This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 13 molecular subtypes across 569 patients, 34 significant findings detected with P value < 0.05 and Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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2q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'CN_CNMF'.
-
6q gain cnv correlated to 'CN_CNMF'.
-
7p gain cnv correlated to 'CN_CNMF'.
-
7q gain cnv correlated to 'CN_CNMF'.
-
10p gain cnv correlated to 'CN_CNMF'.
-
12p gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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20p gain cnv correlated to 'CN_CNMF'.
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20q gain cnv correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
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1p loss cnv correlated to 'MRNA_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF'.
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5p loss cnv correlated to 'MRNASEQ_CNMF'.
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9q loss cnv correlated to 'CN_CNMF'.
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14q loss cnv correlated to 'CN_CNMF'.
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15q loss cnv correlated to 'MIR_CNMF' and 'CN_CNMF'.
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17q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
2p gain | 178 (31%) | 391 |
1e-05 (0.0104) |
1e-05 (0.0104) |
0.821 (1.00) |
0.00042 (0.42) |
1e-05 (0.0104) |
0.0388 (1.00) |
0.0942 (1.00) |
0.00014 (0.142) |
0.00158 (1.00) |
0.823 (1.00) |
0.0268 (1.00) |
0.792 (1.00) |
1 (1.00) |
12p gain | 250 (44%) | 319 |
8e-05 (0.0814) |
0.00076 (0.755) |
0.742 (1.00) |
0.0004 (0.4) |
1e-05 (0.0104) |
0.305 (1.00) |
0.319 (1.00) |
0.00038 (0.381) |
0.00188 (1.00) |
0.183 (1.00) |
0.00023 (0.232) |
0.303 (1.00) |
0.11 (1.00) |
20q gain | 320 (56%) | 249 |
1e-05 (0.0104) |
0.00034 (0.342) |
0.672 (1.00) |
0.0001 (0.101) |
1e-05 (0.0104) |
0.662 (1.00) |
0.0787 (1.00) |
0.00889 (1.00) |
0.136 (1.00) |
0.258 (1.00) |
0.00496 (1.00) |
0.674 (1.00) |
0.509 (1.00) |
2q gain | 150 (26%) | 419 |
0.00044 (0.44) |
5e-05 (0.051) |
0.984 (1.00) |
0.00491 (1.00) |
1e-05 (0.0104) |
0.0987 (1.00) |
0.407 (1.00) |
0.00371 (1.00) |
0.0187 (1.00) |
0.611 (1.00) |
0.00614 (1.00) |
0.105 (1.00) |
0.726 (1.00) |
13q gain | 60 (11%) | 509 |
0.00591 (1.00) |
0.0002 (0.202) |
0.574 (1.00) |
0.0166 (1.00) |
0.00016 (0.162) |
0.593 (1.00) |
0.317 (1.00) |
0.231 (1.00) |
0.43 (1.00) |
0.192 (1.00) |
0.0722 (1.00) |
0.941 (1.00) |
0.686 (1.00) |
15q loss | 276 (49%) | 293 |
0.00051 (0.508) |
0.0134 (1.00) |
9e-05 (0.0914) |
0.00036 (0.361) |
1e-05 (0.0104) |
0.375 (1.00) |
0.814 (1.00) |
0.0663 (1.00) |
0.616 (1.00) |
0.00662 (1.00) |
0.00082 (0.812) |
0.0299 (1.00) |
0.00253 (1.00) |
1q gain | 218 (38%) | 351 |
0.78 (1.00) |
0.27 (1.00) |
0.695 (1.00) |
0.229 (1.00) |
1e-05 (0.0104) |
0.453 (1.00) |
0.507 (1.00) |
0.435 (1.00) |
0.276 (1.00) |
0.204 (1.00) |
0.0984 (1.00) |
0.116 (1.00) |
0.176 (1.00) |
3q gain | 268 (47%) | 301 |
0.975 (1.00) |
0.806 (1.00) |
0.257 (1.00) |
0.429 (1.00) |
2e-05 (0.0204) |
0.594 (1.00) |
0.256 (1.00) |
0.696 (1.00) |
0.926 (1.00) |
0.181 (1.00) |
0.0879 (1.00) |
0.118 (1.00) |
0.206 (1.00) |
5p gain | 196 (34%) | 373 |
0.593 (1.00) |
0.671 (1.00) |
0.854 (1.00) |
0.736 (1.00) |
0.00012 (0.122) |
0.485 (1.00) |
0.0883 (1.00) |
0.13 (1.00) |
0.537 (1.00) |
0.23 (1.00) |
0.634 (1.00) |
0.632 (1.00) |
0.181 (1.00) |
6p gain | 166 (29%) | 403 |
0.511 (1.00) |
0.00438 (1.00) |
0.901 (1.00) |
0.0129 (1.00) |
1e-05 (0.0104) |
0.864 (1.00) |
0.228 (1.00) |
0.158 (1.00) |
0.0079 (1.00) |
0.361 (1.00) |
0.065 (1.00) |
0.436 (1.00) |
0.864 (1.00) |
6q gain | 96 (17%) | 473 |
0.655 (1.00) |
0.0525 (1.00) |
0.822 (1.00) |
0.0202 (1.00) |
1e-05 (0.0104) |
0.788 (1.00) |
0.997 (1.00) |
0.00505 (1.00) |
0.0222 (1.00) |
0.194 (1.00) |
0.0297 (1.00) |
0.469 (1.00) |
0.643 (1.00) |
7p gain | 181 (32%) | 388 |
0.631 (1.00) |
0.535 (1.00) |
0.072 (1.00) |
0.103 (1.00) |
1e-05 (0.0104) |
0.503 (1.00) |
0.402 (1.00) |
0.567 (1.00) |
0.698 (1.00) |
0.925 (1.00) |
0.115 (1.00) |
0.363 (1.00) |
0.435 (1.00) |
7q gain | 198 (35%) | 371 |
0.653 (1.00) |
0.0847 (1.00) |
0.297 (1.00) |
0.379 (1.00) |
2e-05 (0.0204) |
0.463 (1.00) |
0.247 (1.00) |
0.925 (1.00) |
0.643 (1.00) |
0.153 (1.00) |
0.633 (1.00) |
0.0538 (1.00) |
0.451 (1.00) |
10p gain | 184 (32%) | 385 |
0.00397 (1.00) |
0.021 (1.00) |
0.679 (1.00) |
0.376 (1.00) |
1e-05 (0.0104) |
0.979 (1.00) |
0.0101 (1.00) |
0.0111 (1.00) |
0.124 (1.00) |
0.56 (1.00) |
0.00065 (0.646) |
0.511 (1.00) |
0.892 (1.00) |
12q gain | 174 (31%) | 395 |
0.00601 (1.00) |
0.0569 (1.00) |
0.651 (1.00) |
0.0486 (1.00) |
1e-05 (0.0104) |
0.0256 (1.00) |
0.255 (1.00) |
0.00185 (1.00) |
0.00847 (1.00) |
0.102 (1.00) |
0.0111 (1.00) |
0.581 (1.00) |
0.101 (1.00) |
19p gain | 167 (29%) | 402 |
0.0685 (1.00) |
0.441 (1.00) |
0.568 (1.00) |
0.116 (1.00) |
6e-05 (0.0611) |
0.0555 (1.00) |
0.21 (1.00) |
0.235 (1.00) |
0.471 (1.00) |
0.369 (1.00) |
0.334 (1.00) |
0.544 (1.00) |
0.981 (1.00) |
19q gain | 160 (28%) | 409 |
0.208 (1.00) |
0.768 (1.00) |
0.861 (1.00) |
0.184 (1.00) |
1e-05 (0.0104) |
0.494 (1.00) |
0.38 (1.00) |
0.206 (1.00) |
0.437 (1.00) |
0.272 (1.00) |
0.677 (1.00) |
0.434 (1.00) |
0.991 (1.00) |
20p gain | 282 (50%) | 287 |
0.00144 (1.00) |
0.00106 (1.00) |
0.725 (1.00) |
0.00076 (0.755) |
1e-05 (0.0104) |
0.341 (1.00) |
0.332 (1.00) |
0.00267 (1.00) |
0.123 (1.00) |
0.224 (1.00) |
0.00166 (1.00) |
0.602 (1.00) |
0.813 (1.00) |
1p loss | 61 (11%) | 508 |
0.0297 (1.00) |
0.00011 (0.112) |
0.605 (1.00) |
0.239 (1.00) |
0.451 (1.00) |
0.0351 (1.00) |
0.203 (1.00) |
0.632 (1.00) |
0.509 (1.00) |
0.447 (1.00) |
0.306 (1.00) |
0.0408 (1.00) |
0.138 (1.00) |
3p loss | 95 (17%) | 474 |
0.04 (1.00) |
0.00094 (0.926) |
0.889 (1.00) |
0.0061 (1.00) |
8e-05 (0.0814) |
0.634 (1.00) |
0.278 (1.00) |
0.0623 (1.00) |
0.00643 (1.00) |
0.124 (1.00) |
0.0921 (1.00) |
0.921 (1.00) |
0.743 (1.00) |
5p loss | 129 (23%) | 440 |
0.0963 (1.00) |
0.028 (1.00) |
0.486 (1.00) |
0.0833 (1.00) |
0.0215 (1.00) |
0.108 (1.00) |
0.0775 (1.00) |
0.00017 (0.172) |
0.0481 (1.00) |
0.665 (1.00) |
0.0872 (1.00) |
0.383 (1.00) |
0.388 (1.00) |
9q loss | 280 (49%) | 289 |
0.00488 (1.00) |
0.0141 (1.00) |
0.226 (1.00) |
0.0247 (1.00) |
1e-05 (0.0104) |
0.594 (1.00) |
0.585 (1.00) |
0.00456 (1.00) |
0.0515 (1.00) |
0.187 (1.00) |
0.0502 (1.00) |
0.257 (1.00) |
0.0887 (1.00) |
14q loss | 208 (37%) | 361 |
0.212 (1.00) |
0.165 (1.00) |
0.968 (1.00) |
0.492 (1.00) |
1e-05 (0.0104) |
0.98 (1.00) |
0.61 (1.00) |
0.00393 (1.00) |
0.0466 (1.00) |
0.801 (1.00) |
0.32 (1.00) |
0.975 (1.00) |
0.772 (1.00) |
17q loss | 376 (66%) | 193 |
0.0603 (1.00) |
0.0211 (1.00) |
0.0261 (1.00) |
0.0103 (1.00) |
0.969 (1.00) |
0.434 (1.00) |
0.335 (1.00) |
0.492 (1.00) |
0.0947 (1.00) |
0.058 (1.00) |
0.621 (1.00) |
0.00013 (0.132) |
0.121 (1.00) |
1p gain | 166 (29%) | 403 |
0.106 (1.00) |
0.325 (1.00) |
0.119 (1.00) |
0.685 (1.00) |
0.00258 (1.00) |
0.0924 (1.00) |
0.308 (1.00) |
0.612 (1.00) |
0.949 (1.00) |
0.215 (1.00) |
0.618 (1.00) |
0.151 (1.00) |
0.339 (1.00) |
3p gain | 154 (27%) | 415 |
0.339 (1.00) |
0.389 (1.00) |
0.0441 (1.00) |
0.374 (1.00) |
0.0126 (1.00) |
1 (1.00) |
0.406 (1.00) |
0.783 (1.00) |
0.766 (1.00) |
0.918 (1.00) |
0.821 (1.00) |
0.906 (1.00) |
1 (1.00) |
4p gain | 57 (10%) | 512 |
0.246 (1.00) |
0.19 (1.00) |
0.00486 (1.00) |
0.0595 (1.00) |
0.134 (1.00) |
0.456 (1.00) |
0.397 (1.00) |
0.606 (1.00) |
0.841 (1.00) |
0.32 (1.00) |
0.0186 (1.00) |
0.583 (1.00) |
0.158 (1.00) |
4q gain | 32 (6%) | 537 |
0.673 (1.00) |
0.696 (1.00) |
0.153 (1.00) |
0.207 (1.00) |
0.0371 (1.00) |
0.27 (1.00) |
0.45 (1.00) |
0.764 (1.00) |
0.856 (1.00) |
0.374 (1.00) |
0.0442 (1.00) |
0.495 (1.00) |
0.166 (1.00) |
5q gain | 60 (11%) | 509 |
0.0834 (1.00) |
0.244 (1.00) |
0.802 (1.00) |
0.832 (1.00) |
0.51 (1.00) |
0.441 (1.00) |
0.389 (1.00) |
0.709 (1.00) |
0.413 (1.00) |
0.496 (1.00) |
0.81 (1.00) |
0.629 (1.00) |
0.311 (1.00) |
8p gain | 117 (21%) | 452 |
0.0709 (1.00) |
0.00363 (1.00) |
0.299 (1.00) |
0.362 (1.00) |
0.715 (1.00) |
0.136 (1.00) |
0.00705 (1.00) |
0.616 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.496 (1.00) |
0.177 (1.00) |
0.0663 (1.00) |
8q gain | 238 (42%) | 331 |
0.02 (1.00) |
0.00093 (0.917) |
0.0614 (1.00) |
0.2 (1.00) |
0.175 (1.00) |
0.32 (1.00) |
0.387 (1.00) |
0.0308 (1.00) |
0.0862 (1.00) |
0.464 (1.00) |
0.865 (1.00) |
0.293 (1.00) |
0.379 (1.00) |
9p gain | 91 (16%) | 478 |
0.113 (1.00) |
0.424 (1.00) |
0.238 (1.00) |
0.866 (1.00) |
0.019 (1.00) |
0.395 (1.00) |
0.727 (1.00) |
0.693 (1.00) |
0.412 (1.00) |
0.186 (1.00) |
0.186 (1.00) |
0.496 (1.00) |
0.329 (1.00) |
9q gain | 45 (8%) | 524 |
0.252 (1.00) |
0.303 (1.00) |
0.0907 (1.00) |
0.534 (1.00) |
0.17 (1.00) |
0.577 (1.00) |
0.0266 (1.00) |
0.486 (1.00) |
0.09 (1.00) |
0.499 (1.00) |
0.754 (1.00) |
0.474 (1.00) |
0.503 (1.00) |
10q gain | 108 (19%) | 461 |
0.00375 (1.00) |
0.00919 (1.00) |
0.242 (1.00) |
0.118 (1.00) |
0.0012 (1.00) |
0.765 (1.00) |
0.0622 (1.00) |
0.105 (1.00) |
0.22 (1.00) |
0.728 (1.00) |
0.244 (1.00) |
0.96 (1.00) |
0.294 (1.00) |
11p gain | 76 (13%) | 493 |
0.711 (1.00) |
0.1 (1.00) |
0.64 (1.00) |
0.468 (1.00) |
0.343 (1.00) |
0.0282 (1.00) |
0.026 (1.00) |
0.0592 (1.00) |
0.0359 (1.00) |
0.561 (1.00) |
0.839 (1.00) |
0.892 (1.00) |
0.361 (1.00) |
11q gain | 114 (20%) | 455 |
0.456 (1.00) |
0.338 (1.00) |
0.876 (1.00) |
0.12 (1.00) |
0.0394 (1.00) |
0.165 (1.00) |
0.00037 (0.371) |
0.302 (1.00) |
0.158 (1.00) |
0.514 (1.00) |
0.808 (1.00) |
0.842 (1.00) |
0.762 (1.00) |
14q gain | 58 (10%) | 511 |
0.141 (1.00) |
0.191 (1.00) |
0.406 (1.00) |
0.699 (1.00) |
0.799 (1.00) |
0.331 (1.00) |
0.173 (1.00) |
0.505 (1.00) |
0.57 (1.00) |
0.657 (1.00) |
0.632 (1.00) |
0.563 (1.00) |
0.718 (1.00) |
15q gain | 39 (7%) | 530 |
0.846 (1.00) |
0.481 (1.00) |
0.0852 (1.00) |
0.755 (1.00) |
0.419 (1.00) |
0.114 (1.00) |
0.108 (1.00) |
0.735 (1.00) |
0.933 (1.00) |
0.316 (1.00) |
0.2 (1.00) |
0.526 (1.00) |
0.109 (1.00) |
16p gain | 58 (10%) | 511 |
0.00273 (1.00) |
0.00482 (1.00) |
0.402 (1.00) |
0.177 (1.00) |
0.089 (1.00) |
0.343 (1.00) |
0.0346 (1.00) |
0.651 (1.00) |
0.799 (1.00) |
0.123 (1.00) |
0.0808 (1.00) |
0.197 (1.00) |
0.0636 (1.00) |
16q gain | 30 (5%) | 539 |
0.00087 (0.86) |
0.0433 (1.00) |
0.162 (1.00) |
0.221 (1.00) |
0.688 (1.00) |
0.45 (1.00) |
0.0266 (1.00) |
1 (1.00) |
0.361 (1.00) |
0.00097 (0.954) |
0.105 (1.00) |
0.00249 (1.00) |
0.00061 (0.607) |
17p gain | 22 (4%) | 547 |
0.433 (1.00) |
0.112 (1.00) |
0.0561 (1.00) |
0.0522 (1.00) |
0.225 (1.00) |
0.5 (1.00) |
0.408 (1.00) |
0.212 (1.00) |
0.00336 (1.00) |
0.175 (1.00) |
0.837 (1.00) |
0.411 (1.00) |
0.67 (1.00) |
17q gain | 49 (9%) | 520 |
0.322 (1.00) |
0.0441 (1.00) |
0.86 (1.00) |
0.0487 (1.00) |
0.791 (1.00) |
0.448 (1.00) |
0.277 (1.00) |
0.937 (1.00) |
0.0229 (1.00) |
0.791 (1.00) |
0.849 (1.00) |
0.455 (1.00) |
0.93 (1.00) |
18p gain | 117 (21%) | 452 |
0.228 (1.00) |
0.133 (1.00) |
0.928 (1.00) |
0.403 (1.00) |
0.00512 (1.00) |
0.0222 (1.00) |
0.11 (1.00) |
0.812 (1.00) |
0.689 (1.00) |
0.352 (1.00) |
0.234 (1.00) |
0.348 (1.00) |
0.306 (1.00) |
18q gain | 71 (12%) | 498 |
0.648 (1.00) |
0.237 (1.00) |
0.285 (1.00) |
0.359 (1.00) |
0.0518 (1.00) |
0.513 (1.00) |
0.398 (1.00) |
0.486 (1.00) |
0.271 (1.00) |
0.108 (1.00) |
0.196 (1.00) |
0.055 (1.00) |
0.102 (1.00) |
21q gain | 109 (19%) | 460 |
0.29 (1.00) |
0.881 (1.00) |
0.961 (1.00) |
0.582 (1.00) |
0.00136 (1.00) |
0.456 (1.00) |
0.393 (1.00) |
0.337 (1.00) |
0.843 (1.00) |
0.0237 (1.00) |
0.0431 (1.00) |
0.0991 (1.00) |
0.763 (1.00) |
22q gain | 25 (4%) | 544 |
0.565 (1.00) |
0.585 (1.00) |
0.901 (1.00) |
0.634 (1.00) |
0.126 (1.00) |
0.366 (1.00) |
0.262 (1.00) |
0.464 (1.00) |
0.529 (1.00) |
0.0541 (1.00) |
0.0548 (1.00) |
0.0914 (1.00) |
0.042 (1.00) |
xq gain | 104 (18%) | 465 |
0.554 (1.00) |
0.728 (1.00) |
0.836 (1.00) |
0.211 (1.00) |
0.00236 (1.00) |
0.276 (1.00) |
0.791 (1.00) |
0.797 (1.00) |
0.822 (1.00) |
0.552 (1.00) |
0.364 (1.00) |
0.476 (1.00) |
0.541 (1.00) |
1q loss | 39 (7%) | 530 |
0.0955 (1.00) |
0.00814 (1.00) |
0.121 (1.00) |
0.704 (1.00) |
0.978 (1.00) |
0.352 (1.00) |
0.523 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.934 (1.00) |
0.24 (1.00) |
0.71 (1.00) |
2p loss | 53 (9%) | 516 |
0.932 (1.00) |
0.0417 (1.00) |
0.823 (1.00) |
0.441 (1.00) |
0.514 (1.00) |
0.482 (1.00) |
0.895 (1.00) |
0.64 (1.00) |
0.816 (1.00) |
0.721 (1.00) |
0.4 (1.00) |
0.601 (1.00) |
0.779 (1.00) |
2q loss | 59 (10%) | 510 |
0.968 (1.00) |
0.261 (1.00) |
0.761 (1.00) |
0.145 (1.00) |
0.779 (1.00) |
0.795 (1.00) |
0.945 (1.00) |
0.679 (1.00) |
0.928 (1.00) |
0.677 (1.00) |
0.35 (1.00) |
0.665 (1.00) |
0.245 (1.00) |
3q loss | 41 (7%) | 528 |
0.0206 (1.00) |
0.0467 (1.00) |
0.304 (1.00) |
0.0546 (1.00) |
0.00598 (1.00) |
1 (1.00) |
0.627 (1.00) |
0.252 (1.00) |
0.0768 (1.00) |
0.223 (1.00) |
0.00223 (1.00) |
0.288 (1.00) |
0.221 (1.00) |
4p loss | 312 (55%) | 257 |
0.464 (1.00) |
0.0276 (1.00) |
0.282 (1.00) |
0.521 (1.00) |
0.00436 (1.00) |
0.144 (1.00) |
0.131 (1.00) |
0.612 (1.00) |
0.436 (1.00) |
0.0667 (1.00) |
0.13 (1.00) |
0.0546 (1.00) |
0.559 (1.00) |
4q loss | 355 (62%) | 214 |
0.287 (1.00) |
0.114 (1.00) |
0.451 (1.00) |
0.646 (1.00) |
0.00155 (1.00) |
0.101 (1.00) |
0.016 (1.00) |
0.356 (1.00) |
0.351 (1.00) |
0.14 (1.00) |
0.113 (1.00) |
0.0272 (1.00) |
0.264 (1.00) |
5q loss | 218 (38%) | 351 |
0.0005 (0.499) |
0.0017 (1.00) |
0.775 (1.00) |
0.0136 (1.00) |
0.00083 (0.821) |
0.0458 (1.00) |
0.117 (1.00) |
0.0009 (0.888) |
0.145 (1.00) |
0.549 (1.00) |
0.0106 (1.00) |
0.301 (1.00) |
0.128 (1.00) |
6p loss | 164 (29%) | 405 |
0.962 (1.00) |
0.0189 (1.00) |
0.37 (1.00) |
0.47 (1.00) |
0.0594 (1.00) |
0.701 (1.00) |
0.896 (1.00) |
0.412 (1.00) |
0.0435 (1.00) |
0.48 (1.00) |
0.101 (1.00) |
0.318 (1.00) |
0.946 (1.00) |
6q loss | 239 (42%) | 330 |
0.963 (1.00) |
0.0771 (1.00) |
0.435 (1.00) |
0.0989 (1.00) |
0.0178 (1.00) |
0.625 (1.00) |
0.653 (1.00) |
0.0186 (1.00) |
0.021 (1.00) |
0.792 (1.00) |
0.572 (1.00) |
0.923 (1.00) |
0.88 (1.00) |
7p loss | 118 (21%) | 451 |
0.982 (1.00) |
0.356 (1.00) |
0.433 (1.00) |
0.71 (1.00) |
0.302 (1.00) |
0.599 (1.00) |
0.277 (1.00) |
0.621 (1.00) |
0.587 (1.00) |
0.536 (1.00) |
0.804 (1.00) |
0.779 (1.00) |
0.589 (1.00) |
7q loss | 81 (14%) | 488 |
0.333 (1.00) |
0.0863 (1.00) |
0.348 (1.00) |
0.301 (1.00) |
0.92 (1.00) |
0.821 (1.00) |
0.0697 (1.00) |
0.476 (1.00) |
0.311 (1.00) |
0.123 (1.00) |
0.821 (1.00) |
0.503 (1.00) |
0.416 (1.00) |
8p loss | 271 (48%) | 298 |
0.741 (1.00) |
0.892 (1.00) |
0.241 (1.00) |
0.946 (1.00) |
0.00357 (1.00) |
0.118 (1.00) |
0.301 (1.00) |
0.483 (1.00) |
0.705 (1.00) |
0.701 (1.00) |
0.0376 (1.00) |
0.81 (1.00) |
0.405 (1.00) |
8q loss | 88 (15%) | 481 |
0.00809 (1.00) |
0.00479 (1.00) |
0.522 (1.00) |
0.263 (1.00) |
0.00185 (1.00) |
0.0215 (1.00) |
0.233 (1.00) |
0.00094 (0.926) |
0.028 (1.00) |
0.662 (1.00) |
0.124 (1.00) |
0.76 (1.00) |
0.398 (1.00) |
9p loss | 255 (45%) | 314 |
0.00321 (1.00) |
0.00637 (1.00) |
0.512 (1.00) |
0.186 (1.00) |
0.00812 (1.00) |
0.791 (1.00) |
0.544 (1.00) |
0.898 (1.00) |
0.108 (1.00) |
0.0541 (1.00) |
0.256 (1.00) |
0.0638 (1.00) |
0.0378 (1.00) |
10p loss | 94 (17%) | 475 |
0.296 (1.00) |
1 (1.00) |
0.262 (1.00) |
0.369 (1.00) |
0.562 (1.00) |
0.602 (1.00) |
0.0604 (1.00) |
0.814 (1.00) |
0.638 (1.00) |
0.45 (1.00) |
0.812 (1.00) |
0.423 (1.00) |
0.252 (1.00) |
10q loss | 122 (21%) | 447 |
0.973 (1.00) |
0.86 (1.00) |
0.00395 (1.00) |
0.328 (1.00) |
0.0815 (1.00) |
0.365 (1.00) |
0.371 (1.00) |
0.662 (1.00) |
0.724 (1.00) |
0.766 (1.00) |
0.347 (1.00) |
0.87 (1.00) |
0.0592 (1.00) |
11p loss | 193 (34%) | 376 |
0.239 (1.00) |
0.0115 (1.00) |
0.546 (1.00) |
0.309 (1.00) |
0.124 (1.00) |
0.0982 (1.00) |
0.612 (1.00) |
0.0405 (1.00) |
0.112 (1.00) |
0.473 (1.00) |
0.143 (1.00) |
0.0772 (1.00) |
0.097 (1.00) |
11q loss | 144 (25%) | 425 |
0.356 (1.00) |
0.8 (1.00) |
0.179 (1.00) |
0.538 (1.00) |
0.0155 (1.00) |
0.462 (1.00) |
0.71 (1.00) |
0.271 (1.00) |
0.798 (1.00) |
0.514 (1.00) |
0.215 (1.00) |
0.102 (1.00) |
0.27 (1.00) |
12p loss | 78 (14%) | 491 |
0.003 (1.00) |
0.0108 (1.00) |
0.539 (1.00) |
0.0103 (1.00) |
0.00297 (1.00) |
0.783 (1.00) |
0.133 (1.00) |
0.313 (1.00) |
0.205 (1.00) |
0.00938 (1.00) |
0.00637 (1.00) |
0.00225 (1.00) |
0.0171 (1.00) |
12q loss | 104 (18%) | 465 |
0.0682 (1.00) |
0.0793 (1.00) |
0.759 (1.00) |
0.233 (1.00) |
0.0587 (1.00) |
0.268 (1.00) |
0.557 (1.00) |
0.244 (1.00) |
0.196 (1.00) |
0.0431 (1.00) |
0.0484 (1.00) |
0.111 (1.00) |
0.081 (1.00) |
13q loss | 303 (53%) | 266 |
0.0346 (1.00) |
0.00675 (1.00) |
0.791 (1.00) |
0.013 (1.00) |
0.00584 (1.00) |
0.0104 (1.00) |
0.395 (1.00) |
0.466 (1.00) |
0.418 (1.00) |
0.254 (1.00) |
0.504 (1.00) |
0.096 (1.00) |
0.168 (1.00) |
16p loss | 325 (57%) | 244 |
0.321 (1.00) |
0.827 (1.00) |
0.0375 (1.00) |
0.318 (1.00) |
0.124 (1.00) |
0.804 (1.00) |
0.201 (1.00) |
0.0522 (1.00) |
0.309 (1.00) |
0.0791 (1.00) |
0.0814 (1.00) |
0.112 (1.00) |
0.199 (1.00) |
16q loss | 404 (71%) | 165 |
0.567 (1.00) |
0.857 (1.00) |
0.00361 (1.00) |
0.0974 (1.00) |
0.00174 (1.00) |
0.948 (1.00) |
0.245 (1.00) |
0.204 (1.00) |
0.426 (1.00) |
0.0726 (1.00) |
0.156 (1.00) |
0.0479 (1.00) |
0.175 (1.00) |
17p loss | 471 (83%) | 98 |
0.277 (1.00) |
0.216 (1.00) |
0.18 (1.00) |
0.17 (1.00) |
0.482 (1.00) |
0.55 (1.00) |
0.24 (1.00) |
0.101 (1.00) |
0.058 (1.00) |
0.47 (1.00) |
0.476 (1.00) |
0.137 (1.00) |
0.419 (1.00) |
18p loss | 234 (41%) | 335 |
0.416 (1.00) |
0.894 (1.00) |
0.509 (1.00) |
0.0224 (1.00) |
0.235 (1.00) |
0.312 (1.00) |
0.00629 (1.00) |
0.0231 (1.00) |
0.113 (1.00) |
0.837 (1.00) |
0.541 (1.00) |
0.61 (1.00) |
0.776 (1.00) |
18q loss | 290 (51%) | 279 |
0.316 (1.00) |
0.878 (1.00) |
0.407 (1.00) |
0.978 (1.00) |
0.971 (1.00) |
0.812 (1.00) |
0.0478 (1.00) |
0.0113 (1.00) |
0.0898 (1.00) |
0.977 (1.00) |
0.779 (1.00) |
0.822 (1.00) |
0.787 (1.00) |
19p loss | 181 (32%) | 388 |
0.986 (1.00) |
0.44 (1.00) |
0.236 (1.00) |
0.0228 (1.00) |
0.017 (1.00) |
0.0208 (1.00) |
0.859 (1.00) |
0.745 (1.00) |
0.255 (1.00) |
0.8 (1.00) |
0.106 (1.00) |
0.861 (1.00) |
0.601 (1.00) |
19q loss | 172 (30%) | 397 |
0.823 (1.00) |
0.39 (1.00) |
0.284 (1.00) |
0.0153 (1.00) |
0.0386 (1.00) |
0.091 (1.00) |
0.617 (1.00) |
1 (1.00) |
0.483 (1.00) |
0.363 (1.00) |
0.0901 (1.00) |
0.418 (1.00) |
0.797 (1.00) |
20p loss | 49 (9%) | 520 |
0.498 (1.00) |
0.833 (1.00) |
0.221 (1.00) |
0.686 (1.00) |
0.128 (1.00) |
0.102 (1.00) |
0.2 (1.00) |
0.012 (1.00) |
0.00055 (0.548) |
0.0008 (0.793) |
0.173 (1.00) |
0.00631 (1.00) |
0.485 (1.00) |
20q loss | 31 (5%) | 538 |
0.115 (1.00) |
0.498 (1.00) |
0.0382 (1.00) |
0.505 (1.00) |
0.512 (1.00) |
0.0484 (1.00) |
0.097 (1.00) |
0.132 (1.00) |
0.0136 (1.00) |
0.136 (1.00) |
0.378 (1.00) |
0.0648 (1.00) |
0.202 (1.00) |
21q loss | 195 (34%) | 374 |
0.82 (1.00) |
0.0532 (1.00) |
0.386 (1.00) |
0.179 (1.00) |
0.397 (1.00) |
0.651 (1.00) |
0.438 (1.00) |
0.585 (1.00) |
0.408 (1.00) |
0.688 (1.00) |
0.729 (1.00) |
0.144 (1.00) |
0.422 (1.00) |
22q loss | 421 (74%) | 148 |
0.00517 (1.00) |
0.0929 (1.00) |
0.0359 (1.00) |
0.136 (1.00) |
0.00034 (0.342) |
0.0705 (1.00) |
0.00953 (1.00) |
0.191 (1.00) |
0.129 (1.00) |
0.0425 (1.00) |
0.609 (1.00) |
0.0496 (1.00) |
0.0237 (1.00) |
xq loss | 273 (48%) | 296 |
0.0588 (1.00) |
0.164 (1.00) |
0.289 (1.00) |
0.87 (1.00) |
0.00584 (1.00) |
0.387 (1.00) |
0.0453 (1.00) |
0.495 (1.00) |
0.898 (1.00) |
0.799 (1.00) |
0.402 (1.00) |
0.896 (1.00) |
0.159 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
1Q GAIN MUTATED | 58 | 57 | 103 |
1Q GAIN WILD-TYPE | 116 | 149 | 86 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
2P GAIN MUTATED | 93 | 44 | 36 |
2P GAIN WILD-TYPE | 122 | 172 | 90 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
2P GAIN MUTATED | 76 | 48 | 49 |
2P GAIN WILD-TYPE | 234 | 110 | 40 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
2P GAIN MUTATED | 35 | 47 | 96 |
2P GAIN WILD-TYPE | 139 | 159 | 93 |
P value = 0.00014 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
2P GAIN MUTATED | 31 | 12 | 45 |
2P GAIN WILD-TYPE | 69 | 55 | 46 |
P value = 5e-05 (Fisher's exact test), Q value = 0.051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
2Q GAIN MUTATED | 69 | 36 | 41 |
2Q GAIN WILD-TYPE | 241 | 122 | 48 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
2Q GAIN MUTATED | 29 | 40 | 81 |
2Q GAIN WILD-TYPE | 145 | 166 | 108 |
P value = 2e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
3Q GAIN MUTATED | 63 | 89 | 116 |
3Q GAIN WILD-TYPE | 111 | 117 | 73 |
P value = 0.00012 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
5P GAIN MUTATED | 38 | 78 | 80 |
5P GAIN WILD-TYPE | 136 | 128 | 109 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
6P GAIN MUTATED | 30 | 57 | 79 |
6P GAIN WILD-TYPE | 144 | 149 | 110 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
6Q GAIN MUTATED | 12 | 31 | 53 |
6Q GAIN WILD-TYPE | 162 | 175 | 136 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
7P GAIN MUTATED | 46 | 47 | 88 |
7P GAIN WILD-TYPE | 128 | 159 | 101 |
P value = 2e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
7Q GAIN MUTATED | 47 | 60 | 91 |
7Q GAIN WILD-TYPE | 127 | 146 | 98 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
10P GAIN MUTATED | 39 | 48 | 97 |
10P GAIN WILD-TYPE | 135 | 158 | 92 |
P value = 8e-05 (Fisher's exact test), Q value = 0.081
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
12P GAIN MUTATED | 119 | 75 | 49 |
12P GAIN WILD-TYPE | 96 | 141 | 77 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
12P GAIN MUTATED | 55 | 69 | 126 |
12P GAIN WILD-TYPE | 119 | 137 | 63 |
P value = 0.00023 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 105 | 71 | 165 | 106 |
12P GAIN MUTATED | 27 | 39 | 81 | 46 |
12P GAIN WILD-TYPE | 78 | 32 | 84 | 60 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
12Q GAIN MUTATED | 40 | 38 | 96 |
12Q GAIN WILD-TYPE | 134 | 168 | 93 |
P value = 2e-04 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
13Q GAIN MUTATED | 19 | 20 | 19 |
13Q GAIN WILD-TYPE | 291 | 138 | 70 |
P value = 0.00016 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
13Q GAIN MUTATED | 22 | 8 | 30 |
13Q GAIN WILD-TYPE | 152 | 198 | 159 |
P value = 6e-05 (Fisher's exact test), Q value = 0.061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
19P GAIN MUTATED | 34 | 56 | 77 |
19P GAIN WILD-TYPE | 140 | 150 | 112 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
19Q GAIN MUTATED | 33 | 49 | 78 |
19Q GAIN WILD-TYPE | 141 | 157 | 111 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
20P GAIN MUTATED | 64 | 85 | 133 |
20P GAIN WILD-TYPE | 110 | 121 | 56 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
20Q GAIN MUTATED | 143 | 95 | 76 |
20Q GAIN WILD-TYPE | 72 | 121 | 50 |
P value = 1e-04 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_10 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 85 | 57 | 58 | 82 | 34 | 75 | 34 | 36 | 52 | 42 |
20Q GAIN MUTATED | 35 | 30 | 35 | 40 | 24 | 41 | 26 | 21 | 42 | 19 |
20Q GAIN WILD-TYPE | 50 | 27 | 23 | 42 | 10 | 34 | 8 | 15 | 10 | 23 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
20Q GAIN MUTATED | 68 | 103 | 149 |
20Q GAIN WILD-TYPE | 106 | 103 | 40 |
P value = 0.00011 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 310 | 158 | 89 |
1P LOSS MUTATED | 30 | 9 | 21 |
1P LOSS WILD-TYPE | 280 | 149 | 68 |
P value = 8e-05 (Fisher's exact test), Q value = 0.081
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
3P LOSS MUTATED | 21 | 24 | 50 |
3P LOSS WILD-TYPE | 153 | 182 | 139 |
P value = 0.00017 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
5P LOSS MUTATED | 21 | 10 | 39 |
5P LOSS WILD-TYPE | 79 | 57 | 52 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
9Q LOSS MUTATED | 81 | 68 | 131 |
9Q LOSS WILD-TYPE | 93 | 138 | 58 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
14Q LOSS MUTATED | 52 | 61 | 95 |
14Q LOSS WILD-TYPE | 122 | 145 | 94 |
P value = 9e-05 (Fisher's exact test), Q value = 0.091
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 159 | 164 | 232 |
15Q LOSS MUTATED | 62 | 70 | 137 |
15Q LOSS WILD-TYPE | 97 | 94 | 95 |
P value = 1e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
15Q LOSS MUTATED | 66 | 78 | 132 |
15Q LOSS WILD-TYPE | 108 | 128 | 57 |
P value = 0.00013 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 195 | 157 |
17Q LOSS MUTATED | 46 | 145 | 107 |
17Q LOSS WILD-TYPE | 49 | 50 | 50 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtypes file = OV-TP.transferedmergedcluster.txt
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Number of patients = 569
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Number of significantly arm-level cnvs = 80
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Number of molecular subtypes = 13
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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.