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 Chi-square test_P Chi-square 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 Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 12 (3%) 451 NA NA NA NA 9.3956e-05 0.0683 3.2784e-05 0.0242 0.024148 1 1 1 7.741e-09 6.08e-06 0.00082717 0.565 3.1443e-05 0.0232 0.0014437 0.961 0.00013655 0.098 0.0064145 1 1q gain 18 (4%) 445 NA NA NA NA 0.00011016 0.0794 0.00013065 0.0939 0.43569 1 0.73827 1 0.00010733 0.0776 0.051277 1 0.00894 1 0.24994 1 0.00035284 0.246 0.20048 1 2p gain 11 (2%) 452 NA NA NA NA 0.048877 1 0.046013 1 0.31113 1 0.43043 1 1.6747e-06 0.00126 0.13897 1 0.035588 1 0.15396 1 0.069525 1 0.1806 1 2q gain 10 (2%) 453 NA NA NA NA 0.089793 1 0.031449 1 0.31113 1 0.43043 1 2.6037e-07 0.000199 0.23729 1 0.072846 1 0.21042 1 0.090928 1 0.21617 1 3p gain 11 (2%) 452 NA NA NA NA 0.35148 1 0.1818 1 0.46396 1 0.44682 1 0.0077231 1 0.38843 1 0.14273 1 0.48082 1 0.26077 1 0.1806 1 3q gain 8 (2%) 455 NA NA NA NA 0.21528 1 0.063978 1 0.055985 1 0.74032 1 0.00015127 0.108 0.36048 1 0.13473 1 0.47907 1 0.21142 1 0.36226 1 4p gain 12 (3%) 451 NA NA NA NA 0.0067975 1 0.036101 1 0.032748 1 0.7866 1 0.0028807 1 0.010894 1 0.05632 1 0.15396 1 0.24029 1 0.070233 1 4q gain 5 (1%) 458 NA NA NA NA 0.051273 1 0.12047 1 0.11301 1 0.66838 1 0.018476 1 0.58583 1 0.17669 1 0.48547 1 0.030316 1 0.035883 1 5p gain 9 (2%) 454 NA NA NA NA 0.0027544 1 0.0047315 1 0.021682 1 1 1 5.7119e-05 0.0419 0.065242 1 0.0061718 1 0.10683 1 0.0059436 1 0.015216 1 5q gain 7 (2%) 456 NA NA NA NA 0.0036085 1 0.0016571 1 NA NA NA NA 0.010878 1 0.24231 1 0.011463 1 0.26681 1 0.014088 1 0.20013 1 6p gain 7 (2%) 456 NA NA NA NA 0.0058309 1 0.048566 1 0.037839 1 0.46484 1 0.12747 1 0.030682 1 0.13749 1 0.019996 1 0.023116 1 0.20013 1 7p gain 117 (25%) 346 0.7446 1 0.64812 1 7.3336e-48 6.12e-45 5.9674e-24 4.9e-21 0.00087435 0.596 0.017696 1 8.504e-17 6.95e-14 1.3195e-06 0.000999 3.5253e-08 2.74e-05 0.0016992 1 6.7886e-10 5.37e-07 0.28912 1 7q gain 145 (31%) 318 0.7639 1 0.49526 1 3.8178e-45 3.18e-42 1.9185e-19 1.57e-16 0.0053135 1 0.038605 1 6.9359e-12 5.56e-09 6.8358e-07 0.00052 2.397e-07 0.000184 0.0020175 1 1.2774e-07 9.85e-05 0.57924 1 8p gain 39 (8%) 424 NA NA NA NA 1.1518e-05 0.00857 0.014029 1 0.066672 1 0.56602 1 0.10868 1 0.10185 1 0.30782 1 0.47758 1 0.29598 1 0.21461 1 8q gain 49 (11%) 414 0.051852 1 0.30256 1 2.0038e-06 0.00151 0.0006511 0.448 0.012919 1 0.61811 1 0.0014262 0.953 0.021346 1 0.016635 1 0.47548 1 0.0053038 1 0.1892 1 9p gain 17 (4%) 446 NA NA NA NA 0.0078385 1 0.14454 1 0.29435 1 0.81972 1 0.016702 1 0.3538 1 0.40573 1 0.43363 1 0.12569 1 0.24344 1 9q gain 22 (5%) 441 NA NA NA NA 0.0033949 1 0.21899 1 0.25818 1 0.66107 1 0.0022224 1 0.36729 1 0.043564 1 0.36319 1 0.017273 1 0.025165 1 10p gain 47 (10%) 416 1 1 0.087863 1 1.625e-14 1.32e-11 6.1336e-13 4.94e-10 0.023328 1 0.54644 1 2.342e-09 1.85e-06 3.5535e-06 0.00267 0.014485 1 0.58181 1 0.016137 1 0.78889 1 10q gain 7 (2%) 456 NA NA NA NA 0.00023412 0.165 0.23255 1 0.2669 1 0.46484 1 0.00029124 0.203 0.53957 1 0.0074508 1 0.42961 1 0.10833 1 0.72993 1 11p gain 29 (6%) 434 NA NA NA NA 0.10951 1 0.0012085 0.811 0.026963 1 0.49573 1 0.0039547 1 0.019695 1 0.3694 1 0.77315 1 0.17091 1 0.62984 1 11q gain 50 (11%) 413 0.61538 1 0.11658 1 0.22891 1 0.018471 1 0.083688 1 0.14103 1 0.061382 1 0.072622 1 0.53936 1 0.78136 1 0.32032 1 0.7823 1 12p gain 30 (6%) 433 0.75385 1 0.087863 1 0.00020633 0.146 0.076419 1 0.26076 1 0.87476 1 0.14253 1 0.06208 1 0.029703 1 0.11083 1 0.02108 1 0.16629 1 12q gain 15 (3%) 448 NA NA NA NA 0.0077095 1 0.03862 1 0.17332 1 1 1 0.030946 1 0.13233 1 0.043116 1 0.028976 1 0.0038505 1 0.028413 1 13q gain 5 (1%) 458 NA NA NA NA 0.051273 1 0.13552 1 0.79242 1 1 1 0.62588 1 0.71914 1 0.76148 1 1 1 0.83655 1 1 1 14q gain 3 (1%) 460 NA NA NA NA 1 1 1 1 NA NA NA NA 0.9023 1 0.41577 1 0.37154 1 1 1 0.28139 1 0.60782 1 15q gain 10 (2%) 453 NA NA NA NA 0.045693 1 0.029401 1 0.11375 1 0.46484 1 0.0048322 1 0.12514 1 0.024417 1 0.55595 1 0.10174 1 0.1535 1 16p gain 15 (3%) 448 NA NA NA NA 0.22119 1 0.485 1 0.56065 1 0.65772 1 0.092931 1 0.13753 1 0.23592 1 0.21114 1 0.013619 1 0.0023444 1 16q gain 16 (3%) 447 NA NA NA NA 0.033936 1 0.22851 1 0.46901 1 0.73827 1 0.0010084 0.681 0.16163 1 0.67891 1 0.29297 1 0.29549 1 0.0043942 1 17p gain 17 (4%) 446 NA NA NA NA 0.5806 1 0.50536 1 0.34585 1 0.77096 1 0.00078601 0.538 0.27962 1 0.0013889 0.929 0.20889 1 0.0036202 1 0.051244 1 17q gain 19 (4%) 444 NA NA NA NA 0.49962 1 0.33916 1 0.34585 1 0.77096 1 0.0023828 1 0.16558 1 0.0026308 1 0.085905 1 0.067541 1 0.035572 1 18p gain 15 (3%) 448 NA NA NA NA 7.8966e-05 0.0577 0.010874 1 0.022636 1 0.20533 1 1.534e-10 1.22e-07 0.019448 1 0.72208 1 0.11838 1 0.41261 1 0.062963 1 18q gain 12 (3%) 451 NA NA NA NA 0.00094008 0.637 0.0079647 1 0.08038 1 0.14214 1 3.4797e-08 2.71e-05 0.021448 1 0.3682 1 0.023383 1 0.19546 1 0.02173 1 19p gain 89 (19%) 374 0.22111 1 0.83612 1 1.4586e-09 1.15e-06 4.9723e-16 4.05e-13 0.61625 1 0.40581 1 3.2241e-10 2.56e-07 0.00021553 0.152 8.4558e-05 0.0616 0.54902 1 5.8007e-07 0.000443 0.52053 1 19q gain 24 (5%) 439 NA NA NA NA 6.1238e-14 4.95e-11 3.9175e-15 3.18e-12 0.065771 1 0.18725 1 7.9428e-12 6.35e-09 0.00023711 0.166 3.6791e-09 2.9e-06 0.0035848 1 9.7219e-11 7.75e-08 0.182 1 20p gain 42 (9%) 421 NA NA NA NA 5.9697e-12 4.79e-09 3.4539e-13 2.79e-10 0.0010111 0.681 0.1579 1 7.6235e-08 5.91e-05 0.0043993 1 2.6138e-06 0.00197 0.027702 1 1.739e-10 1.38e-07 0.21284 1 20q gain 42 (9%) 421 NA NA NA NA 5.9697e-12 4.79e-09 5.6922e-14 4.61e-11 0.00089846 0.611 0.1097 1 7.1428e-10 5.64e-07 0.0006732 0.462 6.2835e-08 4.88e-05 0.0018911 1 2.1939e-12 1.77e-09 0.065571 1 21q gain 23 (5%) 440 NA NA NA NA 0.020186 1 0.0019977 1 0.10983 1 0.53086 1 0.051397 1 0.92357 1 0.25171 1 0.86848 1 0.31768 1 0.72689 1 22q gain 17 (4%) 446 NA NA NA NA 0.10928 1 0.00082004 0.561 1 1 0.5601 1 0.0037951 1 0.0079602 1 0.5193 1 0.47976 1 0.29576 1 0.3749 1 xq gain 35 (8%) 428 NA NA NA NA 1.7869e-08 1.4e-05 8.2173e-07 0.000625 0.23894 1 0.72046 1 0.0098696 1 0.0011517 0.774 0.25813 1 0.34068 1 0.14256 1 0.41827 1 1p loss 168 (36%) 295 0.028572 1 0.00017271 0.123 6.3613e-47 5.3e-44 4.6023e-95 3.87e-92 0.0003111 0.217 0.142 1 9.1284e-52 7.64e-49 9.0562e-65 7.59e-62 1.6999e-22 1.39e-19 2.0828e-06 0.00157 7.0658e-27 5.82e-24 0.00012366 0.089 1q loss 23 (5%) 440 0.34359 1 0.14393 1 0.81124 1 0.12727 1 0.5517 1 0.54013 1 0.34089 1 0.30407 1 0.8487 1 0.66664 1 0.33625 1 0.23906 1 2p loss 19 (4%) 444 NA NA NA NA 3.4511e-05 0.0254 0.068176 1 0.33106 1 1 1 0.11017 1 0.023264 1 0.1458 1 0.088329 1 0.74927 1 0.0082933 1 2q loss 18 (4%) 445 NA NA NA NA 5.8245e-06 0.00435 0.0089558 1 0.0692 1 0.62827 1 0.082202 1 0.0055137 1 0.68248 1 0.43363 1 0.043781 1 0.004585 1 3p loss 25 (5%) 438 NA NA NA NA 0.0025499 1 0.14594 1 0.0065168 1 0.48289 1 8.5982e-05 0.0626 0.0056695 1 0.023287 1 0.16468 1 0.02976 1 0.037668 1 3q loss 25 (5%) 438 0.17504 1 0.56068 1 0.005978 1 0.22079 1 0.25799 1 0.19137 1 0.00019962 0.142 0.068188 1 0.036388 1 0.11491 1 0.15078 1 0.037668 1 4p loss 67 (14%) 396 1 1 0.60733 1 0.016401 1 4.7718e-10 3.78e-07 0.42939 1 0.02872 1 3.5377e-08 2.75e-05 5.9383e-07 0.000452 0.0045997 1 0.065452 1 0.0018777 1 0.67552 1 4q loss 85 (18%) 378 1 1 0.19622 1 0.0038495 1 8.2886e-09 6.51e-06 0.26354 1 0.053242 1 1.2741e-07 9.84e-05 8.2297e-05 0.0601 0.00076286 0.523 0.014465 1 0.00040475 0.28 0.40883 1 5p loss 32 (7%) 431 0.7446 1 0.042206 1 3.676e-06 0.00276 0.0010659 0.717 0.84862 1 1 1 0.20614 1 0.045955 1 0.12965 1 0.56205 1 0.61281 1 0.18982 1 5q loss 29 (6%) 434 0.44623 1 0.018246 1 8.7829e-07 0.000667 0.0024214 1 0.021796 1 0.50804 1 1.6699e-07 0.000129 0.0041609 1 0.061966 1 0.10754 1 0.008037 1 0.00023046 0.162 6p loss 28 (6%) 435 NA NA NA NA 0.037668 1 0.17771 1 0.18595 1 0.70781 1 0.342 1 0.54575 1 0.86936 1 0.5409 1 0.72751 1 0.45255 1 6q loss 57 (12%) 406 NA NA NA NA 0.00062827 0.433 0.006974 1 0.25362 1 0.39785 1 0.15343 1 0.059337 1 0.25402 1 0.20723 1 0.098853 1 0.19066 1 7p loss 3 (1%) 460 NA NA NA NA 0.45562 1 0.33193 1 NA NA NA NA 0.93706 1 1 1 0.88711 1 1 1 0.9427 1 1 1 7q loss 3 (1%) 460 NA NA NA NA 0.039781 1 0.33193 1 NA NA NA NA 0.93706 1 1 1 0.56439 1 1 1 0.35052 1 1 1 8p loss 17 (4%) 446 0.61538 1 0.0013675 0.916 1.5039e-05 0.0112 9.5961e-05 0.0697 0.018505 1 0.62827 1 2.0814e-07 0.00016 0.0034664 1 2.9345e-05 0.0217 0.12818 1 2.3237e-05 0.0172 0.046286 1 8q loss 11 (2%) 452 NA NA NA NA 0.00014248 0.102 1.5904e-05 0.0118 0.080624 1 0.74032 1 0.00010831 0.0782 0.021448 1 0.00028472 0.199 0.15396 1 0.00023077 0.162 0.1806 1 9p loss 107 (23%) 356 0.38387 1 0.26997 1 4.2154e-06 0.00315 0.00027447 0.192 0.031773 1 0.066426 1 0.00094386 0.639 0.028845 1 0.13001 1 0.84862 1 0.24754 1 0.54875 1 9q loss 46 (10%) 417 NA NA NA NA 0.39265 1 0.42196 1 0.60738 1 0.50613 1 0.025779 1 0.47899 1 0.80746 1 0.69485 1 0.50615 1 0.58597 1 10p loss 76 (16%) 387 0.27077 1 0.56068 1 4.575e-40 3.79e-37 2.7548e-49 2.3e-46 2.5375e-07 0.000194 0.0023175 1 2.1549e-37 1.78e-34 1.0938e-08 8.56e-06 1.5811e-15 1.29e-12 2.8033e-05 0.0207 1.1275e-28 9.29e-26 0.0014335 0.956 10q loss 91 (20%) 372 0.27077 1 0.56068 1 1.4746e-33 1.22e-30 2.7543e-40 2.29e-37 1.3209e-06 0.000999 0.00087376 0.596 2.7616e-35 2.28e-32 4.6876e-11 3.74e-08 2.7647e-16 2.25e-13 4.1679e-06 0.00312 1.1873e-25 9.76e-23 0.0015608 1 11p loss 56 (12%) 407 1 1 0.013836 1 5.0232e-14 4.07e-11 1.2271e-10 9.77e-08 0.012703 1 0.5899 1 5.1515e-12 4.14e-09 8.7269e-09 6.84e-06 0.0027173 1 0.045836 1 0.0066317 1 0.0028726 1 11q loss 19 (4%) 444 NA NA NA NA 0.00020156 0.143 0.00014685 0.105 0.017879 1 1 1 8.751e-08 6.77e-05 0.0042467 1 0.0022623 1 0.034241 1 0.0029323 1 0.0070532 1 12p loss 25 (5%) 438 NA NA NA NA 0.031326 1 0.0069621 1 0.60346 1 0.50965 1 0.67309 1 0.079463 1 0.075698 1 0.35004 1 0.10656 1 0.67936 1 12q loss 47 (10%) 416 1 1 0.087863 1 2.1107e-08 1.65e-05 2.3596e-07 0.000181 0.58318 1 0.61259 1 0.036458 1 0.0003864 0.269 0.018961 1 0.44197 1 0.0015999 1 0.60465 1 13q loss 104 (22%) 359 0.1801 1 0.00061812 0.427 3.5021e-08 2.73e-05 0.027012 1 0.026271 1 0.49032 1 0.004681 1 0.011664 1 0.022631 1 0.23209 1 0.031098 1 0.070074 1 14q loss 70 (15%) 393 0.46711 1 0.47324 1 0.00039797 0.276 0.00015091 0.108 0.045908 1 0.14769 1 5.6952e-05 0.0418 0.011531 1 0.00062816 0.433 0.20839 1 0.00010356 0.0751 0.0052941 1 15q loss 45 (10%) 418 1 1 0.89231 1 0.06662 1 0.000585 0.405 0.27699 1 0.047616 1 0.0001043 0.0755 0.007513 1 0.095474 1 0.5177 1 0.0867 1 0.35845 1 16p loss 13 (3%) 450 NA NA NA NA 0.0032142 1 0.060774 1 0.86477 1 0.44682 1 4.5318e-05 0.0333 1 1 0.3902 1 1 1 0.51922 1 0.18686 1 16q loss 20 (4%) 443 NA NA NA NA 0.0037711 1 0.0024945 1 0.37381 1 0.21908 1 0.028165 1 0.39635 1 0.47168 1 0.45255 1 0.55632 1 0.47924 1 17p loss 14 (3%) 449 NA NA NA NA 0.0046768 1 0.094484 1 1 1 0.60489 1 0.040861 1 0.094064 1 0.037773 1 0.014159 1 0.0085557 1 0.015901 1 17q loss 9 (2%) 454 NA NA NA NA 0.057978 1 0.13796 1 0.83523 1 0.44682 1 0.4069 1 0.22724 1 0.057934 1 0.1753 1 0.095859 1 0.27124 1 18p loss 63 (14%) 400 0.32144 1 0.31568 1 0.43979 1 0.035151 1 0.57345 1 0.080072 1 0.56109 1 0.71924 1 0.036019 1 0.22201 1 0.55969 1 0.51917 1 18q loss 58 (13%) 405 0.34359 1 0.21231 1 0.1435 1 0.0018251 1 0.28483 1 0.20172 1 0.10215 1 0.18144 1 0.55918 1 0.35318 1 0.37156 1 0.61483 1 19p loss 21 (5%) 442 0.84676 1 0.31129 1 0.36553 1 0.75741 1 0.10256 1 0.66107 1 0.0082923 1 0.11305 1 0.47216 1 0.45255 1 0.75968 1 0.33531 1 19q loss 190 (41%) 273 0.18314 1 0.15869 1 1.1097e-35 9.18e-33 1.0677e-75 8.96e-73 0.038416 1 0.11799 1 6.8457e-42 5.69e-39 1.3275e-49 1.11e-46 1.8284e-16 1.49e-13 7.9416e-06 0.00592 3.0037e-20 2.46e-17 0.00025911 0.182 20p loss 5 (1%) 458 NA NA NA NA 0.051273 1 0.13552 1 0.79242 1 1 1 1.0498e-06 0.000796 0.58583 1 0.21325 1 0.22497 1 0.14181 1 0.41676 1 20q loss 3 (1%) 460 NA NA NA NA 0.15468 1 0.49376 1 NA NA NA NA 0.00195 1 0.2926 1 0.27935 1 0.10657 1 0.11147 1 0.017334 1 21q loss 33 (7%) 430 0.61538 1 0.40684 1 0.00015928 0.114 0.0022137 1 0.46096 1 0.83387 1 0.0143 1 0.00097605 0.66 0.21184 1 0.012999 1 0.21889 1 0.073984 1 22q loss 50 (11%) 413 0.81538 1 0.10604 1 7.6935e-12 6.15e-09 1.0351e-07 8e-05 7.5833e-05 0.0555 0.040536 1 2.0184e-07 0.000155 0.00018654 0.132 0.072267 1 0.3882 1 0.0078331 1 0.048483 1 xq loss 60 (13%) 403 0.83946 1 0.022012 1 0.33762 1 0.00091077 0.618 0.047422 1 0.0088422 1 1.0461e-05 0.00779 0.00016191 0.115 0.0021919 1 0.93082 1 0.0049882 1 0.29823 1