(All_Metastatic cohort)
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 78 arm-level results and 8 molecular subtypes across 244 patients, 33 significant findings detected with Q value < 0.25.
-
1q gain cnv correlated to 'CN_CNMF'.
-
6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
7q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
8p gain cnv correlated to 'CN_CNMF'.
-
8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
11q gain cnv correlated to 'CN_CNMF'.
-
12p gain cnv correlated to 'CN_CNMF'.
-
13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
15q gain cnv correlated to 'CN_CNMF'.
-
19q gain cnv correlated to 'MRNASEQ_CNMF'.
-
20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
20q gain cnv correlated to 'CN_CNMF'.
-
21q gain cnv correlated to 'METHLYATION_CNMF'.
-
6q loss cnv correlated to 'CN_CNMF'.
-
9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
11q loss cnv correlated to 'CN_CNMF'.
-
14q loss cnv correlated to 'CN_CNMF'.
-
15q loss cnv correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
10q loss | 112 (46%) | 132 |
3.02e-10 (1.87e-07) |
9.78e-05 (0.0587) |
0.539 (1.00) |
0.192 (1.00) |
2.52e-07 (0.000154) |
0.000187 (0.112) |
0.516 (1.00) |
0.659 (1.00) |
10p loss | 103 (42%) | 141 |
2.19e-07 (0.000134) |
5.53e-05 (0.0333) |
0.44 (1.00) |
0.158 (1.00) |
3.92e-07 (0.000239) |
0.000441 (0.259) |
0.202 (1.00) |
0.323 (1.00) |
6p gain | 76 (31%) | 168 |
2.21e-10 (1.37e-07) |
1.87e-05 (0.0113) |
0.0894 (1.00) |
0.589 (1.00) |
0.17 (1.00) |
0.133 (1.00) |
0.012 (1.00) |
0.000527 (0.309) |
7p gain | 101 (41%) | 143 |
3.05e-10 (1.89e-07) |
0.109 (1.00) |
0.195 (1.00) |
0.298 (1.00) |
0.000225 (0.134) |
0.0343 (1.00) |
0.826 (1.00) |
0.431 (1.00) |
7q gain | 104 (43%) | 140 |
6.52e-12 (4.05e-09) |
0.236 (1.00) |
0.13 (1.00) |
0.167 (1.00) |
0.00014 (0.0839) |
0.0308 (1.00) |
0.319 (1.00) |
0.108 (1.00) |
8q gain | 78 (32%) | 166 |
1.6e-09 (9.87e-07) |
2.01e-05 (0.0121) |
0.603 (1.00) |
0.924 (1.00) |
0.000609 (0.356) |
0.00968 (1.00) |
0.424 (1.00) |
0.62 (1.00) |
13q gain | 39 (16%) | 205 |
7e-06 (0.00424) |
2.3e-05 (0.0138) |
0.399 (1.00) |
0.174 (1.00) |
0.0193 (1.00) |
0.0545 (1.00) |
0.394 (1.00) |
0.477 (1.00) |
20p gain | 70 (29%) | 174 |
6.08e-06 (0.00369) |
0.00195 (1.00) |
0.345 (1.00) |
0.904 (1.00) |
0.000225 (0.134) |
0.00204 (1.00) |
0.05 (1.00) |
0.167 (1.00) |
9p loss | 134 (55%) | 110 |
3.31e-08 (2.03e-05) |
1.93e-05 (0.0117) |
0.188 (1.00) |
0.131 (1.00) |
0.000721 (0.419) |
0.000627 (0.366) |
0.74 (1.00) |
0.532 (1.00) |
1q gain | 77 (32%) | 167 |
7.15e-09 (4.4e-06) |
0.00845 (1.00) |
0.366 (1.00) |
0.172 (1.00) |
0.0745 (1.00) |
0.625 (1.00) |
0.205 (1.00) |
0.0163 (1.00) |
8p gain | 49 (20%) | 195 |
1.16e-09 (7.16e-07) |
0.0118 (1.00) |
0.0562 (1.00) |
0.364 (1.00) |
0.0153 (1.00) |
0.0398 (1.00) |
0.733 (1.00) |
0.438 (1.00) |
11q gain | 15 (6%) | 229 |
0.000314 (0.186) |
0.413 (1.00) |
0.307 (1.00) |
0.72 (1.00) |
0.0213 (1.00) |
0.298 (1.00) |
0.776 (1.00) |
0.0625 (1.00) |
12p gain | 23 (9%) | 221 |
4.41e-07 (0.000268) |
0.147 (1.00) |
0.883 (1.00) |
0.928 (1.00) |
0.00711 (1.00) |
0.0841 (1.00) |
0.317 (1.00) |
0.441 (1.00) |
15q gain | 35 (14%) | 209 |
2e-06 (0.00122) |
0.42 (1.00) |
0.567 (1.00) |
0.912 (1.00) |
0.546 (1.00) |
0.243 (1.00) |
0.833 (1.00) |
0.0954 (1.00) |
19q gain | 20 (8%) | 224 |
0.00761 (1.00) |
0.0396 (1.00) |
0.415 (1.00) |
0.678 (1.00) |
0.000299 (0.177) |
0.0684 (1.00) |
0.727 (1.00) |
0.834 (1.00) |
20q gain | 89 (36%) | 155 |
1.66e-08 (1.02e-05) |
0.00199 (1.00) |
0.448 (1.00) |
0.802 (1.00) |
0.0026 (1.00) |
0.0664 (1.00) |
0.382 (1.00) |
0.42 (1.00) |
21q gain | 29 (12%) | 215 |
0.0384 (1.00) |
0.000261 (0.155) |
0.182 (1.00) |
0.402 (1.00) |
0.0461 (1.00) |
0.00908 (1.00) |
0.47 (1.00) |
0.956 (1.00) |
6q loss | 90 (37%) | 154 |
0.000111 (0.0664) |
0.000705 (0.41) |
0.354 (1.00) |
0.454 (1.00) |
0.00158 (0.91) |
0.0675 (1.00) |
0.622 (1.00) |
0.278 (1.00) |
11q loss | 64 (26%) | 180 |
0.000382 (0.225) |
0.0246 (1.00) |
0.916 (1.00) |
0.764 (1.00) |
0.0965 (1.00) |
0.00748 (1.00) |
0.68 (1.00) |
0.645 (1.00) |
14q loss | 54 (22%) | 190 |
6.92e-08 (4.24e-05) |
0.0508 (1.00) |
0.411 (1.00) |
0.276 (1.00) |
0.00397 (1.00) |
0.328 (1.00) |
0.522 (1.00) |
0.436 (1.00) |
15q loss | 15 (6%) | 229 |
0.00027 (0.16) |
0.0849 (1.00) |
0.651 (1.00) |
0.138 (1.00) |
0.632 (1.00) |
0.884 (1.00) |
0.208 (1.00) |
0.0568 (1.00) |
1p gain | 28 (11%) | 216 |
0.00929 (1.00) |
0.265 (1.00) |
0.148 (1.00) |
0.517 (1.00) |
0.0178 (1.00) |
0.139 (1.00) |
0.711 (1.00) |
0.223 (1.00) |
2p gain | 30 (12%) | 214 |
0.00321 (1.00) |
0.307 (1.00) |
0.0696 (1.00) |
0.391 (1.00) |
0.0113 (1.00) |
0.0173 (1.00) |
0.0831 (1.00) |
0.0226 (1.00) |
2q gain | 28 (11%) | 216 |
0.00246 (1.00) |
0.475 (1.00) |
0.0198 (1.00) |
0.384 (1.00) |
0.0035 (1.00) |
0.00468 (1.00) |
0.0083 (1.00) |
0.00169 (0.973) |
3p gain | 23 (9%) | 221 |
0.058 (1.00) |
0.0677 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.174 (1.00) |
0.271 (1.00) |
0.577 (1.00) |
0.758 (1.00) |
3q gain | 30 (12%) | 214 |
0.158 (1.00) |
0.164 (1.00) |
0.565 (1.00) |
0.594 (1.00) |
0.366 (1.00) |
0.497 (1.00) |
0.848 (1.00) |
0.67 (1.00) |
4p gain | 24 (10%) | 220 |
0.00178 (1.00) |
0.0523 (1.00) |
0.979 (1.00) |
0.469 (1.00) |
0.733 (1.00) |
0.526 (1.00) |
0.697 (1.00) |
0.586 (1.00) |
4q gain | 20 (8%) | 224 |
0.00101 (0.588) |
0.0357 (1.00) |
0.923 (1.00) |
0.945 (1.00) |
0.514 (1.00) |
0.535 (1.00) |
0.458 (1.00) |
0.614 (1.00) |
5p gain | 28 (11%) | 216 |
0.00966 (1.00) |
0.265 (1.00) |
0.758 (1.00) |
0.819 (1.00) |
0.849 (1.00) |
0.201 (1.00) |
0.249 (1.00) |
0.754 (1.00) |
5q gain | 14 (6%) | 230 |
0.0213 (1.00) |
0.389 (1.00) |
0.629 (1.00) |
0.404 (1.00) |
0.45 (1.00) |
0.167 (1.00) |
0.359 (1.00) |
0.193 (1.00) |
6q gain | 18 (7%) | 226 |
0.25 (1.00) |
0.0564 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.746 (1.00) |
0.245 (1.00) |
0.454 (1.00) |
0.698 (1.00) |
9p gain | 9 (4%) | 235 |
0.761 (1.00) |
0.144 (1.00) |
0.12 (1.00) |
0.435 (1.00) |
0.395 (1.00) |
0.805 (1.00) |
0.766 (1.00) |
0.459 (1.00) |
9q gain | 10 (4%) | 234 |
0.0983 (1.00) |
0.468 (1.00) |
0.236 (1.00) |
0.6 (1.00) |
0.784 (1.00) |
0.836 (1.00) |
0.766 (1.00) |
0.341 (1.00) |
11p gain | 17 (7%) | 227 |
0.00986 (1.00) |
0.901 (1.00) |
0.147 (1.00) |
0.474 (1.00) |
0.0172 (1.00) |
0.483 (1.00) |
0.541 (1.00) |
0.0761 (1.00) |
12q gain | 11 (5%) | 233 |
0.000691 (0.403) |
0.629 (1.00) |
0.847 (1.00) |
0.807 (1.00) |
0.046 (1.00) |
0.0261 (1.00) |
0.421 (1.00) |
0.231 (1.00) |
14q gain | 16 (7%) | 228 |
0.0348 (1.00) |
0.0614 (1.00) |
0.0431 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.484 (1.00) |
0.801 (1.00) |
16p gain | 16 (7%) | 228 |
0.000554 (0.324) |
0.00913 (1.00) |
0.452 (1.00) |
0.724 (1.00) |
0.0378 (1.00) |
0.125 (1.00) |
0.674 (1.00) |
0.512 (1.00) |
16q gain | 15 (6%) | 229 |
0.0154 (1.00) |
0.0462 (1.00) |
0.192 (1.00) |
0.527 (1.00) |
0.0373 (1.00) |
0.231 (1.00) |
0.743 (1.00) |
0.228 (1.00) |
17p gain | 16 (7%) | 228 |
0.0636 (1.00) |
0.207 (1.00) |
0.719 (1.00) |
0.79 (1.00) |
0.317 (1.00) |
0.465 (1.00) |
0.432 (1.00) |
0.475 (1.00) |
17q gain | 28 (11%) | 216 |
0.0214 (1.00) |
0.0441 (1.00) |
0.702 (1.00) |
0.293 (1.00) |
0.408 (1.00) |
0.193 (1.00) |
0.153 (1.00) |
0.542 (1.00) |
18p gain | 27 (11%) | 217 |
0.0511 (1.00) |
0.161 (1.00) |
0.91 (1.00) |
0.801 (1.00) |
0.0754 (1.00) |
0.0714 (1.00) |
0.356 (1.00) |
0.293 (1.00) |
18q gain | 16 (7%) | 228 |
0.0348 (1.00) |
0.219 (1.00) |
0.536 (1.00) |
0.308 (1.00) |
0.236 (1.00) |
0.0449 (1.00) |
1 (1.00) |
0.927 (1.00) |
19p gain | 16 (7%) | 228 |
0.00812 (1.00) |
0.028 (1.00) |
0.623 (1.00) |
0.204 (1.00) |
0.00382 (1.00) |
0.00207 (1.00) |
0.285 (1.00) |
0.801 (1.00) |
22q gain | 59 (24%) | 185 |
0.00209 (1.00) |
0.197 (1.00) |
0.803 (1.00) |
0.933 (1.00) |
0.527 (1.00) |
0.867 (1.00) |
0.717 (1.00) |
0.581 (1.00) |
Xq gain | 4 (2%) | 240 |
0.829 (1.00) |
0.835 (1.00) |
1 (1.00) |
0.507 (1.00) |
0.038 (1.00) |
0.118 (1.00) |
0.566 (1.00) |
0.422 (1.00) |
1p loss | 15 (6%) | 229 |
0.0605 (1.00) |
0.0256 (1.00) |
0.383 (1.00) |
0.416 (1.00) |
0.116 (1.00) |
0.359 (1.00) |
0.459 (1.00) |
0.927 (1.00) |
1q loss | 7 (3%) | 237 |
0.0637 (1.00) |
0.345 (1.00) |
0.545 (1.00) |
0.563 (1.00) |
0.179 (1.00) |
0.525 (1.00) |
0.7 (1.00) |
0.734 (1.00) |
2p loss | 18 (7%) | 226 |
0.00883 (1.00) |
0.106 (1.00) |
0.306 (1.00) |
0.0384 (1.00) |
0.533 (1.00) |
0.276 (1.00) |
0.00126 (0.73) |
0.0017 (0.976) |
2q loss | 19 (8%) | 225 |
0.0225 (1.00) |
0.0171 (1.00) |
0.208 (1.00) |
0.15 (1.00) |
0.376 (1.00) |
0.237 (1.00) |
0.0023 (1.00) |
0.00987 (1.00) |
3p loss | 22 (9%) | 222 |
0.0585 (1.00) |
0.0761 (1.00) |
0.382 (1.00) |
0.364 (1.00) |
0.0021 (1.00) |
0.027 (1.00) |
0.778 (1.00) |
0.479 (1.00) |
3q loss | 19 (8%) | 225 |
0.0735 (1.00) |
0.0606 (1.00) |
0.421 (1.00) |
0.209 (1.00) |
0.0675 (1.00) |
0.343 (1.00) |
0.954 (1.00) |
0.315 (1.00) |
4p loss | 30 (12%) | 214 |
0.322 (1.00) |
0.193 (1.00) |
0.342 (1.00) |
0.132 (1.00) |
0.00477 (1.00) |
0.221 (1.00) |
0.403 (1.00) |
0.482 (1.00) |
4q loss | 31 (13%) | 213 |
0.142 (1.00) |
0.0664 (1.00) |
0.308 (1.00) |
0.0206 (1.00) |
0.00645 (1.00) |
0.0285 (1.00) |
0.291 (1.00) |
0.143 (1.00) |
5p loss | 32 (13%) | 212 |
0.701 (1.00) |
0.262 (1.00) |
0.272 (1.00) |
0.333 (1.00) |
0.366 (1.00) |
0.283 (1.00) |
0.0912 (1.00) |
0.166 (1.00) |
5q loss | 46 (19%) | 198 |
0.515 (1.00) |
0.0436 (1.00) |
0.0689 (1.00) |
0.553 (1.00) |
0.47 (1.00) |
0.536 (1.00) |
0.578 (1.00) |
0.86 (1.00) |
6p loss | 28 (11%) | 216 |
0.00857 (1.00) |
0.215 (1.00) |
0.467 (1.00) |
0.347 (1.00) |
0.332 (1.00) |
0.251 (1.00) |
0.209 (1.00) |
0.11 (1.00) |
7p loss | 7 (3%) | 237 |
0.799 (1.00) |
0.0348 (1.00) |
0.664 (1.00) |
0.471 (1.00) |
0.716 (1.00) |
0.786 (1.00) |
0.618 (1.00) |
1 (1.00) |
7q loss | 6 (2%) | 238 |
0.676 (1.00) |
0.0911 (1.00) |
0.779 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.875 (1.00) |
1 (1.00) |
1 (1.00) |
8p loss | 28 (11%) | 216 |
0.0679 (1.00) |
0.111 (1.00) |
0.057 (1.00) |
0.486 (1.00) |
0.0594 (1.00) |
0.349 (1.00) |
0.202 (1.00) |
0.133 (1.00) |
8q loss | 5 (2%) | 239 |
1 (1.00) |
0.0705 (1.00) |
0.139 (1.00) |
0.515 (1.00) |
0.327 (1.00) |
0.285 (1.00) |
0.853 (1.00) |
1 (1.00) |
9q loss | 100 (41%) | 144 |
0.00566 (1.00) |
0.000441 (0.259) |
0.448 (1.00) |
0.364 (1.00) |
0.346 (1.00) |
0.794 (1.00) |
0.766 (1.00) |
0.464 (1.00) |
11p loss | 57 (23%) | 187 |
0.00219 (1.00) |
0.0018 (1.00) |
0.484 (1.00) |
0.27 (1.00) |
0.0799 (1.00) |
0.00919 (1.00) |
0.223 (1.00) |
0.417 (1.00) |
12p loss | 15 (6%) | 229 |
0.167 (1.00) |
0.00881 (1.00) |
0.5 (1.00) |
0.814 (1.00) |
0.277 (1.00) |
0.298 (1.00) |
0.776 (1.00) |
0.599 (1.00) |
12q loss | 24 (10%) | 220 |
0.00538 (1.00) |
0.00239 (1.00) |
0.839 (1.00) |
0.875 (1.00) |
0.546 (1.00) |
0.356 (1.00) |
0.886 (1.00) |
0.947 (1.00) |
13q loss | 36 (15%) | 208 |
0.322 (1.00) |
0.454 (1.00) |
0.172 (1.00) |
0.656 (1.00) |
0.389 (1.00) |
0.609 (1.00) |
0.121 (1.00) |
0.236 (1.00) |
16p loss | 22 (9%) | 222 |
0.0216 (1.00) |
0.00567 (1.00) |
0.956 (1.00) |
0.204 (1.00) |
0.313 (1.00) |
0.39 (1.00) |
0.109 (1.00) |
0.321 (1.00) |
16q loss | 46 (19%) | 198 |
0.00583 (1.00) |
0.0292 (1.00) |
0.571 (1.00) |
0.373 (1.00) |
0.0213 (1.00) |
0.0791 (1.00) |
0.134 (1.00) |
0.146 (1.00) |
17p loss | 50 (20%) | 194 |
0.619 (1.00) |
0.175 (1.00) |
0.493 (1.00) |
0.688 (1.00) |
0.0519 (1.00) |
0.978 (1.00) |
0.749 (1.00) |
0.398 (1.00) |
17q loss | 22 (9%) | 222 |
0.0805 (1.00) |
0.514 (1.00) |
0.387 (1.00) |
0.47 (1.00) |
0.0553 (1.00) |
0.562 (1.00) |
0.663 (1.00) |
1 (1.00) |
18p loss | 48 (20%) | 196 |
0.00385 (1.00) |
0.00436 (1.00) |
0.372 (1.00) |
0.415 (1.00) |
0.000886 (0.514) |
0.0473 (1.00) |
0.978 (1.00) |
0.815 (1.00) |
18q loss | 44 (18%) | 200 |
0.0128 (1.00) |
0.0182 (1.00) |
0.0502 (1.00) |
0.188 (1.00) |
0.0934 (1.00) |
0.55 (1.00) |
0.932 (1.00) |
0.666 (1.00) |
19p loss | 19 (8%) | 225 |
0.21 (1.00) |
0.54 (1.00) |
0.00578 (1.00) |
0.536 (1.00) |
0.149 (1.00) |
0.137 (1.00) |
0.485 (1.00) |
0.641 (1.00) |
19q loss | 19 (8%) | 225 |
0.22 (1.00) |
0.366 (1.00) |
0.654 (1.00) |
0.347 (1.00) |
0.376 (1.00) |
0.544 (1.00) |
0.685 (1.00) |
0.641 (1.00) |
20p loss | 12 (5%) | 232 |
0.528 (1.00) |
0.422 (1.00) |
0.153 (1.00) |
0.744 (1.00) |
0.615 (1.00) |
0.288 (1.00) |
0.0858 (1.00) |
0.459 (1.00) |
20q loss | 3 (1%) | 241 |
0.503 (1.00) |
0.187 (1.00) |
0.636 (1.00) |
0.303 (1.00) |
0.793 (1.00) |
1 (1.00) |
||
21q loss | 28 (11%) | 216 |
0.261 (1.00) |
0.265 (1.00) |
0.823 (1.00) |
0.634 (1.00) |
0.436 (1.00) |
0.751 (1.00) |
0.903 (1.00) |
0.552 (1.00) |
22q loss | 19 (8%) | 225 |
0.498 (1.00) |
0.205 (1.00) |
0.591 (1.00) |
0.428 (1.00) |
0.598 (1.00) |
0.517 (1.00) |
0.103 (1.00) |
0.583 (1.00) |
Xq loss | 10 (4%) | 234 |
0.277 (1.00) |
0.00329 (1.00) |
0.283 (1.00) |
0.188 (1.00) |
0.335 (1.00) |
0.0616 (1.00) |
0.243 (1.00) |
0.501 (1.00) |
P value = 7.15e-09 (Fisher's exact test), Q value = 4.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
1Q GAIN MUTATED | 46 | 16 | 15 |
1Q GAIN WILD-TYPE | 34 | 53 | 80 |
P value = 2.21e-10 (Fisher's exact test), Q value = 1.4e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
6P GAIN MUTATED | 48 | 12 | 16 |
6P GAIN WILD-TYPE | 32 | 57 | 79 |
P value = 1.87e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
6P GAIN MUTATED | 31 | 30 | 15 |
6P GAIN WILD-TYPE | 30 | 59 | 79 |
P value = 3.05e-10 (Fisher's exact test), Q value = 1.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
7P GAIN MUTATED | 35 | 48 | 18 |
7P GAIN WILD-TYPE | 45 | 21 | 77 |
P value = 0.000225 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
7P GAIN MUTATED | 47 | 19 | 35 |
7P GAIN WILD-TYPE | 32 | 51 | 57 |
P value = 6.52e-12 (Fisher's exact test), Q value = 4.1e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
7Q GAIN MUTATED | 30 | 53 | 21 |
7Q GAIN WILD-TYPE | 50 | 16 | 74 |
P value = 0.00014 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
7Q GAIN MUTATED | 49 | 21 | 34 |
7Q GAIN WILD-TYPE | 30 | 49 | 58 |
P value = 1.16e-09 (Fisher's exact test), Q value = 7.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
8P GAIN MUTATED | 17 | 29 | 3 |
8P GAIN WILD-TYPE | 63 | 40 | 92 |
P value = 1.6e-09 (Fisher's exact test), Q value = 9.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
8Q GAIN MUTATED | 35 | 34 | 9 |
8Q GAIN WILD-TYPE | 45 | 35 | 86 |
P value = 2.01e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
8Q GAIN MUTATED | 34 | 25 | 19 |
8Q GAIN WILD-TYPE | 27 | 64 | 75 |
P value = 0.000314 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
11Q GAIN MUTATED | 3 | 11 | 1 |
11Q GAIN WILD-TYPE | 77 | 58 | 94 |
P value = 4.41e-07 (Fisher's exact test), Q value = 0.00027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
12P GAIN MUTATED | 7 | 16 | 0 |
12P GAIN WILD-TYPE | 73 | 53 | 95 |
P value = 7e-06 (Fisher's exact test), Q value = 0.0042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
13Q GAIN MUTATED | 22 | 14 | 3 |
13Q GAIN WILD-TYPE | 58 | 55 | 92 |
P value = 2.3e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
13Q GAIN MUTATED | 19 | 16 | 4 |
13Q GAIN WILD-TYPE | 42 | 73 | 90 |
P value = 2e-06 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
15Q GAIN MUTATED | 7 | 23 | 5 |
15Q GAIN WILD-TYPE | 73 | 46 | 90 |
P value = 0.000299 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
19Q GAIN MUTATED | 13 | 0 | 6 |
19Q GAIN WILD-TYPE | 66 | 70 | 86 |
P value = 6.08e-06 (Fisher's exact test), Q value = 0.0037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
20P GAIN MUTATED | 26 | 32 | 12 |
20P GAIN WILD-TYPE | 54 | 37 | 83 |
P value = 0.000225 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
20P GAIN MUTATED | 36 | 11 | 23 |
20P GAIN WILD-TYPE | 43 | 59 | 69 |
P value = 1.66e-08 (Fisher's exact test), Q value = 1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
20Q GAIN MUTATED | 36 | 39 | 14 |
20Q GAIN WILD-TYPE | 44 | 30 | 81 |
P value = 0.000261 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
21Q GAIN MUTATED | 15 | 11 | 3 |
21Q GAIN WILD-TYPE | 46 | 78 | 91 |
P value = 0.000111 (Fisher's exact test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
6Q LOSS MUTATED | 35 | 35 | 20 |
6Q LOSS WILD-TYPE | 45 | 34 | 75 |
P value = 3.31e-08 (Fisher's exact test), Q value = 2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
9P LOSS MUTATED | 56 | 48 | 30 |
9P LOSS WILD-TYPE | 24 | 21 | 65 |
P value = 1.93e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
9P LOSS MUTATED | 40 | 60 | 34 |
9P LOSS WILD-TYPE | 21 | 29 | 60 |
P value = 2.19e-07 (Fisher's exact test), Q value = 0.00013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
10P LOSS MUTATED | 38 | 44 | 21 |
10P LOSS WILD-TYPE | 42 | 25 | 74 |
P value = 5.53e-05 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
10P LOSS MUTATED | 36 | 43 | 24 |
10P LOSS WILD-TYPE | 25 | 46 | 70 |
P value = 3.92e-07 (Fisher's exact test), Q value = 0.00024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
10P LOSS MUTATED | 51 | 15 | 36 |
10P LOSS WILD-TYPE | 28 | 55 | 56 |
P value = 3.02e-10 (Fisher's exact test), Q value = 1.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
10Q LOSS MUTATED | 41 | 50 | 21 |
10Q LOSS WILD-TYPE | 39 | 19 | 74 |
P value = 9.78e-05 (Fisher's exact test), Q value = 0.059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 61 | 89 | 94 |
10Q LOSS MUTATED | 35 | 50 | 27 |
10Q LOSS WILD-TYPE | 26 | 39 | 67 |
P value = 2.52e-07 (Fisher's exact test), Q value = 0.00015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 70 | 92 |
10Q LOSS MUTATED | 55 | 18 | 39 |
10Q LOSS WILD-TYPE | 24 | 52 | 53 |
P value = 0.000187 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 57 | 122 |
10Q LOSS MUTATED | 26 | 40 | 46 |
10Q LOSS WILD-TYPE | 36 | 17 | 76 |
P value = 0.000382 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
11Q LOSS MUTATED | 33 | 17 | 14 |
11Q LOSS WILD-TYPE | 47 | 52 | 81 |
P value = 6.92e-08 (Fisher's exact test), Q value = 4.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
14Q LOSS MUTATED | 18 | 30 | 6 |
14Q LOSS WILD-TYPE | 62 | 39 | 89 |
P value = 0.00027 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 69 | 95 |
15Q LOSS MUTATED | 12 | 2 | 1 |
15Q LOSS WILD-TYPE | 68 | 67 | 94 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = SKCM-All_Metastatic.transferedmergedcluster.txt
-
Number of patients = 244
-
Number of significantly arm-level cnvs = 78
-
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.