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 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 1p gain 15 (3%) 560 0.40567 1 0.10203 1 0.93194 1 0.49686 1 0.26047 1 0.11777 1 0.17804 1 0.33015 1 0.11131 1 0.91089 1 1q gain 80 (14%) 495 0.48395 1 0.8552 1 0.015823 1 0.92569 1 0.62534 1 0.73607 1 0.12824 1 0.075768 1 0.072884 1 0.97845 1 2p gain 60 (10%) 515 0.016908 1 0.0049882 1 0.0081555 1 0.00025563 0.172 0.07017 1 0.59599 1 0.00022405 0.152 0.00013733 0.0937 0.2161 1 0.020869 1 2q gain 59 (10%) 516 0.0036769 1 0.00391 1 0.0010069 0.666 5.8199e-06 0.00407 0.36308 1 0.79478 1 0.00023412 0.158 0.00082411 0.547 0.25079 1 0.050357 1 3p gain 36 (6%) 539 0.1259 1 0.43337 1 0.00018128 0.123 0.25722 1 0.29198 1 0.34557 1 0.2599 1 0.88499 1 0.20792 1 0.36632 1 3q gain 53 (9%) 522 0.22025 1 0.094667 1 2.4908e-06 0.00175 0.035341 1 0.016764 1 0.41726 1 0.074996 1 0.58768 1 0.11128 1 0.54357 1 4p gain 6 (1%) 569 NA NA NA NA 0.062196 1 0.22614 1 0.20597 1 0.48497 1 NA NA NA NA 0.13662 1 0.052496 1 4q gain 7 (1%) 568 0.70431 1 1 1 0.24967 1 0.787 1 1 1 0.61883 1 NA NA NA NA 0.38271 1 0.80878 1 5p gain 60 (10%) 515 0.11285 1 0.7076 1 0.0015014 0.985 0.17846 1 0.27364 1 0.99002 1 0.40113 1 0.39993 1 0.7844 1 0.35435 1 5q gain 33 (6%) 542 0.45687 1 0.53436 1 0.0035603 1 0.35577 1 0.36743 1 0.76396 1 0.72984 1 0.44647 1 0.81846 1 0.48285 1 6p gain 77 (13%) 498 0.24622 1 0.0049188 1 1.5453e-06 0.00109 0.40135 1 0.2221 1 0.53897 1 0.02271 1 0.22684 1 0.84813 1 0.39161 1 6q gain 71 (12%) 504 0.37518 1 0.019854 1 7.4722e-07 0.000531 0.15877 1 0.34677 1 0.38279 1 0.06068 1 0.57524 1 0.74931 1 0.25108 1 7p gain 290 (50%) 285 0.00044346 0.298 0.0088723 1 1.8943e-21 1.42e-18 7.2886e-07 0.000518 0.24702 1 0.0087241 1 3.7185e-08 2.69e-05 9.5428e-05 0.0652 0.070344 1 0.030432 1 7q gain 255 (44%) 320 0.00064412 0.43 0.013397 1 6.9527e-16 5.14e-13 8.6118e-06 0.00601 0.29031 1 0.078548 1 8.7918e-07 0.000623 1.2379e-05 0.00862 0.24522 1 0.15535 1 8p gain 108 (19%) 467 0.94582 1 0.74582 1 1.0033e-08 7.27e-06 0.43331 1 0.58065 1 0.10124 1 0.18083 1 0.44035 1 0.49022 1 0.89065 1 8q gain 235 (41%) 340 0.069295 1 0.62149 1 1.0571e-33 7.98e-31 0.0094198 1 0.21686 1 0.41345 1 0.0010965 0.724 0.026497 1 0.45899 1 0.63306 1 9p gain 79 (14%) 496 0.41996 1 0.84253 1 0.17843 1 0.79019 1 0.70606 1 0.72977 1 0.53853 1 0.85475 1 0.78008 1 0.78126 1 9q gain 64 (11%) 511 0.47606 1 0.92298 1 0.214 1 0.43338 1 0.26228 1 0.49615 1 0.98879 1 0.69074 1 0.4082 1 0.73861 1 10p gain 28 (5%) 547 0.13658 1 0.8464 1 0.009811 1 0.012541 1 0.96177 1 0.97042 1 0.61731 1 0.044579 1 0.6164 1 0.49637 1 10q gain 13 (2%) 562 0.69094 1 0.58915 1 0.19283 1 0.043666 1 0.43377 1 0.08886 1 0.44811 1 0.076189 1 0.69363 1 0.90189 1 11p gain 39 (7%) 536 0.063043 1 0.654 1 1.7136e-05 0.0119 0.00021429 0.146 0.78095 1 0.73264 1 0.049079 1 0.00015336 0.104 0.24559 1 0.88201 1 11q gain 39 (7%) 536 0.10161 1 0.031637 1 1.3278e-06 0.000939 0.00091055 0.603 0.76461 1 0.50318 1 0.035611 1 0.0052563 1 0.55893 1 0.40622 1 12p gain 93 (16%) 482 0.36191 1 0.81826 1 0.25584 1 0.017053 1 0.63632 1 0.29191 1 0.023201 1 0.013443 1 0.21996 1 0.11247 1 12q gain 78 (14%) 497 0.31523 1 0.72067 1 0.098608 1 0.0019341 1 0.81221 1 0.28767 1 0.035315 1 0.01536 1 0.22169 1 0.16642 1 13q gain 314 (55%) 261 1.0021e-07 7.24e-05 2.4368e-05 0.0168 1.6222e-37 1.23e-34 1.7064e-08 1.24e-05 0.085458 1 0.026046 1 8.5412e-09 6.2e-06 6.3955e-07 0.000455 0.010037 1 0.44955 1 14q gain 19 (3%) 556 0.49483 1 0.55001 1 0.030087 1 0.70858 1 0.31348 1 0.51711 1 0.060477 1 0.047976 1 1 1 0.37109 1 15q gain 7 (1%) 568 NA NA NA NA 0.51457 1 0.88163 1 1 1 0.14409 1 1 1 0.24372 1 0.86981 1 0.37371 1 16p gain 96 (17%) 479 0.097522 1 0.084417 1 1.2625e-16 9.37e-14 0.010804 1 0.29727 1 0.085783 1 0.022796 1 0.13645 1 0.57733 1 0.34666 1 16q gain 96 (17%) 479 0.043277 1 0.068344 1 3.0211e-18 2.25e-15 0.0039079 1 0.35052 1 0.068954 1 0.019816 1 0.060159 1 0.46459 1 0.27723 1 17p gain 13 (2%) 562 0.77999 1 0.0060489 1 1 1 0.84961 1 0.71452 1 0.67333 1 0.015683 1 0.0089989 1 0.69363 1 0.90189 1 17q gain 67 (12%) 508 0.045525 1 0.063861 1 0.00026856 0.181 0.0014284 0.938 0.17537 1 0.14176 1 1.4683e-05 0.0102 0.0019486 1 0.078543 1 0.35388 1 18p gain 21 (4%) 554 0.19204 1 0.01685 1 0.00061013 0.408 0.0095456 1 0.94878 1 0.79498 1 0.13285 1 0.39087 1 0.56836 1 0.39747 1 18q gain 12 (2%) 563 NA NA NA NA 0.17246 1 0.0072864 1 0.32661 1 0.71088 1 0.12238 1 0.85815 1 0.10546 1 0.13438 1 19p gain 52 (9%) 523 0.16712 1 0.22776 1 5.843e-05 0.0401 0.023588 1 0.21528 1 0.25758 1 0.42326 1 0.47411 1 0.71797 1 0.74542 1 19q gain 61 (11%) 514 0.01235 1 0.02492 1 0.012239 1 0.071518 1 0.015545 1 0.049624 1 0.50709 1 0.51206 1 0.83213 1 0.49525 1 20p gain 288 (50%) 287 6.0603e-05 0.0415 6.7132e-09 4.88e-06 4.248e-22 3.19e-19 7.6737e-05 0.0525 0.029685 1 0.040306 1 3.1963e-07 0.000229 3.2029e-07 0.000229 0.62537 1 0.47156 1 20q gain 403 (70%) 172 1.2304e-18 9.18e-16 2.683e-17 1.99e-14 2.2246e-46 1.68e-43 9.0386e-13 6.64e-10 0.01099 1 2.2821e-05 0.0158 9.0343e-18 6.72e-15 1.1305e-13 8.32e-11 0.46311 1 0.10066 1 21q gain 19 (3%) 556 0.43625 1 0.38118 1 0.0026802 1 0.70858 1 0.55823 1 0.052266 1 0.61942 1 0.83363 1 0.68566 1 0.14321 1 22q gain 7 (1%) 568 0.69094 1 0.0060489 1 0.23406 1 0.46578 1 0.66888 1 0.032985 1 0.68907 1 0.49881 1 0.45861 1 0.59561 1 Xq gain 17 (3%) 558 0.14672 1 0.73499 1 0.016685 1 0.33848 1 0.0040371 1 0.4769 1 0.84629 1 1 1 0.48172 1 0.70461 1 1p loss 68 (12%) 507 0.078358 1 0.0032744 1 7.5476e-06 0.00528 3.8428e-05 0.0264 0.4806 1 0.82835 1 0.076382 1 0.0082272 1 0.19261 1 0.62049 1 1q loss 25 (4%) 550 0.55788 1 0.021479 1 0.082264 1 0.031495 1 0.60347 1 0.49802 1 0.1581 1 0.32381 1 0.42483 1 0.72532 1 2p loss 10 (2%) 565 1 1 0.43464 1 0.073513 1 NA NA 0.44803 1 0.58521 1 NA NA NA NA 0.015125 1 0.013286 1 2q loss 8 (1%) 567 0.74087 1 0.44409 1 0.54823 1 NA NA 0.56996 1 0.58231 1 NA NA NA NA 0.058427 1 0.045527 1 3p loss 35 (6%) 540 0.93812 1 0.53032 1 0.83112 1 0.83463 1 0.75751 1 0.79155 1 0.44134 1 0.15697 1 0.10485 1 0.72944 1 3q loss 17 (3%) 558 0.6182 1 0.81564 1 0.75688 1 0.015667 1 0.39473 1 0.59495 1 0.3845 1 0.18399 1 0.73957 1 0.7721 1 4p loss 122 (21%) 453 0.10576 1 0.105 1 5.4975e-11 4.01e-08 0.0035973 1 0.27388 1 0.72913 1 0.0061971 1 0.057158 1 0.045027 1 0.76936 1 4q loss 113 (20%) 462 0.096187 1 0.063801 1 3.1754e-12 2.33e-09 0.0016838 1 0.58887 1 0.44149 1 0.0021315 1 0.053451 1 0.012191 1 0.56362 1 5p loss 34 (6%) 541 0.2914 1 0.43337 1 0.00054432 0.365 0.034068 1 1 1 0.63006 1 0.23394 1 0.035241 1 0.96862 1 0.82879 1 5q loss 60 (10%) 515 0.016307 1 0.091686 1 5.5316e-07 0.000394 0.081603 1 0.73539 1 0.53871 1 0.021113 1 0.09854 1 0.96346 1 0.57856 1 6p loss 18 (3%) 557 0.11691 1 0.0742 1 0.026043 1 0.2767 1 0.76394 1 0.83592 1 0.88965 1 0.60116 1 0.60161 1 0.92285 1 6q loss 33 (6%) 542 0.4568 1 0.338 1 0.09827 1 1 1 0.025209 1 0.47045 1 0.73685 1 0.67654 1 0.26225 1 0.29769 1 7q loss 3 (1%) 572 NA NA NA NA 0.21176 1 NA NA 0.78716 1 0.73685 1 NA NA NA NA 0.76387 1 1 1 8p loss 145 (25%) 430 0.011681 1 0.0046329 1 1.1426e-18 8.53e-16 0.00037323 0.251 0.47852 1 0.098448 1 0.11036 1 0.15185 1 0.51503 1 0.73021 1 8q loss 12 (2%) 563 0.60297 1 0.63949 1 0.082808 1 0.58001 1 0.052123 1 0.3299 1 1 1 0.8276 1 0.15853 1 0.27077 1 9p loss 39 (7%) 536 0.56409 1 0.12011 1 2.8967e-05 0.02 0.0015809 1 0.063458 1 0.15733 1 0.10225 1 0.022105 1 0.12745 1 1 1 9q loss 37 (6%) 538 0.048413 1 0.013528 1 1.9547e-06 0.00138 3.4176e-05 0.0235 0.093971 1 0.39851 1 0.021351 1 0.016716 1 0.049149 1 0.81952 1 10p loss 40 (7%) 535 0.70439 1 0.40096 1 0.00086224 0.572 0.41929 1 0.15082 1 0.15961 1 0.40869 1 0.53216 1 0.13213 1 0.59051 1 10q loss 46 (8%) 529 0.34014 1 0.56823 1 1.4367e-06 0.00101 0.15314 1 0.6091 1 0.27871 1 0.10225 1 0.2311 1 0.71404 1 0.81051 1 11p loss 40 (7%) 535 0.79678 1 1 1 0.0097676 1 0.70583 1 0.86742 1 0.56214 1 0.071558 1 0.083775 1 0.11333 1 0.35936 1 11q loss 51 (9%) 524 0.97545 1 0.85752 1 0.0016581 1 0.23178 1 0.83532 1 0.4532 1 0.099677 1 0.50904 1 0.12883 1 0.83548 1 12p loss 33 (6%) 542 0.11383 1 0.26366 1 5.424e-07 0.000387 0.25849 1 0.70196 1 0.6851 1 0.20105 1 0.46045 1 0.54148 1 0.22186 1 12q loss 28 (5%) 547 0.13127 1 0.052412 1 1.1071e-06 0.000784 0.52201 1 0.64801 1 0.69748 1 0.14256 1 0.18877 1 0.6164 1 0.6809 1 13q loss 12 (2%) 563 0.3244 1 0.10757 1 0.049459 1 0.22645 1 0.091511 1 0.16402 1 0.23575 1 0.66836 1 0.7263 1 0.40273 1 14q loss 143 (25%) 432 4.758e-06 0.00334 2.485e-07 0.000178 1.1184e-31 8.43e-29 1.9699e-07 0.000142 0.0012361 0.813 0.010377 1 1.7256e-07 0.000124 0.00070476 0.469 0.11445 1 0.70906 1 15q loss 156 (27%) 419 0.014365 1 0.011679 1 2.0874e-24 1.57e-21 0.015774 1 0.86073 1 0.61199 1 1.1894e-05 0.00829 0.00057188 0.383 0.3675 1 0.24605 1 16p loss 15 (3%) 560 0.25556 1 0.59763 1 0.09948 1 0.22645 1 0.51701 1 0.91027 1 0.58888 1 0.60116 1 1 1 0.91089 1 16q loss 17 (3%) 558 0.013057 1 0.50638 1 0.0022089 1 0.49228 1 0.71452 1 0.85154 1 0.091107 1 0.12148 1 0.13425 1 0.25684 1 17p loss 252 (44%) 323 0.00024224 0.164 0.0016454 1 5.4882e-22 4.12e-19 2.4395e-07 0.000175 0.7686 1 0.36683 1 3.2518e-06 0.00228 0.00079532 0.529 0.027 1 0.49718 1 17q loss 45 (8%) 530 0.76207 1 0.5585 1 0.0023038 1 0.85708 1 0.92076 1 0.75067 1 0.10108 1 0.10474 1 0.11572 1 0.63456 1 18p loss 324 (56%) 251 9.8728e-15 7.29e-12 8.5148e-12 6.23e-09 4.2634e-47 3.23e-44 4.3282e-19 3.24e-16 0.087657 1 0.0012275 0.809 5.387e-16 3.99e-13 2.735e-11 2e-08 0.065035 1 0.7872 1 18q loss 352 (61%) 223 1.4203e-12 1.04e-09 1.9645e-11 1.44e-08 6.8004e-51 5.16e-48 8.0336e-21 6.02e-18 0.13872 1 0.012816 1 3.958e-16 2.93e-13 3.6833e-09 2.68e-06 0.0093757 1 0.37782 1 19p loss 20 (3%) 555 0.49008 1 0.59763 1 1.4622e-05 0.0102 0.024428 1 1 1 0.18158 1 0.0015479 1 0.0028882 1 0.23499 1 0.37109 1 19q loss 18 (3%) 557 0.49008 1 0.59763 1 0.00023546 0.159 0.096499 1 0.77835 1 0.85927 1 0.0015479 1 0.0028882 1 0.42424 1 0.097617 1 20p loss 47 (8%) 528 0.16877 1 0.17976 1 4.5625e-07 0.000326 0.039019 1 0.92519 1 0.17183 1 0.57735 1 0.39072 1 0.55412 1 0.48621 1 21q loss 114 (20%) 461 0.058799 1 0.31932 1 3.6397e-05 0.025 0.055504 1 0.084084 1 0.47873 1 0.23518 1 0.3916 1 0.11838 1 0.3424 1 22q loss 122 (21%) 453 0.06793 1 0.003803 1 7.7977e-14 5.75e-11 0.35208 1 0.25688 1 0.40929 1 0.067555 1 0.064607 1 0.066218 1 0.10019 1 Xq loss 11 (2%) 564 0.76543 1 0.83939 1 0.33904 1 0.44599 1 0.81707 1 0.41009 1 0.01571 1 0.067381 1 0.51495 1 0.65187 1