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 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 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 1p gain 23 (4%) 491 1 1 1 1 1.2977e-07 0.000104 0.001635 1 0.0013723 0.878 0.0061724 1 0.011148 1 0.0019676 1 0.00057185 0.385 0.26083 1 0.024995 1 0.024438 1 1q gain 51 (10%) 463 0.41028 1 0.41105 1 1.739e-15 1.51e-12 0.036895 1 0.087509 1 0.031246 1 1.8455e-05 0.0137 0.0003644 0.251 2.1621e-05 0.016 0.95431 1 0.030816 1 0.012968 1 2p gain 76 (15%) 438 0.56067 1 0.40029 1 2.5277e-09 2.08e-06 0.20097 1 0.011792 1 0.87127 1 0.16516 1 0.035061 1 0.64367 1 0.092769 1 0.068226 1 0.092169 1 2q gain 77 (15%) 437 0.56067 1 0.40029 1 2.1372e-07 0.00017 0.29955 1 0.011511 1 0.93353 1 0.15625 1 0.035353 1 0.71198 1 0.092769 1 0.14957 1 0.06886 1 3p gain 20 (4%) 494 0.053628 1 0.062305 1 0.00038028 0.262 0.58508 1 0.044393 1 0.00059042 0.396 0.0050634 1 0.0021316 1 6.1301e-05 0.0443 0.00020037 0.141 0.0020248 1 0.062799 1 3q gain 60 (12%) 454 0.012193 1 0.018801 1 2.992e-11 2.52e-08 0.011088 1 0.0005637 0.38 5.9745e-07 0.000468 1.3025e-05 0.00979 1.8656e-06 0.00144 1.4503e-08 1.18e-05 4.11e-06 0.00313 0.00018116 0.128 0.11098 1 4p gain 13 (3%) 501 NA NA NA NA 0.066822 1 0.377 1 0.25321 1 0.0017483 1 0.00041753 0.285 0.069184 1 0.00020836 0.146 0.022606 1 0.04843 1 6.8806e-05 0.0495 4q gain 13 (3%) 501 NA NA NA NA 0.27281 1 0.4491 1 0.25321 1 0.020053 1 0.00041753 0.285 0.14424 1 0.00020836 0.146 0.022606 1 0.04843 1 6.8806e-05 0.0495 5p gain 190 (37%) 324 0.83527 1 0.77796 1 0.00010055 0.0719 0.17234 1 0.084287 1 0.11267 1 0.01276 1 0.00077043 0.509 0.10875 1 0.80736 1 0.12817 1 0.54011 1 5q gain 204 (40%) 310 0.29223 1 0.21196 1 0.0072302 1 0.38892 1 0.39791 1 0.10276 1 0.073103 1 0.004592 1 0.56599 1 0.36722 1 0.22025 1 0.41665 1 6p gain 11 (2%) 503 NA NA NA NA 0.20224 1 0.34049 1 0.067197 1 0.58657 1 0.79359 1 0.84603 1 0.79606 1 1 1 0.84479 1 0.25694 1 6q gain 9 (2%) 505 NA NA NA NA 0.092594 1 0.56926 1 0.01678 1 0.76641 1 1 1 1 1 1 1 0.77855 1 1 1 0.44652 1 7p gain 168 (33%) 346 0.41594 1 0.57703 1 9.5326e-14 8.24e-11 0.006273 1 1.608e-05 0.012 0.001785 1 0.00012737 0.0908 0.0018137 1 0.0063545 1 0.64774 1 0.03771 1 0.26091 1 7q gain 169 (33%) 345 0.41594 1 0.57703 1 1.2362e-13 1.06e-10 0.015616 1 2.7813e-05 0.0205 0.00069173 0.461 0.00014448 0.102 0.0015943 1 0.0079715 1 0.42935 1 0.052025 1 0.037532 1 8p gain 31 (6%) 483 NA NA NA NA 6.2901e-09 5.13e-06 0.00096443 0.627 0.0095995 1 0.20166 1 1.9133e-05 0.0142 0.00032891 0.227 6.9829e-06 0.00529 0.005817 1 0.005203 1 0.048524 1 8q gain 59 (11%) 455 0.22618 1 0.32459 1 9.2983e-19 8.15e-16 6.5387e-06 0.00496 5.2134e-05 0.0379 0.021314 1 8.3582e-12 7.08e-09 1.1988e-09 9.88e-07 6.4942e-11 5.44e-08 0.0024 1 6.5068e-07 0.000508 0.0025459 1 9p gain 13 (3%) 501 NA NA NA NA 0.010615 1 0.90154 1 0.80592 1 0.71552 1 0.23751 1 0.40884 1 0.93798 1 0.016571 1 0.72708 1 0.52894 1 9q gain 12 (2%) 502 NA NA NA NA 0.00080601 0.53 0.8353 1 0.56846 1 0.29075 1 0.25124 1 0.55519 1 0.80609 1 0.028855 1 1 1 0.73698 1 10p gain 17 (3%) 497 NA NA NA NA 0.00092871 0.606 0.11259 1 0.27557 1 0.47235 1 0.00083984 0.551 0.00017957 0.127 0.074982 1 0.43347 1 0.46558 1 0.1385 1 10q gain 12 (2%) 502 NA NA NA NA 0.0011718 0.756 0.082229 1 0.067334 1 0.54603 1 0.014208 1 0.0075141 1 0.07645 1 0.34781 1 0.37319 1 0.27049 1 11p gain 31 (6%) 483 0.23165 1 0.25217 1 1.4164e-05 0.0106 0.30823 1 0.19528 1 0.24639 1 0.29046 1 0.18161 1 0.31251 1 0.02754 1 0.2054 1 0.33024 1 11q gain 29 (6%) 485 0.34099 1 0.53903 1 0.00027581 0.191 0.18751 1 0.4232 1 0.51319 1 0.54853 1 0.483 1 0.59303 1 0.021835 1 0.52254 1 0.24327 1 12p gain 120 (23%) 394 0.012874 1 0.014228 1 9.5341e-14 8.24e-11 0.00017395 0.123 1.3367e-12 1.14e-09 0.0010333 0.67 1.9085e-11 1.61e-08 2.3652e-12 2.01e-09 1.0992e-10 9.16e-08 0.023612 1 7.3513e-08 5.91e-05 0.0059756 1 12q gain 120 (23%) 394 0.012874 1 0.014228 1 1.7388e-13 1.49e-10 0.00011834 0.0845 1.8657e-13 1.6e-10 0.00043125 0.293 6.3994e-11 5.36e-08 2.3652e-12 2.01e-09 3.2044e-11 2.69e-08 0.051759 1 7.3513e-08 5.91e-05 0.0059756 1 13q gain 22 (4%) 492 NA NA NA NA 0.24913 1 0.010383 1 0.64797 1 0.56881 1 0.074695 1 0.51241 1 0.43162 1 0.71238 1 0.93097 1 0.17829 1 14q gain 16 (3%) 498 0.76851 1 0.78254 1 0.0012732 0.82 0.32823 1 0.012121 1 0.0069981 1 0.019591 1 0.04921 1 0.0098736 1 0.0052486 1 0.37319 1 0.013885 1 15q gain 26 (5%) 488 1 1 1 1 0.0010562 0.683 0.59897 1 0.45203 1 0.15002 1 0.63015 1 0.85627 1 0.67295 1 0.28434 1 0.48932 1 0.36945 1 16p gain 107 (21%) 407 0.28203 1 0.33712 1 0.00082708 0.543 0.39878 1 0.0014674 0.936 0.04981 1 0.013888 1 0.0052391 1 0.06864 1 0.68745 1 0.12292 1 0.27505 1 16q gain 99 (19%) 415 0.23296 1 0.21777 1 0.00043863 0.297 0.22724 1 0.0023038 1 0.063492 1 0.012236 1 0.024196 1 0.024285 1 0.5168 1 0.0301 1 0.31629 1 17p gain 25 (5%) 489 0.018559 1 0.034912 1 2.8378e-05 0.0209 0.72735 1 0.32918 1 0.073361 1 0.23738 1 0.058921 1 0.29576 1 0.055509 1 0.29142 1 0.13384 1 17q gain 31 (6%) 483 0.069157 1 0.098773 1 8.0483e-05 0.0578 0.39423 1 0.49259 1 0.076145 1 0.13418 1 0.017119 1 0.18229 1 0.031931 1 0.11168 1 0.066682 1 18p gain 25 (5%) 489 0.31209 1 0.25229 1 0.081021 1 0.40519 1 0.83155 1 0.19135 1 0.076104 1 0.93608 1 0.68709 1 0.64179 1 0.69148 1 0.17698 1 18q gain 25 (5%) 489 0.31209 1 0.25229 1 0.11692 1 0.41315 1 0.73299 1 0.51027 1 0.076104 1 0.93608 1 0.85862 1 0.64179 1 0.69148 1 0.17698 1 19p gain 51 (10%) 463 0.22618 1 0.32459 1 1.9806e-09 1.63e-06 0.0025242 1 0.009356 1 0.052125 1 0.0046699 1 0.0027681 1 0.00019168 0.135 0.0088533 1 0.026056 1 0.94211 1 19q gain 57 (11%) 457 0.10193 1 0.14864 1 2.3573e-11 1.99e-08 0.00028698 0.199 0.0010206 0.662 0.0061868 1 0.0019696 1 0.0007751 0.512 2.9682e-05 0.0218 0.0033262 1 0.008053 1 0.82835 1 20p gain 111 (22%) 403 0.11564 1 0.16346 1 7.5684e-22 6.67e-19 5.6154e-05 0.0408 1.0713e-07 8.58e-05 0.0017354 1 1.1463e-12 9.78e-10 2.1646e-12 1.84e-09 3.3246e-10 2.76e-07 0.00024148 0.169 6.1763e-07 0.000484 0.031619 1 20q gain 114 (22%) 400 0.045714 1 0.06749 1 2.8202e-23 2.49e-20 5.6154e-05 0.0408 6.7616e-09 5.51e-06 0.00089632 0.586 2.6207e-14 2.27e-11 1.8956e-13 1.62e-10 3.5466e-11 2.98e-08 0.00015388 0.109 2.7048e-07 0.000214 0.019653 1 21q gain 50 (10%) 464 0.26897 1 0.27964 1 3.4252e-06 0.00262 0.0086674 1 0.0011012 0.711 0.50897 1 0.00070514 0.469 0.0018901 1 0.0090762 1 1 1 0.057446 1 0.14145 1 22q gain 40 (8%) 474 0.32729 1 0.028901 1 5.7764e-05 0.0418 0.67931 1 0.37794 1 0.5812 1 0.11002 1 0.14795 1 0.073698 1 0.22791 1 0.015619 1 0.16821 1 xq gain 30 (6%) 484 0.38945 1 0.32803 1 0.20356 1 0.70536 1 0.021708 1 0.01187 1 0.17941 1 0.31743 1 0.43719 1 0.90891 1 0.2941 1 0.19072 1 1p loss 56 (11%) 458 0.001279 0.822 0.0003887 0.267 1.0959e-09 9.04e-07 0.46941 1 0.00049161 0.333 0.17796 1 0.13739 1 0.0026206 1 0.034557 1 1.9705e-08 1.6e-05 0.39409 1 0.0002484 0.173 1q loss 36 (7%) 478 0.010729 1 0.013331 1 5.0319e-10 4.16e-07 0.28899 1 0.010192 1 0.069504 1 0.0041572 1 0.0006778 0.452 0.042093 1 2.54e-08 2.05e-05 0.48807 1 1.4115e-05 0.0106 2p loss 14 (3%) 500 3.5787e-05 0.0261 6.2984e-05 0.0454 1.3759e-06 0.00107 0.66785 1 4.5828e-05 0.0334 2.3548e-06 0.00181 2.389e-07 0.00019 4.7333e-09 3.88e-06 8.4032e-05 0.0602 4.5032e-12 3.82e-09 0.074089 1 1.6425e-13 1.41e-10 2q loss 14 (3%) 500 0.00024867 0.173 0.00038936 0.267 1.3759e-06 0.00107 1 1 0.00031624 0.219 2.3548e-06 0.00181 2.389e-07 0.00019 6.3947e-08 5.15e-05 2.3246e-05 0.0172 2.5255e-10 2.1e-07 0.074089 1 1.6425e-13 1.41e-10 3p loss 370 (72%) 144 0.0034866 1 0.00066344 0.443 4.7214e-24 4.18e-21 0.020668 1 0.019708 1 0.0048183 1 1.7167e-08 1.39e-05 3.3584e-10 2.78e-07 0.016449 1 2.8143e-05 0.0207 0.12799 1 5.2707e-06 0.004 3q loss 102 (20%) 412 0.71975 1 0.71847 1 0.00040706 0.278 0.35862 1 0.17274 1 0.084517 1 0.18705 1 0.28968 1 0.90605 1 0.16651 1 0.18545 1 0.34207 1 4p loss 71 (14%) 443 0.53135 1 0.38886 1 3.038e-09 2.49e-06 0.0013598 0.872 0.084529 1 0.33647 1 0.0018307 1 0.001661 1 0.84687 1 0.31241 1 0.074322 1 0.3747 1 4q loss 65 (13%) 449 0.38705 1 0.34568 1 1.0368e-11 8.77e-09 0.00052903 0.358 0.051013 1 0.19873 1 0.0007696 0.509 9.7825e-06 0.00739 0.38181 1 0.1413 1 0.040575 1 0.29318 1 5p loss 7 (1%) 507 NA NA NA NA 0.022751 1 0.29091 1 0.65716 1 0.2869 1 0.026634 1 0.020876 1 0.028471 1 0.035394 1 NA NA NA NA 5q loss 6 (1%) 508 NA NA NA NA 0.048911 1 0.53395 1 0.47139 1 0.62591 1 0.045315 1 0.047501 1 0.060248 1 0.0053338 1 NA NA NA NA 6p loss 99 (19%) 415 0.011254 1 0.0028151 1 8.4777e-16 7.38e-13 0.00072253 0.48 3.739e-06 0.00285 0.00025843 0.18 3.0524e-08 2.47e-05 5.756e-07 0.000452 7.9898e-11 6.68e-08 0.00027829 0.193 4.38e-07 0.000345 0.0096066 1 6q loss 126 (25%) 388 0.047526 1 0.021165 1 6.5753e-15 5.69e-12 0.043405 1 2.5682e-05 0.019 0.0032678 1 0.00013393 0.0952 0.0049725 1 3.8577e-07 0.000304 0.023316 1 0.00013175 0.0938 0.080071 1 7p loss 3 (1%) 511 NA NA NA NA 0.18065 1 NA NA NA NA NA NA 0.058084 1 0.12839 1 0.055624 1 0.28915 1 0.058067 1 0.64978 1 7q loss 4 (1%) 510 NA NA NA NA 0.091473 1 0.36257 1 0.097958 1 1 1 0.049093 1 0.061549 1 0.033514 1 0.51949 1 0.058067 1 0.64978 1 8p loss 136 (26%) 378 0.35372 1 0.42649 1 8.214e-05 0.0589 0.21585 1 0.18521 1 0.29062 1 0.06917 1 0.066076 1 0.083482 1 0.054194 1 0.1504 1 0.32392 1 8q loss 67 (13%) 447 0.64737 1 0.74664 1 0.13285 1 0.10561 1 0.2891 1 0.48572 1 0.70745 1 0.59358 1 0.58861 1 0.33427 1 0.2373 1 0.51485 1 9p loss 146 (28%) 368 0.004171 1 0.00053301 0.36 2.0616e-47 1.83e-44 1.7559e-19 1.54e-16 4.8897e-06 0.00372 0.00093462 0.608 2.1213e-22 1.87e-19 1.1769e-25 1.04e-22 2.9656e-15 2.57e-12 3.4902e-05 0.0255 1.0379e-10 8.66e-08 0.0024222 1 9q loss 147 (29%) 367 0.010069 1 0.0014349 0.917 3.0559e-46 2.71e-43 1.8014e-18 1.58e-15 1.0599e-06 0.000824 0.0015911 1 6.7853e-23 5.99e-20 3.2585e-25 2.89e-22 1.2924e-16 1.13e-13 0.00015857 0.112 4.5506e-10 3.76e-07 0.00043017 0.293 10p loss 66 (13%) 448 0.17348 1 0.23862 1 4.9617e-09 4.06e-06 0.055321 1 0.74237 1 0.26738 1 0.17548 1 0.31593 1 0.066988 1 0.026962 1 0.090587 1 0.083959 1 10q loss 87 (17%) 427 0.31524 1 0.36049 1 2.1212e-08 1.72e-05 0.0071475 1 0.99022 1 0.14926 1 0.10962 1 0.18593 1 0.10864 1 0.12792 1 0.13816 1 0.02138 1 11p loss 18 (4%) 496 NA NA NA NA 3.3998e-05 0.0249 0.047325 1 0.13967 1 0.55314 1 0.15013 1 0.066196 1 0.18099 1 0.047559 1 0.064433 1 0.1135 1 11q loss 23 (4%) 491 0.18897 1 0.20731 1 5.9057e-07 0.000464 0.014251 1 0.10125 1 0.41768 1 0.012636 1 0.0039088 1 0.028216 1 0.11292 1 0.028451 1 0.22716 1 12p loss 3 (1%) 511 NA NA NA NA 0.34351 1 NA NA NA NA NA NA 0.43658 1 1 1 0.44733 1 0.44785 1 NA NA NA NA 12q loss 4 (1%) 510 NA NA NA NA 0.57723 1 NA NA 0.52479 1 0.18488 1 1 1 1 1 0.21252 1 0.75642 1 NA NA NA NA 13q loss 69 (13%) 445 0.0030403 1 0.0045545 1 9.3251e-11 7.79e-08 0.00073734 0.489 7.6632e-06 0.00579 0.0030671 1 4.0978e-06 0.00312 3.542e-07 0.00028 3.2289e-06 0.00247 0.0019374 1 0.050021 1 0.0084363 1 14q loss 214 (42%) 300 3.1171e-05 0.0228 4.3065e-05 0.0314 6.373e-18 5.58e-15 6.2116e-08 5.01e-05 1.0117e-13 8.72e-11 1.2787e-07 0.000102 1.9674e-21 1.73e-18 7.8869e-16 6.88e-13 2.4086e-11 2.03e-08 0.16478 1 8.2463e-07 0.000642 2.8956e-05 0.0213 15q loss 35 (7%) 479 0.11774 1 0.12687 1 2.5903e-10 2.15e-07 0.0078729 1 0.041965 1 0.4139 1 3.1992e-06 0.00245 8.1493e-07 0.000636 0.0023116 1 0.077961 1 0.0023059 1 0.42142 1 16p loss 10 (2%) 504 NA NA NA NA 0.27549 1 0.63136 1 0.036005 1 0.83662 1 0.29266 1 0.045009 1 0.26908 1 0.12509 1 0.37319 1 0.54552 1 16q loss 15 (3%) 499 NA NA NA NA 0.060168 1 0.34392 1 0.05764 1 0.59467 1 0.199 1 0.0059297 1 0.1029 1 0.034093 1 0.70976 1 0.71489 1 17p loss 45 (9%) 469 0.00013537 0.0961 0.00027063 0.188 5.3523e-09 4.38e-06 0.13987 1 0.0051073 1 0.0016327 1 1.6084e-06 0.00124 1.4045e-07 0.000112 9.5891e-08 7.69e-05 1.6947e-06 0.00131 0.033483 1 0.019891 1 17q loss 28 (5%) 486 0.00061803 0.414 0.00091193 0.595 2.4215e-06 0.00186 0.58508 1 0.15674 1 0.023748 1 0.00038636 0.265 5.8652e-05 0.0424 1.1448e-05 0.00863 9.1408e-07 0.000711 0.16006 1 1.8147e-05 0.0135 18p loss 91 (18%) 423 0.057359 1 0.13502 1 1.3644e-13 1.17e-10 2.6816e-07 0.000212 3.0725e-08 2.48e-05 0.0018299 1 7.0848e-19 6.22e-16 1.8899e-15 1.64e-12 3.6147e-11 3.03e-08 1.702e-05 0.0127 4.4229e-07 0.000348 0.0086229 1 18q loss 93 (18%) 421 0.046805 1 0.064915 1 2.2901e-13 1.96e-10 1.9663e-06 0.00152 1.9858e-07 0.000158 0.0067011 1 6.4189e-18 5.61e-15 4.0978e-15 3.55e-12 1.1052e-10 9.2e-08 1.3993e-05 0.0105 1.6751e-07 0.000134 0.0023338 1 19p loss 11 (2%) 503 NA NA NA NA 0.00042566 0.29 0.060367 1 0.00058958 0.396 0.00078757 0.519 0.16512 1 0.017552 1 0.26904 1 0.17825 1 0.11468 1 0.0082664 1 19q loss 4 (1%) 510 NA NA NA NA 0.013448 1 NA NA 0.88973 1 0.16833 1 0.35162 1 0.38764 1 0.83014 1 1 1 NA NA NA NA 20p loss 8 (2%) 506 NA NA NA NA 0.22297 1 1 1 0.058197 1 1 1 0.090709 1 0.44503 1 0.015546 1 0.081109 1 NA NA NA NA 20q loss 3 (1%) 511 NA NA NA NA 0.18065 1 NA NA NA NA NA NA 0.058084 1 0.76285 1 0.055624 1 0.00883 1 NA NA NA NA 21q loss 55 (11%) 459 0.026008 1 0.030636 1 9.2451e-09 7.53e-06 0.024137 1 0.027744 1 0.0078775 1 0.0057273 1 0.0013451 0.864 0.0099019 1 0.00084949 0.556 0.213 1 0.016975 1 22q loss 39 (8%) 475 0.010053 1 0.015526 1 5.8477e-09 4.78e-06 0.0069517 1 0.0042271 1 0.035821 1 6.2408e-07 0.000488 2.8401e-06 0.00218 1.1754e-05 0.00885 0.12697 1 0.00065593 0.439 0.49849 1 xq loss 46 (9%) 468 0.02379 1 0.0091659 1 1.9654e-05 0.0146 0.022161 1 0.14324 1 0.0038202 1 0.055348 1 0.0041925 1 0.015832 1 1.4272e-05 0.0107 0.027045 1 0.016682 1