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 30 (7%) 397 0.80979 1 0.6576 1 0.026562 1 1 1 0.012554 1 0.085835 1 0.70078 1 0.042613 1 0.66923 1 0.6113 1 0.7789 1 1 1 1q gain 75 (18%) 352 0.52759 1 0.68588 1 0.0019352 1 0.20562 1 0.24286 1 0.029786 1 0.43902 1 0.03363 1 0.92505 1 0.95713 1 0.034187 1 0.76521 1 2p gain 74 (17%) 353 0.074272 1 0.035959 1 0.00037341 0.294 0.019539 1 0.11231 1 0.40351 1 0.007583 1 0.015475 1 0.39593 1 0.062272 1 0.28185 1 0.0034718 1 2q gain 70 (16%) 357 0.074272 1 0.035959 1 0.00020938 0.167 0.023294 1 0.28899 1 0.51786 1 0.030607 1 0.053457 1 0.49339 1 0.11076 1 0.47093 1 0.167 1 3p gain 42 (10%) 385 0.13733 1 0.13714 1 2.0621e-05 0.0173 0.36985 1 0.15078 1 0.041684 1 0.035523 1 0.22558 1 0.67828 1 0.33281 1 0.59493 1 0.21832 1 3q gain 61 (14%) 366 0.096621 1 0.0040264 1 7.8958e-08 6.9e-05 0.076689 1 0.096321 1 0.052149 1 8.1952e-05 0.0669 0.012194 1 0.65849 1 0.28026 1 0.15411 1 0.49736 1 4p gain 9 (2%) 418 NA NA NA NA 0.016367 1 0.38021 1 0.31576 1 0.70831 1 0.37451 1 0.17746 1 0.60974 1 0.88734 1 0.50543 1 1 1 4q gain 15 (4%) 412 0.12729 1 0.3199 1 0.0073873 1 1 1 0.0067975 1 0.74547 1 0.23575 1 0.23679 1 0.14268 1 0.096558 1 0.3941 1 1 1 5p gain 63 (15%) 364 0.35704 1 0.15349 1 0.034911 1 0.44648 1 0.51756 1 0.9639 1 0.66698 1 0.00622 1 0.84996 1 0.3189 1 0.20984 1 0.55772 1 5q gain 39 (9%) 388 0.78376 1 0.68292 1 0.019139 1 0.49155 1 0.39224 1 0.45286 1 0.52982 1 0.065461 1 0.5463 1 0.44379 1 0.7998 1 1 1 6p gain 79 (19%) 348 0.072134 1 2.0499e-05 0.0173 4.3913e-10 3.91e-07 0.068673 1 0.64613 1 0.59617 1 0.0025582 1 0.00057541 0.448 0.58419 1 0.29551 1 0.0019478 1 0.2198 1 6q gain 72 (17%) 355 0.18973 1 0.0011453 0.862 7.7808e-08 6.81e-05 0.2536 1 0.95035 1 0.2417 1 0.023399 1 0.018941 1 0.51578 1 0.4593 1 0.00018821 0.151 0.16693 1 7p gain 233 (55%) 194 0.0062031 1 0.0010711 0.809 4.5578e-15 4.16e-12 0.00063478 0.489 0.00027878 0.221 0.0098189 1 9.4942e-09 8.35e-06 1.0141e-08 8.91e-06 0.53604 1 0.0095884 1 9.1385e-06 0.00774 0.94622 1 7q gain 211 (49%) 216 0.0040723 1 0.003122 1 6.8818e-10 6.12e-07 0.015038 1 0.0059737 1 0.0098751 1 4.344e-07 0.000377 1.4704e-07 0.000128 0.47803 1 0.0053079 1 2.9485e-05 0.0246 0.86833 1 8p gain 123 (29%) 304 0.96317 1 0.4815 1 0.0024882 1 0.84453 1 0.51399 1 0.16129 1 0.024222 1 0.10144 1 0.59653 1 0.31904 1 0.92558 1 0.3853 1 8q gain 212 (50%) 215 0.87178 1 0.14272 1 4.7108e-18 4.32e-15 0.0097878 1 0.12741 1 0.043741 1 0.0013298 0.997 0.0015602 1 0.72366 1 0.79036 1 0.024451 1 0.054287 1 9p gain 74 (17%) 353 0.19755 1 0.061108 1 0.0036064 1 0.70526 1 0.001851 1 0.58421 1 0.36958 1 0.38092 1 0.85898 1 0.97936 1 0.076174 1 0.80834 1 9q gain 65 (15%) 362 0.1707 1 0.022137 1 0.036674 1 0.64171 1 0.0004025 0.316 0.59832 1 0.51784 1 0.85826 1 0.41064 1 0.46053 1 0.30851 1 0.82161 1 10p gain 32 (7%) 395 0.59691 1 0.8884 1 0.035071 1 0.50136 1 0.024107 1 0.049878 1 0.26369 1 0.065337 1 0.40228 1 0.18219 1 0.0093291 1 0.51061 1 10q gain 18 (4%) 409 0.16982 1 0.82865 1 0.27889 1 0.105 1 0.36322 1 0.79393 1 1 1 0.69849 1 0.74727 1 0.37975 1 0.037088 1 0.32433 1 11p gain 50 (12%) 377 0.00074376 0.569 0.00028292 0.224 1.0818e-10 9.69e-08 0.00012536 0.102 0.076177 1 0.091774 1 7.777e-05 0.0637 0.0014556 1 0.88975 1 0.026281 1 0.012843 1 0.13538 1 11q gain 48 (11%) 379 0.00020437 0.163 9.2074e-05 0.0748 1.387e-11 1.25e-08 0.00092399 0.701 0.030638 1 0.24239 1 2.4226e-06 0.00208 0.00038026 0.299 0.64375 1 0.0080185 1 0.0065929 1 0.15904 1 12p gain 87 (20%) 340 0.17946 1 0.33864 1 0.04165 1 0.025568 1 0.71716 1 0.92096 1 0.53128 1 0.88465 1 0.27432 1 0.35554 1 0.45607 1 0.67317 1 12q gain 80 (19%) 347 0.19795 1 0.42244 1 0.013074 1 0.0082957 1 0.54466 1 0.75964 1 0.21019 1 0.42004 1 0.11234 1 0.24142 1 0.25343 1 0.44442 1 13q gain 245 (57%) 182 6.2648e-05 0.0514 2.7378e-05 0.0229 2.7982e-31 2.6e-28 0.0017521 1 0.031254 1 0.052336 1 1.6317e-09 1.44e-06 2.8245e-09 2.5e-06 0.42588 1 0.094442 1 5.2592e-06 0.00448 0.55549 1 14q gain 34 (8%) 393 0.3404 1 0.29877 1 0.25419 1 0.63028 1 0.41671 1 0.39002 1 0.28567 1 0.34766 1 0.66188 1 0.85399 1 0.295 1 0.74504 1 15q gain 11 (3%) 416 1 1 0.31456 1 0.36738 1 0.20275 1 0.080765 1 0.16718 1 0.86374 1 0.86029 1 0.92307 1 0.61883 1 0.67487 1 0.55468 1 16p gain 102 (24%) 325 4.4702e-05 0.0368 3.7046e-05 0.0307 1.4186e-20 1.31e-17 0.098211 1 0.16035 1 0.27739 1 7.7787e-05 0.0637 8.5983e-06 0.00731 0.5576 1 0.0015195 1 0.011617 1 0.87814 1 16q gain 99 (23%) 328 3.1249e-05 0.0261 6.0574e-05 0.0498 1.0671e-19 9.83e-17 0.19389 1 0.22755 1 0.2867 1 8.1845e-05 0.0669 2.4268e-05 0.0204 0.71847 1 0.00070928 0.545 0.0032947 1 0.61578 1 17p gain 25 (6%) 402 0.84075 1 0.18934 1 0.25582 1 0.50898 1 0.2135 1 0.61628 1 0.13375 1 0.11853 1 0.4977 1 0.35018 1 0.93942 1 0.77869 1 17q gain 75 (18%) 352 0.12221 1 0.094481 1 1.8963e-07 0.000165 0.0010144 0.769 0.3448 1 0.057522 1 6.6076e-07 0.000573 0.00036703 0.289 0.022894 1 0.47285 1 0.15173 1 0.32369 1 18p gain 22 (5%) 405 0.091833 1 0.46284 1 8.6021e-06 0.00731 0.00050109 0.392 0.82899 1 0.6358 1 0.020199 1 0.0050516 1 0.18142 1 0.049489 1 0.26789 1 0.43022 1 18q gain 14 (3%) 413 0.1437 1 0.63479 1 0.0016039 1 0.0029128 1 0.59656 1 0.19399 1 0.0039025 1 0.059055 1 0.41483 1 0.12145 1 0.1454 1 0.48541 1 19p gain 67 (16%) 360 0.14845 1 0.073181 1 3.9875e-05 0.0329 0.068077 1 0.25905 1 0.21143 1 0.0077433 1 0.017036 1 0.077909 1 0.0076362 1 0.0050995 1 0.32416 1 19q gain 76 (18%) 351 0.087031 1 0.012907 1 0.0051744 1 0.35829 1 0.041477 1 0.086439 1 0.035246 1 0.016913 1 0.18129 1 0.0078987 1 0.022284 1 0.14974 1 20p gain 229 (54%) 198 0.0012161 0.915 1.0061e-06 0.000868 4.129e-13 3.75e-10 0.00073968 0.567 0.041265 1 0.15311 1 2.2169e-08 1.94e-05 2.3461e-06 0.00202 0.64579 1 0.011543 1 0.00070373 0.541 0.81645 1 20q gain 302 (71%) 125 3.636e-10 3.25e-07 4.4104e-11 3.96e-08 2.2939e-36 2.13e-33 2.0614e-12 1.86e-09 9.418e-05 0.0764 0.00018864 0.151 2.3478e-23 2.17e-20 1.6401e-18 1.51e-15 0.89823 1 8.2292e-05 0.0671 1.1072e-12 1e-09 0.26175 1 21q gain 21 (5%) 406 0.035655 1 0.27469 1 0.026279 1 0.89352 1 0.73056 1 1 1 0.57523 1 0.34028 1 0.22224 1 0.22904 1 0.3698 1 1 1 22q gain 10 (2%) 417 1 1 1 1 0.12906 1 0.38021 1 0.63669 1 1 1 0.2667 1 0.15926 1 1 1 0.83945 1 0.85792 1 0.12522 1 xq gain 68 (16%) 359 0.035082 1 0.29714 1 0.0028656 1 0.16903 1 0.25569 1 0.1628 1 0.44054 1 0.15323 1 0.27769 1 0.76242 1 0.21967 1 0.41923 1 1p loss 91 (21%) 336 0.027515 1 0.059696 1 6.8913e-11 6.18e-08 0.00092171 0.701 0.57684 1 0.54683 1 9.1535e-05 0.0744 8.9419e-06 0.00758 0.7774 1 0.003912 1 0.0042894 1 0.0067383 1 1q loss 52 (12%) 375 0.2731 1 0.54392 1 3.6034e-05 0.03 0.060943 1 0.43931 1 0.22673 1 0.0046263 1 0.0024394 1 0.65163 1 0.010923 1 0.0065362 1 0.106 1 2p loss 6 (1%) 421 0.89774 1 0.31456 1 0.033855 1 NA NA 0.70306 1 1 1 0.17283 1 0.34069 1 0.63943 1 0.43036 1 NA NA NA NA 2q loss 7 (2%) 420 1 1 0.15598 1 0.185 1 NA NA 0.30984 1 0.46454 1 0.064362 1 0.20067 1 0.38933 1 0.32825 1 NA NA NA NA 3p loss 50 (12%) 377 0.7802 1 0.36383 1 0.0039866 1 0.13602 1 0.60518 1 0.56646 1 0.044292 1 0.048033 1 0.6091 1 0.50306 1 0.00060374 0.467 0.47484 1 3q loss 31 (7%) 396 0.82499 1 1 1 0.029028 1 0.55784 1 0.39633 1 0.49239 1 0.72171 1 0.38654 1 0.24662 1 0.9081 1 0.012411 1 0.35225 1 4p loss 127 (30%) 300 8.4542e-05 0.0688 0.0074671 1 2.365e-14 2.15e-11 0.00045801 0.359 0.10455 1 0.096616 1 4.0195e-06 0.00343 1.6054e-06 0.00138 0.45203 1 0.057519 1 2.7298e-05 0.0229 0.53096 1 4q loss 115 (27%) 312 0.00016271 0.131 0.0064741 1 2.0618e-14 1.88e-11 9.4627e-06 0.00801 0.10445 1 0.19434 1 0.0003405 0.269 3.4014e-06 0.00291 0.21914 1 0.022857 1 4.4047e-05 0.0363 0.24614 1 5p loss 54 (13%) 373 0.63591 1 0.86461 1 0.00015536 0.125 0.0083871 1 0.3292 1 0.55796 1 0.030329 1 0.011525 1 0.72916 1 0.53673 1 0.094723 1 0.93444 1 5q loss 74 (17%) 353 0.30633 1 0.18044 1 6.7673e-07 0.000586 0.0066613 1 0.0089425 1 0.0072873 1 3.7062e-05 0.0307 3.4615e-06 0.00296 0.97922 1 0.4593 1 0.0022012 1 1 1 6p loss 33 (8%) 394 1 1 1 1 0.59467 1 0.51491 1 0.18595 1 0.57624 1 0.96054 1 0.68529 1 0.61308 1 0.11381 1 0.033121 1 0.21401 1 6q loss 44 (10%) 383 0.82195 1 0.81084 1 0.96119 1 0.36705 1 0.20186 1 0.20165 1 0.77207 1 0.73348 1 0.58051 1 0.16833 1 0.28649 1 0.4441 1 7q loss 3 (1%) 424 NA NA NA NA 0.11832 1 0.615 1 NA NA NA NA 0.42229 1 0.61854 1 0.56127 1 0.59972 1 NA NA NA NA 8p loss 133 (31%) 294 0.023502 1 0.0016996 1 3.206e-16 2.93e-13 3.6338e-05 0.0302 0.010537 1 0.0010883 0.821 3.5029e-07 0.000304 4.3333e-06 0.00369 0.5603 1 0.10861 1 2.8521e-06 0.00244 0.47407 1 8q loss 23 (5%) 404 0.80979 1 0.6576 1 0.0038285 1 0.33957 1 0.27401 1 0.10795 1 0.90339 1 0.14055 1 0.5093 1 0.076816 1 0.14916 1 0.49035 1 9p loss 49 (11%) 378 0.57125 1 0.013623 1 3.9782e-05 0.0329 0.0024693 1 0.88566 1 0.34046 1 0.00073984 0.567 0.00054262 0.424 0.36921 1 0.12602 1 0.00082995 0.632 0.24695 1 9q loss 49 (11%) 378 0.11811 1 0.060601 1 3.9782e-05 0.0329 0.00024513 0.195 0.96705 1 0.35639 1 0.00028423 0.225 0.00054262 0.424 0.43779 1 0.0086883 1 1.3169e-05 0.0111 0.35196 1 10p loss 64 (15%) 363 0.020994 1 0.033981 1 2.9439e-08 2.58e-05 0.0038794 1 0.013592 1 0.124 1 9.7805e-06 0.00826 0.000196 0.157 0.48686 1 0.0060618 1 0.001341 1 0.55035 1 10q loss 68 (16%) 359 0.02472 1 0.017668 1 2.5007e-10 2.24e-07 0.00057458 0.448 0.012108 1 0.063813 1 3.6553e-06 0.00312 3.26e-05 0.0272 0.61035 1 0.050816 1 0.00014808 0.12 0.84245 1 11p loss 49 (11%) 378 0.22558 1 0.041045 1 0.0023201 1 0.021611 1 0.72298 1 0.69292 1 0.21139 1 0.022664 1 0.82366 1 0.70267 1 0.00023854 0.19 0.80755 1 11q loss 59 (14%) 368 0.04223 1 0.0020698 1 0.00031219 0.247 0.001286 0.966 0.60141 1 0.87104 1 0.12377 1 0.017997 1 0.85143 1 0.38293 1 0.00021871 0.175 0.58342 1 12p loss 44 (10%) 383 0.061639 1 0.011297 1 1.6582e-10 1.48e-07 0.042046 1 0.40144 1 0.60017 1 0.00024624 0.196 0.0027774 1 0.86715 1 0.21068 1 0.0028921 1 0.66421 1 12q loss 47 (11%) 380 0.10982 1 0.010531 1 3.7574e-09 3.31e-06 0.013644 1 0.51298 1 0.68619 1 2.9391e-05 0.0246 0.00069231 0.533 0.94371 1 0.10495 1 0.00059558 0.462 0.18923 1 13q loss 12 (3%) 415 0.87394 1 0.19429 1 0.15658 1 0.040553 1 0.001601 1 0.008184 1 0.76444 1 0.21624 1 0.59751 1 0.071649 1 0.07925 1 0.15011 1 14q loss 128 (30%) 299 7.3259e-07 0.000634 1.6461e-06 0.00142 1.9304e-28 1.79e-25 7.3269e-07 0.000634 0.0017995 1 0.045247 1 1.7742e-11 1.6e-08 3.8196e-10 3.41e-07 0.25253 1 7.0019e-05 0.0574 2.2407e-05 0.0188 0.084721 1 15q loss 145 (34%) 282 0.0017216 1 0.0020458 1 8.8286e-21 8.15e-18 0.00060014 0.465 0.012251 1 0.03246 1 2.8509e-09 2.52e-06 1.5741e-08 1.38e-05 0.85247 1 0.0001381 0.112 4.5835e-05 0.0377 0.42877 1 16p loss 27 (6%) 400 0.40597 1 0.71065 1 1 1 0.42884 1 0.39227 1 0.33501 1 0.067337 1 0.13574 1 0.50856 1 0.25221 1 0.2481 1 0.39213 1 16q loss 25 (6%) 402 0.40597 1 0.71065 1 0.59502 1 0.59112 1 0.13654 1 0.25112 1 0.28023 1 0.43422 1 0.40419 1 0.62562 1 0.19556 1 0.78103 1 17p loss 222 (52%) 205 2.0969e-07 0.000183 1.0695e-06 0.000922 4.8624e-29 4.51e-26 1.2834e-09 1.14e-06 0.019678 1 0.00092282 0.701 2.7946e-12 2.52e-09 4.5585e-13 4.13e-10 0.79079 1 0.10008 1 9.3916e-10 8.34e-07 0.11687 1 17q loss 61 (14%) 366 0.11319 1 0.68588 1 0.00058772 0.457 0.013836 1 0.57436 1 0.47572 1 0.058881 1 0.017916 1 0.56933 1 0.25084 1 0.0032512 1 0.030092 1 18p loss 237 (56%) 190 1.4606e-12 1.32e-09 7.6271e-10 6.78e-07 1.0469e-44 9.76e-42 8.2259e-18 7.53e-15 0.00075088 0.574 0.00060703 0.469 4.677e-24 4.33e-21 6.1473e-18 5.64e-15 1 1 0.0064521 1 7.557e-15 6.88e-12 0.0093992 1 18q loss 252 (59%) 175 6.3991e-12 5.77e-09 9.6007e-10 8.52e-07 1.1223e-42 1.04e-39 2.9462e-15 2.69e-12 0.0041836 1 0.00081399 0.621 1.2341e-25 1.14e-22 7.589e-18 6.95e-15 0.70069 1 0.010111 1 2.2623e-13 2.05e-10 0.082179 1 19p loss 38 (9%) 389 1 1 0.16701 1 0.027993 1 0.3771 1 0.60608 1 0.25972 1 0.090236 1 0.0053177 1 0.041343 1 0.49904 1 0.46829 1 0.04611 1 19q loss 32 (7%) 395 0.83826 1 0.2968 1 0.06015 1 0.53063 1 0.18047 1 0.11948 1 0.26053 1 0.023527 1 0.33848 1 0.72302 1 0.36899 1 0.12859 1 20p loss 43 (10%) 384 0.19429 1 0.13714 1 0.0010509 0.794 0.20455 1 0.86312 1 0.4709 1 0.069627 1 0.12952 1 0.87855 1 0.14673 1 0.12411 1 0.086273 1 20q loss 6 (1%) 421 NA NA NA NA 1 1 0.82201 1 0.032052 1 1 1 0.87533 1 0.76899 1 1 1 1 1 0.19834 1 0.31943 1 21q loss 117 (27%) 310 0.009922 1 0.0075797 1 5.0974e-09 4.49e-06 0.060574 1 0.22921 1 0.18586 1 0.0044825 1 0.00062107 0.479 0.4651 1 0.29778 1 0.0018001 1 0.46209 1 22q loss 138 (32%) 289 0.00041772 0.327 0.00019004 0.152 1.6611e-18 1.53e-15 0.0003207 0.253 0.17036 1 0.63997 1 2.6584e-07 0.000231 0.00017317 0.139 0.1361 1 0.0010438 0.79 1.0405e-05 0.00878 0.29058 1 xq loss 46 (11%) 381 0.029763 1 0.19962 1 0.01049 1 0.24701 1 0.08566 1 0.20454 1 0.16775 1 0.3248 1 0.078532 1 0.52108 1 0.049774 1 0.20004 1