Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL nCNV (%) nWild-Type Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 5 (1%) 488 NA NA NA NA 0.62741 1 NA NA 0.43887 1 0.035855 1 0.84555 1 0.85029 1 0.51881 1 1 1 1q gain 32 (6%) 461 0.61119 1 1 1 1.0459e-05 0.00625 0.45189 1 0.43377 1 0.19022 1 0.0097169 1 0.15038 1 0.019589 1 0.85766 1 2p gain 48 (10%) 445 0.56067 1 0.47247 1 1.0848e-06 0.000671 0.65317 1 0.046154 1 0.78296 1 0.14408 1 0.078453 1 0.4915 1 0.34803 1 2q gain 49 (10%) 444 0.56067 1 0.47247 1 4.9027e-05 0.0282 0.82441 1 0.052756 1 0.86158 1 0.051935 1 0.049818 1 0.44216 1 0.34803 1 3p gain 7 (1%) 486 NA NA NA NA 0.38574 1 1 1 0.10217 1 0.0032938 1 0.29418 1 0.16078 1 0.011147 1 0.13611 1 3q gain 27 (5%) 466 0.082325 1 0.085132 1 6.5793e-05 0.0375 0.080411 1 0.007183 1 0.00010715 0.0606 0.00039457 0.214 0.0093127 1 0.0010381 0.536 0.0029769 1 4p gain 8 (2%) 485 NA NA NA NA 0.2057 1 0.60825 1 0.42832 1 0.080261 1 0.025659 1 0.37796 1 0.015548 1 0.2643 1 4q gain 8 (2%) 485 NA NA NA NA 0.67035 1 0.79533 1 0.87831 1 0.33815 1 0.011216 1 0.5092 1 0.041127 1 0.2643 1 5p gain 141 (29%) 352 0.59284 1 0.59153 1 1.2527e-05 0.00745 0.44108 1 0.081729 1 0.054605 1 0.045779 1 0.0084423 1 0.021627 1 0.054383 1 5q gain 156 (32%) 337 0.10537 1 0.12107 1 5.8712e-05 0.0336 0.37509 1 0.1584 1 0.17451 1 0.038112 1 0.0051214 1 0.045065 1 0.011492 1 6p gain 6 (1%) 487 NA NA NA NA 0.77018 1 0.55518 1 0.8188 1 0.87678 1 0.21454 1 0.44902 1 0.44091 1 0.19183 1 6q gain 5 (1%) 488 NA NA NA NA 0.53168 1 0.79533 1 0.57144 1 0.62591 1 0.44232 1 0.57135 1 0.8329 1 0.10409 1 7p gain 127 (26%) 366 0.87675 1 0.93891 1 5.0545e-06 0.00305 0.054291 1 0.00026802 0.147 0.0056517 1 0.067954 1 0.082377 1 0.0016959 0.855 0.64057 1 7q gain 129 (26%) 364 0.87675 1 0.93891 1 1.3614e-05 0.00809 0.041704 1 0.00011777 0.0663 0.00071795 0.378 0.058061 1 0.13146 1 0.00070459 0.372 0.88818 1 8p gain 14 (3%) 479 NA NA NA NA 5.418e-05 0.0311 0.079578 1 0.086779 1 0.14595 1 0.00097842 0.509 0.00068297 0.361 0.010547 1 0.010667 1 8q gain 34 (7%) 459 0.053628 1 0.058091 1 2.747e-07 0.000173 0.0010457 0.536 0.010176 1 0.044916 1 1.1473e-07 7.26e-05 4.879e-05 0.0281 1.8826e-05 0.011 0.0040385 1 9p gain 8 (2%) 485 NA NA NA NA 0.74129 1 0.24924 1 0.17017 1 0.17028 1 0.10317 1 0.05713 1 0.73368 1 0.042444 1 9q gain 8 (2%) 485 NA NA NA NA 0.28254 1 1 1 0.10371 1 0.33815 1 0.52284 1 0.63567 1 0.6185 1 0.36177 1 10p gain 6 (1%) 487 NA NA NA NA 0.39007 1 1 1 0.98053 1 1 1 0.267 1 0.31138 1 0.38654 1 0.57569 1 10q gain 4 (1%) 489 NA NA NA NA 0.18428 1 1 1 0.71582 1 0.61472 1 0.68786 1 0.50758 1 0.32529 1 0.55868 1 11p gain 17 (3%) 476 0.76851 1 0.77815 1 0.00052935 0.284 0.77137 1 0.43744 1 0.3949 1 0.49103 1 0.26531 1 0.69928 1 0.47838 1 11q gain 15 (3%) 478 0.76851 1 0.77815 1 0.0011789 0.601 0.69815 1 0.54134 1 0.48032 1 0.58591 1 0.50493 1 0.64658 1 0.47846 1 12p gain 78 (16%) 415 0.19401 1 0.16527 1 7.9908e-07 0.000496 0.0010394 0.536 5.6676e-07 0.000354 0.013931 1 1.1022e-05 0.00658 1.8938e-05 0.0111 3.7201e-07 0.000233 0.32421 1 12q gain 78 (16%) 415 0.19401 1 0.16527 1 7.9908e-07 0.000496 0.0010394 0.536 5.6676e-07 0.000354 0.014143 1 1.1022e-05 0.00658 1.8938e-05 0.0111 3.7201e-07 0.000233 0.32421 1 13q gain 14 (3%) 479 NA NA NA NA 0.74221 1 0.076952 1 0.46728 1 0.77086 1 0.068473 1 0.63576 1 0.15674 1 0.49268 1 14q gain 5 (1%) 488 NA NA NA NA 0.049557 1 0.60825 1 0.86889 1 0.059647 1 0.0035445 1 0.047744 1 0.12185 1 0.068463 1 15q gain 14 (3%) 479 NA NA NA NA 0.094725 1 0.57818 1 0.64372 1 0.23718 1 0.11643 1 0.37881 1 0.8803 1 0.72568 1 16p gain 65 (13%) 428 0.10023 1 0.21177 1 0.15276 1 0.68944 1 0.01148 1 0.066314 1 0.63473 1 0.11281 1 0.31767 1 0.35671 1 16q gain 58 (12%) 435 0.07055 1 0.17117 1 0.17461 1 0.90922 1 0.044287 1 0.12194 1 0.69647 1 0.33614 1 0.43321 1 0.59421 1 17p gain 16 (3%) 477 0.0052247 1 0.0066496 1 0.00035713 0.195 0.4196 1 0.32105 1 0.033572 1 0.19135 1 0.032663 1 0.4043 1 0.046398 1 17q gain 22 (4%) 471 0.0082659 1 0.010223 1 0.0048052 1 0.11876 1 0.55304 1 0.054698 1 0.25322 1 0.0094887 1 0.24864 1 0.0059539 1 18p gain 18 (4%) 475 0.076398 1 0.039003 1 0.23818 1 0.15286 1 0.31926 1 0.14269 1 0.097694 1 0.40967 1 0.28798 1 0.64109 1 18q gain 18 (4%) 475 0.076398 1 0.039003 1 0.23818 1 0.15286 1 0.31926 1 0.14269 1 0.097694 1 0.40967 1 0.28798 1 0.64109 1 19p gain 25 (5%) 468 0.18897 1 0.1968 1 3.3746e-05 0.0195 0.33956 1 0.044845 1 0.39709 1 0.042771 1 0.011532 1 0.025373 1 0.067951 1 19q gain 28 (6%) 465 0.053628 1 0.058091 1 3.0044e-06 0.00184 0.20068 1 0.055965 1 0.15391 1 0.018535 1 0.004142 1 0.0082806 1 0.028284 1 20p gain 66 (13%) 427 0.10193 1 0.10973 1 1.0457e-12 6.91e-10 0.00067423 0.358 0.00045333 0.244 0.00097912 0.509 3.5945e-06 0.0022 5.2899e-06 0.00318 4.4671e-06 0.00272 0.0080605 1 20q gain 68 (14%) 425 0.075297 1 0.092006 1 6.2337e-14 4.13e-11 0.00067423 0.358 3.5385e-05 0.0205 0.00085487 0.447 3.298e-07 0.000207 1.4673e-06 0.000907 2.0898e-07 0.000132 0.0055059 1 21q gain 33 (7%) 460 0.82033 1 0.81457 1 0.00011721 0.0661 0.09858 1 0.036798 1 0.83574 1 0.070901 1 0.080022 1 0.30691 1 1 1 22q gain 25 (5%) 468 0.58042 1 0.039003 1 0.00039943 0.216 0.075575 1 0.45167 1 0.21702 1 0.82643 1 0.84565 1 0.82318 1 0.64945 1 Xq gain 11 (2%) 482 0.41403 1 0.43151 1 0.63929 1 0.57818 1 0.39249 1 0.48252 1 0.19785 1 0.2766 1 0.1526 1 0.16993 1 1p loss 32 (6%) 461 0.00083595 0.438 6.1992e-05 0.0355 0.0039487 1 0.19754 1 5.0549e-08 3.23e-05 0.00043538 0.235 0.012254 1 4.6432e-06 0.00281 0.0039972 1 1.361e-08 8.74e-06 1q loss 21 (4%) 472 0.021718 1 0.0028644 1 2.0871e-05 0.0122 0.90381 1 0.00016788 0.0938 0.0019091 0.958 6.6528e-05 0.0379 6.2684e-07 0.00039 0.019672 1 7.5387e-09 4.85e-06 2p loss 10 (2%) 483 0.00024867 0.137 0.00037409 0.204 1.5215e-05 0.00896 0.45635 1 1.3686e-05 0.00812 0.00018904 0.105 4.7244e-07 0.000295 1.8734e-08 1.2e-05 0.00057471 0.306 8.7237e-11 5.68e-08 2q loss 11 (2%) 482 0.00024867 0.137 0.00037409 0.204 4.754e-06 0.00288 1 1 0.00012943 0.0725 4.4152e-05 0.0255 8.96e-08 5.68e-05 7.9136e-08 5.03e-05 0.00023817 0.131 8.8269e-10 5.71e-07 3p loss 304 (62%) 189 0.012955 1 0.010206 1 6.3714e-24 4.24e-21 0.00052055 0.28 0.0001198 0.0673 1.7769e-05 0.0104 3.8542e-11 2.52e-08 7.0891e-10 4.59e-07 4.3958e-06 0.00268 6.9642e-08 4.44e-05 3q loss 73 (15%) 420 0.70139 1 0.69959 1 0.0014361 0.725 0.19173 1 0.18206 1 0.0066057 1 0.51828 1 0.80379 1 0.012182 1 0.33802 1 4p loss 35 (7%) 458 0.28864 1 0.29647 1 0.065781 1 0.27395 1 0.81614 1 0.94781 1 0.088816 1 0.36552 1 0.39336 1 0.70702 1 4q loss 28 (6%) 465 1 1 1 1 0.00022145 0.122 0.25535 1 0.25143 1 0.31278 1 0.063101 1 0.05733 1 0.78215 1 0.5118 1 6p loss 58 (12%) 435 0.013899 1 0.0028988 1 4.2674e-12 2.8e-09 0.0089899 1 0.00012166 0.0683 7.0349e-06 0.00422 0.00072213 0.38 0.0010519 0.538 6.3989e-09 4.13e-06 0.00019148 0.106 6q loss 82 (17%) 411 0.039296 1 0.012516 1 6.3378e-17 4.21e-14 0.12101 1 0.0013994 0.708 0.0010327 0.534 0.20388 1 0.47751 1 1.4309e-05 0.00847 0.00030994 0.17 8p loss 94 (19%) 399 0.77713 1 0.78081 1 0.047016 1 0.70561 1 0.72351 1 0.49983 1 0.18497 1 0.63325 1 0.21504 1 0.8631 1 8q loss 37 (8%) 456 0.49011 1 0.58627 1 0.74744 1 0.25514 1 0.53952 1 0.7855 1 0.11152 1 0.026589 1 0.28801 1 0.90796 1 9p loss 87 (18%) 406 0.37846 1 0.069376 1 9.2257e-25 6.15e-22 3.5676e-12 2.35e-09 0.0046325 1 0.0072553 1 1.3893e-11 9.1e-09 2.7121e-12 1.79e-09 7.473e-09 4.82e-06 0.1249 1 9q loss 92 (19%) 401 0.37846 1 0.069376 1 4.4289e-26 2.96e-23 4.2989e-13 2.85e-10 0.00099938 0.518 0.010359 1 1.315e-12 8.68e-10 3.9392e-14 2.62e-11 4.6723e-10 3.03e-07 0.11845 1 10p loss 32 (6%) 461 0.026008 1 0.02869 1 0.0002012 0.111 0.38225 1 0.19525 1 0.036955 1 0.012254 1 0.019724 1 0.56897 1 0.010113 1 10q loss 48 (10%) 445 0.097195 1 0.11948 1 0.0026344 1 0.040882 1 0.22014 1 0.012532 1 0.094952 1 0.12585 1 0.35687 1 0.17052 1 11p loss 5 (1%) 488 NA NA NA NA 0.12092 1 0.60825 1 0.15609 1 0.035855 1 0.35902 1 0.46204 1 0.60843 1 0.40395 1 11q loss 7 (1%) 486 NA NA NA NA 0.05266 1 0.82585 1 0.053318 1 0.21517 1 0.37721 1 0.31138 1 0.33437 1 0.30093 1 13q loss 31 (6%) 462 0.025253 1 0.02806 1 6.3588e-05 0.0363 0.24729 1 0.001372 0.698 0.0013857 0.703 0.0024962 1 0.00045951 0.247 7.4275e-05 0.0422 0.001046 0.536 14q loss 158 (32%) 335 0.0017916 0.901 0.00095642 0.498 2.0238e-10 1.32e-07 3.0568e-05 0.0177 6.6084e-12 4.34e-09 2.0759e-07 0.000131 6.9702e-11 4.55e-08 2.8039e-07 0.000176 2.873e-06 0.00177 0.0027346 1 15q loss 12 (2%) 481 0.58042 1 0.58403 1 0.021316 1 0.37272 1 0.45072 1 0.70387 1 0.073285 1 0.13618 1 0.21091 1 0.22794 1 16q loss 5 (1%) 488 NA NA NA NA 0.013543 1 NA NA 0.16723 1 0.45624 1 1 1 0.29246 1 0.56905 1 0.42444 1 17p loss 25 (5%) 468 0.00011676 0.066 0.00017823 0.0995 4.3019e-06 0.00262 0.90782 1 2.9244e-05 0.017 5.1787e-06 0.00312 1.9025e-06 0.00117 1.5033e-08 9.64e-06 1.6275e-08 1.04e-05 8.3533e-09 5.37e-06 17q loss 12 (2%) 481 0.00066805 0.355 0.00077017 0.404 0.00022423 0.124 0.45635 1 1.4598e-05 0.00863 1.0235e-05 0.00613 1.9121e-06 0.00118 7.9136e-08 5.03e-05 7.6646e-05 0.0435 8.5008e-11 5.54e-08 18p loss 46 (9%) 447 0.19401 1 0.43305 1 3.017e-06 0.00185 0.01939 1 0.018255 1 0.0047251 1 6.0578e-06 0.00364 0.00019604 0.109 4.6294e-06 0.00281 0.0088683 1 18q loss 48 (10%) 445 0.2588 1 0.23793 1 3.6093e-06 0.00221 0.032401 1 0.055096 1 0.012751 1 2.8663e-05 0.0167 0.00057363 0.306 1.514e-05 0.00893 0.0013782 0.7 19p loss 4 (1%) 489 NA NA NA NA 0.18428 1 0.33163 1 0.2794 1 0.035855 1 0.34103 1 0.37884 1 0.88045 1 0.77451 1 20p loss 6 (1%) 487 NA NA NA NA 0.047496 1 1 1 0.017173 1 0.87678 1 0.267 1 0.74728 1 0.092089 1 0.19183 1 21q loss 32 (6%) 461 0.014517 1 0.021914 1 0.00036659 0.2 0.47862 1 0.0050057 1 0.039896 1 0.0019241 0.964 1.7176e-05 0.0101 0.032198 1 0.00056956 0.305 22q loss 11 (2%) 482 NA NA NA NA 0.0050112 1 0.16071 1 0.046179 1 0.39292 1 0.00088773 0.463 0.019143 1 0.3732 1 0.81646 1 Xq loss 7 (1%) 486 0.039423 1 0.077238 1 0.30836 1 0.82585 1 0.38057 1 0.56426 1 0.067592 1 0.0076322 1 0.02786 1 0.0068545 1