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 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 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 1p gain 58 (12%) 414 1 1 1 1 3.6007e-08 2.55e-05 0.00056497 0.359 0.081519 1 0.024133 1 0.22951 1 0.43329 1 0.54153 1 0.89021 1 1q gain 177 (38%) 295 0.46488 1 0.88479 1 0.035246 1 1.8806e-05 0.0127 0.13068 1 0.14618 1 0.082445 1 0.37626 1 0.49123 1 0.12238 1 2p gain 50 (11%) 422 0.03123 1 0.015087 1 6.9979e-08 4.95e-05 3.8879e-06 0.00268 0.078071 1 0.030149 1 0.032133 1 0.00078312 0.489 0.0018558 1 0.0050342 1 2q gain 45 (10%) 427 0.0302 1 0.025306 1 1.6942e-06 0.00118 7.9235e-07 0.000553 0.25214 1 0.27599 1 0.1102 1 0.017121 1 0.0055667 1 0.043863 1 3p gain 13 (3%) 459 NA NA NA NA 0.032214 1 0.046198 1 0.13709 1 0.27068 1 0.019844 1 0.17133 1 0.71961 1 0.29796 1 3q gain 29 (6%) 443 NA NA NA NA 0.002502 1 0.0023517 1 0.078299 1 0.022215 1 0.057657 1 0.50189 1 0.1038 1 0.21768 1 4p gain 30 (6%) 442 0.55363 1 0.41815 1 0.0035245 1 0.010189 1 0.072717 1 0.034995 1 0.75286 1 0.17232 1 0.21094 1 0.12834 1 4q gain 11 (2%) 461 NA NA NA NA 0.037947 1 0.83822 1 0.2221 1 0.27068 1 0.25101 1 0.089353 1 0.10105 1 0.041273 1 5p gain 178 (38%) 294 0.48692 1 0.4185 1 9.1029e-15 6.64e-12 0.15626 1 0.23307 1 0.63629 1 0.050236 1 0.12861 1 0.50057 1 0.66769 1 5q gain 56 (12%) 416 0.017738 1 0.64431 1 0.045138 1 0.00074201 0.466 0.54134 1 0.18722 1 0.033978 1 0.10639 1 0.13608 1 0.58744 1 6p gain 71 (15%) 401 0.29183 1 0.05069 1 0.01985 1 3.7746e-06 0.0026 0.0093568 1 0.26104 1 0.044557 1 0.22879 1 0.14082 1 0.097336 1 6q gain 20 (4%) 452 NA NA NA NA 0.40991 1 0.0096519 1 0.10777 1 0.064469 1 0.74606 1 0.59355 1 0.0606 1 0.0019832 1 7p gain 154 (33%) 318 0.75419 1 0.5228 1 3.0761e-18 2.25e-15 1.9669e-06 0.00137 8.9258e-05 0.0589 0.0094814 1 2.917e-08 2.07e-05 0.00010504 0.069 0.00075593 0.474 0.0034688 1 7q gain 111 (24%) 361 0.38828 1 0.70175 1 5.8646e-09 4.19e-06 0.0004719 0.302 0.078881 1 0.29831 1 1.3704e-05 0.00931 8.8709e-05 0.0586 0.052486 1 0.08103 1 8p gain 59 (12%) 413 NA NA NA NA 3.7361e-10 2.7e-07 0.0032345 1 0.59752 1 0.84164 1 0.005802 1 0.0092203 1 0.85939 1 0.084505 1 8q gain 144 (31%) 328 0.064056 1 0.19076 1 1.9041e-21 1.39e-18 3.3188e-07 0.000233 0.035664 1 0.0042398 1 0.00096998 0.6 0.0013896 0.852 1.6795e-05 0.0113 1.4583e-05 0.00989 9p gain 14 (3%) 458 NA NA NA NA 0.01734 1 0.011241 1 1 1 0.84262 1 0.014563 1 0.91325 1 0.71961 1 0.39763 1 9q gain 7 (1%) 465 NA NA NA NA 0.27415 1 0.5904 1 0.39223 1 0.26858 1 0.014299 1 0.39218 1 0.43904 1 0.34455 1 10p gain 49 (10%) 423 NA NA NA NA 0.041705 1 0.00011027 0.0723 0.16869 1 0.16046 1 0.3271 1 0.37843 1 0.13239 1 0.65653 1 10q gain 28 (6%) 444 NA NA NA NA 0.10669 1 0.023719 1 0.55524 1 0.18774 1 0.16048 1 0.16396 1 0.7009 1 0.18142 1 11p gain 35 (7%) 437 NA NA NA NA 0.052748 1 0.041882 1 0.1006 1 0.47594 1 0.58289 1 0.15677 1 0.077261 1 0.057367 1 11q gain 51 (11%) 421 0.11976 1 0.15726 1 0.00091473 0.568 0.013133 1 0.00082362 0.514 0.019571 1 0.030404 1 0.00182 1 0.0033017 1 0.005661 1 12p gain 57 (12%) 415 0.56496 1 0.13192 1 3.0173e-14 2.2e-11 8.574e-05 0.0568 0.17972 1 0.1154 1 0.010308 1 0.0007369 0.464 0.0062177 1 0.0065043 1 12q gain 46 (10%) 426 0.56496 1 0.13192 1 2.8963e-12 2.1e-09 0.00018438 0.12 0.15757 1 0.089273 1 0.02287 1 0.004544 1 0.021689 1 0.003944 1 13q gain 15 (3%) 457 NA NA NA NA 0.22626 1 0.027219 1 0.43272 1 0.29381 1 0.45464 1 0.12994 1 0.3984 1 0.9382 1 14q gain 56 (12%) 416 NA NA NA NA 4.9039e-06 0.00336 2.9768e-06 0.00206 0.12705 1 0.51774 1 0.00051885 0.331 0.0067847 1 0.012568 1 0.0056206 1 15q gain 14 (3%) 458 NA NA NA NA 0.26273 1 0.54151 1 0.81901 1 0.5781 1 0.10611 1 0.34098 1 0.92878 1 0.35106 1 16p gain 67 (14%) 405 0.35825 1 0.32152 1 0.32844 1 0.00034914 0.226 0.087838 1 0.44803 1 0.041951 1 0.048384 1 0.013574 1 0.036528 1 16q gain 42 (9%) 430 0.19234 1 0.051411 1 0.42796 1 0.0097721 1 0.025313 1 0.025242 1 0.15718 1 0.22442 1 0.13208 1 0.0018319 1 17p gain 28 (6%) 444 NA NA NA NA 8.7254e-06 0.00596 0.00042658 0.275 0.66456 1 0.53278 1 0.48494 1 0.88121 1 0.12916 1 0.56946 1 17q gain 78 (17%) 394 0.044722 1 0.70175 1 4.6891e-08 3.32e-05 1.3902e-06 0.000969 0.42297 1 0.19877 1 0.0095393 1 0.044701 1 0.060059 1 0.070639 1 18p gain 42 (9%) 430 NA NA NA NA 2.1329e-06 0.00148 0.0011183 0.691 0.071061 1 0.20947 1 0.22384 1 0.065175 1 0.024195 1 0.028095 1 18q gain 26 (6%) 446 NA NA NA NA 2.196e-05 0.0148 0.00060846 0.386 0.089952 1 0.037314 1 0.013885 1 0.0068186 1 0.099087 1 0.011389 1 19p gain 6 (1%) 466 NA NA NA NA 0.77335 1 0.37216 1 0.7761 1 1 1 0.86142 1 0.86399 1 0.20967 1 0.5892 1 19q gain 22 (5%) 450 NA NA NA NA 0.00046067 0.296 0.17589 1 0.40228 1 0.014388 1 0.99249 1 0.72181 1 0.023728 1 0.10393 1 20p gain 61 (13%) 411 0.023526 1 0.012653 1 3.0574e-06 0.00211 2.7756e-05 0.0186 0.024914 1 0.68732 1 0.00046548 0.298 0.00082577 0.514 0.069924 1 0.022081 1 20q gain 76 (16%) 396 0.0023737 1 0.0021899 1 4.7968e-07 0.000336 5.0053e-09 3.58e-06 0.0013155 0.809 0.091419 1 6.8393e-05 0.0453 0.0014122 0.864 0.0053017 1 0.010638 1 21q gain 41 (9%) 431 0.19234 1 0.15726 1 4.9992e-05 0.0332 3.4241e-05 0.0229 0.09138 1 0.052338 1 0.43821 1 0.058398 1 0.42274 1 0.39048 1 22q gain 20 (4%) 452 NA NA NA NA 0.060988 1 0.12997 1 0.78173 1 0.17219 1 0.55852 1 0.80578 1 0.022442 1 0.17922 1 Xq gain 19 (4%) 453 0.7496 1 0.59113 1 0.00023724 0.154 0.042457 1 0.43272 1 0.5983 1 0.057972 1 0.47969 1 0.37808 1 0.17922 1 1p loss 28 (6%) 444 NA NA NA NA 0.0044453 1 0.00021355 0.139 0.11126 1 0.19883 1 0.0073213 1 0.11958 1 0.46527 1 0.48921 1 1q loss 11 (2%) 461 NA NA NA NA 0.061871 1 0.081099 1 0.2221 1 0.015141 1 0.39442 1 0.094926 1 0.20381 1 0.29371 1 2p loss 6 (1%) 466 NA NA NA NA 0.93066 1 0.46619 1 1 1 0.61732 1 0.65456 1 0.57925 1 0.36946 1 1 1 2q loss 4 (1%) 468 NA NA NA NA 0.1486 1 0.22703 1 NA NA NA NA NA NA NA NA 1 1 0.48678 1 3p loss 93 (20%) 379 0.2081 1 0.17643 1 0.00045648 0.294 1.5326e-05 0.0104 0.15622 1 0.4015 1 0.042608 1 0.0059013 1 0.0096212 1 0.062539 1 3q loss 56 (12%) 416 0.55363 1 0.41815 1 0.010691 1 0.0033496 1 0.34086 1 0.93304 1 0.010293 1 0.29635 1 0.036624 1 0.57518 1 4p loss 38 (8%) 434 NA NA NA NA 1.2563e-05 0.00854 6.4378e-05 0.0427 0.19181 1 0.24819 1 9.9851e-05 0.0657 4.9084e-06 0.00336 0.0018334 1 0.059857 1 4q loss 45 (10%) 427 0.0060484 1 0.0070565 1 2.2044e-10 1.59e-07 4.2432e-07 0.000297 0.46872 1 0.5783 1 6.6428e-09 4.74e-06 1.8737e-09 1.34e-06 0.0015314 0.933 0.00072427 0.456 5p loss 15 (3%) 457 NA NA NA NA 0.006451 1 0.0080031 1 0.30598 1 0.77738 1 0.16176 1 0.040267 1 0.088793 1 0.029156 1 5q loss 58 (12%) 414 0.023526 1 0.012653 1 3.4011e-05 0.0228 1.0066e-05 0.00686 0.038819 1 0.098574 1 0.0014436 0.882 0.0082675 1 0.0059251 1 0.053257 1 6p loss 38 (8%) 434 0.33468 1 0.30806 1 0.025173 1 0.037418 1 0.20205 1 0.53707 1 0.36147 1 0.86316 1 0.33359 1 0.76003 1 6q loss 105 (22%) 367 0.80335 1 0.72164 1 0.070422 1 4.3992e-06 0.00303 0.1041 1 0.033507 1 0.015404 1 0.68616 1 0.24447 1 0.66427 1 7p loss 14 (3%) 458 0.55363 1 0.41815 1 0.0072296 1 0.31247 1 0.52239 1 0.93754 1 0.054262 1 0.11482 1 1 1 0.87174 1 7q loss 17 (4%) 455 0.52998 1 0.18587 1 0.030531 1 0.41084 1 0.68724 1 0.82053 1 0.28973 1 0.18619 1 0.73838 1 0.72635 1 8p loss 118 (25%) 354 0.10434 1 0.17288 1 4.7485e-14 3.45e-11 1.9961e-06 0.00139 0.1732 1 0.028147 1 0.0032526 1 0.025622 1 0.061846 1 0.02407 1 8q loss 17 (4%) 455 NA NA NA NA 0.00094334 0.585 0.090013 1 0.001241 0.766 0.0052641 1 0.55244 1 0.049171 1 0.72063 1 0.67667 1 9p loss 139 (29%) 333 0.15472 1 0.20593 1 2.7013e-08 1.92e-05 2.5852e-05 0.0173 0.34531 1 0.049049 1 0.15957 1 0.0072592 1 0.75693 1 0.30863 1 9q loss 117 (25%) 355 0.46164 1 0.47514 1 8.1724e-08 5.76e-05 1.0698e-08 7.62e-06 0.3234 1 0.144 1 0.056388 1 0.0065209 1 0.14693 1 0.0035211 1 10p loss 35 (7%) 437 0.90089 1 0.8178 1 0.00070668 0.446 0.00088884 0.553 0.052545 1 0.099122 1 0.14129 1 0.044292 1 0.023404 1 0.14638 1 10q loss 45 (10%) 427 0.7496 1 0.59113 1 0.0012414 0.766 0.0045419 1 0.015725 1 0.058513 1 0.077889 1 0.31418 1 0.26924 1 0.66884 1 11p loss 32 (7%) 440 0.33468 1 0.10222 1 0.0005298 0.337 0.84564 1 0.0045403 1 0.026834 1 0.013168 1 0.0020054 1 0.079305 1 0.17712 1 11q loss 29 (6%) 443 0.47379 1 0.15726 1 0.0027079 1 0.49977 1 0.010249 1 0.025131 1 0.21015 1 0.12562 1 0.32584 1 1 1 12p loss 37 (8%) 435 0.7282 1 0.8178 1 0.22911 1 0.00065309 0.413 0.81934 1 0.53401 1 0.0036641 1 0.51506 1 0.66013 1 0.40313 1 12q loss 23 (5%) 449 NA NA NA NA 0.078702 1 0.13092 1 0.88633 1 0.30468 1 0.90907 1 0.83913 1 0.86049 1 0.41612 1 13q loss 109 (23%) 363 0.084587 1 0.041059 1 3.554e-21 2.6e-18 6.4648e-07 0.000452 0.28492 1 0.0093561 1 0.10623 1 0.0005975 0.379 0.0042418 1 0.029906 1 14q loss 46 (10%) 426 0.40121 1 0.41815 1 0.0631 1 0.02449 1 0.030579 1 0.004879 1 0.5297 1 0.76642 1 0.23607 1 0.56153 1 15q loss 95 (20%) 377 0.40454 1 0.21903 1 5.2574e-12 3.81e-09 1.4103e-09 1.02e-06 0.48115 1 0.018752 1 0.0013241 0.813 3.6014e-05 0.024 0.00078019 0.488 9.7445e-05 0.0642 16p loss 37 (8%) 435 NA NA NA NA 0.0003069 0.199 0.001816 1 0.044709 1 0.28061 1 0.010634 1 0.075492 1 0.041468 1 0.052101 1 16q loss 56 (12%) 416 0.015881 1 1 1 4.6443e-06 0.00319 0.0014839 0.905 0.0059521 1 0.0085501 1 0.017919 1 0.14791 1 0.011571 1 0.12178 1 17p loss 109 (23%) 363 0.12966 1 0.30099 1 5.858e-06 0.00401 0.0035343 1 0.057179 1 0.20966 1 0.20048 1 0.70906 1 0.81923 1 0.46522 1 17q loss 17 (4%) 455 NA NA NA NA 0.1551 1 0.02222 1 0.066137 1 0.89735 1 0.058919 1 0.37054 1 0.67333 1 0.53357 1 18p loss 75 (16%) 397 0.41986 1 0.41218 1 1.1432e-05 0.00779 0.019843 1 0.88021 1 0.22337 1 0.44205 1 0.68965 1 0.88901 1 0.54548 1 18q loss 108 (23%) 364 0.41986 1 0.41218 1 1.6812e-09 1.21e-06 0.00016049 0.105 0.30099 1 0.12927 1 0.21554 1 0.1597 1 0.63156 1 0.98774 1 19p loss 112 (24%) 360 0.64867 1 0.68791 1 1.5576e-09 1.12e-06 7.1483e-08 5.05e-05 0.86711 1 0.68957 1 0.00063164 0.4 0.018333 1 0.00024033 0.156 0.056165 1 19q loss 67 (14%) 405 0.71049 1 0.72164 1 0.00019019 0.124 0.028818 1 0.77814 1 0.43291 1 0.073794 1 0.098059 1 0.020346 1 0.082573 1 20p loss 61 (13%) 411 0.19188 1 0.41218 1 0.00019416 0.126 0.053462 1 0.0063065 1 0.025187 1 0.1372 1 0.051839 1 0.61369 1 0.42287 1 20q loss 24 (5%) 448 NA NA NA NA 0.26161 1 0.13942 1 0.32479 1 0.3064 1 0.27637 1 0.87134 1 0.95141 1 0.14112 1 21q loss 66 (14%) 406 NA NA NA NA 3.0301e-12 2.2e-09 9.9995e-08 7.04e-05 0.10286 1 0.017555 1 6.5991e-09 4.71e-06 2.7593e-07 0.000194 1.4826e-05 0.01 2.3111e-05 0.0155 22q loss 90 (19%) 382 0.30751 1 0.32108 1 5.7463e-10 4.14e-07 4.5583e-05 0.0304 0.0090911 1 0.010973 1 0.00036353 0.234 0.00047578 0.304 0.0022101 1 0.00017034 0.111 Xq loss 11 (2%) 461 NA NA NA NA 0.25276 1 0.28051 1 0.7403 1 0.57183 1 0.32382 1 0.25499 1 0.65969 1 0.69312 1