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 13 (3%) 499 NA NA NA NA 0.00017 0.116 0.00012 0.0832 0.02456 1 1 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.0079999 1 9.9999e-06 0.0084 9.9999e-05 0.0698 9.9999e-06 0.0084 1q gain 23 (4%) 489 NA NA NA NA 0.00073999 0.48 0.00031 0.209 0.43297 1 0.60496 1 3e-05 0.0216 0.00046 0.306 0.35621 1 0.00339 1 0.00145 0.911 0.0051299 1 2p gain 14 (3%) 498 NA NA NA NA 0.060249 1 0.02841 1 0.31065 1 0.34481 1 0.01316 1 0.00084999 0.546 0.42576 1 0.13568 1 0.10998 1 0.17009 1 2q gain 13 (3%) 499 NA NA NA NA 0.13799 1 0.02302 1 0.31102 1 0.34615 1 0.03497 1 0.00056999 0.376 0.37507 1 0.03427 1 0.091189 1 0.10544 1 3p gain 11 (2%) 501 NA NA NA NA 0.35407 1 0.18063 1 0.46369 1 0.20173 1 0.10754 1 0.11045 1 0.15111 1 0.096269 1 0.19999 1 0.18427 1 3q gain 8 (2%) 504 NA NA NA NA 0.21555 1 0.067999 1 0.055239 1 0.36701 1 0.062819 1 0.0037 1 0.34562 1 0.083629 1 0.12861 1 0.14229 1 4p gain 13 (3%) 499 NA NA NA NA 0.01152 1 0.0195 1 0.0332 1 0.89511 1 0.0082499 1 0.0016 0.998 0.195 1 0.27239 1 0.087599 1 0.068069 1 4q gain 6 (1%) 506 NA NA NA NA 0.0367 1 0.04325 1 0.11314 1 0.6686 1 0.0157 1 0.00357 1 0.26269 1 0.2161 1 0.04999 1 0.15764 1 5p gain 11 (2%) 501 NA NA NA NA 0.01184 1 0.00212 1 0.02178 1 0.6067 1 7.9999e-05 0.0562 9.9999e-05 0.0698 0.02362 1 0.03076 1 0.00017 0.116 0.0081999 1 5q gain 8 (2%) 504 NA NA NA NA 0.00318 1 0.00015 0.103 NA NA NA NA 0.00016 0.11 0.00016 0.11 0.01298 1 0.00071999 0.469 0.00016 0.11 0.00079999 0.516 6p gain 7 (1%) 505 NA NA NA NA 0.00072999 0.474 0.04663 1 0.03754 1 0.51717 1 0.44126 1 0.097689 1 0.02645 1 0.04218 1 0.01998 1 0.02438 1 7p gain 120 (23%) 392 0.74314 1 0.78138 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00037 0.248 0.01143 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00385 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 7q gain 150 (29%) 362 0.76605 1 0.51964 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00412 1 0.19959 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.01068 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 8p gain 45 (9%) 467 NA NA NA NA 9.9999e-06 0.0084 0.00288 1 0.063359 1 0.16069 1 0.01889 1 0.0053499 1 0.56502 1 0.25547 1 0.058079 1 0.03675 1 8q gain 55 (11%) 457 0.052679 1 0.40773 1 9.9999e-06 0.0084 0.00016 0.11 0.01118 1 0.058079 1 0.00125 0.792 0.00044 0.293 0.21539 1 0.0264 1 0.0028 1 0.00219 1 9p gain 17 (3%) 495 NA NA NA NA 0.01129 1 0.14321 1 0.29689 1 0.53099 1 0.066179 1 0.03618 1 0.8583 1 0.074729 1 0.28258 1 0.0492 1 9q gain 23 (4%) 489 NA NA NA NA 0.01993 1 0.13243 1 0.25654 1 0.054579 1 0.03022 1 0.01296 1 0.55976 1 0.065559 1 0.03779 1 0.04748 1 10p gain 56 (11%) 456 1 1 0.04191 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.02094 1 0.55351 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.063949 1 0.092459 1 0.00395 1 0.00089999 0.574 10q gain 12 (2%) 500 NA NA NA NA 5.9999e-05 0.0426 0.03895 1 0.26581 1 0.51666 1 0.085329 1 0.03699 1 0.12293 1 0.55409 1 0.077469 1 0.47279 1 11p gain 31 (6%) 481 NA NA NA NA 0.079419 1 0.00055999 0.37 0.02596 1 0.1084 1 0.01005 1 0.0033 1 0.10129 1 0.02035 1 0.18407 1 0.00153 0.958 11q gain 58 (11%) 454 0.61409 1 0.58015 1 0.33495 1 0.01557 1 0.081369 1 0.03162 1 0.061379 1 0.03815 1 0.37045 1 0.0277 1 0.40359 1 0.00377 1 12p gain 32 (6%) 480 0.75416 1 0.58269 1 7.9999e-05 0.0562 0.04792 1 0.25975 1 0.31013 1 0.01947 1 0.056929 1 0.03578 1 0.01804 1 0.00413 1 0.02311 1 12q gain 16 (3%) 496 NA NA NA NA 0.00061999 0.407 0.04586 1 0.29378 1 0.53268 1 0.0061099 1 0.086459 1 0.025 1 0.060739 1 0.00126 0.798 0.0235 1 13q gain 6 (1%) 506 NA NA NA NA 0.37416 1 0.43552 1 0.79421 1 0.79357 1 0.23459 1 0.47408 1 0.43413 1 0.26547 1 0.87568 1 0.49157 1 14q gain 4 (1%) 508 NA NA NA NA 1 1 0.89199 1 NA NA NA NA 0.70979 1 0.59574 1 0.49674 1 0.62438 1 0.13969 1 0.32406 1 15q gain 11 (2%) 501 NA NA NA NA 0.00206 1 0.02083 1 0.04498 1 0.21643 1 0.04951 1 0.01317 1 0.11042 1 0.14232 1 0.03286 1 0.108 1 16p gain 16 (3%) 496 NA NA NA NA 0.51873 1 0.53498 1 0.56162 1 0.6976 1 0.15132 1 0.091919 1 0.1777 1 0.34103 1 0.40386 1 0.14017 1 16q gain 19 (4%) 493 NA NA NA NA 0.0448 1 0.23315 1 0.47277 1 0.51604 1 0.15452 1 0.03383 1 0.057709 1 0.97682 1 0.24937 1 0.49076 1 17p gain 20 (4%) 492 NA NA NA NA 0.29842 1 0.30157 1 0.3453 1 0.88583 1 0.18822 1 0.04646 1 0.15013 1 0.34829 1 0.085529 1 0.19332 1 17q gain 23 (4%) 489 NA NA NA NA 0.60251 1 0.1817 1 0.34649 1 0.88528 1 0.34839 1 0.12095 1 0.074279 1 0.30905 1 0.31221 1 0.12703 1 18p gain 16 (3%) 496 NA NA NA NA 6.9999e-05 0.0493 0.0080499 1 0.02248 1 0.44237 1 0.0264 1 0.0095599 1 0.64308 1 0.33442 1 0.31291 1 0.20452 1 18q gain 13 (3%) 499 NA NA NA NA 0.00076999 0.498 0.01034 1 0.082009 1 0.59752 1 0.00149 0.934 3e-04 0.202 0.63388 1 0.059659 1 0.083569 1 0.01547 1 19p gain 101 (20%) 411 0.22041 1 1 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.67475 1 0.42366 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.01136 1 0.00164 1 9.9999e-06 0.0084 2e-05 0.0145 19q gain 25 (5%) 487 NA NA NA NA 9.9999e-06 0.0084 9.9999e-06 0.0084 0.058689 1 0.39594 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00291 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 20p gain 43 (8%) 469 NA NA NA NA 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00071999 0.469 0.17471 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.11177 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 20q gain 43 (8%) 469 NA NA NA NA 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00062999 0.412 0.14531 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.04294 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 21q gain 24 (5%) 488 NA NA NA NA 0.0105 1 0.00275 1 0.10846 1 0.39204 1 0.42476 1 0.21141 1 0.7229 1 0.10308 1 0.32887 1 0.20814 1 22q gain 23 (4%) 489 NA NA NA NA 0.01315 1 9.9999e-06 0.0084 1 1 0.68649 1 0.0014 0.882 0.00031 0.209 0.30483 1 0.04092 1 0.03375 1 0.00013 0.0898 xq gain 40 (8%) 472 NA NA NA NA 9.9999e-06 0.0084 9.9999e-06 0.0084 0.23432 1 0.71619 1 5.9999e-05 0.0426 2e-05 0.0145 0.071149 1 0.0224 1 0.0225 1 0.0064299 1 1p loss 183 (36%) 329 0.02834 1 0.00028 0.189 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00018 0.123 0.37314 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 1q loss 23 (4%) 489 0.3451 1 0.15196 1 0.73528 1 0.03665 1 0.67621 1 0.54413 1 0.39139 1 0.20117 1 0.16538 1 0.26001 1 0.29277 1 0.29638 1 2p loss 21 (4%) 491 NA NA NA NA 4e-05 0.0286 0.056829 1 0.33135 1 1 1 0.16494 1 0.03073 1 0.15106 1 0.25914 1 0.37948 1 0.15136 1 2q loss 18 (4%) 494 NA NA NA NA 0.00011 0.0763 0.0087099 1 0.068509 1 0.60629 1 0.42569 1 0.12542 1 0.02836 1 0.40019 1 0.43817 1 0.24157 1 3p loss 30 (6%) 482 NA NA NA NA 0.00039 0.261 0.16428 1 0.0063399 1 0.2685 1 0.03931 1 0.02185 1 0.0084899 1 0.01478 1 0.01388 1 0.01234 1 3q loss 28 (5%) 484 0.17278 1 0.88192 1 0.00138 0.871 0.15097 1 0.25675 1 0.76784 1 0.073489 1 0.063129 1 0.15733 1 0.16992 1 0.1429 1 0.02069 1 4p loss 71 (14%) 441 1 1 0.78176 1 0.051039 1 9.9999e-06 0.0084 0.35243 1 1 1 5e-05 0.0356 9.9999e-06 0.0084 2e-05 0.0145 2e-05 0.0145 0.02053 1 9.9999e-06 0.0084 4q loss 91 (18%) 421 1 1 0.40303 1 0.01561 1 9.9999e-06 0.0084 0.25765 1 0.93168 1 0.00082999 0.534 3e-05 0.0216 9.9999e-06 0.0084 9.9999e-06 0.0084 0.065049 1 9.9999e-06 0.0084 5p loss 34 (7%) 478 0.74239 1 0.066899 1 9.9999e-06 0.0084 0.00047 0.312 0.91655 1 0.95314 1 0.17241 1 0.04394 1 0.070909 1 0.36598 1 0.36586 1 0.1316 1 5q loss 33 (6%) 479 0.44563 1 0.23576 1 9.9999e-06 0.0084 0.00018 0.123 0.01978 1 0.11649 1 0.02653 1 0.0065899 1 3e-05 0.0216 0.092869 1 0.061789 1 0.00159 0.994 6p loss 30 (6%) 482 NA NA NA NA 0.00135 0.853 0.12271 1 0.18666 1 0.68774 1 0.37943 1 0.45963 1 0.67495 1 0.17749 1 0.67405 1 0.0075199 1 6q loss 63 (12%) 449 NA NA NA NA 9.9999e-06 0.0084 0.00178 1 0.2532 1 0.56525 1 0.078709 1 0.01946 1 0.00499 1 0.01155 1 0.01628 1 0.0068099 1 7p loss 3 (1%) 509 NA NA NA NA 0.60528 1 0.32556 1 NA NA NA NA 1 1 0.89605 1 1 1 0.70867 1 1 1 0.63466 1 7q loss 3 (1%) 509 NA NA NA NA 0.04766 1 0.3249 1 NA NA NA NA 0.37286 1 0.17612 1 1 1 0.88935 1 0.59875 1 0.63384 1 8p loss 17 (3%) 495 0.61414 1 0.04368 1 9.9999e-06 0.0084 5e-05 0.0356 0.01846 1 0.15345 1 9.9999e-06 0.0084 2e-05 0.0145 0.078119 1 0.00087999 0.564 5.9999e-05 0.0426 0.00196 1 8q loss 11 (2%) 501 NA NA NA NA 9.9999e-05 0.0698 3e-05 0.0216 0.080349 1 0.366 1 8.9999e-05 0.063 8.9999e-05 0.063 0.11898 1 0.00266 1 0.00059999 0.394 0.00289 1 9p loss 118 (23%) 394 0.38337 1 0.26617 1 9.9999e-06 0.0084 5.9999e-05 0.0426 0.03099 1 0.02035 1 0.092829 1 0.050149 1 0.85584 1 0.16807 1 0.38931 1 0.04953 1 9q loss 51 (10%) 461 NA NA NA NA 0.053509 1 0.24079 1 0.6212 1 0.34076 1 0.47381 1 0.13887 1 0.36013 1 0.92429 1 0.87338 1 0.33756 1 10p loss 83 (16%) 429 0.27088 1 0.88309 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00087999 0.564 9.9999e-06 0.0084 9.9999e-06 0.0084 6.9999e-05 0.0493 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 10q loss 96 (19%) 416 0.2709 1 0.88163 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00051999 0.344 9.9999e-06 0.0084 9.9999e-06 0.0084 2e-05 0.0145 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 11p loss 63 (12%) 449 1 1 0.03116 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.01199 1 0.72635 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.00067999 0.443 0.00024 0.163 0.00095999 0.611 0.00025 0.169 11q loss 21 (4%) 491 NA NA NA NA 0.00012 0.0832 9.9999e-05 0.0698 0.01771 1 0.65026 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.062659 1 0.00061999 0.407 0.0014 0.882 0.00015 0.103 12p loss 26 (5%) 486 NA NA NA NA 0.0097399 1 0.011 1 0.60522 1 1 1 0.40126 1 0.32646 1 0.055519 1 0.46922 1 0.34925 1 0.38123 1 12q loss 51 (10%) 461 1 1 0.58209 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.68536 1 0.11195 1 0.0068599 1 0.00265 1 0.00369 1 0.30158 1 0.1584 1 0.16011 1 13q loss 115 (22%) 397 0.18144 1 4e-05 0.0286 9.9999e-06 0.0084 0.04179 1 0.02435 1 0.62731 1 0.01393 1 0.00394 1 0.10673 1 0.14941 1 0.02105 1 0.084899 1 14q loss 80 (16%) 432 0.4649 1 0.26768 1 0.00025 0.169 0.00057999 0.382 0.04557 1 0.11603 1 2e-05 0.0145 2e-05 0.0145 0.01056 1 0.00081999 0.528 0.00039 0.261 0.00046 0.306 15q loss 51 (10%) 461 1 1 0.70709 1 0.23978 1 0.00047 0.312 0.27223 1 0.04619 1 0.00122 0.775 0.00166 1 0.39479 1 0.3413 1 0.076159 1 0.04486 1 16p loss 14 (3%) 498 NA NA NA NA 0.00337 1 0.12572 1 0.86586 1 0.20211 1 0.02839 1 0.11847 1 0.59221 1 0.75227 1 0.5285 1 0.77686 1 16q loss 22 (4%) 490 NA NA NA NA 0.00359 1 0.0064399 1 0.37458 1 0.065719 1 0.01743 1 0.092379 1 0.64736 1 0.16927 1 0.54813 1 0.055149 1 17p loss 13 (3%) 499 NA NA NA NA 0.01477 1 0.21386 1 1 1 0.7829 1 0.0137 1 0.063929 1 0.26911 1 0.0069399 1 0.071789 1 0.02438 1 17q loss 8 (2%) 504 NA NA NA NA 0.11238 1 0.25788 1 0.83541 1 0.50904 1 0.27712 1 0.53186 1 0.15905 1 0.14828 1 0.17178 1 0.15201 1 18p loss 68 (13%) 444 0.32039 1 0.03091 1 0.55999 1 0.02601 1 0.58037 1 0.10594 1 0.13761 1 0.03111 1 0.48393 1 0.5575 1 0.21432 1 0.71058 1 18q loss 62 (12%) 450 0.34132 1 0.15211 1 0.17617 1 0.00035 0.235 0.28442 1 0.097339 1 0.03188 1 0.00347 1 0.050469 1 0.34635 1 0.12213 1 0.43642 1 19p loss 23 (4%) 489 0.84637 1 0.43142 1 0.53908 1 0.82197 1 0.10134 1 0.80977 1 0.73541 1 0.65014 1 0.43876 1 0.15548 1 0.53092 1 0.17218 1 19q loss 209 (41%) 303 0.18259 1 0.01341 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.03819 1 0.33026 1 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 9.9999e-06 0.0084 20p loss 7 (1%) 505 NA NA NA NA 0.22107 1 0.22737 1 0.79287 1 1 1 0.26651 1 0.3921 1 1 1 0.31998 1 0.31687 1 0.17819 1 20q loss 3 (1%) 509 NA NA NA NA 0.24072 1 0.49134 1 NA NA NA NA 0.02322 1 0.13805 1 0.21631 1 0.70491 1 0.56871 1 0.63368 1 21q loss 36 (7%) 476 0.61559 1 0.04242 1 9.9999e-06 0.0084 0.00047 0.312 0.46253 1 0.65398 1 0.00090999 0.58 0.00063999 0.418 0.37843 1 0.11442 1 0.01856 1 0.00465 1 22q loss 57 (11%) 455 0.81537 1 0.0065499 1 9.9999e-06 0.0084 9.9999e-06 0.0084 5.9999e-05 0.0426 0.03982 1 9.9999e-06 0.0084 9.9999e-06 0.0084 0.50135 1 0.00441 1 0.00288 1 0.00019 0.129 xq loss 69 (13%) 443 0.83896 1 0.26623 1 0.70518 1 0.00496 1 0.04364 1 0.01988 1 5e-05 0.0356 9.9999e-06 0.0084 0.00077999 0.504 0.00088999 0.569 0.00028 0.189 5.9999e-05 0.0426