0.25 (1.00) |
0.133 (1.00) |
22q gain | 5 (14%) | 31 |
0.342 (1.00) |
0.599 (1.00) |
0.81 (1.00) |
1 (1.00) |
0.0856 (1.00) |
0.287 (1.00) |
0.848 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.928 (1.00) |
1p loss | 4 (11%) | 32 |
1 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.752 (1.00) |
0.657 (1.00) |
0.61 (1.00) |
0.815 (1.00) |
0.794 (1.00) |
0.626 (1.00) |
0.813 (1.00) |
3p loss | 22 (61%) | 14 |
0.00222 (0.366) |
0.252 (1.00) |
1 (1.00) |
0.0616 (1.00) |
0.62 (1.00) |
0.0119 (0.561) |
0.772 (1.00) |
0.586 (1.00) |
0.499 (1.00) |
0.991 (1.00) |
3q loss | 3 (8%) | 33 |
0.593 (1.00) |
0.479 (1.00) |
0.163 (1.00) |
0.022 (0.649) |
0.69 (1.00) |
0.613 (1.00) |
0.559 (1.00) |
0.394 (1.00) |
||
4p loss | 10 (28%) | 26 |
0.274 (1.00) |
0.101 (1.00) |
1 (1.00) |
1 (1.00) |
0.223 (1.00) |
0.322 (1.00) |
0.787 (1.00) |
0.646 (1.00) |
0.709 (1.00) |
0.288 (1.00) |
4q loss | 13 (36%) | 23 |
1 (1.00) |
0.39 (1.00) |
0.618 (1.00) |
0.688 (1.00) |
0.369 (1.00) |
0.391 (1.00) |
0.46 (1.00) |
0.839 (1.00) |
0.736 (1.00) |
0.368 (1.00) |
6p loss | 5 (14%) | 31 |
0.65 (1.00) |
0.0226 (0.649) |
0.702 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.983 (1.00) |
0.371 (1.00) |
0.24 (1.00) |
0.63 (1.00) |
0.982 (1.00) |
7p loss | 4 (11%) | 32 |
0.605 (1.00) |
0.426 (1.00) |
0.43 (1.00) |
0.28 (1.00) |
0.516 (1.00) |
0.904 (1.00) |
1 (1.00) |
0.858 (1.00) |
||
7q loss | 4 (11%) | 32 |
1 (1.00) |
0.423 (1.00) |
0.428 (1.00) |
0.285 (1.00) |
0.321 (1.00) |
0.277 (1.00) |
0.287 (1.00) |
0.391 (1.00) |
||
8p loss | 10 (28%) | 26 |
0.717 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.0174 (0.636) |
0.0775 (1.00) |
0.0935 (1.00) |
0.0375 (0.883) |
0.26 (1.00) |
0.172 (1.00) |
8q loss | 3 (8%) | 33 |
0.593 (1.00) |
0.262 (1.00) |
0.765 (1.00) |
0.524 (1.00) |
0.242 (1.00) |
0.793 (1.00) |
0.769 (1.00) |
0.0756 (1.00) |
1 (1.00) |
0.133 (1.00) |
9p loss | 18 (50%) | 18 |
1 (1.00) |
0.284 (1.00) |
0.269 (1.00) |
0.00665 (0.53) |
0.694 (1.00) |
0.298 (1.00) |
0.186 (1.00) |
0.127 (1.00) |
0.5 (1.00) |
0.591 (1.00) |
9q loss | 19 (53%) | 17 |
1 (1.00) |
0.77 (1.00) |
0.259 (1.00) |
0.0114 (0.561) |
0.581 (1.00) |
0.132 (1.00) |
0.71 (1.00) |
0.37 (1.00) |
0.192 (1.00) |
0.604 (1.00) |
10p loss | 6 (17%) | 30 |
1 (1.00) |
0.861 (1.00) |
0.206 (1.00) |
0.111 (1.00) |
0.733 (1.00) |
0.362 (1.00) |
0.58 (1.00) |
0.777 (1.00) |
0.677 (1.00) |
0.015 (0.584) |
10q loss | 5 (14%) | 31 |
0.167 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.409 (1.00) |
0.982 (1.00) |
0.85 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.557 (1.00) |
11p loss | 8 (22%) | 28 |
0.434 (1.00) |
1 (1.00) |
0.0656 (1.00) |
0.488 (1.00) |
0.207 (1.00) |
0.531 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.694 (1.00) |
0.389 (1.00) |
11q loss | 9 (25%) | 27 |
0.255 (1.00) |
1 (1.00) |
0.268 (1.00) |
0.482 (1.00) |
0.0727 (1.00) |
0.474 (1.00) |
0.766 (1.00) |
0.583 (1.00) |
0.705 (1.00) |
0.759 (1.00) |
12q loss | 3 (8%) | 33 |
0.231 (1.00) |
0.478 (1.00) |
0.326 (1.00) |
0.155 (1.00) |
0.608 (1.00) |
1 (1.00) |
1 (1.00) |
0.399 (1.00) |
||
13q loss | 15 (42%) | 21 |
1 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.516 (1.00) |
0.631 (1.00) |
0.744 (1.00) |
0.757 (1.00) |
0.312 (1.00) |
0.736 (1.00) |
0.335 (1.00) |
14q loss | 13 (36%) | 23 |
0.014 (0.576) |
0.564 (1.00) |
0.247 (1.00) |
0.00727 (0.53) |
1 (1.00) |
0.0436 (0.9) |
1 (1.00) |
0.911 (1.00) |
0.484 (1.00) |
0.281 (1.00) |
15q loss | 5 (14%) | 31 |
0.342 (1.00) |
0.596 (1.00) |
1 (1.00) |
1 (1.00) |
0.085 (1.00) |
0.288 (1.00) |
0.511 (1.00) |
0.755 (1.00) |
0.63 (1.00) |
0.982 (1.00) |
16p loss | 4 (11%) | 32 |
1 (1.00) |
1 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.739 (1.00) |
0.966 (1.00) |
0.626 (1.00) |
0.187 (1.00) |
||
16q loss | 7 (19%) | 29 |
0.684 (1.00) |
0.333 (1.00) |
0.392 (1.00) |
0.429 (1.00) |
0.662 (1.00) |
0.414 (1.00) |
0.659 (1.00) |
0.0193 (0.637) |
1 (1.00) |
0.662 (1.00) |
17p loss | 10 (28%) | 26 |
0.717 (1.00) |
0.52 (1.00) |
0.858 (1.00) |
1 (1.00) |
0.115 (1.00) |
0.352 (1.00) |
0.252 (1.00) |
0.291 (1.00) |
1 (1.00) |
0.143 (1.00) |
18p loss | 6 (17%) | 30 |
1 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.48 (1.00) |
0.45 (1.00) |
0.603 (1.00) |
0.24 (1.00) |
0.571 (1.00) |
0.367 (1.00) |
0.307 (1.00) |
18q loss | 8 (22%) | 28 |
0.236 (1.00) |
0.701 (1.00) |
0.583 (1.00) |
0.839 (1.00) |
0.103 (1.00) |
0.614 (1.00) |
0.132 (1.00) |
0.252 (1.00) |
0.424 (1.00) |
0.063 (1.00) |
19p loss | 4 (11%) | 32 |
0.605 (1.00) |
0.296 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.683 (1.00) |
0.0514 (0.997) |
0.242 (1.00) |
0.125 (1.00) |
0.00803 (0.53) |
19q loss | 3 (8%) | 33 |
1 (1.00) |
0.482 (1.00) |
0.327 (1.00) |
0.733 (1.00) |
0.862 (1.00) |
1 (1.00) |
1 (1.00) |
0.579 (1.00) |
||
20p loss | 5 (14%) | 31 |
1 (1.00) |
0.595 (1.00) |
0.0319 (0.78) |
0.519 (1.00) |
0.0977 (1.00) |
0.415 (1.00) |
0.376 (1.00) |
0.0113 (0.561) |
||
21q loss | 15 (42%) | 21 |
0.311 (1.00) |
1 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.133 (1.00) |
0.288 (1.00) |
0.337 (1.00) |
0.629 (1.00) |
0.31 (1.00) |
0.69 (1.00) |
22q loss | 5 (14%) | 31 |
0.65 (1.00) |
0.838 (1.00) |
0.704 (1.00) |
0.376 (1.00) |
0.331 (1.00) |
0.152 (1.00) |
0.677 (1.00) |
0.805 (1.00) |
0.376 (1.00) |
0.401 (1.00) |
xp loss | 15 (42%) | 21 |
0.00185 (0.366) |
0.0271 (0.694) |
0.65 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.265 (1.00) |
0.574 (1.00) |
0.961 (1.00) |
0.501 (1.00) |
0.996 (1.00) |
xq loss | 15 (42%) | 21 |
0.00185 (0.366) |
0.0273 (0.694) |
0.649 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.265 (1.00) |
0.573 (1.00) |
0.962 (1.00) |
0.501 (1.00) |
0.996 (1.00) |
P value = 0.000242 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 19 | 17 |
6Q LOSS MUTATED | 5 | 15 |
6Q LOSS WILD-TYPE | 14 | 2 |
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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/19780560/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/20125181/CHOL-TP.transferedmergedcluster.txt
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Number of patients = 36
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Number of significantly arm-level cnvs = 66
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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.