Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL MIR_CNMF MIR_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 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q 1p gain 166 (29%) 403 0.10528 1 0.17636 1 0.11996 1 0.24892 1 0.0024112 1 0.15457 1 0.087496 1 0.61901 1 0.6009 1 0.79657 1 0.21517 1 0.88474 1 0.15483 1 0.2312 1 1q gain 218 (38%) 351 0.77551 1 0.34752 1 0.70491 1 0.14668 1 9.7777e-08 0.000108 0.0057376 1 0.45568 1 0.9924 1 0.43565 1 0.5668 1 0.20539 1 0.34981 1 0.1132 1 0.17882 1 2p gain 178 (31%) 391 1.4765e-06 0.00163 1.9591e-06 0.00216 0.81085 1 0.00010085 0.109 2.3559e-11 2.62e-08 1.3229e-07 0.000147 0.03756 1 0.28498 1 0.00012718 0.137 0.007203 1 0.81214 1 0.26356 1 0.79707 1 0.29879 1 2q gain 150 (26%) 419 0.0004172 0.446 1.8237e-05 0.0199 0.97858 1 0.0032521 1 4.4206e-09 4.91e-06 0.00014332 0.154 0.097911 1 0.71579 1 0.003696 1 0.018846 1 0.60612 1 0.86885 1 0.10762 1 0.13141 1 3p gain 154 (27%) 415 0.33746 1 0.65768 1 0.043112 1 0.55432 1 0.013003 1 0.83882 1 1 1 0.89584 1 0.77177 1 0.43611 1 0.91572 1 0.4058 1 0.89978 1 0.1345 1 3q gain 268 (47%) 301 0.97127 1 0.77982 1 0.25149 1 0.59989 1 3.5328e-06 0.00388 0.018835 1 0.58504 1 0.33895 1 0.69826 1 0.64297 1 0.1826 1 0.14938 1 0.11876 1 0.39988 1 4p gain 57 (10%) 512 0.24264 1 0.24592 1 0.005163 1 0.3189 1 0.12822 1 0.11685 1 0.47226 1 0.18222 1 0.59501 1 0.4388 1 0.3225 1 0.061869 1 0.57353 1 0.089674 1 4q gain 32 (6%) 537 0.65659 1 0.76672 1 0.1549 1 0.57678 1 0.0351 1 0.017561 1 0.27447 1 0.60671 1 0.77389 1 0.514 1 0.37551 1 0.0067237 1 0.48214 1 0.40421 1 5p gain 196 (34%) 373 0.58594 1 0.98637 1 0.8542 1 0.66316 1 6.7944e-05 0.0737 0.19367 1 0.48289 1 0.24558 1 0.12303 1 0.44321 1 0.22965 1 0.55046 1 0.62054 1 0.052513 1 5q gain 60 (11%) 509 0.082902 1 0.22247 1 0.79911 1 0.5021 1 0.49881 1 0.50703 1 0.42353 1 0.24175 1 0.73505 1 0.48959 1 0.498 1 0.60269 1 0.64553 1 0.49481 1 6p gain 166 (29%) 403 0.50973 1 0.13657 1 0.897 1 0.087145 1 1.3819e-06 0.00152 8.6125e-05 0.0933 0.86043 1 0.14365 1 0.15779 1 0.84229 1 0.35016 1 0.59014 1 0.44142 1 0.22026 1 6q gain 96 (17%) 473 0.64763 1 0.097345 1 0.81906 1 0.1739 1 3.0644e-07 0.000339 1.3515e-05 0.0148 0.80172 1 0.67745 1 0.004992 1 0.26062 1 0.19489 1 0.25312 1 0.46672 1 0.070471 1 7p gain 181 (32%) 388 0.62288 1 0.86102 1 0.071605 1 0.15583 1 7.5679e-07 0.000835 0.00010972 0.118 0.50501 1 0.37976 1 0.56131 1 0.47049 1 0.92132 1 0.30252 1 0.36602 1 0.62015 1 7q gain 198 (35%) 371 0.64568 1 0.26683 1 0.29732 1 0.55578 1 1.6935e-05 0.0185 0.0014507 1 0.44822 1 0.19881 1 0.9195 1 0.69065 1 0.14814 1 0.7475 1 0.05431 1 0.73861 1 8p gain 117 (21%) 452 0.068549 1 0.012823 1 0.29801 1 0.019304 1 0.71429 1 0.79609 1 0.13126 1 0.17504 1 0.6099 1 0.65633 1 0.10635 1 0.12576 1 0.17526 1 0.063857 1 8q gain 238 (42%) 331 0.020567 1 0.0066496 1 0.060981 1 0.11889 1 0.1798 1 0.4461 1 0.31683 1 0.52606 1 0.030002 1 0.20355 1 0.46125 1 0.5964 1 0.28893 1 0.64094 1 9p gain 91 (16%) 478 0.107 1 0.83224 1 0.23917 1 0.77338 1 0.018828 1 0.0083242 1 0.39565 1 0.92198 1 0.6793 1 0.16424 1 0.18614 1 0.32282 1 0.4881 1 0.15788 1 9q gain 45 (8%) 524 0.24773 1 0.21604 1 0.094325 1 0.64075 1 0.18148 1 0.22196 1 0.56493 1 0.22644 1 0.47142 1 0.020304 1 0.48657 1 0.70347 1 0.43859 1 0.75222 1 10p gain 184 (32%) 385 0.0044155 1 0.062179 1 0.67059 1 0.029914 1 1.4469e-10 1.61e-07 0.00017352 0.186 0.97447 1 0.24079 1 0.011248 1 0.46726 1 0.54294 1 0.62505 1 0.50668 1 0.22119 1 10q gain 108 (19%) 461 0.0037944 1 0.033936 1 0.23803 1 0.0092155 1 0.0012588 1 0.090941 1 0.75893 1 0.63065 1 0.10754 1 0.44657 1 0.73603 1 0.68976 1 0.94895 1 0.36092 1 11p gain 76 (13%) 493 0.68443 1 0.30279 1 0.62396 1 0.84927 1 0.34408 1 0.013986 1 0.027628 1 0.033835 1 0.060162 1 0.24072 1 0.55279 1 0.65203 1 0.866 1 1 1 11q gain 114 (20%) 455 0.44578 1 0.38667 1 0.86334 1 0.086197 1 0.04062 1 0.0016085 1 0.16382 1 0.016596 1 0.28942 1 0.079992 1 0.52068 1 0.79919 1 0.8425 1 0.66935 1 12p gain 250 (44%) 319 4.3983e-05 0.0478 8.8845e-05 0.0961 0.7444 1 0.00072617 0.771 1.0548e-13 1.18e-10 1.8378e-07 0.000203 0.29915 1 0.56455 1 0.00038275 0.41 0.0042574 1 0.18279 1 0.30651 1 0.29706 1 0.13672 1 12q gain 174 (31%) 395 0.006272 1 5.087e-05 0.0552 0.64404 1 0.33933 1 2.0379e-12 2.28e-09 5.4901e-06 0.00602 0.025795 1 0.26303 1 0.0018935 1 0.0041541 1 0.10209 1 0.11017 1 0.57134 1 0.12152 1 13q gain 60 (11%) 509 0.0064065 1 0.035226 1 0.56834 1 3.2104e-05 0.035 0.00012537 0.135 4.8999e-06 0.00538 0.57693 1 0.45309 1 0.24551 1 0.82556 1 0.18795 1 1 1 0.95449 1 0.91051 1 14q gain 58 (10%) 511 0.1466 1 0.52484 1 0.40119 1 0.28666 1 0.8008 1 0.73348 1 0.32853 1 0.12541 1 0.49591 1 0.32366 1 0.6377 1 0.68132 1 0.5646 1 0.42618 1 15q gain 39 (7%) 530 0.84289 1 0.57206 1 0.09418 1 0.28382 1 0.40126 1 0.5696 1 0.11049 1 0.23227 1 0.75344 1 0.53068 1 0.29795 1 0.36167 1 0.51782 1 0.15758 1 16p gain 58 (10%) 511 0.0026485 1 0.0027881 1 0.40119 1 0.59947 1 0.085011 1 0.018167 1 0.34783 1 0.014196 1 0.63718 1 0.66485 1 0.12835 1 0.14192 1 0.1948 1 0.044426 1 16q gain 30 (5%) 539 0.00082801 0.878 0.013346 1 0.16886 1 0.47814 1 0.68676 1 0.0036905 1 0.43296 1 0.23208 1 1 1 0.15102 1 0.00092452 0.977 0.034471 1 0.0027153 1 0.0065006 1 17p gain 22 (4%) 547 0.42343 1 0.55557 1 0.064971 1 0.45537 1 0.22445 1 0.24144 1 0.48347 1 0.51086 1 0.20321 1 0.70474 1 0.17366 1 0.47436 1 0.41234 1 0.23751 1 17q gain 49 (9%) 520 0.33505 1 0.16493 1 0.85431 1 0.69224 1 0.77411 1 0.29692 1 0.46168 1 0.43713 1 0.90011 1 0.90482 1 0.77063 1 0.83611 1 0.44311 1 0.82658 1 18p gain 117 (21%) 452 0.23058 1 0.12241 1 0.92065 1 0.44075 1 0.0047316 1 0.00047208 0.503 0.023059 1 0.10714 1 0.77878 1 0.7773 1 0.35531 1 0.93841 1 0.34241 1 0.78256 1 18q gain 71 (12%) 498 0.64541 1 0.47133 1 0.28554 1 0.37468 1 0.053789 1 0.037989 1 0.53171 1 0.35912 1 0.48182 1 0.13268 1 0.11232 1 0.37894 1 0.053969 1 0.45851 1 19p gain 167 (29%) 402 0.067639 1 0.18066 1 0.56607 1 0.73872 1 4.183e-05 0.0455 0.029489 1 0.05556 1 0.63249 1 0.23231 1 0.48433 1 0.37588 1 0.19979 1 0.54525 1 0.8092 1 19q gain 160 (28%) 409 0.20752 1 0.45644 1 0.86108 1 0.47432 1 4.5444e-06 0.00499 0.09891 1 0.48455 1 0.89644 1 0.20753 1 0.25728 1 0.26863 1 0.1521 1 0.44288 1 0.90296 1 20p gain 282 (50%) 287 0.0013803 1 0.0061415 1 0.71849 1 0.0006145 0.654 1.004e-11 1.12e-08 2.7299e-08 3.03e-05 0.33702 1 0.22023 1 0.0027322 1 0.33769 1 0.22409 1 0.91775 1 0.60183 1 0.70572 1 20q gain 320 (56%) 249 8.7646e-06 0.0096 0.0014567 1 0.66994 1 0.00020432 0.219 4.5014e-15 5.04e-12 2.582e-10 2.87e-07 0.65944 1 0.023174 1 0.0089567 1 0.84301 1 0.25894 1 0.92368 1 0.66757 1 0.48304 1 21q gain 109 (19%) 460 0.29251 1 0.22099 1 0.96646 1 0.96431 1 0.0011725 1 0.016759 1 0.44308 1 0.52263 1 0.32724 1 0.090223 1 0.023863 1 0.50224 1 0.10211 1 0.25802 1 22q gain 25 (4%) 544 0.52571 1 0.82466 1 0.88393 1 0.76304 1 0.12956 1 0.21572 1 0.36989 1 0.80039 1 0.4651 1 0.69133 1 0.061305 1 0.094762 1 0.087296 1 0.11885 1 xq gain 104 (18%) 465 0.55266 1 0.50424 1 0.82407 1 0.71544 1 0.0024111 1 0.87835 1 0.26476 1 0.37353 1 0.77664 1 0.8806 1 0.54118 1 0.87561 1 0.46411 1 0.29177 1 1p loss 61 (11%) 508 0.028793 1 0.015419 1 0.59423 1 0.13984 1 0.45744 1 0.25904 1 0.035674 1 0.34085 1 0.58478 1 0.48959 1 0.44444 1 0.63628 1 0.042262 1 0.36141 1 1q loss 39 (7%) 530 0.097879 1 0.010473 1 0.11897 1 0.68867 1 0.95866 1 0.31933 1 0.32606 1 0.79304 1 0.46838 1 0.20166 1 0.95033 1 1 1 0.25434 1 0.87596 1 2p loss 53 (9%) 516 0.89932 1 0.83327 1 0.8145 1 0.72354 1 0.51845 1 0.71906 1 0.47039 1 0.52471 1 0.61173 1 0.48383 1 0.71786 1 0.1172 1 0.59626 1 0.90649 1 2q loss 59 (10%) 510 0.96451 1 0.62892 1 0.76021 1 0.1015 1 0.751 1 0.62986 1 0.79636 1 0.8863 1 0.6324 1 0.33023 1 0.67004 1 0.23233 1 0.64753 1 0.41715 1 3p loss 95 (17%) 474 0.04064 1 0.026826 1 0.88598 1 0.020234 1 0.00010564 0.114 0.0026991 1 0.62965 1 0.29273 1 0.059518 1 0.85678 1 0.12706 1 0.94316 1 0.90923 1 0.0019353 1 3q loss 41 (7%) 528 0.021082 1 0.012289 1 0.29701 1 0.13472 1 0.0059998 1 0.0013917 1 1 1 0.61425 1 0.23446 1 0.7168 1 0.23523 1 0.10173 1 0.27879 1 0.0070587 1 4p loss 312 (55%) 257 0.46636 1 0.3045 1 0.27673 1 0.02725 1 0.004066 1 0.60195 1 0.14483 1 0.29753 1 0.60767 1 0.86109 1 0.068707 1 0.0076303 1 0.052535 1 0.026215 1 4q loss 355 (62%) 214 0.28214 1 0.26416 1 0.4457 1 0.035897 1 0.0013738 1 0.66821 1 0.10278 1 0.083683 1 0.35896 1 0.17255 1 0.13547 1 0.00040804 0.436 0.027152 1 0.040186 1 5p loss 129 (23%) 440 0.094204 1 0.087747 1 0.48875 1 0.0045296 1 0.020905 1 0.0067517 1 0.10793 1 0.67665 1 0.00013705 0.147 0.50963 1 0.65375 1 0.52384 1 0.38358 1 0.051191 1 5q loss 218 (38%) 351 0.00052984 0.564 0.029978 1 0.7659 1 0.0022249 1 0.00088549 0.937 1.4135e-07 0.000156 0.045211 1 0.20417 1 0.0010143 1 0.64664 1 0.53968 1 0.60045 1 0.29725 1 0.43915 1 6p loss 164 (29%) 405 0.96807 1 0.4679 1 0.37108 1 0.72543 1 0.060357 1 0.11343 1 0.70234 1 0.59656 1 0.40862 1 0.52916 1 0.47581 1 0.67323 1 0.32241 1 0.63509 1 6q loss 239 (42%) 330 0.95857 1 0.41209 1 0.43946 1 0.53572 1 0.017142 1 0.071043 1 0.62303 1 0.39432 1 0.020212 1 0.03141 1 0.79164 1 0.94252 1 0.91084 1 0.44504 1 7p loss 118 (21%) 451 0.98115 1 0.60176 1 0.43039 1 0.3865 1 0.30034 1 0.14155 1 0.59237 1 0.79618 1 0.63185 1 0.026221 1 0.52733 1 0.40991 1 0.76645 1 0.4158 1 7q loss 81 (14%) 488 0.34319 1 0.40813 1 0.34207 1 0.39225 1 0.91736 1 0.10861 1 0.81506 1 0.22255 1 0.47682 1 0.16252 1 0.12476 1 1 1 0.50175 1 0.90826 1 8p loss 271 (48%) 298 0.74273 1 0.87676 1 0.24032 1 0.73604 1 0.0035872 1 0.10885 1 0.12005 1 0.16617 1 0.47569 1 0.84223 1 0.68625 1 0.026757 1 0.80207 1 0.26881 1 8q loss 88 (15%) 481 0.0074995 1 0.058058 1 0.53295 1 0.085812 1 0.0019115 1 0.034658 1 0.02209 1 0.21308 1 0.00087254 0.924 0.03711 1 0.64629 1 0.36966 1 0.76451 1 0.50103 1 9p loss 255 (45%) 314 0.0031873 1 0.034646 1 0.51157 1 0.10426 1 0.0083444 1 0.070079 1 0.78714 1 0.50513 1 0.8825 1 0.35347 1 0.053138 1 0.37129 1 0.062501 1 0.2861 1 9q loss 280 (49%) 289 0.0051497 1 0.03755 1 0.22212 1 0.011252 1 2.1934e-12 2.45e-09 0.003672 1 0.58504 1 1 1 0.0044382 1 0.40694 1 0.18314 1 0.17849 1 0.25129 1 0.092881 1 10p loss 94 (17%) 475 0.29704 1 0.74957 1 0.25767 1 0.16197 1 0.56627 1 0.27632 1 0.58937 1 0.12157 1 0.79931 1 0.26597 1 0.43351 1 0.56276 1 0.40462 1 0.49536 1 10q loss 122 (21%) 447 0.96359 1 0.4578 1 0.0040881 1 0.18708 1 0.081 1 0.0011542 1 0.35485 1 0.026291 1 0.6795 1 0.19123 1 0.76163 1 0.77102 1 0.84985 1 0.76522 1 11p loss 193 (34%) 376 0.23663 1 0.029225 1 0.54164 1 0.57579 1 0.12351 1 0.03523 1 0.10013 1 0.56323 1 0.038901 1 0.10271 1 0.47586 1 0.092545 1 0.077671 1 0.12088 1 11q loss 144 (25%) 425 0.36054 1 0.31976 1 0.17713 1 0.62354 1 0.015705 1 0.093636 1 0.4639 1 0.64312 1 0.26324 1 0.2527 1 0.51069 1 0.14611 1 0.10213 1 0.043754 1 12p loss 78 (14%) 491 0.0028241 1 0.02393 1 0.53566 1 0.14754 1 0.0029046 1 0.25471 1 0.77121 1 0.23359 1 0.32706 1 0.33665 1 0.0097071 1 0.0043462 1 0.0023028 1 0.0081847 1 12q loss 104 (18%) 465 0.067687 1 0.0056592 1 0.75993 1 0.62344 1 0.058932 1 0.2026 1 0.26377 1 0.65623 1 0.23772 1 0.017318 1 0.045881 1 0.020394 1 0.10819 1 0.030974 1 13q loss 303 (53%) 266 0.034305 1 0.04252 1 0.78714 1 0.18203 1 0.0060543 1 1.3607e-05 0.0149 0.010015 1 0.018215 1 0.47237 1 0.97754 1 0.25284 1 0.8251 1 0.093821 1 0.94798 1 14q loss 208 (37%) 361 0.20994 1 0.10123 1 0.97365 1 0.90849 1 1.3452e-05 0.0147 0.0032295 1 0.97094 1 0.81193 1 0.0038262 1 0.14844 1 0.79809 1 0.7972 1 0.96999 1 0.44965 1 15q loss 276 (49%) 293 0.00042977 0.459 0.0011826 1 0.00010449 0.113 0.00063422 0.674 4.3069e-12 4.81e-09 3.9783e-07 0.000439 0.37104 1 0.4129 1 0.065618 1 0.83912 1 0.0068962 1 0.28771 1 0.030015 1 0.0010229 1 16p loss 325 (57%) 244 0.3192 1 0.56528 1 0.037586 1 0.50347 1 0.12281 1 0.095659 1 0.79956 1 0.52263 1 0.052791 1 0.43327 1 0.080246 1 0.11591 1 0.11344 1 0.09828 1 16q loss 404 (71%) 165 0.56468 1 0.40566 1 0.0034451 1 0.30189 1 0.0020545 1 0.062689 1 0.94758 1 0.84429 1 0.20923 1 0.42664 1 0.069985 1 0.055641 1 0.048665 1 0.098261 1 17p loss 471 (83%) 98 0.2777 1 0.22124 1 0.17874 1 0.52402 1 0.46958 1 0.20772 1 0.53483 1 0.19632 1 0.10168 1 0.26822 1 0.47505 1 0.362 1 0.13438 1 0.63894 1 17q loss 376 (66%) 193 0.059135 1 0.038961 1 0.02632 1 0.57655 1 0.9677 1 0.50492 1 0.43156 1 0.20898 1 0.46955 1 0.423 1 0.056242 1 0.41801 1 7.6601e-05 0.083 0.77918 1 18p loss 234 (41%) 335 0.41764 1 0.21937 1 0.50971 1 0.086365 1 0.23635 1 0.0032276 1 0.31066 1 0.0027908 1 0.023587 1 0.50411 1 0.83951 1 0.5077 1 0.61117 1 0.79773 1 18q loss 290 (51%) 279 0.3172 1 0.082105 1 0.40087 1 0.72857 1 0.97319 1 0.10595 1 0.80555 1 0.011642 1 0.010758 1 0.2143 1 0.96878 1 0.92669 1 0.8199 1 0.72116 1 19p loss 181 (32%) 388 0.98694 1 0.90574 1 0.23103 1 0.51532 1 0.016747 1 0.032377 1 0.021526 1 0.63 1 0.74526 1 0.72551 1 0.79522 1 0.89245 1 0.86004 1 1 1 19q loss 172 (30%) 397 0.82909 1 0.39409 1 0.2855 1 0.81173 1 0.037954 1 0.1321 1 0.094134 1 0.34611 1 1 1 0.79246 1 0.36786 1 0.63493 1 0.40957 1 0.75484 1 20p loss 49 (9%) 520 0.49462 1 0.97281 1 0.22292 1 0.4459 1 0.12053 1 0.27199 1 0.09935 1 0.11412 1 0.013089 1 0.11636 1 0.00076692 0.814 0.43421 1 0.0065317 1 0.70281 1 20q loss 31 (5%) 538 0.12613 1 0.48537 1 0.035955 1 0.46923 1 0.52355 1 0.61933 1 0.053298 1 0.033567 1 0.12631 1 0.24747 1 0.13098 1 0.24558 1 0.059892 1 0.71461 1 21q loss 195 (34%) 374 0.81619 1 0.38018 1 0.38312 1 0.32734 1 0.39742 1 0.14061 1 0.641 1 0.29235 1 0.58435 1 0.5879 1 0.68053 1 0.91708 1 0.14461 1 0.86714 1 22q loss 421 (74%) 148 0.0047292 1 0.038038 1 0.036212 1 0.035171 1 0.00035022 0.375 0.0040606 1 0.069668 1 0.18748 1 0.18415 1 0.75668 1 0.040205 1 0.63073 1 0.05013 1 0.26426 1 xq loss 273 (48%) 296 0.058284 1 0.23458 1 0.28875 1 0.32203 1 0.006002 1 0.09727 1 0.37307 1 0.010222 1 0.49006 1 0.52091 1 0.78808 1 0.73052 1 0.88817 1 0.91215 1