This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 79 arm-level results and 8 molecular subtypes across 352 patients, 62 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3p gain cnv correlated to 'METHLYATION_CNMF'.
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3q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9p gain cnv correlated to 'CN_CNMF'.
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11p gain cnv correlated to 'CN_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
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14q gain cnv correlated to 'CN_CNMF'.
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16p gain cnv correlated to 'METHLYATION_CNMF'.
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17p gain cnv correlated to 'CN_CNMF'.
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18p gain cnv correlated to 'CN_CNMF'.
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18q gain cnv correlated to 'METHLYATION_CNMF'.
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20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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22q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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4q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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10p loss cnv correlated to 'CN_CNMF'.
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10q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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11p loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'METHLYATION_CNMF'.
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18q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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21q loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 62 significant findings detected.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Chi-square test | Chi-square 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 | |
4p loss | 0 (0%) | 270 |
5.83e-12 (3.66e-09) |
2.98e-08 (1.83e-05) |
0.135 (1.00) |
0.0374 (1.00) |
0.00227 (1.00) |
0.000123 (0.0709) |
5.82e-05 (0.0344) |
0.0591 (1.00) |
12p gain | 0 (0%) | 287 |
1.64e-07 (1e-04) |
1.89e-05 (0.0113) |
0.663 (1.00) |
0.725 (1.00) |
0.00399 (1.00) |
0.000612 (0.346) |
9.95e-05 (0.0581) |
0.00889 (1.00) |
5q loss | 0 (0%) | 289 |
2.15e-14 (1.36e-11) |
7.27e-10 (4.54e-07) |
0.434 (1.00) |
0.528 (1.00) |
0.00575 (1.00) |
4.53e-05 (0.0269) |
0.0369 (1.00) |
1 (1.00) |
13q loss | 0 (0%) | 280 |
2.38e-07 (0.000145) |
9.48e-10 (5.9e-07) |
0.315 (1.00) |
0.439 (1.00) |
0.0286 (1.00) |
2.38e-05 (0.0142) |
0.00756 (1.00) |
0.203 (1.00) |
16q loss | 0 (0%) | 323 |
0.00704 (1.00) |
4.19e-05 (0.025) |
0.0347 (1.00) |
0.00546 (1.00) |
4.72e-07 (0.000287) |
1.34e-08 (8.24e-06) |
0.000498 (0.282) |
0.00763 (1.00) |
2p gain | 0 (0%) | 321 |
9.19e-05 (0.0537) |
0.000103 (0.0598) |
0.368 (1.00) |
0.802 (1.00) |
0.0146 (1.00) |
0.0236 (1.00) |
0.471 (1.00) |
0.0838 (1.00) |
3q gain | 0 (0%) | 240 |
0.000825 (0.464) |
4.27e-05 (0.0254) |
0.228 (1.00) |
0.52 (1.00) |
0.0178 (1.00) |
0.00384 (1.00) |
0.000112 (0.0649) |
0.387 (1.00) |
7p gain | 0 (0%) | 274 |
2.95e-05 (0.0176) |
0.000406 (0.231) |
0.623 (1.00) |
0.64 (1.00) |
0.817 (1.00) |
0.939 (1.00) |
0.758 (1.00) |
0.364 (1.00) |
7q gain | 0 (0%) | 304 |
7.08e-10 (4.43e-07) |
1.01e-06 (0.000612) |
0.488 (1.00) |
0.92 (1.00) |
0.275 (1.00) |
0.112 (1.00) |
0.16 (1.00) |
0.762 (1.00) |
8q gain | 0 (0%) | 207 |
4.97e-09 (3.08e-06) |
0.000341 (0.195) |
0.52 (1.00) |
0.219 (1.00) |
0.52 (1.00) |
0.519 (1.00) |
0.426 (1.00) |
0.0661 (1.00) |
20p gain | 0 (0%) | 284 |
7.5e-06 (0.00451) |
7.9e-05 (0.0466) |
0.062 (1.00) |
0.175 (1.00) |
0.617 (1.00) |
0.365 (1.00) |
0.219 (1.00) |
0.263 (1.00) |
20q gain | 0 (0%) | 280 |
8.46e-07 (0.000515) |
0.000112 (0.0651) |
0.924 (1.00) |
0.884 (1.00) |
0.495 (1.00) |
0.726 (1.00) |
0.564 (1.00) |
0.179 (1.00) |
22q gain | 0 (0%) | 310 |
0.00016 (0.0919) |
8.21e-05 (0.0484) |
0.641 (1.00) |
0.405 (1.00) |
0.0775 (1.00) |
0.019 (1.00) |
0.397 (1.00) |
0.95 (1.00) |
1p loss | 0 (0%) | 336 |
4.35e-10 (2.72e-07) |
9.7e-07 (0.000589) |
0.114 (1.00) |
0.123 (1.00) |
0.0129 (1.00) |
0.0156 (1.00) |
0.0183 (1.00) |
0.517 (1.00) |
3p loss | 0 (0%) | 219 |
8.24e-13 (5.18e-10) |
3.16e-07 (0.000193) |
0.304 (1.00) |
0.766 (1.00) |
0.365 (1.00) |
0.176 (1.00) |
0.138 (1.00) |
0.765 (1.00) |
4q loss | 0 (0%) | 297 |
5.73e-09 (3.54e-06) |
3.38e-06 (0.00204) |
0.293 (1.00) |
0.147 (1.00) |
0.0148 (1.00) |
0.00277 (1.00) |
0.00128 (0.717) |
0.0498 (1.00) |
8p loss | 0 (0%) | 274 |
1.8e-06 (0.00109) |
6.66e-06 (0.00401) |
0.891 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.485 (1.00) |
0.106 (1.00) |
0.477 (1.00) |
9p loss | 0 (0%) | 259 |
1.66e-09 (1.03e-06) |
2.25e-08 (1.38e-05) |
0.484 (1.00) |
0.847 (1.00) |
0.311 (1.00) |
0.0696 (1.00) |
0.00718 (1.00) |
0.241 (1.00) |
10q loss | 0 (0%) | 323 |
8.12e-08 (4.98e-05) |
0.00667 (1.00) |
0.48 (1.00) |
0.742 (1.00) |
0.0334 (1.00) |
0.00123 (0.692) |
4.58e-05 (0.0271) |
0.514 (1.00) |
11q loss | 0 (0%) | 283 |
2.19e-13 (1.38e-10) |
7.28e-05 (0.0431) |
0.864 (1.00) |
0.594 (1.00) |
0.0115 (1.00) |
0.051 (1.00) |
0.0294 (1.00) |
0.792 (1.00) |
18q loss | 0 (0%) | 259 |
1.92e-09 (1.19e-06) |
6.73e-08 (4.13e-05) |
0.386 (1.00) |
0.197 (1.00) |
0.0192 (1.00) |
0.512 (1.00) |
0.0111 (1.00) |
0.211 (1.00) |
1q gain | 0 (0%) | 310 |
0.000122 (0.0707) |
0.00187 (1.00) |
0.49 (1.00) |
0.504 (1.00) |
0.0129 (1.00) |
0.00499 (1.00) |
0.0369 (1.00) |
0.391 (1.00) |
3p gain | 0 (0%) | 323 |
0.489 (1.00) |
8.26e-05 (0.0486) |
0.0468 (1.00) |
0.583 (1.00) |
0.00323 (1.00) |
0.00326 (1.00) |
0.000463 (0.263) |
0.113 (1.00) |
5p gain | 0 (0%) | 264 |
5.64e-09 (3.49e-06) |
0.0326 (1.00) |
0.666 (1.00) |
0.43 (1.00) |
0.579 (1.00) |
0.409 (1.00) |
1 (1.00) |
0.506 (1.00) |
9p gain | 0 (0%) | 309 |
0.00011 (0.064) |
0.0595 (1.00) |
0.421 (1.00) |
0.303 (1.00) |
0.288 (1.00) |
0.643 (1.00) |
0.372 (1.00) |
0.744 (1.00) |
11p gain | 0 (0%) | 335 |
0.000202 (0.116) |
0.67 (1.00) |
0.833 (1.00) |
0.399 (1.00) |
0.754 (1.00) |
0.845 (1.00) |
0.819 (1.00) |
0.308 (1.00) |
14q gain | 0 (0%) | 294 |
0.000131 (0.0756) |
0.0159 (1.00) |
0.445 (1.00) |
0.0667 (1.00) |
0.0271 (1.00) |
0.027 (1.00) |
0.0529 (1.00) |
0.0446 (1.00) |
16p gain | 0 (0%) | 330 |
0.00785 (1.00) |
8.45e-05 (0.0496) |
0.0259 (1.00) |
0.362 (1.00) |
0.241 (1.00) |
0.958 (1.00) |
0.781 (1.00) |
0.491 (1.00) |
17p gain | 0 (0%) | 332 |
0.000367 (0.209) |
0.0824 (1.00) |
0.544 (1.00) |
0.468 (1.00) |
0.18 (1.00) |
0.561 (1.00) |
0.181 (1.00) |
0.131 (1.00) |
18p gain | 0 (0%) | 297 |
0.000122 (0.0707) |
0.0581 (1.00) |
0.318 (1.00) |
0.385 (1.00) |
0.114 (1.00) |
0.0049 (1.00) |
0.43 (1.00) |
0.889 (1.00) |
18q gain | 0 (0%) | 332 |
0.0059 (1.00) |
0.000177 (0.102) |
0.531 (1.00) |
0.399 (1.00) |
0.0192 (1.00) |
0.0171 (1.00) |
0.0019 (1.00) |
1 (1.00) |
10p loss | 0 (0%) | 300 |
8.93e-05 (0.0523) |
0.0656 (1.00) |
0.27 (1.00) |
0.594 (1.00) |
0.937 (1.00) |
0.805 (1.00) |
0.571 (1.00) |
0.362 (1.00) |
11p loss | 0 (0%) | 304 |
0.000257 (0.147) |
0.0444 (1.00) |
0.11 (1.00) |
0.699 (1.00) |
0.00173 (0.969) |
0.00598 (1.00) |
0.0297 (1.00) |
0.694 (1.00) |
17p loss | 0 (0%) | 303 |
0.0211 (1.00) |
1.27e-05 (0.00765) |
0.748 (1.00) |
0.567 (1.00) |
0.637 (1.00) |
0.0218 (1.00) |
0.178 (1.00) |
0.699 (1.00) |
21q loss | 0 (0%) | 289 |
2.16e-06 (0.0013) |
0.0109 (1.00) |
0.942 (1.00) |
0.204 (1.00) |
0.892 (1.00) |
0.512 (1.00) |
0.68 (1.00) |
0.722 (1.00) |
1p gain | 0 (0%) | 341 |
0.379 (1.00) |
0.694 (1.00) |
0.955 (1.00) |
0.64 (1.00) |
0.179 (1.00) |
0.34 (1.00) |
0.86 (1.00) |
0.38 (1.00) |
2q gain | 0 (0%) | 331 |
0.00527 (1.00) |
0.00187 (1.00) |
0.509 (1.00) |
0.928 (1.00) |
0.0781 (1.00) |
0.127 (1.00) |
0.567 (1.00) |
0.206 (1.00) |
4p gain | 0 (0%) | 339 |
0.0153 (1.00) |
0.064 (1.00) |
0.231 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.228 (1.00) |
0.0443 (1.00) |
0.217 (1.00) |
4q gain | 0 (0%) | 343 |
0.0661 (1.00) |
0.103 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.63 (1.00) |
0.917 (1.00) |
0.805 (1.00) |
5q gain | 0 (0%) | 324 |
0.0432 (1.00) |
0.693 (1.00) |
1 (1.00) |
1 (1.00) |
0.819 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.424 (1.00) |
6p gain | 0 (0%) | 326 |
0.0172 (1.00) |
0.0466 (1.00) |
0.215 (1.00) |
0.547 (1.00) |
0.902 (1.00) |
0.871 (1.00) |
0.871 (1.00) |
0.0605 (1.00) |
6q gain | 0 (0%) | 333 |
0.412 (1.00) |
0.0821 (1.00) |
0.677 (1.00) |
0.764 (1.00) |
0.727 (1.00) |
0.378 (1.00) |
1 (1.00) |
0.19 (1.00) |
8p gain | 0 (0%) | 299 |
0.00796 (1.00) |
0.002 (1.00) |
0.728 (1.00) |
0.114 (1.00) |
0.381 (1.00) |
0.313 (1.00) |
0.146 (1.00) |
0.273 (1.00) |
9q gain | 0 (0%) | 294 |
0.000686 (0.387) |
0.0312 (1.00) |
0.239 (1.00) |
0.109 (1.00) |
0.215 (1.00) |
0.131 (1.00) |
0.369 (1.00) |
0.516 (1.00) |
10p gain | 0 (0%) | 340 |
0.539 (1.00) |
0.00278 (1.00) |
0.798 (1.00) |
0.752 (1.00) |
0.055 (1.00) |
0.0689 (1.00) |
0.129 (1.00) |
0.238 (1.00) |
10q gain | 0 (0%) | 346 |
0.194 (1.00) |
0.338 (1.00) |
0.57 (1.00) |
0.256 (1.00) |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
1 (1.00) |
11q gain | 0 (0%) | 335 |
0.0297 (1.00) |
0.494 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.284 (1.00) |
0.952 (1.00) |
0.533 (1.00) |
12q gain | 0 (0%) | 326 |
0.194 (1.00) |
0.0042 (1.00) |
0.173 (1.00) |
0.695 (1.00) |
0.0645 (1.00) |
0.00174 (0.973) |
0.0172 (1.00) |
0.0962 (1.00) |
13q gain | 0 (0%) | 334 |
0.101 (1.00) |
0.0352 (1.00) |
0.35 (1.00) |
0.645 (1.00) |
0.603 (1.00) |
0.904 (1.00) |
0.705 (1.00) |
0.308 (1.00) |
15q gain | 0 (0%) | 340 |
0.489 (1.00) |
0.272 (1.00) |
0.542 (1.00) |
0.444 (1.00) |
0.872 (1.00) |
0.255 (1.00) |
0.814 (1.00) |
0.29 (1.00) |
16q gain | 0 (0%) | 322 |
0.0018 (1.00) |
0.00423 (1.00) |
0.783 (1.00) |
0.659 (1.00) |
0.0266 (1.00) |
0.437 (1.00) |
0.884 (1.00) |
0.105 (1.00) |
17q gain | 0 (0%) | 327 |
0.000625 (0.353) |
0.0963 (1.00) |
0.0893 (1.00) |
0.514 (1.00) |
0.19 (1.00) |
0.0519 (1.00) |
0.256 (1.00) |
0.456 (1.00) |
19p gain | 0 (0%) | 340 |
0.332 (1.00) |
0.00495 (1.00) |
0.0945 (1.00) |
0.0843 (1.00) |
0.389 (1.00) |
0.0231 (1.00) |
0.193 (1.00) |
0.238 (1.00) |
19q gain | 0 (0%) | 331 |
0.187 (1.00) |
0.0581 (1.00) |
0.788 (1.00) |
0.402 (1.00) |
0.158 (1.00) |
0.319 (1.00) |
0.115 (1.00) |
0.825 (1.00) |
21q gain | 0 (0%) | 343 |
0.182 (1.00) |
0.773 (1.00) |
1 (1.00) |
1 (1.00) |
0.0193 (1.00) |
0.0552 (1.00) |
0.032 (1.00) |
1 (1.00) |
Xq gain | 0 (0%) | 329 |
0.00145 (0.813) |
0.0888 (1.00) |
0.237 (1.00) |
0.177 (1.00) |
0.503 (1.00) |
0.913 (1.00) |
0.768 (1.00) |
0.918 (1.00) |
2p loss | 0 (0%) | 346 |
0.969 (1.00) |
0.0441 (1.00) |
0.684 (1.00) |
1 (1.00) |
0.115 (1.00) |
0.0743 (1.00) |
0.026 (1.00) |
0.145 (1.00) |
2q loss | 0 (0%) | 342 |
0.394 (1.00) |
0.0939 (1.00) |
0.229 (1.00) |
0.449 (1.00) |
0.0147 (1.00) |
0.014 (1.00) |
0.0837 (1.00) |
0.0243 (1.00) |
3q loss | 0 (0%) | 330 |
0.0168 (1.00) |
0.115 (1.00) |
0.331 (1.00) |
0.428 (1.00) |
0.881 (1.00) |
0.959 (1.00) |
0.286 (1.00) |
0.831 (1.00) |
5p loss | 0 (0%) | 344 |
0.0314 (1.00) |
0.00598 (1.00) |
0.611 (1.00) |
0.821 (1.00) |
0.0763 (1.00) |
0.0888 (1.00) |
0.0122 (1.00) |
0.78 (1.00) |
6p loss | 0 (0%) | 333 |
0.097 (1.00) |
0.0127 (1.00) |
0.00421 (1.00) |
0.169 (1.00) |
0.0317 (1.00) |
0.111 (1.00) |
0.0081 (1.00) |
0.266 (1.00) |
6q loss | 0 (0%) | 331 |
0.199 (1.00) |
0.0701 (1.00) |
0.0106 (1.00) |
0.0725 (1.00) |
0.379 (1.00) |
0.392 (1.00) |
0.0545 (1.00) |
0.308 (1.00) |
7p loss | 0 (0%) | 347 |
0.982 (1.00) |
0.388 (1.00) |
0.391 (1.00) |
0.452 (1.00) |
0.23 (1.00) |
1 (1.00) |
||
7q loss | 0 (0%) | 344 |
0.155 (1.00) |
0.371 (1.00) |
0.752 (1.00) |
0.757 (1.00) |
0.315 (1.00) |
0.906 (1.00) |
0.164 (1.00) |
0.349 (1.00) |
8q loss | 0 (0%) | 345 |
0.322 (1.00) |
0.0604 (1.00) |
0.845 (1.00) |
0.658 (1.00) |
1 (1.00) |
0.496 (1.00) |
0.308 (1.00) |
0.769 (1.00) |
9q loss | 0 (0%) | 321 |
0.00345 (1.00) |
0.0679 (1.00) |
0.9 (1.00) |
0.477 (1.00) |
0.829 (1.00) |
0.855 (1.00) |
0.748 (1.00) |
0.123 (1.00) |
12p loss | 0 (0%) | 339 |
0.0414 (1.00) |
0.139 (1.00) |
0.169 (1.00) |
0.21 (1.00) |
0.468 (1.00) |
0.459 (1.00) |
0.56 (1.00) |
0.261 (1.00) |
12q loss | 0 (0%) | 344 |
0.315 (1.00) |
0.073 (1.00) |
0.766 (1.00) |
0.671 (1.00) |
0.201 (1.00) |
0.308 (1.00) |
0.605 (1.00) |
0.121 (1.00) |
14q loss | 0 (0%) | 334 |
0.409 (1.00) |
0.0415 (1.00) |
0.141 (1.00) |
0.64 (1.00) |
0.0108 (1.00) |
0.0154 (1.00) |
0.00969 (1.00) |
0.327 (1.00) |
15q loss | 0 (0%) | 325 |
0.00387 (1.00) |
0.173 (1.00) |
0.399 (1.00) |
0.318 (1.00) |
0.457 (1.00) |
0.246 (1.00) |
0.272 (1.00) |
0.202 (1.00) |
16p loss | 0 (0%) | 340 |
0.0706 (1.00) |
0.0294 (1.00) |
0.109 (1.00) |
0.294 (1.00) |
0.0414 (1.00) |
0.014 (1.00) |
0.0915 (1.00) |
0.153 (1.00) |
17q loss | 0 (0%) | 346 |
0.0446 (1.00) |
0.0232 (1.00) |
0.438 (1.00) |
0.402 (1.00) |
0.456 (1.00) |
0.861 (1.00) |
0.452 (1.00) |
1 (1.00) |
18p loss | 0 (0%) | 322 |
0.0313 (1.00) |
0.0243 (1.00) |
0.846 (1.00) |
0.344 (1.00) |
0.578 (1.00) |
0.747 (1.00) |
0.264 (1.00) |
0.391 (1.00) |
19p loss | 0 (0%) | 325 |
0.013 (1.00) |
0.113 (1.00) |
0.737 (1.00) |
0.941 (1.00) |
0.118 (1.00) |
0.416 (1.00) |
0.877 (1.00) |
0.00636 (1.00) |
19q loss | 0 (0%) | 331 |
0.0035 (1.00) |
0.18 (1.00) |
0.131 (1.00) |
0.293 (1.00) |
0.694 (1.00) |
0.833 (1.00) |
0.249 (1.00) |
0.244 (1.00) |
20p loss | 0 (0%) | 330 |
0.0283 (1.00) |
0.319 (1.00) |
0.302 (1.00) |
0.814 (1.00) |
0.224 (1.00) |
0.0904 (1.00) |
0.551 (1.00) |
0.267 (1.00) |
20q loss | 0 (0%) | 342 |
0.0222 (1.00) |
0.212 (1.00) |
0.651 (1.00) |
0.779 (1.00) |
0.0359 (1.00) |
0.0468 (1.00) |
0.853 (1.00) |
0.816 (1.00) |
22q loss | 0 (0%) | 326 |
0.00331 (1.00) |
0.0305 (1.00) |
1 (1.00) |
0.779 (1.00) |
0.391 (1.00) |
0.772 (1.00) |
0.00725 (1.00) |
0.801 (1.00) |
Xq loss | 0 (0%) | 344 |
0.0671 (1.00) |
0.0763 (1.00) |
0.903 (1.00) |
0.13 (1.00) |
0.804 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.78 (1.00) |
P value = 0.000122 (Chi-square test), Q value = 0.071
Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
1Q GAIN CNV | 15 | 3 | 14 | 8 | 1 | 1 |
1Q GAIN WILD-TYPE | 67 | 38 | 36 | 84 | 73 | 12 |
Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 9.19e-05 (Chi-square test), Q value = 0.054
Table S2. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
2P GAIN CNV | 12 | 9 | 7 | 1 | 1 | 1 |
2P GAIN WILD-TYPE | 70 | 32 | 43 | 91 | 73 | 12 |
Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 0.000103 (Chi-square test), Q value = 0.06
Table S3. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
2P GAIN CNV | 9 | 6 | 0 | 1 | 13 | 1 | 1 | 0 |
2P GAIN WILD-TYPE | 34 | 41 | 39 | 44 | 45 | 50 | 3 | 19 |
Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 8.26e-05 (Chi-square test), Q value = 0.049
Table S4. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
3P GAIN CNV | 4 | 3 | 0 | 13 | 5 | 1 | 0 | 1 |
3P GAIN WILD-TYPE | 39 | 44 | 39 | 32 | 53 | 50 | 4 | 18 |
Figure S4. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D5V2.png)
P value = 4.27e-05 (Chi-square test), Q value = 0.025
Table S5. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
3Q GAIN CNV | 20 | 17 | 6 | 23 | 25 | 6 | 2 | 3 |
3Q GAIN WILD-TYPE | 23 | 30 | 33 | 22 | 33 | 45 | 2 | 16 |
Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D6V2.png)
P value = 0.000112 (Fisher's exact test), Q value = 0.065
Table S6. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 138 | 100 |
3Q GAIN CNV | 26 | 62 | 23 |
3Q GAIN WILD-TYPE | 87 | 76 | 77 |
Figure S6. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D6V7.png)
P value = 5.64e-09 (Chi-square test), Q value = 3.5e-06
Table S7. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
5P GAIN CNV | 21 | 27 | 11 | 17 | 8 | 4 |
5P GAIN WILD-TYPE | 61 | 14 | 39 | 75 | 66 | 9 |
Figure S7. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 2.95e-05 (Chi-square test), Q value = 0.018
Table S8. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
7P GAIN CNV | 22 | 13 | 22 | 10 | 9 | 2 |
7P GAIN WILD-TYPE | 60 | 28 | 28 | 82 | 65 | 11 |
Figure S8. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 0.000406 (Chi-square test), Q value = 0.23
Table S9. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
7P GAIN CNV | 15 | 12 | 12 | 3 | 21 | 3 | 1 | 3 |
7P GAIN WILD-TYPE | 28 | 35 | 27 | 42 | 37 | 48 | 3 | 16 |
Figure S9. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D13V2.png)
P value = 7.08e-10 (Chi-square test), Q value = 4.4e-07
Table S10. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
7Q GAIN CNV | 13 | 4 | 22 | 5 | 3 | 1 |
7Q GAIN WILD-TYPE | 69 | 37 | 28 | 87 | 71 | 12 |
Figure S10. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D14V1.png)
P value = 1.01e-06 (Chi-square test), Q value = 0.00061
Table S11. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
7Q GAIN CNV | 9 | 6 | 3 | 3 | 21 | 0 | 1 | 0 |
7Q GAIN WILD-TYPE | 34 | 41 | 36 | 42 | 37 | 51 | 3 | 19 |
Figure S11. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D14V2.png)
P value = 4.97e-09 (Chi-square test), Q value = 3.1e-06
Table S12. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
8Q GAIN CNV | 37 | 31 | 16 | 18 | 33 | 10 |
8Q GAIN WILD-TYPE | 45 | 10 | 34 | 74 | 41 | 3 |
Figure S12. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 0.000341 (Chi-square test), Q value = 0.19
Table S13. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
8Q GAIN CNV | 23 | 25 | 19 | 16 | 22 | 8 | 4 | 9 |
8Q GAIN WILD-TYPE | 20 | 22 | 20 | 29 | 36 | 43 | 0 | 10 |
Figure S13. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D16V2.png)
P value = 0.00011 (Chi-square test), Q value = 0.064
Table S14. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
9P GAIN CNV | 8 | 1 | 5 | 12 | 10 | 7 |
9P GAIN WILD-TYPE | 74 | 40 | 45 | 80 | 64 | 6 |
Figure S14. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D17V1.png)
P value = 0.000202 (Chi-square test), Q value = 0.12
Table S15. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
11P GAIN CNV | 1 | 1 | 2 | 3 | 6 | 4 |
11P GAIN WILD-TYPE | 81 | 40 | 48 | 89 | 68 | 9 |
Figure S15. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D21V1.png)
P value = 1.64e-07 (Chi-square test), Q value = 1e-04
Table S16. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
12P GAIN CNV | 11 | 14 | 22 | 9 | 6 | 3 |
12P GAIN WILD-TYPE | 71 | 27 | 28 | 83 | 68 | 10 |
Figure S16. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 1.89e-05 (Chi-square test), Q value = 0.011
Table S17. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
12P GAIN CNV | 13 | 7 | 0 | 10 | 23 | 4 | 1 | 2 |
12P GAIN WILD-TYPE | 30 | 40 | 39 | 35 | 35 | 47 | 3 | 17 |
Figure S17. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D23V2.png)
P value = 9.95e-05 (Fisher's exact test), Q value = 0.058
Table S18. Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 138 | 100 |
12P GAIN CNV | 14 | 41 | 10 |
12P GAIN WILD-TYPE | 99 | 97 | 90 |
Figure S18. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D23V7.png)
P value = 0.000131 (Chi-square test), Q value = 0.076
Table S19. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
14Q GAIN CNV | 19 | 9 | 11 | 1 | 13 | 5 |
14Q GAIN WILD-TYPE | 63 | 32 | 39 | 91 | 61 | 8 |
Figure S19. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D26V1.png)
P value = 8.45e-05 (Chi-square test), Q value = 0.05
Table S20. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
16P GAIN CNV | 8 | 5 | 1 | 1 | 2 | 1 | 2 | 0 |
16P GAIN WILD-TYPE | 35 | 42 | 38 | 44 | 56 | 50 | 2 | 19 |
Figure S20. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D28V2.png)
P value = 0.000367 (Chi-square test), Q value = 0.21
Table S21. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
17P GAIN CNV | 7 | 2 | 9 | 2 | 0 | 0 |
17P GAIN WILD-TYPE | 75 | 39 | 41 | 90 | 74 | 13 |
Figure S21. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D30V1.png)
P value = 0.000122 (Chi-square test), Q value = 0.071
Table S22. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
18P GAIN CNV | 12 | 11 | 16 | 7 | 5 | 4 |
18P GAIN WILD-TYPE | 70 | 30 | 34 | 85 | 69 | 9 |
Figure S22. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D32V1.png)
P value = 0.000177 (Chi-square test), Q value = 0.1
Table S23. Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
18Q GAIN CNV | 2 | 0 | 0 | 9 | 8 | 0 | 0 | 1 |
18Q GAIN WILD-TYPE | 41 | 47 | 39 | 36 | 50 | 51 | 4 | 18 |
Figure S23. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D33V2.png)
P value = 7.5e-06 (Chi-square test), Q value = 0.0045
Table S24. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
20P GAIN CNV | 15 | 20 | 11 | 7 | 13 | 2 |
20P GAIN WILD-TYPE | 67 | 21 | 39 | 85 | 61 | 11 |
Figure S24. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D36V1.png)
P value = 7.9e-05 (Chi-square test), Q value = 0.047
Table S25. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
20P GAIN CNV | 11 | 17 | 3 | 9 | 16 | 2 | 3 | 2 |
20P GAIN WILD-TYPE | 32 | 30 | 36 | 36 | 42 | 49 | 1 | 17 |
Figure S25. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D36V2.png)
P value = 8.46e-07 (Chi-square test), Q value = 0.00051
Table S26. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
20Q GAIN CNV | 16 | 21 | 13 | 6 | 13 | 3 |
20Q GAIN WILD-TYPE | 66 | 20 | 37 | 86 | 61 | 10 |
Figure S26. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D37V1.png)
P value = 0.000112 (Chi-square test), Q value = 0.065
Table S27. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
20Q GAIN CNV | 14 | 17 | 5 | 6 | 16 | 2 | 3 | 4 |
20Q GAIN WILD-TYPE | 29 | 30 | 34 | 39 | 42 | 49 | 1 | 15 |
Figure S27. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D37V2.png)
P value = 0.00016 (Chi-square test), Q value = 0.092
Table S28. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
22Q GAIN CNV | 10 | 5 | 15 | 3 | 6 | 3 |
22Q GAIN WILD-TYPE | 72 | 36 | 35 | 89 | 68 | 10 |
Figure S28. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D39V1.png)
P value = 8.21e-05 (Chi-square test), Q value = 0.048
Table S29. Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
22Q GAIN CNV | 5 | 5 | 2 | 2 | 19 | 5 | 0 | 0 |
22Q GAIN WILD-TYPE | 38 | 42 | 37 | 43 | 39 | 46 | 4 | 19 |
Figure S29. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D39V2.png)
P value = 4.35e-10 (Chi-square test), Q value = 2.7e-07
Table S30. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
1P LOSS CNV | 3 | 0 | 12 | 0 | 1 | 0 |
1P LOSS WILD-TYPE | 79 | 41 | 38 | 92 | 73 | 13 |
Figure S30. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D41V1.png)
P value = 9.7e-07 (Chi-square test), Q value = 0.00059
Table S31. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
1P LOSS CNV | 2 | 0 | 0 | 1 | 12 | 0 | 1 | 0 |
1P LOSS WILD-TYPE | 41 | 47 | 39 | 44 | 46 | 51 | 3 | 19 |
Figure S31. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D41V2.png)
P value = 8.24e-13 (Chi-square test), Q value = 5.2e-10
Table S32. Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
3P LOSS CNV | 44 | 19 | 32 | 5 | 28 | 5 |
3P LOSS WILD-TYPE | 38 | 22 | 18 | 87 | 46 | 8 |
Figure S32. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D44V1.png)
P value = 3.16e-07 (Chi-square test), Q value = 0.00019
Table S33. Gene #44: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
3P LOSS CNV | 22 | 20 | 15 | 9 | 33 | 3 | 2 | 10 |
3P LOSS WILD-TYPE | 21 | 27 | 24 | 36 | 25 | 48 | 2 | 9 |
Figure S33. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D44V2.png)
P value = 5.83e-12 (Chi-square test), Q value = 3.7e-09
Table S34. Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
4P LOSS CNV | 27 | 6 | 30 | 8 | 11 | 0 |
4P LOSS WILD-TYPE | 55 | 35 | 20 | 84 | 63 | 13 |
Figure S34. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D46V1.png)
P value = 2.98e-08 (Chi-square test), Q value = 1.8e-05
Table S35. Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
4P LOSS CNV | 12 | 5 | 7 | 12 | 31 | 1 | 1 | 3 |
4P LOSS WILD-TYPE | 31 | 42 | 32 | 33 | 27 | 50 | 3 | 16 |
Figure S35. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D46V2.png)
P value = 0.000123 (Fisher's exact test), Q value = 0.071
Table S36. Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
4P LOSS CNV | 20 | 9 | 43 |
4P LOSS WILD-TYPE | 75 | 75 | 77 |
Figure S36. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D46V6.png)
P value = 5.82e-05 (Fisher's exact test), Q value = 0.034
Table S37. Gene #46: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 138 | 100 |
4P LOSS CNV | 23 | 48 | 11 |
4P LOSS WILD-TYPE | 90 | 90 | 89 |
Figure S37. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D46V7.png)
P value = 5.73e-09 (Chi-square test), Q value = 3.5e-06
Table S38. Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
4Q LOSS CNV | 13 | 6 | 23 | 4 | 9 | 0 |
4Q LOSS WILD-TYPE | 69 | 35 | 27 | 88 | 65 | 13 |
Figure S38. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D47V1.png)
P value = 3.38e-06 (Chi-square test), Q value = 0.002
Table S39. Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
4Q LOSS CNV | 10 | 7 | 4 | 6 | 22 | 0 | 0 | 0 |
4Q LOSS WILD-TYPE | 33 | 40 | 35 | 39 | 36 | 51 | 4 | 19 |
Figure S39. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D47V2.png)
P value = 2.15e-14 (Chi-square test), Q value = 1.4e-11
Table S40. Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
5Q LOSS CNV | 16 | 17 | 24 | 1 | 5 | 0 |
5Q LOSS WILD-TYPE | 66 | 24 | 26 | 91 | 69 | 13 |
Figure S40. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D49V1.png)
P value = 7.27e-10 (Chi-square test), Q value = 4.5e-07
Table S41. Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
5Q LOSS CNV | 19 | 11 | 1 | 4 | 23 | 0 | 0 | 2 |
5Q LOSS WILD-TYPE | 24 | 36 | 38 | 41 | 35 | 51 | 4 | 17 |
Figure S41. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D49V2.png)
P value = 4.53e-05 (Fisher's exact test), Q value = 0.027
Table S42. Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
5Q LOSS CNV | 16 | 6 | 38 |
5Q LOSS WILD-TYPE | 79 | 78 | 82 |
Figure S42. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D49V6.png)
P value = 1.8e-06 (Chi-square test), Q value = 0.0011
Table S43. Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
8P LOSS CNV | 31 | 9 | 12 | 2 | 20 | 4 |
8P LOSS WILD-TYPE | 51 | 32 | 38 | 90 | 54 | 9 |
Figure S43. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D54V1.png)
P value = 6.66e-06 (Chi-square test), Q value = 0.004
Table S44. Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
8P LOSS CNV | 9 | 18 | 16 | 4 | 12 | 1 | 0 | 2 |
8P LOSS WILD-TYPE | 34 | 29 | 23 | 41 | 46 | 50 | 4 | 17 |
Figure S44. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D54V2.png)
P value = 1.66e-09 (Chi-square test), Q value = 1e-06
Table S45. Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
9P LOSS CNV | 28 | 20 | 21 | 2 | 21 | 1 |
9P LOSS WILD-TYPE | 54 | 21 | 29 | 90 | 53 | 12 |
Figure S45. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D56V1.png)
P value = 2.25e-08 (Chi-square test), Q value = 1.4e-05
Table S46. Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
9P LOSS CNV | 24 | 12 | 9 | 5 | 25 | 1 | 2 | 5 |
9P LOSS WILD-TYPE | 19 | 35 | 30 | 40 | 33 | 50 | 2 | 14 |
Figure S46. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D56V2.png)
P value = 8.93e-05 (Chi-square test), Q value = 0.052
Table S47. Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
10P LOSS CNV | 12 | 10 | 12 | 1 | 12 | 5 |
10P LOSS WILD-TYPE | 70 | 31 | 38 | 91 | 62 | 8 |
Figure S47. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D58V1.png)
P value = 8.12e-08 (Chi-square test), Q value = 5e-05
Table S48. Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
10Q LOSS CNV | 5 | 5 | 15 | 2 | 2 | 0 |
10Q LOSS WILD-TYPE | 77 | 36 | 35 | 90 | 72 | 13 |
Figure S48. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D59V1.png)
P value = 4.58e-05 (Fisher's exact test), Q value = 0.027
Table S49. Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 138 | 100 |
10Q LOSS CNV | 6 | 22 | 1 |
10Q LOSS WILD-TYPE | 107 | 116 | 99 |
Figure S49. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D59V7.png)
P value = 0.000257 (Chi-square test), Q value = 0.15
Table S50. Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
11P LOSS CNV | 22 | 7 | 9 | 5 | 5 | 0 |
11P LOSS WILD-TYPE | 60 | 34 | 41 | 87 | 69 | 13 |
Figure S50. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D60V1.png)
P value = 2.19e-13 (Chi-square test), Q value = 1.4e-10
Table S51. Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
11Q LOSS CNV | 41 | 3 | 9 | 13 | 2 | 1 |
11Q LOSS WILD-TYPE | 41 | 38 | 41 | 79 | 72 | 12 |
Figure S51. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D61V1.png)
P value = 7.28e-05 (Chi-square test), Q value = 0.043
Table S52. Gene #61: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
11Q LOSS CNV | 5 | 6 | 11 | 19 | 12 | 1 | 1 | 3 |
11Q LOSS WILD-TYPE | 38 | 41 | 28 | 26 | 46 | 50 | 3 | 16 |
Figure S52. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D61V2.png)
P value = 2.38e-07 (Chi-square test), Q value = 0.00015
Table S53. Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
13Q LOSS CNV | 19 | 12 | 24 | 8 | 8 | 1 |
13Q LOSS WILD-TYPE | 63 | 29 | 26 | 84 | 66 | 12 |
Figure S53. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D64V1.png)
P value = 9.48e-10 (Chi-square test), Q value = 5.9e-07
Table S54. Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
13Q LOSS CNV | 25 | 7 | 5 | 9 | 14 | 0 | 0 | 2 |
13Q LOSS WILD-TYPE | 18 | 40 | 34 | 36 | 44 | 51 | 4 | 17 |
Figure S54. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D64V2.png)
P value = 2.38e-05 (Fisher's exact test), Q value = 0.014
Table S55. Gene #64: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
13Q LOSS CNV | 16 | 6 | 39 |
13Q LOSS WILD-TYPE | 79 | 78 | 81 |
Figure S55. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D64V6.png)
P value = 4.19e-05 (Chi-square test), Q value = 0.025
Table S56. Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
16Q LOSS CNV | 4 | 0 | 1 | 11 | 8 | 0 | 0 | 0 |
16Q LOSS WILD-TYPE | 39 | 47 | 38 | 34 | 50 | 51 | 4 | 19 |
Figure S56. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D68V2.png)
P value = 4.72e-07 (Fisher's exact test), Q value = 0.00029
Table S57. Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
16Q LOSS CNV | 21 | 1 | 1 |
16Q LOSS WILD-TYPE | 97 | 90 | 89 |
Figure S57. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D68V5.png)
P value = 1.34e-08 (Fisher's exact test), Q value = 8.2e-06
Table S58. Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
16Q LOSS CNV | 0 | 1 | 22 |
16Q LOSS WILD-TYPE | 95 | 83 | 98 |
Figure S58. Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D68V6.png)
P value = 1.27e-05 (Chi-square test), Q value = 0.0076
Table S59. Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
17P LOSS CNV | 17 | 8 | 1 | 6 | 7 | 1 | 1 | 2 |
17P LOSS WILD-TYPE | 26 | 39 | 38 | 39 | 51 | 50 | 3 | 17 |
Figure S59. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D69V2.png)
P value = 1.92e-09 (Chi-square test), Q value = 1.2e-06
Table S60. Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
18Q LOSS CNV | 26 | 19 | 12 | 1 | 31 | 4 |
18Q LOSS WILD-TYPE | 56 | 22 | 38 | 91 | 43 | 9 |
Figure S60. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D72V1.png)
P value = 6.73e-08 (Chi-square test), Q value = 4.1e-05
Table S61. Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 43 | 47 | 39 | 45 | 58 | 51 | 4 | 19 |
18Q LOSS CNV | 20 | 22 | 14 | 2 | 15 | 3 | 3 | 5 |
18Q LOSS WILD-TYPE | 23 | 25 | 25 | 43 | 43 | 48 | 1 | 14 |
Figure S61. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D72V2.png)
P value = 2.16e-06 (Chi-square test), Q value = 0.0013
Table S62. Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 82 | 41 | 50 | 92 | 74 | 13 |
21Q LOSS CNV | 21 | 7 | 14 | 0 | 15 | 6 |
21Q LOSS WILD-TYPE | 61 | 34 | 36 | 92 | 59 | 7 |
Figure S62. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D77V1.png)
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = HNSC-TP.transferedmergedcluster.txt
-
Number of patients = 352
-
Number of significantly arm-level cnvs = 79
-
Number of molecular subtypes = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.