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 21 (6%) 337 0.97137 1 0.65195 1 0.2131 1 0.21659 1 0.86661 1 0.23188 1 0.71876 1 0.14049 1 0.24425 1 0.61357 1 1q gain 74 (21%) 284 0.13272 1 0.10044 1 1.4978e-05 0.0112 0.011057 1 0.62705 1 0.52188 1 0.0032918 1 0.0017889 1 0.046228 1 0.085224 1 2p gain 85 (24%) 273 0.010309 1 0.016172 1 4.6924e-09 3.61e-06 1.9583e-05 0.0147 0.10485 1 0.36985 1 0.016498 1 0.00053126 0.38 0.98288 1 0.24943 1 2q gain 39 (11%) 319 0.21552 1 0.067931 1 0.00038047 0.276 0.0090505 1 0.44865 1 0.49672 1 0.0045574 1 0.0046095 1 0.85461 1 0.36056 1 3p gain 42 (12%) 316 0.53925 1 0.21493 1 0.0079748 1 0.00080209 0.569 0.74142 1 0.6165 1 0.13492 1 0.065087 1 0.88411 1 0.25139 1 3q gain 162 (45%) 196 0.071969 1 0.6531 1 0.023822 1 0.034291 1 0.49518 1 0.53657 1 0.44057 1 0.30541 1 0.72606 1 0.46491 1 4p gain 14 (4%) 344 0.1484 1 0.14985 1 0.02323 1 0.14883 1 0.19414 1 0.49317 1 0.012351 1 0.16277 1 1 1 0.92412 1 4q gain 7 (2%) 351 0.36322 1 1 1 0.45563 1 NA NA NA NA NA NA 0.76682 1 0.3559 1 0.60951 1 0.74029 1 5p gain 163 (46%) 195 0.88631 1 0.84628 1 0.00018495 0.135 0.023824 1 0.28218 1 0.3023 1 0.15037 1 0.60176 1 0.4408 1 0.12464 1 5q gain 34 (9%) 324 0.091217 1 0.37059 1 0.036728 1 0.041372 1 0.66077 1 0.57816 1 0.15364 1 0.39191 1 0.68061 1 0.079143 1 6p gain 31 (9%) 327 0.0010169 0.716 0.0085349 1 0.00522 1 0.35112 1 0.57973 1 0.23705 1 0.044452 1 0.0014127 0.982 0.92334 1 1 1 6q gain 19 (5%) 339 0.0032122 1 0.017402 1 0.0052616 1 0.028344 1 0.72102 1 0.55515 1 0.18584 1 0.0011177 0.782 0.69595 1 0.42265 1 7p gain 94 (26%) 264 0.12859 1 0.17084 1 4.075e-05 0.0302 0.001063 0.746 0.8081 1 0.86728 1 0.25497 1 0.099375 1 0.92224 1 0.0099388 1 7q gain 88 (25%) 270 0.065972 1 0.097862 1 4.5017e-11 3.49e-08 3.6029e-06 0.00273 0.62196 1 0.70035 1 0.022673 1 0.026029 1 0.38394 1 0.0016374 1 8p gain 47 (13%) 311 0.12873 1 0.14267 1 0.19393 1 0.70558 1 0.78294 1 0.42749 1 0.070516 1 0.004551 1 0.25053 1 0.17832 1 8q gain 101 (28%) 257 0.036525 1 0.024581 1 0.014142 1 0.082371 1 0.75626 1 0.87702 1 0.011459 1 0.0012792 0.892 0.08233 1 0.15975 1 9p gain 19 (5%) 339 0.28964 1 0.13856 1 0.10235 1 0.92965 1 0.17317 1 0.0002552 0.186 0.0096746 1 0.017195 1 0.43646 1 0.05322 1 9q gain 28 (8%) 330 0.069877 1 0.029367 1 0.034214 1 0.084003 1 0.075259 1 0.0024803 1 0.0017707 1 0.0014985 1 0.25357 1 0.041263 1 10p gain 16 (4%) 342 0.2079 1 1 1 0.5923 1 0.22402 1 0.4632 1 0.10702 1 0.5246 1 1 1 0.86928 1 0.82033 1 10q gain 6 (2%) 352 NA NA NA NA 0.52601 1 0.22273 1 0.10424 1 0.65065 1 0.57843 1 1 1 0.4934 1 1 1 11p gain 19 (5%) 339 0.90823 1 0.73368 1 0.87637 1 0.30594 1 0.79371 1 0.44486 1 0.8346 1 0.78914 1 0.43646 1 0.85224 1 11q gain 22 (6%) 336 0.041129 1 0.19349 1 0.20918 1 0.20665 1 0.94581 1 0.3808 1 0.43215 1 0.042257 1 0.85961 1 0.7551 1 12p gain 97 (27%) 261 0.014628 1 0.11889 1 1.7744e-05 0.0133 0.20845 1 0.18155 1 0.81732 1 0.15278 1 0.056541 1 0.77491 1 0.4886 1 12q gain 43 (12%) 315 0.029591 1 0.1428 1 2.3369e-05 0.0175 0.19635 1 0.14445 1 0.75934 1 0.53408 1 0.0086919 1 0.34848 1 0.28344 1 13q gain 8 (2%) 350 0.76867 1 1 1 0.60549 1 0.11755 1 0.28732 1 0.35113 1 0.13224 1 0.083452 1 0.7573 1 0.76466 1 14q gain 35 (10%) 323 0.086925 1 0.56842 1 0.94969 1 0.78048 1 0.86152 1 0.66415 1 0.34169 1 0.5218 1 0.080698 1 0.13884 1 15q gain 33 (9%) 325 0.2078 1 0.032532 1 0.010001 1 0.029594 1 0.21509 1 0.021403 1 0.0067201 1 0.057487 1 0.050167 1 0.0019332 1 16p gain 16 (4%) 342 0.58909 1 1 1 0.0009712 0.686 0.35504 1 0.72102 1 0.29146 1 0.52116 1 0.2662 1 0.86928 1 0.93367 1 16q gain 21 (6%) 337 0.23729 1 0.84377 1 8.244e-05 0.0608 0.62986 1 0.39681 1 0.12697 1 0.34511 1 0.73497 1 0.21787 1 0.59236 1 17p gain 9 (3%) 349 0.29798 1 0.08809 1 0.0037853 1 0.11755 1 0.068533 1 0.40643 1 0.35357 1 0.025972 1 0.28405 1 0.039515 1 17q gain 37 (10%) 321 0.012958 1 0.028176 1 1.0913e-07 8.32e-05 0.0033558 1 0.41942 1 0.75017 1 0.003283 1 0.0061884 1 0.52817 1 0.18562 1 18p gain 56 (16%) 302 0.0025961 1 9.5207e-06 0.00718 0.00024463 0.178 0.18518 1 0.13987 1 0.15047 1 0.039102 1 0.0097742 1 0.64855 1 0.10224 1 18q gain 39 (11%) 319 0.0024775 1 4.9465e-05 0.0367 0.0087195 1 0.65186 1 0.17522 1 0.060638 1 0.0087331 1 0.0040363 1 0.19332 1 0.055534 1 19p gain 35 (10%) 323 0.051591 1 0.16251 1 6.254e-05 0.0463 0.0046664 1 0.00049193 0.354 0.00194 1 0.069535 1 0.0086564 1 0.072342 1 0.3136 1 19q gain 50 (14%) 308 0.057664 1 0.7726 1 0.028504 1 0.69223 1 0.06802 1 0.021402 1 0.26977 1 0.077472 1 0.64232 1 0.95245 1 20p gain 97 (27%) 261 0.13174 1 0.037917 1 4.2859e-06 0.00324 0.05944 1 0.55805 1 0.28168 1 0.32182 1 0.32208 1 0.34252 1 0.014841 1 20q gain 88 (25%) 270 0.59314 1 0.46392 1 4.872e-06 0.00368 0.21554 1 0.76462 1 0.32782 1 0.10335 1 0.0031357 1 0.52293 1 0.018214 1 21q gain 18 (5%) 340 0.96811 1 0.42462 1 0.65475 1 0.03244 1 0.5776 1 0.96528 1 0.69725 1 0.35358 1 0.76091 1 0.1757 1 22q gain 84 (23%) 274 0.0036214 1 0.0085753 1 4.046e-05 0.0301 0.013083 1 0.25811 1 0.0075331 1 0.070527 1 0.056273 1 0.98288 1 0.012239 1 Xq gain 9 (3%) 349 0.76867 1 1 1 0.11583 1 0.62397 1 0.44953 1 0.58442 1 0.77288 1 0.15446 1 0.67831 1 0.21005 1 1p loss 52 (15%) 306 0.0024775 1 0.0004187 0.304 1.7728e-09 1.37e-06 1.1942e-06 0.000908 0.21129 1 0.12361 1 0.00076617 0.544 0.0070651 1 0.24255 1 0.021507 1 1q loss 9 (3%) 349 NA NA NA NA 0.24973 1 0.35508 1 0.73727 1 0.75546 1 0.38529 1 0.2856 1 1 1 0.81074 1 2p loss 3 (1%) 355 NA NA NA NA 0.30658 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2q loss 11 (3%) 347 0.39507 1 1 1 0.0039379 1 0.012553 1 0.73758 1 0.58442 1 0.76877 1 0.78818 1 0.54024 1 0.74177 1 3p loss 148 (41%) 210 0.050134 1 0.44773 1 6.6408e-05 0.0491 3.0921e-05 0.023 0.66763 1 0.23475 1 0.64893 1 0.023334 1 0.76848 1 0.084304 1 3q loss 26 (7%) 332 0.26082 1 0.70138 1 0.032875 1 0.059066 1 0.77369 1 0.94141 1 0.38396 1 0.076884 1 0.74473 1 0.91318 1 4p loss 149 (42%) 209 0.17085 1 0.031897 1 2.2628e-08 1.74e-05 3.56e-08 2.72e-05 0.061908 1 0.45626 1 0.44112 1 0.033125 1 0.29969 1 0.23246 1 4q loss 128 (36%) 230 0.0079594 1 0.00097462 0.687 1.2995e-09 1e-06 3.743e-06 0.00283 0.017669 1 0.19428 1 0.013676 1 0.00387 1 0.070216 1 0.0068404 1 5p loss 24 (7%) 334 0.19793 1 0.51386 1 0.026942 1 0.24759 1 0.30886 1 0.43803 1 0.72729 1 0.39286 1 1 1 0.82951 1 5q loss 137 (38%) 221 0.18503 1 0.36302 1 7.552e-08 5.77e-05 1.6484e-09 1.27e-06 0.10332 1 0.1077 1 0.24583 1 0.38198 1 0.44545 1 0.28648 1 6p loss 34 (9%) 324 0.079844 1 0.016367 1 0.00037315 0.271 0.0018796 1 0.075465 1 0.031057 1 0.0037054 1 0.0092401 1 0.52045 1 0.21245 1 6q loss 40 (11%) 318 0.08274 1 0.011644 1 0.002303 1 0.016915 1 0.074785 1 0.14213 1 0.064435 1 0.1167 1 1 1 0.82558 1 7p loss 22 (6%) 336 0.40774 1 0.83372 1 0.0025297 1 0.019565 1 0.50184 1 0.10885 1 0.46247 1 0.18677 1 0.096789 1 0.10443 1 7q loss 11 (3%) 347 0.47205 1 0.8485 1 0.074627 1 0.50859 1 1 1 0.69466 1 0.082478 1 0.044966 1 0.38277 1 0.37702 1 8p loss 105 (29%) 253 0.27633 1 0.39643 1 3.4931e-06 0.00265 0.01541 1 0.21675 1 0.96612 1 0.3975 1 0.52535 1 0.78688 1 0.52413 1 8q loss 12 (3%) 346 0.2079 1 0.26173 1 0.0094108 1 0.30261 1 0.29598 1 0.62935 1 0.30341 1 0.067364 1 0.25044 1 0.85023 1 9p loss 149 (42%) 209 0.059096 1 0.49841 1 1.1684e-11 9.09e-09 2.8124e-08 2.15e-05 0.91629 1 0.32487 1 0.93589 1 0.59406 1 0.93637 1 0.70982 1 9q loss 94 (26%) 264 0.0026004 1 0.003846 1 5.6792e-11 4.4e-08 1.0237e-05 0.00771 0.93688 1 0.27375 1 0.0012543 0.876 9.5625e-05 0.0704 0.31352 1 0.011887 1 10p loss 81 (23%) 277 0.054263 1 0.13391 1 7.5739e-08 5.78e-05 8.397e-07 0.000639 1 1 0.063843 1 0.0033998 1 0.01083 1 0.076949 1 0.00020129 0.147 10q loss 82 (23%) 276 0.0091286 1 0.00015338 0.112 4.1372e-11 3.21e-08 2.7478e-05 0.0205 0.16927 1 0.0026251 1 0.00050315 0.361 0.00088588 0.626 0.055077 1 0.00043695 0.316 11p loss 57 (16%) 301 0.011825 1 0.31148 1 0.00069311 0.493 0.00058281 0.415 0.045323 1 0.013425 1 0.14037 1 0.094103 1 0.87233 1 0.37189 1 11q loss 37 (10%) 321 0.32228 1 0.56841 1 3.0968e-05 0.023 0.0005716 0.408 0.069466 1 0.24561 1 0.048409 1 0.054028 1 0.38413 1 0.27294 1 12p loss 6 (2%) 352 NA NA NA NA 0.69034 1 0.17942 1 NA NA NA NA 0.22465 1 0.43092 1 0.43222 1 0.57106 1 12q loss 5 (1%) 353 NA NA NA NA 0.53198 1 0.17942 1 0.29619 1 0.43741 1 0.77511 1 0.091656 1 1 1 0.57106 1 13q loss 137 (38%) 221 0.20016 1 0.62629 1 1.2154e-08 9.33e-06 0.00047833 0.344 0.16163 1 0.35516 1 0.45238 1 0.58169 1 0.8083 1 0.041159 1 14q loss 67 (19%) 291 0.00058 0.414 0.021694 1 0.00049266 0.354 0.0011143 0.781 0.046073 1 0.016406 1 0.00010097 0.0742 6.4037e-09 4.92e-06 0.43363 1 0.061445 1 15q loss 40 (11%) 318 0.76434 1 0.11493 1 0.33612 1 0.0011491 0.803 0.0076185 1 0.00174 1 0.16922 1 0.011927 1 0.18777 1 0.35944 1 16p loss 55 (15%) 303 0.42164 1 0.42298 1 0.00016533 0.121 0.017551 1 0.41149 1 0.30133 1 0.33435 1 0.036748 1 0.30169 1 0.013348 1 16q loss 70 (20%) 288 0.065068 1 0.2372 1 0.0021031 1 0.011611 1 0.11136 1 0.17126 1 0.15364 1 0.0005197 0.372 0.90345 1 0.001294 0.901 17p loss 129 (36%) 229 0.10165 1 1 1 0.00012684 0.0931 7.3077e-05 0.0539 0.013307 1 0.112 1 0.49882 1 0.43679 1 0.19723 1 0.0021764 1 17q loss 22 (6%) 336 0.14736 1 0.19349 1 0.10382 1 0.012325 1 0.30306 1 0.94307 1 0.00084512 0.598 0.035177 1 0.8173 1 0.34969 1 18p loss 40 (11%) 318 0.83533 1 0.90723 1 0.013412 1 0.061173 1 0.27799 1 0.7177 1 0.021688 1 0.17933 1 0.66749 1 0.68581 1 18q loss 73 (20%) 285 0.58036 1 0.84409 1 0.0054811 1 0.1109 1 0.19345 1 0.56069 1 0.24372 1 0.91935 1 0.071808 1 0.98226 1 19p loss 60 (17%) 298 0.039371 1 0.045029 1 0.00047626 0.343 0.1852 1 0.70826 1 0.82708 1 0.0010458 0.735 2.3793e-05 0.0178 0.0021214 1 0.00044217 0.319 19q loss 40 (11%) 318 0.54085 1 0.2427 1 0.24893 1 0.022161 1 0.036643 1 0.11058 1 0.8114 1 0.13795 1 0.23457 1 0.34176 1 20p loss 17 (5%) 341 0.26792 1 0.023682 1 0.10135 1 0.20635 1 0.040797 1 0.57518 1 0.8022 1 0.59665 1 0.40102 1 0.3995 1 20q loss 20 (6%) 338 0.037591 1 0.020284 1 0.021311 1 0.14039 1 0.077419 1 0.46574 1 0.012559 1 0.010769 1 0.54089 1 0.16277 1 21q loss 111 (31%) 247 0.024673 1 0.016071 1 9.7269e-10 7.53e-07 1.3138e-05 0.00988 0.33796 1 0.22874 1 0.011505 1 0.015864 1 0.0096864 1 0.61048 1 22q loss 35 (10%) 323 0.05705 1 0.15715 1 0.50924 1 0.75426 1 0.60696 1 0.18797 1 0.45957 1 0.052444 1 0.10303 1 0.45872 1 Xq loss 14 (4%) 344 0.63366 1 1 1 0.4284 1 0.66447 1 0.28072 1 0.00042381 0.307 0.67435 1 0.85314 1 0.33458 1 0.31303 1