Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 46 (8%) 543 0.24048 1 0.40761 1 0.0074223 1 0.47524 1 0.0053473 1 0.09229 1 0.98888 1 0.28255 1 0.30545 1 0.55162 1 0.036707 1 0.56053 1 1q gain 113 (19%) 476 0.7587 1 0.90665 1 0.005774 1 0.33632 1 0.12604 1 0.13115 1 0.79587 1 0.11002 1 0.17124 1 0.066956 1 0.015153 1 0.72526 1 2p gain 114 (19%) 475 0.041423 1 0.005163 1 0.00027062 0.223 0.006087 1 0.61735 1 0.33039 1 2.171e-06 0.0019 0.001195 0.944 0.044918 1 0.0091987 1 0.24264 1 0.00078563 0.626 2q gain 112 (19%) 477 0.027306 1 0.0018266 1 6.3189e-06 0.00548 0.0015665 1 0.64465 1 0.56966 1 0.00025186 0.208 0.0012149 0.957 0.1114 1 0.042873 1 0.41892 1 0.042105 1 3p gain 68 (12%) 521 0.014939 1 0.54055 1 1.9102e-05 0.0164 0.14905 1 0.1268 1 0.23352 1 0.3945 1 0.16606 1 0.14761 1 0.23122 1 0.06003 1 0.55638 1 3q gain 94 (16%) 495 0.036045 1 0.039924 1 6.0974e-10 5.51e-07 0.0077158 1 0.12491 1 0.20701 1 0.018475 1 0.010554 1 0.044201 1 0.42389 1 0.0048624 1 0.74549 1 4p gain 17 (3%) 572 0.81462 1 0.46238 1 0.0046022 1 0.26878 1 0.1541 1 0.20676 1 0.075098 1 0.4563 1 0.55661 1 1 1 0.25691 1 0.09313 1 4q gain 19 (3%) 570 0.22764 1 0.25959 1 0.052058 1 0.79346 1 0.11399 1 0.43884 1 0.13668 1 0.025681 1 0.32773 1 0.084118 1 0.05548 1 0.77137 1 5p gain 98 (17%) 491 0.49441 1 0.72949 1 0.00094642 0.751 0.85615 1 0.19792 1 0.88472 1 0.01507 1 0.0099944 1 0.80177 1 0.89014 1 0.015274 1 0.95755 1 5q gain 62 (11%) 527 0.75836 1 0.90115 1 0.0022064 1 0.7552 1 0.71323 1 0.79154 1 0.23395 1 0.10475 1 0.73253 1 0.28756 1 0.28612 1 0.44025 1 6p gain 119 (20%) 470 0.015059 1 0.0033683 1 3.141e-09 2.82e-06 0.22534 1 0.85065 1 0.74025 1 0.093643 1 0.01317 1 0.45145 1 0.8922 1 0.013502 1 0.3174 1 6q gain 106 (18%) 483 0.16276 1 0.045263 1 7.5961e-10 6.85e-07 0.243 1 0.822 1 0.24976 1 0.14605 1 0.052003 1 0.35185 1 0.44453 1 0.0026724 1 0.20734 1 7p gain 334 (57%) 255 0.00046068 0.374 0.00033861 0.277 3.2833e-21 3.05e-18 4.7496e-06 0.00414 0.009025 1 0.030065 1 1.6325e-08 1.46e-05 3.3573e-09 3.01e-06 0.0058437 1 0.0043971 1 7.2913e-06 0.00631 0.53211 1 7q gain 298 (51%) 291 0.00015805 0.132 0.0016669 1 2.0285e-13 1.86e-10 0.00025039 0.207 0.13355 1 0.10628 1 1.6248e-07 0.000145 3.471e-07 0.000307 0.013238 1 0.043049 1 4.6923e-05 0.0399 0.22709 1 8p gain 163 (28%) 426 0.91468 1 0.43181 1 8.5816e-08 7.68e-05 0.89914 1 0.44452 1 0.022446 1 0.0013276 1 0.0024394 1 0.23121 1 0.15173 1 0.76497 1 0.17716 1 8q gain 303 (51%) 286 0.34689 1 0.011443 1 4.7025e-39 4.41e-36 0.021176 1 0.0885 1 0.12544 1 2.4191e-05 0.0208 1.1053e-05 0.00953 0.3568 1 0.36894 1 0.061456 1 0.27519 1 9p gain 116 (20%) 473 0.53714 1 0.79299 1 0.41201 1 0.5322 1 0.12763 1 0.41733 1 0.82591 1 0.21593 1 0.97693 1 0.62098 1 0.082945 1 0.6831 1 9q gain 98 (17%) 491 0.64167 1 0.37485 1 0.71477 1 0.80341 1 0.091975 1 0.24353 1 0.93519 1 0.76969 1 0.55935 1 0.94138 1 0.7152 1 0.90328 1 10p gain 44 (7%) 545 0.10926 1 0.56883 1 0.10655 1 0.89198 1 0.10916 1 0.13667 1 0.55403 1 0.26258 1 0.48765 1 0.14825 1 0.041226 1 0.42185 1 10q gain 24 (4%) 565 0.91122 1 0.4311 1 0.75967 1 0.12251 1 0.16938 1 0.46482 1 0.99014 1 0.91528 1 0.49063 1 0.68427 1 0.12602 1 0.81223 1 11p gain 80 (14%) 509 0.013124 1 0.03059 1 1.2023e-07 0.000107 0.00010305 0.0864 0.66089 1 0.59085 1 0.00077054 0.615 0.00027616 0.227 0.283 1 0.092212 1 0.0082716 1 0.67236 1 11q gain 73 (12%) 516 0.017275 1 0.010779 1 1.66e-07 0.000148 8.0135e-05 0.0676 0.19428 1 0.59583 1 1.0178e-06 0.000896 3.2586e-06 0.00284 0.29742 1 0.067559 1 0.0001277 0.107 0.23656 1 12p gain 123 (21%) 466 0.35104 1 0.71686 1 0.03529 1 0.0051821 1 0.52921 1 0.81694 1 0.83527 1 0.74221 1 0.50628 1 0.54832 1 0.19191 1 0.58095 1 12q gain 107 (18%) 482 0.24943 1 0.77616 1 0.024253 1 0.003087 1 0.57186 1 0.77509 1 0.49192 1 0.4987 1 0.33845 1 0.27927 1 0.073592 1 0.13489 1 13q gain 354 (60%) 235 4.1087e-07 0.000363 5.3813e-05 0.0456 2.9839e-35 2.8e-32 1.7807e-07 0.000158 0.24329 1 0.42157 1 1.2604e-07 0.000112 5.8117e-07 0.000512 0.00063131 0.506 0.34974 1 3.1882e-07 0.000282 0.047728 1 14q gain 42 (7%) 547 0.73514 1 0.35174 1 0.31776 1 0.85144 1 0.78023 1 0.88516 1 0.38004 1 0.82113 1 0.86715 1 0.61974 1 0.58519 1 0.79979 1 15q gain 14 (2%) 575 0.29716 1 0.28202 1 0.042499 1 0.71421 1 0.17348 1 0.27174 1 0.93406 1 1 1 1 1 0.76198 1 0.71493 1 0.42444 1 16p gain 141 (24%) 448 0.011838 1 0.037312 1 8.6052e-20 7.98e-17 0.013968 1 0.16496 1 0.21803 1 5.5413e-05 0.0469 3.3554e-05 0.0287 0.47157 1 0.95823 1 0.015656 1 0.20784 1 16q gain 138 (23%) 451 0.0085513 1 0.013895 1 6.5492e-21 6.08e-18 0.025842 1 0.23207 1 0.20277 1 0.00018563 0.154 1.6977e-05 0.0146 0.7916 1 0.84258 1 0.0028079 1 0.072219 1 17p gain 35 (6%) 554 0.44149 1 0.027856 1 0.63934 1 1 1 0.19978 1 0.94963 1 0.28522 1 0.45696 1 0.16141 1 0.79963 1 0.58603 1 0.51895 1 17q gain 106 (18%) 483 0.011996 1 0.012137 1 9.1945e-05 0.0775 0.0060374 1 0.27536 1 0.26579 1 5.6865e-06 0.00494 0.007229 1 0.0023926 1 0.094835 1 0.39347 1 0.52134 1 18p gain 30 (5%) 559 0.30855 1 0.10087 1 0.0082763 1 0.00026766 0.221 0.60184 1 0.68387 1 0.081913 1 0.019516 1 0.60525 1 0.14619 1 0.11989 1 0.74827 1 18q gain 19 (3%) 570 0.044864 1 0.023098 1 0.069822 1 0.00060924 0.489 0.67272 1 0.36383 1 0.019469 1 0.069445 1 0.23903 1 0.15362 1 0.042166 1 0.90369 1 19p gain 99 (17%) 490 0.41647 1 0.32944 1 3.206e-06 0.0028 0.047994 1 0.1604 1 0.19184 1 0.26594 1 0.094881 1 0.07924 1 0.31757 1 0.074635 1 0.1231 1 19q gain 107 (18%) 482 0.077843 1 0.034498 1 6.6552e-05 0.0562 0.083222 1 0.03203 1 0.28105 1 0.56538 1 0.23692 1 0.29927 1 0.75279 1 0.10025 1 0.078013 1 20p gain 338 (57%) 251 0.0002405 0.199 1.7429e-06 0.00153 5.1105e-10 4.62e-07 0.00027201 0.224 0.018701 1 0.16289 1 0.00010816 0.0905 0.00059661 0.48 0.34273 1 0.60892 1 0.00065606 0.526 0.75929 1 20q gain 446 (76%) 143 1.2527e-13 1.15e-10 5.159e-13 4.71e-10 1.044e-33 9.77e-31 1.0478e-17 9.67e-15 0.0052665 1 0.012784 1 1.4524e-18 1.34e-15 3.412e-14 3.13e-11 0.020272 1 0.1513 1 4.7978e-12 4.37e-09 0.00047566 0.386 21q gain 31 (5%) 558 0.31161 1 0.57994 1 0.042641 1 0.62687 1 0.48693 1 0.31818 1 0.81416 1 0.35113 1 0.41695 1 0.51259 1 0.25253 1 0.86135 1 22q gain 22 (4%) 567 0.11691 1 0.32339 1 0.051264 1 0.41867 1 0.84305 1 0.45925 1 0.17082 1 0.19769 1 0.66855 1 0.30206 1 0.13031 1 0.95612 1 xq gain 101 (17%) 488 0.25826 1 0.60489 1 0.00018572 0.154 0.19732 1 0.10967 1 0.042472 1 0.47467 1 0.16854 1 0.35144 1 0.96222 1 0.69627 1 0.45734 1 1p loss 130 (22%) 459 0.066725 1 0.036989 1 1.9218e-07 0.000171 0.00057925 0.467 0.98364 1 0.60943 1 0.0037351 1 2.1478e-05 0.0184 0.28624 1 0.11511 1 0.044948 1 0.026429 1 1q loss 73 (12%) 516 0.23595 1 0.054492 1 9.6918e-06 0.00837 0.31196 1 0.85991 1 0.73533 1 0.00027602 0.227 0.0015024 1 0.7461 1 0.029614 1 0.13306 1 0.0073048 1 2p loss 17 (3%) 572 1 1 0.85829 1 0.0016008 1 0.045157 1 0.34711 1 1 1 0.21322 1 0.064196 1 0.096144 1 0.11261 1 0.74121 1 0.7046 1 2q loss 13 (2%) 576 0.80524 1 0.41119 1 0.030534 1 0.26277 1 0.53458 1 0.66563 1 0.41333 1 0.042945 1 0.16001 1 0.049563 1 0.19737 1 0.68605 1 3p loss 65 (11%) 524 0.34946 1 0.62337 1 0.53624 1 0.39256 1 0.53417 1 0.75729 1 0.76991 1 0.30998 1 0.7605 1 0.10732 1 0.060853 1 0.16678 1 3q loss 42 (7%) 547 0.24561 1 0.029158 1 0.45726 1 0.1914 1 0.32385 1 0.83552 1 0.71194 1 0.50877 1 0.5814 1 0.11746 1 0.33717 1 0.38029 1 4p loss 185 (31%) 404 0.02913 1 0.13668 1 4.229e-12 3.85e-09 0.00093269 0.741 0.4752 1 0.81914 1 0.00028949 0.237 2.7132e-05 0.0233 0.080997 1 0.082261 1 6.2816e-05 0.0531 0.15137 1 4q loss 178 (30%) 411 0.042373 1 0.15915 1 1.2145e-14 1.12e-11 5.4567e-06 0.00475 0.75577 1 0.5067 1 0.0005695 0.46 0.00010051 0.0844 0.10437 1 0.053148 1 0.0010358 0.82 0.010679 1 5p loss 80 (14%) 509 0.37111 1 0.91249 1 0.00054082 0.438 0.018453 1 0.68463 1 0.10753 1 0.788 1 0.070446 1 1 1 0.44514 1 0.10894 1 0.013983 1 5q loss 113 (19%) 476 0.0093405 1 0.11021 1 1.9633e-06 0.00172 0.031843 1 0.1132 1 0.60847 1 0.024447 1 0.00071064 0.568 0.62294 1 0.11563 1 0.00055911 0.452 0.020957 1 6p loss 45 (8%) 544 0.54892 1 0.36977 1 0.16088 1 0.8537 1 0.072745 1 0.2054 1 0.90337 1 0.2792 1 0.46672 1 0.55162 1 0.068306 1 0.071587 1 6q loss 67 (11%) 522 0.43263 1 0.23862 1 0.10104 1 0.51127 1 0.22991 1 0.20829 1 0.28221 1 0.25473 1 0.512 1 0.252 1 0.78488 1 0.5559 1 7q loss 4 (1%) 585 NA NA NA NA 0.097955 1 1 1 1 1 0.62605 1 0.57387 1 1 1 1 1 0.52554 1 NA NA NA NA 8p loss 206 (35%) 383 0.0092326 1 0.0074436 1 6.0208e-29 5.63e-26 3.8578e-05 0.0329 0.32768 1 0.0081001 1 0.0032866 1 0.0039646 1 0.54342 1 0.11398 1 0.0010243 0.812 0.038311 1 8q loss 31 (5%) 558 0.6828 1 0.88811 1 0.042698 1 0.63732 1 0.85314 1 0.89494 1 0.37826 1 0.13015 1 0.61735 1 0.68588 1 0.54133 1 0.27293 1 9p loss 71 (12%) 518 0.47593 1 0.26112 1 0.00034373 0.28 0.004475 1 0.83739 1 0.036226 1 0.00037662 0.307 0.006601 1 0.20257 1 0.041058 1 0.001528 1 0.074934 1 9q loss 70 (12%) 519 0.049763 1 0.035581 1 4.7449e-05 0.0403 0.001233 0.969 0.92893 1 0.03213 1 0.00018677 0.155 0.010566 1 0.4665 1 0.022016 1 0.00021189 0.176 0.021792 1 10p loss 96 (16%) 493 0.011786 1 0.10842 1 3.5005e-07 0.000309 0.030935 1 0.018113 1 0.73635 1 0.00049742 0.403 0.001426 1 0.2112 1 0.11998 1 0.020268 1 0.0036791 1 10q loss 104 (18%) 485 0.023525 1 0.29324 1 5.212e-12 4.74e-09 0.010214 1 0.013772 1 0.36713 1 0.00011884 0.0993 4.9251e-05 0.0418 0.68366 1 0.21886 1 0.00043396 0.353 0.00058243 0.469 11p loss 73 (12%) 516 0.94301 1 0.60472 1 0.0574 1 0.097489 1 0.50881 1 0.87144 1 0.90397 1 0.19231 1 0.96497 1 0.33883 1 0.087837 1 0.26016 1 11q loss 89 (15%) 500 0.82945 1 0.90263 1 0.016037 1 0.015598 1 0.9498 1 0.75809 1 0.98947 1 0.65488 1 0.79563 1 0.089433 1 0.14944 1 0.41756 1 12p loss 68 (12%) 521 0.069775 1 0.097003 1 7.7955e-10 7.02e-07 0.15905 1 0.86358 1 0.42418 1 0.079253 1 0.023688 1 0.81771 1 0.91819 1 0.0062379 1 0.11255 1 12q loss 68 (12%) 521 0.12959 1 0.050629 1 1.1212e-09 1.01e-06 0.10881 1 0.62464 1 0.71321 1 0.015392 1 0.0089447 1 0.26753 1 0.60067 1 0.0080598 1 0.075926 1 13q loss 20 (3%) 569 0.29721 1 0.13239 1 0.039125 1 0.39041 1 0.29241 1 0.070624 1 0.73969 1 0.22917 1 0.7416 1 0.6608 1 0.018895 1 0.20385 1 14q loss 193 (33%) 396 0.00026442 0.218 4.4526e-05 0.0379 6.7977e-27 6.35e-24 1.8771e-06 0.00164 0.0025846 1 0.098607 1 7.2619e-11 6.59e-08 3.6011e-05 0.0308 0.13322 1 0.96328 1 1.1967e-07 0.000107 0.11762 1 15q loss 217 (37%) 372 0.00010248 0.086 0.0011656 0.922 1.749e-21 1.63e-18 0.0012245 0.964 0.2369 1 0.37928 1 1.0841e-05 0.00936 4.2118e-07 0.000371 0.82509 1 0.61834 1 6.4843e-06 0.00562 0.23349 1 16p loss 36 (6%) 553 0.10712 1 0.076341 1 0.57536 1 1 1 0.22793 1 0.18423 1 0.70647 1 0.178 1 0.63235 1 0.28129 1 0.8254 1 0.48894 1 16q loss 39 (7%) 550 0.026713 1 0.24208 1 0.039063 1 0.63726 1 0.24851 1 0.26976 1 0.91841 1 0.76259 1 0.56309 1 0.67537 1 1 1 0.95508 1 17p loss 323 (55%) 266 2.7798e-05 0.0238 0.00044806 0.364 3.1325e-26 2.92e-23 2.3731e-08 2.13e-05 0.12235 1 0.11056 1 1.0203e-06 0.000897 2.7161e-07 0.000241 0.035294 1 0.036562 1 1.0579e-06 0.000929 0.27645 1 17q loss 85 (14%) 504 0.9595 1 0.48536 1 0.02425 1 0.3081 1 0.80252 1 0.81027 1 0.79999 1 0.034301 1 0.83456 1 0.46821 1 0.11706 1 0.19014 1 18p loss 362 (61%) 227 1.9112e-12 1.74e-09 3.5402e-10 3.21e-07 1.7086e-39 1.6e-36 2.2366e-22 2.08e-19 0.028551 1 0.01799 1 9.4783e-22 8.82e-19 7.1857e-17 6.63e-14 0.0097903 1 0.48502 1 3.3899e-16 3.12e-13 0.00030672 0.251 18q loss 388 (66%) 201 1.3893e-11 1.26e-08 3.6762e-10 3.33e-07 1.088e-40 1.02e-37 9.3792e-20 8.69e-17 0.049327 1 0.083795 1 3.9644e-18 3.66e-15 1.663e-15 1.53e-12 0.00083374 0.664 0.1282 1 6.0937e-14 5.59e-11 0.0013721 1 19p loss 61 (10%) 528 0.37266 1 0.20154 1 9.6847e-05 0.0814 0.35437 1 0.68944 1 0.77717 1 0.085089 1 0.011998 1 0.15656 1 0.00015589 0.13 0.48673 1 0.013793 1 19q loss 53 (9%) 536 0.65173 1 0.017995 1 0.0012008 0.947 0.70986 1 0.12049 1 0.88066 1 0.13481 1 0.031826 1 0.21586 1 0.0015004 1 0.23593 1 0.077242 1 20p loss 61 (10%) 528 0.1157 1 0.35453 1 0.0050509 1 0.029476 1 0.77676 1 0.7131 1 0.15826 1 0.043342 1 0.73884 1 0.96717 1 0.10561 1 0.039557 1 20q loss 5 (1%) 584 NA NA NA NA 0.87838 1 0.18428 1 0.093893 1 0.6491 1 0.39639 1 0.73222 1 0.82802 1 1 1 NA NA NA NA 21q loss 184 (31%) 405 0.026489 1 0.038986 1 5.9449e-06 0.00516 0.018896 1 0.70392 1 0.090404 1 9.3295e-05 0.0786 0.001461 1 0.1244 1 0.075744 1 0.0027422 1 0.1651 1 22q loss 193 (33%) 396 0.0051952 1 0.0054946 1 4.4667e-13 4.08e-10 0.024187 1 0.77586 1 0.90831 1 0.03142 1 0.01016 1 0.96405 1 0.37968 1 0.00069589 0.557 0.16997 1 xq loss 71 (12%) 518 0.98545 1 0.95618 1 0.053944 1 0.035357 1 0.054814 1 0.24496 1 0.65257 1 0.28016 1 0.055709 1 0.17348 1 0.53812 1 0.1667 1