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 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 Fisher's exact test_P Fisher's exact test_Q 1p gain 5 (1%) 488 NA NA NA NA 0.62741 1 NA NA 1 1 0.02481 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 0.14001 1 0.12199 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 0.000676 0.65317 1 0.8984 1 0.93377 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 0.0281 0.82441 1 0.95967 1 0.83841 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 0.17184 1 0.001886 0.962 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 0.0373 0.080411 1 0.020587 1 0.0017834 0.913 0.00039457 0.215 0.0093127 1 0.0010381 0.543 0.0029769 1 4p gain 8 (2%) 485 NA NA NA NA 0.2057 1 0.60825 1 0.17184 1 0.06103 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 0.22558 1 0.3706 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 0.47281 1 0.25674 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 0.0335 0.37509 1 0.48919 1 0.39926 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 0.22558 1 0.66572 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 0.28768 1 0.44495 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 0.051204 1 0.01095 1 0.067954 1 0.082377 1 0.0016959 0.87 0.64057 1 7q gain 129 (26%) 364 0.87675 1 0.93891 1 1.3614e-05 0.00809 0.041704 1 0.0086082 1 0.0013133 0.678 0.058061 1 0.13146 1 0.00070459 0.376 0.88818 1 8p gain 14 (3%) 479 NA NA NA NA 5.418e-05 0.0309 0.079578 1 9.1202e-05 0.0513 0.20434 1 0.00097842 0.513 0.00068297 0.365 0.010547 1 0.010667 1 8q gain 34 (7%) 459 0.053628 1 0.058091 1 2.747e-07 0.000174 0.0010457 0.544 6.4228e-06 0.00386 0.058778 1 1.1473e-07 7.27e-05 4.879e-05 0.028 1.8826e-05 0.0111 0.0040385 1 9p gain 8 (2%) 485 NA NA NA NA 0.74129 1 0.24924 1 0.085679 1 0.27994 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 0.78296 1 0.06103 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 1 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 0.53245 1 1 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 0.286 0.77137 1 0.20514 1 0.8904 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 0.61 0.69815 1 0.35798 1 0.8185 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 0.000499 0.0010394 0.543 4.5832e-05 0.0264 0.031852 1 1.1022e-05 0.00658 1.8938e-05 0.0111 3.7201e-07 0.000234 0.32421 1 12q gain 78 (16%) 415 0.19401 1 0.16527 1 7.9908e-07 0.000499 0.0010394 0.543 4.5832e-05 0.0264 0.037143 1 1.1022e-05 0.00658 1.8938e-05 0.0111 3.7201e-07 0.000234 0.32421 1 13q gain 14 (3%) 479 NA NA NA NA 0.74221 1 0.076952 1 0.35798 1 0.38827 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 0.27315 1 0.048221 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 0.93051 1 0.7301 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 0.63436 1 0.21089 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 0.47451 1 0.43392 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 0.196 0.4196 1 0.55339 1 0.16947 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 0.44755 1 0.73026 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 0.34703 1 0.15875 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 0.34703 1 0.15875 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 0.093406 1 0.31033 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 0.00185 0.20068 1 0.041872 1 0.11652 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 0.361 5.0363e-05 0.0288 0.0075563 1 3.5945e-06 0.0022 5.2899e-06 0.00319 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 0.361 3.0332e-05 0.0177 0.0083094 1 3.298e-07 0.000208 1.4673e-06 0.000913 2.0898e-07 0.000132 0.0055059 1 21q gain 33 (7%) 460 0.82033 1 0.81457 1 0.00011721 0.0658 0.09858 1 0.66527 1 0.69068 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 0.217 0.075575 1 0.66401 1 0.25279 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 1 1 0.81561 1 0.19785 1 0.2766 1 0.1526 1 0.16993 1 1p loss 32 (6%) 461 0.00083595 0.441 6.1992e-05 0.0353 0.0039487 1 0.19754 1 0.51559 1 0.0047367 1 0.012254 1 4.6432e-06 0.00282 0.0039972 1 1.361e-08 8.75e-06 1q loss 21 (4%) 472 0.021718 1 0.0028644 1 2.0871e-05 0.0122 0.90381 1 0.64215 1 0.017825 1 6.6528e-05 0.0377 6.2684e-07 0.000392 0.019672 1 7.5387e-09 4.86e-06 2p loss 10 (2%) 483 0.00024867 0.137 0.00037409 0.205 1.5215e-05 0.00899 0.45635 1 0.22558 1 0.00014165 0.0793 4.7244e-07 0.000296 1.8734e-08 1.2e-05 0.00057471 0.309 8.7237e-11 5.69e-08 2q loss 11 (2%) 482 0.00024867 0.137 0.00037409 0.205 4.754e-06 0.00288 1 1 0.1495 1 3.1478e-05 0.0183 8.96e-08 5.69e-05 7.9136e-08 5.04e-05 0.00023817 0.132 8.8269e-10 5.72e-07 3p loss 304 (62%) 189 0.012955 1 0.010206 1 6.3714e-24 4.24e-21 0.00052055 0.282 4.7042e-06 0.00285 3.9514e-05 0.0228 3.8542e-11 2.52e-08 7.0891e-10 4.6e-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 0.738 0.19173 1 0.23624 1 0.0036433 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 0.57969 1 0.94656 1 0.088816 1 0.36552 1 0.39336 1 0.70702 1 4q loss 28 (6%) 465 1 1 1 1 0.00022145 0.123 0.25535 1 0.85728 1 0.2903 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 3.439e-08 2.2e-05 3.5253e-06 0.00216 0.00072213 0.384 0.0010519 0.545 6.3989e-09 4.14e-06 0.00019148 0.107 6q loss 82 (17%) 411 0.039296 1 0.012516 1 6.3378e-17 4.21e-14 0.12101 1 2.912e-06 0.0018 0.00077934 0.412 0.20388 1 0.47751 1 1.4309e-05 0.00849 0.00030994 0.17 8p loss 94 (19%) 399 0.77713 1 0.78081 1 0.047016 1 0.70561 1 0.77793 1 0.70012 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 0.55019 1 0.60626 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 0.00080974 0.428 0.091492 1 1.3893e-11 9.11e-09 2.7121e-12 1.79e-09 7.473e-09 4.83e-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 0.0007375 0.392 0.026405 1 1.315e-12 8.68e-10 3.9392e-14 2.62e-11 4.6723e-10 3.04e-07 0.11845 1 10p loss 32 (6%) 461 0.026008 1 0.02869 1 0.0002012 0.112 0.38225 1 0.4325 1 0.058845 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 0.56538 1 0.018164 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 0.33203 1 0.048221 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 0.38099 1 0.115 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 0.0361 0.24729 1 0.0019409 0.986 0.0041023 1 0.0024962 1 0.00045951 0.25 7.4275e-05 0.042 0.001046 0.544 14q loss 158 (32%) 335 0.0017916 0.916 0.00095642 0.502 2.0238e-10 1.32e-07 3.0568e-05 0.0178 3.0731e-06 0.00189 4.3631e-05 0.0252 6.9702e-11 4.56e-08 2.8039e-07 0.000177 2.873e-06 0.00178 0.0027346 1 15q loss 12 (2%) 481 0.58042 1 0.58403 1 0.021316 1 0.37272 1 0.44115 1 0.52188 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 0.8693 1 0.85429 1 1 1 0.29246 1 0.56905 1 0.42444 1 17p loss 25 (5%) 468 0.00011676 0.0656 0.00017823 0.0996 4.3019e-06 0.00263 0.90782 1 0.0078943 1 3.0562e-05 0.0178 1.9025e-06 0.00118 1.5033e-08 9.65e-06 1.6275e-08 1.04e-05 8.3533e-09 5.38e-06 17q loss 12 (2%) 481 0.00066805 0.359 0.00077017 0.408 0.00022423 0.124 0.45635 1 0.10478 1 6.9394e-06 0.00416 1.9121e-06 0.00119 7.9136e-08 5.04e-05 7.6646e-05 0.0432 8.5008e-11 5.55e-08 18p loss 46 (9%) 447 0.19401 1 0.43305 1 3.017e-06 0.00186 0.01939 1 8.0415e-06 0.00482 0.012934 1 6.0578e-06 0.00365 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 2.1425e-05 0.0125 0.064004 1 2.8663e-05 0.0167 0.00057363 0.309 1.514e-05 0.00896 0.0013782 0.71 19p loss 4 (1%) 489 NA NA NA NA 0.18428 1 0.33163 1 0.03661 1 0.02481 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 0.78296 1 0.66572 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 0.201 0.47862 1 0.90519 1 0.02883 1 0.0019241 0.979 1.7176e-05 0.0101 0.032198 1 0.00056956 0.308 22q loss 11 (2%) 482 NA NA NA NA 0.0050112 1 0.16071 1 0.13311 1 0.19283 1 0.00088773 0.467 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 0.69479 1 0.36044 1 0.067592 1 0.0076322 1 0.02786 1 0.0068545 1