This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 77 arm-level results and 8 molecular subtypes across 139 patients, 5 significant findings detected with Q value < 0.25.
-
8q gain cnv correlated to 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'METHLYATION_CNMF'.
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17p loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 77 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 significant findings detected.
|
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 8q gain | 0 (0%) | 82 |
6.79e-11 (4.16e-08) |
0.551 (1.00) |
0.00951 (1.00) |
0.283 (1.00) |
0.0128 (1.00) |
0.15 (1.00) |
0.0604 (1.00) |
0.193 (1.00) |
| 4q loss | 0 (0%) | 109 |
0.000104 (0.0635) |
0.000651 (0.394) |
0.0582 (1.00) |
0.48 (1.00) |
0.608 (1.00) |
0.7 (1.00) |
0.511 (1.00) |
0.915 (1.00) |
| 8p loss | 0 (0%) | 83 |
1.49e-09 (9.13e-07) |
0.0707 (1.00) |
0.539 (1.00) |
0.554 (1.00) |
0.675 (1.00) |
0.204 (1.00) |
0.664 (1.00) |
0.0865 (1.00) |
| 16q loss | 0 (0%) | 100 |
0.0305 (1.00) |
0.000205 (0.125) |
0.0075 (1.00) |
0.00816 (1.00) |
0.0156 (1.00) |
0.00407 (1.00) |
0.562 (1.00) |
0.00716 (1.00) |
| 17p loss | 0 (0%) | 86 |
0.000213 (0.13) |
0.0692 (1.00) |
0.0155 (1.00) |
0.732 (1.00) |
0.00492 (1.00) |
0.00427 (1.00) |
0.0294 (1.00) |
0.0275 (1.00) |
| 1p gain | 0 (0%) | 124 |
0.153 (1.00) |
0.869 (1.00) |
0.006 (1.00) |
0.0675 (1.00) |
0.323 (1.00) |
0.574 (1.00) |
0.634 (1.00) |
0.794 (1.00) |
| 1q gain | 0 (0%) | 68 |
0.000646 (0.392) |
0.00248 (1.00) |
0.132 (1.00) |
0.0302 (1.00) |
0.273 (1.00) |
0.688 (1.00) |
0.0613 (1.00) |
0.755 (1.00) |
| 2p gain | 0 (0%) | 130 |
0.171 (1.00) |
0.25 (1.00) |
0.147 (1.00) |
0.504 (1.00) |
0.389 (1.00) |
0.784 (1.00) |
0.547 (1.00) |
0.791 (1.00) |
| 2q gain | 0 (0%) | 132 |
0.439 (1.00) |
0.0677 (1.00) |
0.0673 (1.00) |
0.418 (1.00) |
0.459 (1.00) |
0.635 (1.00) |
0.606 (1.00) |
1 (1.00) |
| 3p gain | 0 (0%) | 132 |
0.496 (1.00) |
0.656 (1.00) |
0.592 (1.00) |
0.456 (1.00) |
0.271 (1.00) |
0.476 (1.00) |
0.574 (1.00) |
1 (1.00) |
| 3q gain | 0 (0%) | 132 |
0.496 (1.00) |
0.656 (1.00) |
0.592 (1.00) |
0.456 (1.00) |
0.271 (1.00) |
0.476 (1.00) |
0.574 (1.00) |
1 (1.00) |
| 4p gain | 0 (0%) | 134 |
0.63 (1.00) |
0.267 (1.00) |
0.0494 (1.00) |
0.206 (1.00) |
0.711 (1.00) |
1 (1.00) |
0.299 (1.00) |
1 (1.00) |
| 5p gain | 0 (0%) | 102 |
0.0209 (1.00) |
0.126 (1.00) |
0.384 (1.00) |
0.345 (1.00) |
0.674 (1.00) |
0.816 (1.00) |
0.874 (1.00) |
0.64 (1.00) |
| 5q gain | 0 (0%) | 113 |
0.113 (1.00) |
0.518 (1.00) |
0.388 (1.00) |
0.529 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.672 (1.00) |
0.765 (1.00) |
| 6p gain | 0 (0%) | 115 |
0.0277 (1.00) |
0.0206 (1.00) |
0.843 (1.00) |
0.505 (1.00) |
0.905 (1.00) |
0.848 (1.00) |
0.133 (1.00) |
0.898 (1.00) |
| 6q gain | 0 (0%) | 125 |
0.287 (1.00) |
0.232 (1.00) |
0.821 (1.00) |
0.499 (1.00) |
0.664 (1.00) |
0.655 (1.00) |
0.269 (1.00) |
0.852 (1.00) |
| 7p gain | 0 (0%) | 107 |
0.0969 (1.00) |
0.484 (1.00) |
0.499 (1.00) |
0.554 (1.00) |
0.107 (1.00) |
0.0879 (1.00) |
0.362 (1.00) |
0.283 (1.00) |
| 7q gain | 0 (0%) | 104 |
0.206 (1.00) |
0.011 (1.00) |
0.256 (1.00) |
0.321 (1.00) |
0.0276 (1.00) |
0.0627 (1.00) |
0.233 (1.00) |
0.264 (1.00) |
| 8p gain | 0 (0%) | 122 |
0.466 (1.00) |
0.83 (1.00) |
0.309 (1.00) |
0.0526 (1.00) |
0.854 (1.00) |
0.932 (1.00) |
0.886 (1.00) |
0.802 (1.00) |
| 9p gain | 0 (0%) | 135 |
0.555 (1.00) |
0.479 (1.00) |
0.0947 (1.00) |
0.406 (1.00) |
0.383 (1.00) |
0.221 (1.00) |
0.141 (1.00) |
0.256 (1.00) |
| 9q gain | 0 (0%) | 136 |
0.632 (1.00) |
0.793 (1.00) |
0.258 (1.00) |
0.787 (1.00) |
0.179 (1.00) |
0.344 (1.00) |
0.313 (1.00) |
0.51 (1.00) |
| 10p gain | 0 (0%) | 127 |
0.802 (1.00) |
0.248 (1.00) |
0.733 (1.00) |
0.147 (1.00) |
0.736 (1.00) |
0.623 (1.00) |
0.792 (1.00) |
0.47 (1.00) |
| 10q gain | 0 (0%) | 131 |
0.105 (1.00) |
0.0345 (1.00) |
0.398 (1.00) |
0.181 (1.00) |
0.199 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.769 (1.00) |
| 11p gain | 0 (0%) | 136 |
0.28 (1.00) |
0.793 (1.00) |
0.567 (1.00) |
0.586 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.453 (1.00) |
1 (1.00) |
| 11q gain | 0 (0%) | 136 |
0.499 (1.00) |
0.25 (1.00) |
0.308 (1.00) |
1 (1.00) |
1 (1.00) |
0.51 (1.00) |
||
| 12p gain | 0 (0%) | 135 |
0.455 (1.00) |
0.81 (1.00) |
0.1 (1.00) |
0.0421 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.816 (1.00) |
0.786 (1.00) |
| 12q gain | 0 (0%) | 133 |
0.24 (1.00) |
0.763 (1.00) |
0.188 (1.00) |
0.418 (1.00) |
0.58 (1.00) |
1 (1.00) |
0.412 (1.00) |
0.714 (1.00) |
| 13q gain | 0 (0%) | 133 |
0.004 (1.00) |
0.283 (1.00) |
0.311 (1.00) |
0.129 (1.00) |
0.144 (1.00) |
0.851 (1.00) |
0.191 (1.00) |
1 (1.00) |
| 14q gain | 0 (0%) | 133 |
0.326 (1.00) |
0.166 (1.00) |
0.534 (1.00) |
0.56 (1.00) |
0.871 (1.00) |
0.199 (1.00) |
0.765 (1.00) |
0.393 (1.00) |
| 15q gain | 0 (0%) | 131 |
0.818 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.632 (1.00) |
0.461 (1.00) |
0.13 (1.00) |
0.634 (1.00) |
0.265 (1.00) |
| 16p gain | 0 (0%) | 135 |
0.0368 (1.00) |
0.479 (1.00) |
0.333 (1.00) |
1 (1.00) |
0.625 (1.00) |
0.77 (1.00) |
0.557 (1.00) |
1 (1.00) |
| 17p gain | 0 (0%) | 133 |
0.768 (1.00) |
0.115 (1.00) |
0.979 (1.00) |
0.293 (1.00) |
0.848 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
| 17q gain | 0 (0%) | 111 |
0.0459 (1.00) |
0.583 (1.00) |
0.583 (1.00) |
0.38 (1.00) |
0.938 (1.00) |
0.592 (1.00) |
0.437 (1.00) |
0.251 (1.00) |
| 18p gain | 0 (0%) | 133 |
0.154 (1.00) |
0.212 (1.00) |
0.188 (1.00) |
0.129 (1.00) |
0.35 (1.00) |
0.712 (1.00) |
0.412 (1.00) |
0.852 (1.00) |
| 18q gain | 0 (0%) | 132 |
0.113 (1.00) |
0.0867 (1.00) |
0.101 (1.00) |
0.0698 (1.00) |
0.303 (1.00) |
0.871 (1.00) |
0.231 (1.00) |
0.751 (1.00) |
| 19p gain | 0 (0%) | 128 |
0.488 (1.00) |
0.00776 (1.00) |
0.179 (1.00) |
0.0847 (1.00) |
0.41 (1.00) |
0.389 (1.00) |
0.714 (1.00) |
0.603 (1.00) |
| 19q gain | 0 (0%) | 125 |
0.465 (1.00) |
0.00101 (0.61) |
0.0469 (1.00) |
0.0263 (1.00) |
0.263 (1.00) |
0.255 (1.00) |
0.36 (1.00) |
0.371 (1.00) |
| 20p gain | 0 (0%) | 112 |
0.142 (1.00) |
0.15 (1.00) |
0.0379 (1.00) |
0.38 (1.00) |
0.356 (1.00) |
0.705 (1.00) |
0.691 (1.00) |
0.782 (1.00) |
| 20q gain | 0 (0%) | 111 |
0.098 (1.00) |
0.285 (1.00) |
0.0828 (1.00) |
0.752 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.788 (1.00) |
| 21q gain | 0 (0%) | 133 |
1 (1.00) |
0.267 (1.00) |
0.393 (1.00) |
0.418 (1.00) |
0.72 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
| 22q gain | 0 (0%) | 130 |
0.627 (1.00) |
0.728 (1.00) |
0.134 (1.00) |
0.44 (1.00) |
0.389 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.621 (1.00) |
| Xq gain | 0 (0%) | 131 |
0.428 (1.00) |
0.0873 (1.00) |
0.0575 (1.00) |
0.051 (1.00) |
0.0325 (1.00) |
0.0224 (1.00) |
0.0434 (1.00) |
0.0431 (1.00) |
| 1p loss | 0 (0%) | 121 |
1 (1.00) |
0.0239 (1.00) |
0.062 (1.00) |
0.335 (1.00) |
0.253 (1.00) |
0.359 (1.00) |
0.64 (1.00) |
0.241 (1.00) |
| 1q loss | 0 (0%) | 134 |
0.855 (1.00) |
0.196 (1.00) |
0.14 (1.00) |
0.266 (1.00) |
0.458 (1.00) |
0.811 (1.00) |
0.184 (1.00) |
1 (1.00) |
| 2p loss | 0 (0%) | 135 |
0.257 (1.00) |
0.585 (1.00) |
0.0947 (1.00) |
0.524 (1.00) |
0.383 (1.00) |
0.77 (1.00) |
0.683 (1.00) |
1 (1.00) |
| 2q loss | 0 (0%) | 133 |
0.0494 (1.00) |
0.169 (1.00) |
0.0169 (1.00) |
0.56 (1.00) |
0.205 (1.00) |
0.528 (1.00) |
0.509 (1.00) |
0.815 (1.00) |
| 3p loss | 0 (0%) | 127 |
0.061 (1.00) |
0.0836 (1.00) |
0.000728 (0.441) |
0.00668 (1.00) |
0.0842 (1.00) |
0.306 (1.00) |
0.158 (1.00) |
0.0413 (1.00) |
| 3q loss | 0 (0%) | 133 |
0.154 (1.00) |
0.0519 (1.00) |
0.113 (1.00) |
0.129 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.412 (1.00) |
0.714 (1.00) |
| 4p loss | 0 (0%) | 124 |
0.00217 (1.00) |
0.0195 (1.00) |
0.00825 (1.00) |
0.42 (1.00) |
0.253 (1.00) |
0.793 (1.00) |
0.0723 (1.00) |
1 (1.00) |
| 5p loss | 0 (0%) | 136 |
0.499 (1.00) |
0.347 (1.00) |
0.4 (1.00) |
0.414 (1.00) |
0.478 (1.00) |
0.313 (1.00) |
0.223 (1.00) |
|
| 5q loss | 0 (0%) | 131 |
0.312 (1.00) |
0.0867 (1.00) |
0.896 (1.00) |
0.568 (1.00) |
0.465 (1.00) |
0.58 (1.00) |
0.326 (1.00) |
0.373 (1.00) |
| 6p loss | 0 (0%) | 134 |
0.439 (1.00) |
0.615 (1.00) |
0.309 (1.00) |
0.61 (1.00) |
0.154 (1.00) |
0.413 (1.00) |
0.509 (1.00) |
0.673 (1.00) |
| 6q loss | 0 (0%) | 108 |
0.0667 (1.00) |
0.923 (1.00) |
0.061 (1.00) |
0.436 (1.00) |
0.065 (1.00) |
0.83 (1.00) |
0.0204 (1.00) |
0.791 (1.00) |
| 7p loss | 0 (0%) | 133 |
0.877 (1.00) |
0.52 (1.00) |
0.493 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.308 (1.00) |
0.262 (1.00) |
0.101 (1.00) |
| 7q loss | 0 (0%) | 129 |
0.292 (1.00) |
1 (1.00) |
0.129 (1.00) |
0.565 (1.00) |
0.413 (1.00) |
0.516 (1.00) |
0.391 (1.00) |
0.0853 (1.00) |
| 8q loss | 0 (0%) | 129 |
0.00154 (0.922) |
0.304 (1.00) |
0.321 (1.00) |
0.218 (1.00) |
0.258 (1.00) |
0.273 (1.00) |
0.432 (1.00) |
0.726 (1.00) |
| 9p loss | 0 (0%) | 112 |
0.0274 (1.00) |
0.764 (1.00) |
0.278 (1.00) |
0.842 (1.00) |
0.984 (1.00) |
0.952 (1.00) |
0.923 (1.00) |
0.866 (1.00) |
| 9q loss | 0 (0%) | 113 |
0.00151 (0.904) |
0.384 (1.00) |
0.147 (1.00) |
0.919 (1.00) |
0.769 (1.00) |
0.771 (1.00) |
0.461 (1.00) |
0.777 (1.00) |
| 10p loss | 0 (0%) | 131 |
0.0103 (1.00) |
0.316 (1.00) |
0.0713 (1.00) |
0.204 (1.00) |
0.829 (1.00) |
1 (1.00) |
0.251 (1.00) |
1 (1.00) |
| 10q loss | 0 (0%) | 115 |
0.00105 (0.628) |
0.533 (1.00) |
0.164 (1.00) |
0.44 (1.00) |
0.437 (1.00) |
0.59 (1.00) |
0.183 (1.00) |
0.691 (1.00) |
| 11p loss | 0 (0%) | 129 |
0.0933 (1.00) |
0.101 (1.00) |
0.136 (1.00) |
0.235 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.222 (1.00) |
0.896 (1.00) |
| 11q loss | 0 (0%) | 126 |
0.406 (1.00) |
0.927 (1.00) |
0.082 (1.00) |
0.248 (1.00) |
0.368 (1.00) |
0.703 (1.00) |
0.103 (1.00) |
0.839 (1.00) |
| 12p loss | 0 (0%) | 124 |
0.0141 (1.00) |
0.119 (1.00) |
0.0219 (1.00) |
0.482 (1.00) |
0.805 (1.00) |
0.767 (1.00) |
0.26 (1.00) |
0.918 (1.00) |
| 12q loss | 0 (0%) | 135 |
0.257 (1.00) |
0.793 (1.00) |
0.251 (1.00) |
0.0716 (1.00) |
0.867 (1.00) |
0.77 (1.00) |
0.683 (1.00) |
1 (1.00) |
| 13q loss | 0 (0%) | 98 |
0.000847 (0.512) |
0.428 (1.00) |
0.00124 (0.743) |
0.191 (1.00) |
0.073 (1.00) |
0.548 (1.00) |
0.0514 (1.00) |
0.593 (1.00) |
| 14q loss | 0 (0%) | 105 |
0.00884 (1.00) |
0.358 (1.00) |
0.0411 (1.00) |
0.0064 (1.00) |
0.716 (1.00) |
0.808 (1.00) |
0.252 (1.00) |
0.919 (1.00) |
| 15q loss | 0 (0%) | 124 |
0.174 (1.00) |
0.0387 (1.00) |
0.728 (1.00) |
0.877 (1.00) |
0.323 (1.00) |
0.0604 (1.00) |
0.727 (1.00) |
0.141 (1.00) |
| 16p loss | 0 (0%) | 110 |
0.213 (1.00) |
0.0244 (1.00) |
0.00293 (1.00) |
0.000518 (0.315) |
0.000905 (0.546) |
0.00244 (1.00) |
0.222 (1.00) |
0.00533 (1.00) |
| 17q loss | 0 (0%) | 132 |
0.0227 (1.00) |
0.0867 (1.00) |
0.582 (1.00) |
0.875 (1.00) |
0.856 (1.00) |
0.388 (1.00) |
1 (1.00) |
0.588 (1.00) |
| 18p loss | 0 (0%) | 123 |
0.28 (1.00) |
0.00414 (1.00) |
0.736 (1.00) |
0.732 (1.00) |
0.577 (1.00) |
0.687 (1.00) |
0.695 (1.00) |
0.693 (1.00) |
| 18q loss | 0 (0%) | 120 |
0.0497 (1.00) |
0.00536 (1.00) |
0.117 (1.00) |
0.684 (1.00) |
0.398 (1.00) |
0.643 (1.00) |
0.404 (1.00) |
0.433 (1.00) |
| 19p loss | 0 (0%) | 130 |
0.627 (1.00) |
0.0524 (1.00) |
0.439 (1.00) |
0.586 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.715 (1.00) |
1 (1.00) |
| 19q loss | 0 (0%) | 135 |
1 (1.00) |
0.793 (1.00) |
0.467 (1.00) |
0.83 (1.00) |
0.179 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.51 (1.00) |
| 20p loss | 0 (0%) | 133 |
0.154 (1.00) |
0.52 (1.00) |
0.563 (1.00) |
0.56 (1.00) |
0.523 (1.00) |
0.242 (1.00) |
0.862 (1.00) |
0.202 (1.00) |
| 21q loss | 0 (0%) | 115 |
0.204 (1.00) |
0.912 (1.00) |
0.186 (1.00) |
0.121 (1.00) |
0.498 (1.00) |
0.217 (1.00) |
0.672 (1.00) |
0.343 (1.00) |
| 22q loss | 0 (0%) | 121 |
0.539 (1.00) |
0.362 (1.00) |
0.303 (1.00) |
0.944 (1.00) |
0.272 (1.00) |
0.437 (1.00) |
0.847 (1.00) |
0.672 (1.00) |
| Xq loss | 0 (0%) | 136 |
0.111 (1.00) |
0.793 (1.00) |
0.0388 (1.00) |
0.217 (1.00) |
0.652 (1.00) |
0.228 (1.00) |
0.313 (1.00) |
0.223 (1.00) |
P value = 6.79e-11 (Fisher's exact test), Q value = 4.2e-08
Table S1. Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| 8Q GAIN CNV | 33 | 8 | 16 |
| 8Q GAIN WILD-TYPE | 6 | 40 | 36 |
Figure S1. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000104 (Fisher's exact test), Q value = 0.064
Table S2. Gene #46: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| 4Q LOSS CNV | 6 | 3 | 21 |
| 4Q LOSS WILD-TYPE | 33 | 45 | 31 |
Figure S2. Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1.49e-09 (Fisher's exact test), Q value = 9.1e-07
Table S3. Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| 8P LOSS CNV | 24 | 3 | 29 |
| 8P LOSS WILD-TYPE | 15 | 45 | 23 |
Figure S3. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000205 (Fisher's exact test), Q value = 0.12
Table S4. Gene #67: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 32 | 35 | 56 |
| 16Q LOSS CNV | 4 | 19 | 11 |
| 16Q LOSS WILD-TYPE | 28 | 16 | 45 |
Figure S4. Get High-res Image Gene #67: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.000213 (Fisher's exact test), Q value = 0.13
Table S5. Gene #68: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| 17P LOSS CNV | 8 | 14 | 31 |
| 17P LOSS WILD-TYPE | 31 | 34 | 21 |
Figure S5. Get High-res Image Gene #68: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = LIHC-TP.transferedmergedcluster.txt
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Number of patients = 139
-
Number of significantly arm-level cnvs = 77
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Number of molecular subtypes = 8
-
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 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.
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.