Clinical Features 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 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 68 (13%) 443 0.00010081 0.0715 0.011935 1 0.95702 1 0.84833 1 0.86587 1 0.59441 1 0.69656 1 0.34903 1 0.86429 1 0.70252 1 1q gain 117 (23%) 394 6.88e-07 0.000517 1.7819e-08 1.36e-05 0.28948 1 0.65283 1 0.00021824 0.153 0.00033036 0.229 0.0017658 1 0.2313 1 0.0057873 1 0.038559 1 2p gain 90 (18%) 421 1.6009e-07 0.000122 7.3583e-11 5.72e-08 0.045176 1 0.69515 1 0.049429 1 0.034704 1 0.12493 1 0.47005 1 0.09978 1 0.81335 1 2q gain 69 (14%) 442 2.0381e-06 0.00151 2.6796e-10 2.08e-07 0.53354 1 0.81192 1 0.061878 1 0.030329 1 0.24344 1 1 1 0.14158 1 0.45728 1 3p gain 79 (15%) 432 0.0081509 1 0.00024817 0.173 0.067691 1 0.053103 1 0.0014122 0.938 0.0041075 1 0.0095135 1 0.16617 1 0.044388 1 0.1114 1 3q gain 249 (49%) 262 1.1515e-05 0.00842 4.4262e-07 0.000334 0.68263 1 0.72989 1 0.00066144 0.452 0.0018246 1 0.0012075 0.808 0.27231 1 0.079621 1 0.24745 1 4p gain 39 (8%) 472 0.0025768 1 7.0446e-05 0.0504 0.5761 1 0.8238 1 0.051825 1 0.057942 1 0.1172 1 0.16763 1 0.47295 1 0.2739 1 4q gain 35 (7%) 476 0.10767 1 0.40456 1 1 1 0.84745 1 0.62199 1 0.11579 1 0.91946 1 0.72192 1 0.94833 1 0.46779 1 5p gain 195 (38%) 316 9.2096e-12 7.2e-09 0.0036385 1 0.95817 1 0.60164 1 0.083876 1 0.22641 1 0.60461 1 1 1 0.93184 1 0.97844 1 5q gain 65 (13%) 446 0.032223 1 0.52032 1 0.59502 1 0.707 1 0.76904 1 0.89385 1 0.72847 1 0.33364 1 0.45056 1 0.50295 1 6p gain 80 (16%) 431 1.7901e-06 0.00133 0.003433 1 0.49218 1 0.56312 1 0.66557 1 0.71224 1 0.56712 1 0.44801 1 0.24727 1 0.45954 1 6q gain 61 (12%) 450 2.2384e-05 0.0163 0.041366 1 0.19677 1 0.12706 1 0.074462 1 0.022387 1 0.12466 1 0.67222 1 0.056938 1 0.25362 1 7p gain 180 (35%) 331 1.4389e-09 1.11e-06 7.5703e-10 5.86e-07 0.62432 1 0.52004 1 0.26927 1 0.14479 1 0.68582 1 0.92348 1 0.45239 1 0.85589 1 7q gain 123 (24%) 388 9.4127e-09 7.23e-06 2.988e-11 2.33e-08 0.17555 1 0.91277 1 0.48374 1 0.90284 1 0.0076004 1 0.45374 1 0.48648 1 0.29509 1 8p gain 148 (29%) 363 0.0016399 1 0.078771 1 0.5827 1 0.54171 1 0.3529 1 0.068561 1 0.67664 1 0.31394 1 0.46321 1 0.59045 1 8q gain 304 (59%) 207 3.5603e-07 0.00027 2.0322e-05 0.0148 0.081594 1 0.42634 1 0.11466 1 0.011245 1 0.08395 1 0.0066493 1 0.0075491 1 0.015499 1 9p gain 102 (20%) 409 3.1675e-18 2.52e-15 5.0641e-05 0.0364 0.50396 1 0.058342 1 0.0013933 0.928 0.0085085 1 0.0078637 1 1 1 0.058196 1 0.5584 1 9q gain 136 (27%) 375 4.1692e-14 3.29e-11 0.017806 1 0.129 1 0.20733 1 0.25131 1 0.11299 1 0.65166 1 0.91758 1 0.28638 1 0.67639 1 10p gain 40 (8%) 471 0.058722 1 2.4946e-06 0.00184 0.57872 1 0.5291 1 0.038313 1 0.0041969 1 0.046092 1 0.058863 1 0.87515 1 0.19475 1 10q gain 34 (7%) 477 0.00066525 0.454 0.30454 1 0.097263 1 0.34104 1 0.64915 1 0.38082 1 0.58651 1 0.4641 1 0.83795 1 0.33129 1 11p gain 65 (13%) 446 4.2695e-06 0.00314 7.5386e-06 0.00553 0.93006 1 0.89304 1 0.20949 1 0.036231 1 0.052751 1 0.094559 1 0.18809 1 0.42687 1 11q gain 70 (14%) 441 0.00016823 0.119 7.5831e-05 0.0541 0.52074 1 0.77962 1 0.22944 1 0.033061 1 0.29835 1 0.68819 1 0.89248 1 0.72524 1 12p gain 143 (28%) 368 7.8718e-13 6.17e-10 1.1295e-07 8.6e-05 0.016096 1 0.31798 1 0.015519 1 0.0096169 1 0.066211 1 0.68359 1 0.49794 1 0.53293 1 12q gain 87 (17%) 424 3.8065e-07 0.000288 0.00085121 0.578 0.11851 1 0.12446 1 0.084516 1 0.0052495 1 0.5725 1 0.71704 1 0.74886 1 0.48445 1 13q gain 56 (11%) 455 2.3132e-08 1.76e-05 0.00088583 0.6 0.58842 1 0.50238 1 0.014408 1 0.011601 1 0.24218 1 0.052982 1 0.27718 1 0.028513 1 14q gain 148 (29%) 363 8.8485e-13 6.93e-10 1.8773e-06 0.00139 0.21676 1 0.47922 1 0.014296 1 0.14804 1 0.017363 1 0.0033032 1 0.0076741 1 0.00089547 0.605 15q gain 71 (14%) 440 0.082378 1 0.019909 1 0.38116 1 0.85143 1 0.20636 1 0.070273 1 0.98023 1 0.35826 1 0.84677 1 0.3441 1 16p gain 104 (20%) 407 1.2856e-06 0.00096 2.3448e-06 0.00174 0.33161 1 0.93637 1 0.41003 1 0.57691 1 0.71421 1 1 1 0.55649 1 0.92071 1 16q gain 104 (20%) 407 1.226e-08 9.4e-06 5.6265e-06 0.00413 0.49887 1 0.82604 1 0.15137 1 0.43525 1 0.27145 1 0.067791 1 0.025792 1 0.12262 1 17p gain 66 (13%) 445 8.6668e-07 0.000651 3.0434e-06 0.00224 0.59659 1 0.31058 1 0.0075086 1 0.10165 1 0.086864 1 0.0082608 1 0.26532 1 0.08294 1 17q gain 84 (16%) 427 7.5739e-06 0.00554 0.00023868 0.167 0.57849 1 0.58345 1 0.12657 1 0.27193 1 0.48967 1 0.38551 1 0.95846 1 0.79184 1 18p gain 119 (23%) 392 7.2716e-13 5.71e-10 5.2185e-06 0.00384 0.33276 1 0.76945 1 0.36891 1 0.0007115 0.484 0.65696 1 0.91428 1 0.79383 1 0.58174 1 18q gain 48 (9%) 463 0.002259 1 1.8183e-05 0.0133 0.016803 1 0.40811 1 0.00020599 0.145 2.0916e-05 0.0152 5.0369e-05 0.0362 0.27252 1 0.012024 1 0.11253 1 19p gain 53 (10%) 458 0.0016946 1 3.0449e-07 0.000231 0.089235 1 0.068385 1 0.012203 1 0.0013758 0.919 0.00044244 0.306 0.05043 1 0.50353 1 0.34181 1 19q gain 74 (14%) 437 0.039775 1 5.5203e-05 0.0396 0.95592 1 0.39256 1 0.017596 1 0.0020213 1 0.00055715 0.383 0.09141 1 0.82963 1 0.26385 1 20p gain 188 (37%) 323 2.7308e-06 0.00202 1.0446e-06 0.000781 0.95062 1 0.12045 1 0.10154 1 0.10334 1 0.20373 1 0.0023215 1 0.019071 1 0.023348 1 20q gain 198 (39%) 313 6.2606e-09 4.81e-06 6.0076e-07 0.000452 0.83434 1 0.85702 1 0.10811 1 0.21904 1 0.17264 1 0.004782 1 0.0024965 1 0.0092521 1 21q gain 35 (7%) 476 0.046457 1 0.017213 1 0.015127 1 0.76785 1 0.0066498 1 0.0067671 1 0.10002 1 0.47586 1 0.69534 1 0.67217 1 22q gain 110 (22%) 401 1.8186e-06 0.00135 2.1538e-13 1.7e-10 0.1526 1 0.37624 1 0.28119 1 0.63252 1 0.0011305 0.759 0.57822 1 0.0026262 1 0.75961 1 xq gain 87 (17%) 424 1.4116e-06 0.00105 0.0033306 1 0.25074 1 0.75124 1 0.41473 1 0.42818 1 0.061862 1 0.22054 1 0.65402 1 0.31572 1 1p loss 52 (10%) 459 0.00018181 0.128 1.4488e-08 1.11e-05 0.019997 1 0.53815 1 0.003607 1 0.0058707 1 0.33799 1 0.53892 1 0.21196 1 0.38392 1 1q loss 35 (7%) 476 0.058028 1 0.12382 1 0.77998 1 0.69635 1 0.098035 1 0.22418 1 0.036951 1 0.02728 1 0.055448 1 0.45599 1 2p loss 33 (6%) 478 0.090314 1 0.0037391 1 0.15909 1 0.15253 1 0.10804 1 0.035626 1 0.036499 1 1 1 0.011774 1 0.82327 1 2q loss 42 (8%) 469 0.92168 1 0.038555 1 0.83585 1 0.17175 1 0.73794 1 0.70334 1 0.20668 1 1 1 0.030801 1 0.5135 1 3p loss 287 (56%) 224 2.2895e-26 1.83e-23 6.5167e-21 5.19e-18 0.82318 1 0.12039 1 0.013079 1 0.011789 1 0.14231 1 0.012742 1 0.72031 1 0.44345 1 3q loss 60 (12%) 451 0.013876 1 0.19244 1 0.2626 1 0.84354 1 0.60541 1 0.83364 1 0.9414 1 1 1 0.46461 1 0.79601 1 4p loss 186 (36%) 325 6.96e-20 5.54e-17 4.8469e-14 3.82e-11 0.039159 1 0.59242 1 0.00023096 0.162 6.2299e-05 0.0446 0.37748 1 0.56836 1 0.026957 1 0.022201 1 4q loss 144 (28%) 367 6.6289e-13 5.21e-10 5.019e-07 0.000378 0.46877 1 0.42742 1 0.0077563 1 0.0031926 1 0.23865 1 0.18434 1 0.079711 1 0.033151 1 5p loss 50 (10%) 461 1.5517e-05 0.0113 2.5055e-05 0.0181 0.40711 1 0.43377 1 0.68978 1 0.57802 1 0.76296 1 0.21862 1 0.12422 1 0.43472 1 5q loss 160 (31%) 351 2.3286e-21 1.86e-18 5.3757e-17 4.26e-14 0.24333 1 0.13299 1 0.20504 1 0.0013949 0.928 0.79909 1 0.092301 1 0.71813 1 0.656 1 6p loss 67 (13%) 444 0.0003012 0.209 0.0033866 1 0.029545 1 0.55503 1 0.029437 1 0.052086 1 0.32694 1 0.42007 1 0.2602 1 0.46784 1 6q loss 67 (13%) 444 0.065165 1 0.0095505 1 0.12835 1 0.38412 1 0.76904 1 0.15187 1 0.66977 1 0.49751 1 0.33462 1 0.63007 1 7p loss 28 (5%) 483 0.022189 1 0.041045 1 0.010206 1 0.20746 1 0.47156 1 0.16651 1 0.29964 1 0.84295 1 0.081639 1 0.75068 1 7q loss 42 (8%) 469 0.2016 1 0.38348 1 0.52519 1 0.27131 1 0.32352 1 0.72256 1 0.042263 1 0.50637 1 0.82856 1 0.78461 1 8p loss 184 (36%) 327 5.1771e-11 4.03e-08 2.0173e-06 0.0015 0.54953 1 0.28818 1 0.036355 1 0.00093843 0.633 0.030978 1 0.00056781 0.39 0.00089828 0.606 0.0008613 0.584 8q loss 30 (6%) 481 0.07668 1 0.13362 1 0.75617 1 0.34375 1 0.69792 1 0.79851 1 0.21651 1 1 1 0.74129 1 0.29449 1 9p loss 176 (34%) 335 4.3599e-26 3.48e-23 4.9014e-17 3.89e-14 0.69921 1 0.16434 1 0.29882 1 0.33033 1 0.41071 1 0.84712 1 0.33378 1 0.54824 1 9q loss 83 (16%) 428 2.5682e-10 1.99e-07 1.0203e-06 0.000764 0.98384 1 1 1 0.62424 1 0.84454 1 0.80558 1 0.61864 1 0.13541 1 0.25092 1 10p loss 151 (30%) 360 3.5372e-05 0.0256 0.00061827 0.423 0.31622 1 0.09801 1 0.051014 1 0.13183 1 0.097392 1 0.1077 1 0.24963 1 0.3015 1 10q loss 109 (21%) 402 0.00011333 0.0802 0.0011973 0.802 0.20753 1 0.33021 1 0.014863 1 0.10681 1 0.020854 1 0.82168 1 0.25372 1 0.79319 1 11p loss 134 (26%) 377 2.206e-08 1.69e-05 0.00035283 0.245 0.33024 1 0.90852 1 0.0051974 1 0.037435 1 0.006044 1 0.67815 1 0.38859 1 0.15533 1 11q loss 164 (32%) 347 8.5271e-05 0.0608 2.8491e-07 0.000216 0.25444 1 0.40883 1 0.0049871 1 0.0046944 1 0.26228 1 0.69564 1 0.38767 1 0.8664 1 12p loss 36 (7%) 475 0.64713 1 0.11058 1 0.6461 1 0.60528 1 0.85515 1 0.9231 1 1 1 0.58763 1 0.37049 1 0.64947 1 12q loss 32 (6%) 479 0.016322 1 0.016937 1 0.87131 1 0.26688 1 0.48934 1 0.40669 1 0.97241 1 0.70067 1 0.18654 1 0.49611 1 13q loss 162 (32%) 349 3.744e-15 2.96e-12 9.39e-07 0.000704 0.3772 1 0.80156 1 0.0031617 1 0.00028222 0.196 0.037151 1 0.4309 1 0.33627 1 0.056974 1 14q loss 54 (11%) 457 0.0062509 1 0.0021797 1 0.037227 1 0.41525 1 5.0343e-05 0.0362 0.0010996 0.74 0.0045499 1 0.05043 1 0.23458 1 0.04383 1 15q loss 98 (19%) 413 8.5134e-08 6.49e-05 0.2303 1 0.62524 1 0.41349 1 0.12133 1 0.067019 1 0.72062 1 0.24562 1 0.53106 1 0.35016 1 16p loss 60 (12%) 451 0.00048051 0.331 0.013226 1 0.86737 1 0.72313 1 0.0061866 1 0.06638 1 0.95308 1 0.31654 1 0.82623 1 0.6273 1 16q loss 78 (15%) 433 0.0057899 1 1.5458e-09 1.19e-06 0.47868 1 0.078006 1 1.9246e-10 1.5e-07 1.9268e-09 1.49e-06 0.0022495 1 0.01472 1 0.00056819 0.39 0.00036491 0.253 17p loss 103 (20%) 408 8.5845e-05 0.0611 0.0030679 1 0.39291 1 0.27806 1 0.52278 1 0.076265 1 0.53274 1 0.90979 1 0.2519 1 0.54284 1 17q loss 34 (7%) 477 0.0011234 0.755 0.32588 1 0.90272 1 0.0047845 1 0.4374 1 0.80718 1 0.90427 1 0.35509 1 0.96574 1 0.43321 1 18p loss 101 (20%) 410 0.022107 1 0.00019079 0.135 0.53643 1 0.20344 1 0.26974 1 0.11572 1 0.64432 1 0.24562 1 0.86146 1 0.32043 1 18q loss 208 (41%) 303 1.664e-17 1.32e-14 1.4262e-14 1.13e-11 0.31437 1 0.015061 1 0.0018781 1 0.00068755 0.468 0.0016301 1 0.00026405 0.184 0.14709 1 0.022768 1 19p loss 93 (18%) 418 0.00022879 0.16 2.3814e-05 0.0173 0.70291 1 0.2041 1 0.022682 1 0.10195 1 0.042049 1 0.0027039 1 0.65749 1 0.3289 1 19q loss 82 (16%) 429 9.7754e-05 0.0695 4.96e-05 0.0358 0.12921 1 0.55363 1 0.2088 1 0.67175 1 0.35285 1 0.031877 1 0.7826 1 0.62602 1 20p loss 46 (9%) 465 0.00046094 0.318 0.0062728 1 0.48302 1 0.47588 1 0.083748 1 0.087451 1 0.3359 1 0.034932 1 0.0014417 0.956 0.12189 1 20q loss 28 (5%) 483 0.010799 1 0.018227 1 0.22528 1 0.19148 1 0.02172 1 0.0073053 1 0.026744 1 0.027727 1 0.00019488 0.137 0.01461 1 21q loss 179 (35%) 332 2.6348e-11 2.06e-08 1.9568e-09 1.51e-06 0.57123 1 0.5117 1 0.032996 1 0.12025 1 0.5284 1 0.083702 1 0.72493 1 0.20652 1 22q loss 72 (14%) 439 0.0036418 1 0.003329 1 0.64405 1 0.53815 1 0.0013774 0.919 0.25974 1 0.00058191 0.399 0.1436 1 0.0034228 1 0.43339 1 xq loss 82 (16%) 429 9.793e-05 0.0695 3.6665e-05 0.0265 0.088194 1 0.033628 1 0.030549 1 0.020674 1 0.014837 1 0.3785 1 0.1685 1 0.22808 1