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%) 500 NA NA NA NA 5.9999e-05 0.0427 0.00016 0.111 0.02421 1 1 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.0055799 1 2e-05 0.0147 0.01234 1 0.00014 0.0974 1q gain 23 (4%) 490 NA NA NA NA 0.00023 0.157 0.00056999 0.377 0.43389 1 0.60664 1 5.9999e-05 0.0427 0.00045 0.3 0.12157 1 0.03157 1 0.03081 1 0.056819 1 2p gain 14 (3%) 499 NA NA NA NA 0.01682 1 0.01496 1 0.30882 1 0.34476 1 0.01244 1 0.00103 0.664 0.60302 1 0.02116 1 0.88951 1 0.03994 1 2q gain 13 (3%) 500 NA NA NA NA 0.03809 1 0.01033 1 0.30771 1 0.34271 1 0.03492 1 0.00068999 0.453 0.51244 1 0.01766 1 0.68407 1 0.04567 1 3p gain 11 (2%) 502 NA NA NA NA 0.064709 1 0.32718 1 0.46286 1 0.20284 1 0.10813 1 0.10902 1 0.11864 1 0.2884 1 0.74331 1 0.19922 1 3q gain 8 (2%) 505 NA NA NA NA 0.00191 1 0.10048 1 0.056389 1 0.36638 1 0.062769 1 0.00369 1 0.34173 1 0.13346 1 0.32962 1 0.14968 1 4p gain 13 (3%) 500 NA NA NA NA 0.00060999 0.402 0.0070599 1 0.03239 1 0.89536 1 0.0084399 1 0.00177 1 0.19052 1 0.10552 1 0.33745 1 0.27494 1 4q gain 6 (1%) 507 NA NA NA NA 0.03909 1 0.01762 1 0.11157 1 0.66997 1 0.01425 1 0.00355 1 0.26125 1 0.15005 1 0.38213 1 0.22196 1 5p gain 11 (2%) 502 NA NA NA NA 0.0064399 1 0.00292 1 0.02136 1 0.60878 1 4e-05 0.029 9.9999e-05 0.07 0.02384 1 0.02683 1 0.14249 1 0.01591 1 5q gain 8 (2%) 505 NA NA NA NA 0.00469 1 0.00025 0.17 NA NA NA NA 0.00022 0.15 0.00018 0.124 0.01254 1 0.00097999 0.634 0.0085499 1 0.00058999 0.389 6p gain 7 (1%) 506 NA NA NA NA 0.22467 1 0.0466 1 0.03775 1 0.51814 1 0.43403 1 0.097929 1 0.0234 1 0.063729 1 0.57233 1 0.03296 1 7p gain 121 (24%) 392 0.74486 1 0.7814 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00044 0.293 0.01164 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00263 1 9.9999e-06 0.00836 0.00039 0.262 9.9999e-06 0.00836 7q gain 151 (29%) 362 0.76166 1 0.51971 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00403 1 0.20049 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00328 1 9.9999e-06 0.00836 0.00078999 0.516 9.9999e-06 0.00836 8p gain 46 (9%) 467 NA NA NA NA 8.9999e-05 0.0634 0.00133 0.849 0.063789 1 0.16028 1 0.02234 1 0.0056899 1 0.39073 1 0.41293 1 0.20671 1 0.071049 1 8q gain 56 (11%) 457 0.051479 1 0.40467 1 9.9999e-06 0.00836 5e-05 0.0359 0.0114 1 0.055839 1 0.00153 0.967 0.00049 0.325 0.1907 1 0.11953 1 0.067679 1 0.01541 1 9p gain 17 (3%) 496 NA NA NA NA 0.01562 1 0.14865 1 0.29165 1 0.53063 1 0.064799 1 0.03655 1 0.83857 1 0.02608 1 0.86061 1 0.20397 1 9q gain 24 (5%) 489 NA NA NA NA 0.01235 1 0.10478 1 0.25818 1 0.054329 1 0.03986 1 0.01364 1 0.42996 1 0.01045 1 0.58403 1 0.17303 1 10p gain 57 (11%) 456 1 1 0.04178 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.02112 1 0.553 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.054309 1 0.2951 1 0.47425 1 0.0056499 1 10q gain 12 (2%) 501 NA NA NA NA 0.00132 0.843 0.02035 1 0.26709 1 0.51523 1 0.085429 1 0.03616 1 0.077919 1 0.03032 1 0.57968 1 0.20757 1 11p gain 31 (6%) 482 NA NA NA NA 0.0326 1 0.00088999 0.578 0.02586 1 0.11009 1 0.0093299 1 0.00318 1 0.093679 1 0.02454 1 0.40686 1 0.0081999 1 11q gain 58 (11%) 455 0.61555 1 0.58176 1 0.1776 1 0.0106 1 0.081749 1 0.03072 1 0.062279 1 0.03661 1 0.54644 1 0.04638 1 0.64836 1 0.03188 1 12p gain 33 (6%) 480 0.7543 1 0.57968 1 0.00029 0.196 0.03292 1 0.25854 1 0.30888 1 0.04212 1 0.087529 1 0.087339 1 0.02153 1 0.19073 1 0.5585 1 12q gain 16 (3%) 497 NA NA NA NA 0.0054599 1 0.10209 1 0.29373 1 0.53181 1 0.0054899 1 0.085139 1 0.16502 1 0.059179 1 0.11899 1 0.091009 1 13q gain 6 (1%) 507 NA NA NA NA 0.38187 1 0.39671 1 0.79414 1 0.79482 1 0.23428 1 0.47369 1 0.35196 1 0.5877 1 0.4536 1 0.46914 1 14q gain 4 (1%) 509 NA NA NA NA 0.82572 1 0.75815 1 NA NA NA NA 0.71026 1 0.59043 1 0.21705 1 0.67972 1 0.27047 1 0.75853 1 15q gain 11 (2%) 502 NA NA NA NA 0.00221 1 0.02028 1 0.04491 1 0.2172 1 0.04782 1 0.01337 1 0.17612 1 0.28771 1 0.47463 1 0.096369 1 16p gain 17 (3%) 496 NA NA NA NA 0.48815 1 0.74478 1 0.5602 1 0.69794 1 0.074899 1 0.04791 1 0.11953 1 0.059169 1 0.11009 1 0.51535 1 16q gain 19 (4%) 494 NA NA NA NA 0.26765 1 0.31541 1 0.47018 1 0.51302 1 0.15237 1 0.03404 1 0.054809 1 0.099919 1 0.13934 1 0.52998 1 17p gain 20 (4%) 493 NA NA NA NA 0.48937 1 0.59567 1 0.34755 1 0.88806 1 0.18645 1 0.04546 1 0.18909 1 0.48536 1 0.68694 1 0.65418 1 17q gain 23 (4%) 490 NA NA NA NA 0.68233 1 0.4486 1 0.34723 1 0.88474 1 0.34861 1 0.12073 1 0.10858 1 0.70001 1 0.42451 1 0.35813 1 18p gain 17 (3%) 496 NA NA NA NA 0.00013 0.0906 0.00483 1 0.02325 1 0.44084 1 0.03091 1 0.01161 1 0.83856 1 0.092649 1 0.61181 1 0.03721 1 18q gain 13 (3%) 500 NA NA NA NA 0.00097999 0.634 0.00355 1 0.081009 1 0.59907 1 0.00162 1 0.00023 0.157 0.50908 1 0.01722 1 0.18192 1 0.00453 1 19p gain 100 (19%) 413 0.22028 1 1 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.67689 1 0.42434 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00018 0.124 0.03853 1 0.23493 1 0.00254 1 19q gain 25 (5%) 488 NA NA NA NA 9.9999e-06 0.00836 9.9999e-06 0.00836 0.056639 1 0.39947 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00243 1 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 20p gain 43 (8%) 470 NA NA NA NA 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00066999 0.441 0.17538 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.16025 1 9.9999e-06 0.00836 0.00094999 0.617 9.9999e-06 0.00836 20q gain 43 (8%) 470 NA NA NA NA 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00072999 0.477 0.14376 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.04912 1 9.9999e-06 0.00836 4e-05 0.029 9.9999e-06 0.00836 21q gain 24 (5%) 489 NA NA NA NA 0.0059599 1 0.0119 1 0.10956 1 0.39467 1 0.42805 1 0.21148 1 0.62313 1 0.098319 1 0.72809 1 0.079949 1 22q gain 23 (4%) 490 NA NA NA NA 0.01198 1 4e-05 0.029 1 1 0.68601 1 0.00106 0.681 0.00038 0.255 0.11856 1 0.52654 1 0.04174 1 0.22368 1 xq gain 41 (8%) 472 NA NA NA NA 9.9999e-06 0.00836 9.9999e-06 0.00836 0.2364 1 0.71365 1 9.9999e-05 0.07 9.9999e-06 0.00836 0.01769 1 0.55852 1 0.66957 1 0.01345 1 1p loss 184 (36%) 329 0.02947 1 0.00019 0.131 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00027 0.183 0.4584 1 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 1q loss 25 (5%) 488 0.34443 1 0.15044 1 0.45527 1 0.063169 1 0.47528 1 0.46465 1 0.36098 1 0.2817 1 0.076099 1 0.41302 1 0.16303 1 0.13763 1 2p loss 21 (4%) 492 NA NA NA NA 0.00024 0.163 0.04163 1 0.33314 1 1 1 0.16137 1 0.03031 1 0.072749 1 0.40467 1 0.72901 1 0.25901 1 2q loss 18 (4%) 495 NA NA NA NA 0.00041 0.274 0.0057299 1 0.069449 1 0.60726 1 0.42334 1 0.12483 1 0.02605 1 0.81066 1 0.69093 1 0.38438 1 3p loss 30 (6%) 483 NA NA NA NA 0.0048 1 0.058319 1 0.0063699 1 0.27172 1 0.03801 1 0.02111 1 0.00103 0.664 0.00047 0.312 0.19309 1 0.00293 1 3q loss 28 (5%) 485 0.17582 1 0.88167 1 0.0072299 1 0.13284 1 0.25164 1 0.76891 1 0.072299 1 0.062839 1 0.090319 1 0.01686 1 0.26902 1 0.03544 1 4p loss 71 (14%) 442 1 1 0.78304 1 0.0033 1 9.9999e-06 0.00836 0.35057 1 1 1 4e-05 0.029 9.9999e-06 0.00836 5e-05 0.0359 0.00034 0.229 4e-05 0.029 9.9999e-06 0.00836 4q loss 92 (18%) 421 1 1 0.40449 1 0.0065999 1 9.9999e-06 0.00836 0.25783 1 0.93066 1 0.00070999 0.465 9.9999e-06 0.00836 0.00021 0.144 0.00148 0.937 2e-05 0.0147 2e-05 0.0147 5p loss 34 (7%) 479 0.74502 1 0.066339 1 9.9999e-06 0.00836 9.9999e-05 0.07 0.91518 1 0.95357 1 0.17316 1 0.04353 1 0.10478 1 0.39202 1 0.73326 1 0.32521 1 5q loss 33 (6%) 480 0.44684 1 0.23912 1 9.9999e-06 0.00836 0.00017 0.118 0.0193 1 0.11906 1 0.02719 1 0.0064899 1 8.9999e-05 0.0634 0.16186 1 0.81056 1 0.61002 1 6p loss 30 (6%) 483 NA NA NA NA 0.03329 1 0.058139 1 0.18718 1 0.68523 1 0.37109 1 0.46208 1 0.39974 1 0.40361 1 0.01227 1 0.00304 1 6q loss 63 (12%) 450 NA NA NA NA 7.9999e-05 0.0566 0.00134 0.854 0.25081 1 0.56798 1 0.076459 1 0.01923 1 0.00122 0.781 0.17307 1 0.01369 1 4e-05 0.029 7p loss 3 (1%) 510 NA NA NA NA 0.04989 1 0.24488 1 NA NA NA NA 1 1 0.89528 1 1 1 1 1 NA NA NA NA 7q loss 3 (1%) 510 NA NA NA NA 0.04938 1 0.24292 1 NA NA NA NA 0.37393 1 0.17645 1 1 1 1 1 NA NA NA NA 8p loss 17 (3%) 496 0.61567 1 0.04262 1 2e-05 0.0147 5e-05 0.0359 0.01897 1 0.1524 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.11661 1 0.00145 0.919 0.81642 1 0.00027 0.183 8q loss 11 (2%) 502 NA NA NA NA 2e-04 0.137 2e-05 0.0147 0.082299 1 0.36421 1 7.9999e-05 0.0566 6.9999e-05 0.0497 0.052419 1 0.00067999 0.447 0.37335 1 8.9999e-05 0.0634 9p loss 118 (23%) 395 0.38247 1 0.26639 1 9.9999e-06 0.00836 3e-04 0.203 0.03187 1 0.01977 1 0.094809 1 0.051009 1 0.89356 1 0.22081 1 0.28514 1 0.03461 1 9q loss 51 (10%) 462 NA NA NA NA 0.15257 1 0.46131 1 0.62171 1 0.34272 1 0.46656 1 0.13221 1 0.39623 1 0.82437 1 0.593 1 0.03341 1 10p loss 83 (16%) 430 0.26893 1 0.88129 1 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00111 0.712 9.9999e-06 0.00836 9.9999e-06 0.00836 2e-05 0.0147 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 10q loss 96 (19%) 417 0.27331 1 0.8828 1 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 0.00042 0.281 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 11p loss 63 (12%) 450 1 1 0.03147 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.0122 1 0.7261 1 9.9999e-06 0.00836 9.9999e-06 0.00836 2e-05 0.0147 5e-05 0.0359 0.43427 1 0.01646 1 11q loss 21 (4%) 492 NA NA NA NA 0.00017 0.118 6.9999e-05 0.0497 0.01752 1 0.65163 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.02484 1 6.9999e-05 0.0497 0.49173 1 4e-04 0.268 12p loss 26 (5%) 487 NA NA NA NA 0.00381 1 0.063179 1 0.60593 1 1 1 0.40349 1 0.31959 1 0.079099 1 0.15234 1 0.55274 1 0.92998 1 12q loss 51 (10%) 462 1 1 0.57864 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.68115 1 0.11014 1 0.0070699 1 0.00288 1 0.0058299 1 0.33249 1 0.83443 1 0.80892 1 13q loss 116 (23%) 397 0.17933 1 8.9999e-05 0.0634 5e-05 0.0359 0.0058899 1 0.02625 1 0.62237 1 0.01593 1 0.0051599 1 0.03477 1 0.0132 1 0.29686 1 0.24009 1 14q loss 80 (16%) 433 0.46593 1 0.26641 1 0.00104 0.669 0.00016 0.111 0.04406 1 0.11494 1 2e-05 0.0147 3e-05 0.0218 0.01031 1 0.00082999 0.541 0.01139 1 0.00054999 0.364 15q loss 51 (10%) 462 1 1 0.70572 1 0.02829 1 0.00179 1 0.27113 1 0.04633 1 0.00094999 0.617 0.00139 0.883 0.23484 1 0.47261 1 0.057369 1 0.083879 1 16p loss 14 (3%) 499 NA NA NA NA 0.00495 1 0.04302 1 0.86578 1 0.20067 1 0.02871 1 0.11963 1 0.82285 1 0.35653 1 0.70587 1 0.1357 1 16q loss 22 (4%) 491 NA NA NA NA 0.0058199 1 0.00221 1 0.37586 1 0.068099 1 0.01684 1 0.091899 1 0.6639 1 0.00355 1 0.29538 1 0.0092599 1 17p loss 13 (3%) 500 NA NA NA NA 0.094119 1 0.13245 1 1 1 0.78201 1 0.01386 1 0.062189 1 0.15816 1 0.0063399 1 0.71434 1 0.01141 1 17q loss 8 (2%) 505 NA NA NA NA 0.11593 1 0.20007 1 0.83715 1 0.51038 1 0.27043 1 0.53136 1 0.16208 1 0.26486 1 1 1 0.02348 1 18p loss 68 (13%) 445 0.3206 1 0.02979 1 0.20276 1 0.00138 0.878 0.58152 1 0.10454 1 0.13403 1 0.02925 1 0.59723 1 0.91461 1 0.47059 1 0.51197 1 18q loss 62 (12%) 451 0.34344 1 0.15151 1 0.04626 1 0.00031 0.209 0.28817 1 0.097799 1 0.0309 1 0.00337 1 0.058109 1 0.71208 1 0.42286 1 0.52956 1 19p loss 25 (5%) 488 0.84734 1 0.43291 1 0.52599 1 0.87536 1 0.1027 1 0.80913 1 0.56247 1 0.45842 1 0.13147 1 0.1157 1 0.02592 1 0.055779 1 19q loss 209 (41%) 304 0.18614 1 0.01258 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.03842 1 0.33471 1 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 9.9999e-06 0.00836 20p loss 7 (1%) 506 NA NA NA NA 0.22479 1 0.15609 1 0.79333 1 1 1 0.2598 1 0.39453 1 0.4466 1 0.48198 1 0.71017 1 0.48113 1 20q loss 3 (1%) 510 NA NA NA NA 0.25294 1 0.44614 1 NA NA NA NA 0.02401 1 0.13775 1 0.23353 1 1 1 0.30122 1 0.88765 1 21q loss 36 (7%) 477 0.61234 1 0.04264 1 9.9999e-06 0.00836 0.00021 0.144 0.46439 1 0.65354 1 0.00087999 0.573 0.00046 0.306 0.24899 1 0.02644 1 0.50686 1 0.28816 1 22q loss 57 (11%) 456 0.81751 1 0.0068699 1 9.9999e-06 0.00836 9.9999e-06 0.00836 4e-05 0.029 0.0402 1 9.9999e-06 0.00836 9.9999e-06 0.00836 0.45333 1 0.00033 0.222 0.01159 1 0.00015 0.104 xq loss 69 (13%) 444 0.83731 1 0.26638 1 0.25402 1 0.0121 1 0.04484 1 0.02086 1 5e-05 0.0359 9.9999e-06 0.00836 7.9999e-05 0.0566 0.15048 1 0.0314 1 0.0082499 1