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 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 168 (29%) 411 0.080369 1 0.34895 1 0.12239 1 0.73012 1 0.00038 0.398 0.18323 1 0.10501 1 0.26349 1 0.61128 1 0.9485 1 0.25211 1 0.68318 1 0.23053 1 0.52461 1 1q gain 221 (38%) 358 0.83174 1 0.26915 1 0.70464 1 0.22681 1 9.9999e-06 0.011 0.0086399 1 0.50155 1 0.54798 1 0.43483 1 0.27734 1 0.2289 1 0.10586 1 0.19838 1 0.56172 1 2p gain 186 (32%) 393 9.9999e-06 0.011 2e-05 0.0215 0.88624 1 0.00051999 0.542 9.9999e-06 0.011 9.9999e-06 0.011 0.03568 1 0.077789 1 0.00016 0.17 0.00178 1 0.82206 1 0.02555 1 0.67492 1 0.60836 1 2q gain 155 (27%) 424 0.00056999 0.592 6.9999e-05 0.0746 1 1 0.0073899 1 9.9999e-06 0.011 0.00023 0.243 0.10888 1 0.32216 1 0.00368 1 0.02044 1 0.60874 1 0.0065299 1 1 1 0.74645 1 3p gain 160 (28%) 419 0.43697 1 0.4488 1 0.070029 1 0.52786 1 0.01161 1 0.78562 1 1 1 0.38308 1 0.66019 1 0.68713 1 0.99059 1 0.81871 1 1 1 0.81209 1 3q gain 275 (47%) 304 0.93442 1 0.86673 1 0.34405 1 0.4267 1 9.9999e-06 0.011 0.01631 1 0.63865 1 0.25798 1 0.69382 1 0.92654 1 0.25255 1 0.089319 1 1 1 0.63529 1 4p gain 60 (10%) 519 0.24615 1 0.19198 1 0.00499 1 0.060829 1 0.017 1 0.11924 1 0.46142 1 0.39539 1 0.60576 1 0.83992 1 0.32314 1 0.01796 1 1 1 0.57161 1 4q gain 32 (6%) 547 0.49408 1 0.7636 1 0.21231 1 0.080019 1 0.00461 1 0.0077499 1 0.3504 1 0.2256 1 0.76275 1 0.85673 1 0.22681 1 0.063969 1 NA NA NA NA 5p gain 199 (34%) 380 0.56696 1 0.7102 1 0.8553 1 0.76186 1 0.00041 0.429 0.194 1 0.49521 1 0.072149 1 0.12707 1 0.53995 1 0.17913 1 0.57523 1 0.66563 1 0.2159 1 5q gain 60 (10%) 519 0.058879 1 0.19559 1 0.82216 1 0.89207 1 0.845 1 0.49588 1 0.46419 1 0.36917 1 0.70954 1 0.40717 1 0.38175 1 0.7911 1 0.48052 1 NA NA 6p gain 170 (29%) 409 0.51337 1 0.0042 1 0.90367 1 0.01336 1 9.9999e-06 0.011 8.9999e-05 0.0957 0.86377 1 0.23043 1 0.15873 1 0.0079799 1 0.36132 1 0.064469 1 0.41486 1 0.76166 1 6q gain 97 (17%) 482 0.65987 1 0.051709 1 0.82095 1 0.02206 1 9.9999e-06 0.011 9.9999e-06 0.011 0.78913 1 0.99748 1 0.00475 1 0.02179 1 0.19693 1 0.02947 1 0.3808 1 0.57602 1 7p gain 181 (31%) 398 0.58862 1 0.4752 1 0.084759 1 0.10836 1 9.9999e-06 0.011 0.00025 0.264 0.64634 1 0.49992 1 0.53049 1 0.68336 1 0.96587 1 0.11915 1 1 1 0.76249 1 7q gain 203 (35%) 376 0.65107 1 0.084639 1 0.30048 1 0.38007 1 9.9999e-06 0.011 0.00156 1 0.46 1 0.24804 1 0.92476 1 0.64317 1 0.15111 1 0.62822 1 0.64617 1 0.36889 1 8p gain 119 (21%) 460 0.067949 1 0.0038 1 0.39863 1 0.42058 1 0.69265 1 0.80813 1 0.13672 1 0.00336 1 0.61814 1 1 1 0.13258 1 0.49343 1 0.22078 1 0.10069 1 8q gain 242 (42%) 337 0.0207 1 0.00063999 0.664 0.080719 1 0.14091 1 0.25918 1 0.44846 1 0.31895 1 0.26681 1 0.02995 1 0.085279 1 0.55962 1 0.86309 1 0.03096 1 0.68551 1 9p gain 92 (16%) 487 0.11327 1 0.42311 1 0.23734 1 0.86732 1 0.00273 1 0.0084699 1 0.40013 1 0.72557 1 0.69185 1 0.41161 1 0.1864 1 0.18822 1 0.62406 1 0.6082 1 9q gain 45 (8%) 534 0.25241 1 0.30889 1 0.092569 1 0.53328 1 0.13792 1 0.22362 1 0.57882 1 0.02679 1 0.48333 1 0.091399 1 0.49562 1 0.75236 1 0.45455 1 NA NA 10p gain 188 (32%) 391 0.00417 1 0.02173 1 0.67815 1 0.37647 1 9.9999e-06 0.011 0.00021 0.222 0.97925 1 0.0094699 1 0.01069 1 0.12473 1 0.55747 1 0.00065999 0.684 1 1 0.94057 1 10q gain 111 (19%) 468 0.00423 1 0.0091099 1 0.24002 1 0.11704 1 0.00393 1 0.093539 1 0.76798 1 0.061469 1 0.10534 1 0.22018 1 0.73065 1 0.24703 1 0.64617 1 0.65887 1 11p gain 77 (13%) 502 0.71293 1 0.10014 1 0.63979 1 0.46832 1 0.1364 1 0.01377 1 0.0278 1 0.02617 1 0.058099 1 0.0348 1 0.55874 1 0.83758 1 1 1 NA NA 11q gain 115 (20%) 464 0.39373 1 0.25077 1 0.88324 1 0.18122 1 0.0044 1 0.00187 1 0.20583 1 0.00078999 0.817 0.30346 1 0.15591 1 0.40941 1 0.7788 1 0.32331 1 0.10566 1 12p gain 255 (44%) 324 9.9999e-05 0.106 0.00154 1 0.74146 1 0.00099999 1 9.9999e-06 0.011 9.9999e-06 0.011 0.30503 1 0.31706 1 0.00053999 0.562 0.00378 1 0.2265 1 0.00026 0.274 0.41486 1 0.25149 1 12q gain 177 (31%) 402 0.0046 1 0.056489 1 0.62645 1 0.03414 1 9.9999e-06 0.011 2e-05 0.0215 0.01899 1 0.22128 1 0.00192 1 0.0089999 1 0.10209 1 0.01051 1 0.074303 1 0.29004 1 13q gain 60 (10%) 519 0.0074099 1 0.00035 0.367 0.58624 1 0.025 1 5.9999e-05 0.0641 3e-05 0.0321 0.49236 1 0.40857 1 0.22998 1 0.42713 1 0.15136 1 0.098699 1 0.45455 1 NA NA 14q gain 59 (10%) 520 0.13868 1 0.1915 1 0.40489 1 0.69875 1 0.41089 1 0.74107 1 0.33016 1 0.17153 1 0.50328 1 0.5679 1 0.65598 1 0.63049 1 1 1 NA NA 15q gain 40 (7%) 539 0.84822 1 0.47923 1 0.087589 1 0.75756 1 0.097639 1 0.60447 1 0.11362 1 0.10899 1 0.73801 1 0.93092 1 0.31368 1 0.20348 1 1 1 NA NA 16p gain 59 (10%) 520 0.00232 1 0.0050499 1 0.4053 1 0.17513 1 0.02962 1 0.0176 1 0.34773 1 0.03467 1 0.6499 1 0.79887 1 0.12241 1 0.079979 1 0.48052 1 NA NA 16q gain 31 (5%) 548 0.00094999 0.979 0.04385 1 0.16216 1 0.22078 1 0.2682 1 0.00319 1 0.45486 1 0.02602 1 1 1 0.36353 1 0.00072999 0.756 0.10526 1 1 1 NA NA 17p gain 22 (4%) 557 0.43129 1 0.11279 1 0.055229 1 0.052459 1 0.15361 1 0.23069 1 0.49851 1 0.40636 1 0.21054 1 0.00371 1 0.17423 1 0.83769 1 NA NA NA NA 17q gain 47 (8%) 532 0.42278 1 0.03783 1 0.75812 1 0.0369 1 0.52176 1 0.38887 1 0.58816 1 0.37324 1 0.90164 1 0.02269 1 0.82291 1 0.87857 1 1 1 NA NA 18p gain 120 (21%) 459 0.18394 1 0.098449 1 0.87096 1 0.39185 1 0.00153 1 3e-04 0.316 0.02385 1 0.11053 1 0.8116 1 0.69027 1 0.35034 1 0.23442 1 0.64617 1 0.81217 1 18q gain 72 (12%) 507 0.64378 1 0.16551 1 0.23051 1 0.39028 1 0.02364 1 0.02441 1 0.51441 1 0.39708 1 0.48406 1 0.27136 1 0.10724 1 0.19363 1 1 1 1 1 19p gain 171 (30%) 408 0.075689 1 0.45187 1 0.51745 1 0.115 1 2e-05 0.0215 0.02649 1 0.056649 1 0.32369 1 0.1904 1 0.57891 1 0.26867 1 0.31025 1 1 1 0.74435 1 19q gain 161 (28%) 418 0.25931 1 0.75266 1 0.90709 1 0.16878 1 5.9999e-05 0.0641 0.13252 1 0.47621 1 0.46235 1 0.20492 1 0.43788 1 0.27148 1 0.67393 1 0.59398 1 0.72178 1 20p gain 289 (50%) 290 0.00142 1 0.0011 1 0.72323 1 0.00029 0.305 9.9999e-06 0.011 9.9999e-06 0.011 0.33193 1 0.37085 1 0.00373 1 0.16583 1 0.22498 1 0.00341 1 0.39128 1 0.5235 1 20q gain 328 (57%) 251 3e-05 0.0321 0.00024 0.253 0.66774 1 7.9999e-05 0.0852 9.9999e-06 0.011 9.9999e-06 0.011 0.66023 1 0.082209 1 0.0091499 1 0.13766 1 0.25687 1 0.0051599 1 1 1 0.49506 1 21q gain 109 (19%) 470 0.29148 1 0.8794 1 0.96198 1 0.58227 1 0.00169 1 0.01626 1 0.45602 1 0.39322 1 0.33471 1 0.84288 1 0.02288 1 0.044 1 1 1 NA NA 22q gain 24 (4%) 555 0.36727 1 0.60008 1 0.93209 1 0.60461 1 0.36786 1 0.17037 1 0.39152 1 0.37496 1 0.56252 1 0.60845 1 0.096799 1 0.081479 1 0.57143 1 0.38174 1 xq gain 106 (18%) 473 0.48243 1 0.82769 1 0.8428 1 0.26695 1 0.00048 0.501 0.93344 1 0.31068 1 0.83731 1 0.76224 1 0.92957 1 0.47406 1 0.30021 1 1 1 0.90842 1 1p loss 65 (11%) 514 0.03224 1 0.00033 0.346 0.46525 1 0.19482 1 0.46698 1 0.2906 1 0.02068 1 0.21139 1 0.63212 1 0.508 1 0.44567 1 0.30893 1 1 1 NA NA 1q loss 43 (7%) 536 0.11752 1 0.01436 1 0.058069 1 0.60087 1 0.69029 1 0.38317 1 0.22213 1 0.61943 1 0.46572 1 1 1 0.96918 1 0.93222 1 NA NA NA NA 2p loss 53 (9%) 526 0.93058 1 0.02385 1 0.61744 1 0.48945 1 0.5779 1 0.77485 1 0.48447 1 0.8935 1 0.335 1 0.81594 1 0.72157 1 0.4024 1 0.48052 1 NA NA 2q loss 59 (10%) 520 0.91893 1 0.27022 1 0.69695 1 0.15055 1 0.85515 1 0.68153 1 0.88978 1 0.93776 1 0.4992 1 0.79434 1 0.55607 1 0.22958 1 0.48052 1 NA NA 3p loss 95 (16%) 484 0.02285 1 0.00083999 0.867 0.81814 1 0.0058399 1 0.00054999 0.572 0.00276 1 0.65037 1 0.26712 1 0.062059 1 0.0055899 1 0.12225 1 0.091219 1 1 1 0.1238 1 3q loss 43 (7%) 536 0.01345 1 0.03953 1 0.2856 1 0.057619 1 0.02959 1 0.00292 1 0.93298 1 0.36122 1 0.23149 1 0.091749 1 0.3046 1 0.00112 1 0.59398 1 0.03331 1 4p loss 316 (55%) 263 0.36587 1 0.02323 1 0.28157 1 0.61484 1 0.00416 1 0.48155 1 0.15029 1 0.13159 1 0.42595 1 0.44083 1 0.12008 1 0.19728 1 1 1 0.62388 1 4q loss 362 (63%) 217 0.20751 1 0.081929 1 0.50046 1 0.71552 1 0.00127 1 0.56071 1 0.1206 1 0.01792 1 0.26884 1 0.35036 1 0.21356 1 0.1806 1 1 1 0.36821 1 5p loss 133 (23%) 446 0.074719 1 0.03132 1 0.53926 1 0.087339 1 0.01238 1 0.0070199 1 0.088749 1 0.057269 1 0.00018 0.191 0.04701 1 0.56938 1 0.04992 1 1 1 0.90515 1 5q loss 223 (39%) 356 0.00042 0.439 0.00159 1 0.70848 1 0.01288 1 0.00042 0.439 9.9999e-06 0.011 0.034 1 0.093559 1 0.0011 1 0.14731 1 0.61951 1 0.0067499 1 0.37771 1 0.71855 1 6p loss 165 (28%) 414 0.96958 1 0.02006 1 0.45 1 0.50662 1 0.14711 1 0.11974 1 0.77996 1 0.84868 1 0.40977 1 0.04299 1 0.47974 1 0.10202 1 0.57143 1 0.574 1 6q loss 242 (42%) 337 0.96232 1 0.076219 1 0.43272 1 0.097219 1 0.03411 1 0.071169 1 0.62402 1 0.65775 1 0.01899 1 0.02067 1 0.7922 1 0.57058 1 0.59398 1 0.90202 1 7p loss 121 (21%) 458 0.99117 1 0.40379 1 0.47853 1 0.69941 1 0.11105 1 0.1487 1 0.54109 1 0.32783 1 0.7746 1 0.71162 1 0.53765 1 0.79957 1 0.59398 1 0.20165 1 7q loss 81 (14%) 498 0.33559 1 0.088979 1 0.34727 1 0.29964 1 0.73737 1 0.11046 1 0.8203 1 0.069629 1 0.47809 1 0.3117 1 0.12365 1 0.81991 1 1 1 0.33753 1 8p loss 277 (48%) 302 0.74081 1 0.89033 1 0.24209 1 0.94638 1 0.00241 1 0.11037 1 0.11852 1 0.29714 1 0.48108 1 0.70335 1 0.70114 1 0.03701 1 1 1 0.9401 1 8q loss 90 (16%) 489 0.0076199 1 0.0052099 1 0.51916 1 0.26279 1 0.00106 1 0.03465 1 0.02168 1 0.23401 1 0.00094999 0.979 0.02885 1 0.66294 1 0.12426 1 1 1 0.90108 1 9p loss 262 (45%) 317 0.00323 1 0.0059799 1 0.50959 1 0.18298 1 0.01617 1 0.069069 1 0.79321 1 0.5459 1 0.89902 1 0.10705 1 0.054559 1 0.254 1 0.39128 1 0.15413 1 9q loss 286 (49%) 293 0.0071299 1 0.01301 1 0.22241 1 0.03437 1 9.9999e-06 0.011 0.0053799 1 0.6091 1 0.6818 1 0.0073399 1 0.051689 1 0.22558 1 0.057559 1 1 1 0.62457 1 10p loss 97 (17%) 482 0.22262 1 0.96269 1 0.22104 1 0.33644 1 0.64296 1 0.23236 1 0.59406 1 0.087839 1 0.65211 1 0.55457 1 0.35931 1 0.83334 1 1 1 0.22143 1 10q loss 124 (21%) 455 0.93817 1 0.82514 1 0.00449 1 0.29624 1 0.02292 1 0.00188 1 0.30223 1 0.40683 1 0.77314 1 0.74087 1 0.69267 1 0.37149 1 0.3808 1 0.69546 1 11p loss 198 (34%) 381 0.23948 1 0.01087 1 0.54462 1 0.3105 1 0.19931 1 0.03667 1 0.099969 1 0.61149 1 0.04085 1 0.10998 1 0.47178 1 0.1426 1 0.32331 1 0.80231 1 11q loss 148 (26%) 431 0.29634 1 0.90196 1 0.21114 1 0.5609 1 0.0094599 1 0.070049 1 0.42277 1 0.7668 1 0.26924 1 0.801 1 0.4954 1 0.17637 1 0.59398 1 0.38439 1 12p loss 79 (14%) 500 0.00262 1 0.01101 1 0.65747 1 0.0064899 1 0.00104 1 0.25397 1 0.87027 1 0.15204 1 0.31476 1 0.20086 1 0.0095499 1 0.0061799 1 0.29323 1 0.72506 1 12q loss 105 (18%) 474 0.082589 1 0.083089 1 0.7277 1 0.17038 1 0.02226 1 0.2233 1 0.26552 1 0.55817 1 0.17281 1 0.14871 1 0.02586 1 0.03042 1 0.13534 1 0.04118 1 13q loss 310 (54%) 269 0.02975 1 0.0082199 1 0.80383 1 0.01746 1 0.051519 1 9.9999e-06 0.011 0.0056599 1 0.34393 1 0.46739 1 0.41982 1 0.21729 1 0.53514 1 0.66563 1 0.14952 1 14q loss 215 (37%) 364 0.25003 1 0.1912 1 0.96722 1 0.39814 1 9.9999e-06 0.011 0.00367 1 0.98073 1 0.60711 1 0.00374 1 0.0482 1 0.85452 1 0.40193 1 0.3808 1 0.22387 1 15q loss 280 (48%) 299 0.00049 0.511 0.01631 1 7.9999e-05 0.0852 0.00032 0.336 9.9999e-06 0.011 9.9999e-06 0.011 0.37764 1 0.81294 1 0.066239 1 0.61201 1 0.0081299 1 0.00062999 0.654 0.042731 1 0.62293 1 16p loss 334 (58%) 245 0.37956 1 0.84638 1 0.04024 1 0.35127 1 0.21731 1 0.11499 1 0.76557 1 0.22742 1 0.03972 1 0.24608 1 0.04831 1 0.068309 1 0.67492 1 0.36778 1 16q loss 413 (71%) 166 0.57881 1 0.87001 1 0.00285 1 0.079519 1 0.02816 1 0.064489 1 0.90711 1 0.30834 1 0.19622 1 0.36993 1 0.054129 1 0.12855 1 0.62406 1 0.60647 1 17p loss 478 (83%) 101 0.33687 1 0.22752 1 0.13585 1 0.20463 1 0.59237 1 0.24857 1 0.55368 1 0.18873 1 0.10226 1 0.057129 1 0.4744 1 0.47637 1 1 1 NA NA 17q loss 383 (66%) 196 0.084449 1 0.02832 1 0.01494 1 0.01161 1 0.94398 1 0.55734 1 0.57013 1 0.29374 1 0.53429 1 0.096959 1 0.077569 1 0.71273 1 0.62406 1 0.27761 1 18p loss 235 (41%) 344 0.41113 1 0.95167 1 0.47196 1 0.02137 1 0.54554 1 0.00218 1 0.31326 1 0.0067199 1 0.02384 1 0.11398 1 0.838 1 0.53801 1 0.66563 1 0.57941 1 18q loss 293 (51%) 286 0.34261 1 0.97178 1 0.29636 1 0.95713 1 0.85406 1 0.10448 1 0.71308 1 0.03536 1 0.01144 1 0.091209 1 0.97789 1 0.77867 1 0.66992 1 0.24698 1 19p loss 185 (32%) 394 0.97762 1 0.45421 1 0.32803 1 0.04373 1 0.00498 1 0.0191 1 0.0097199 1 0.88746 1 0.6669 1 0.31277 1 0.67488 1 0.11867 1 0.011499 1 0.12558 1 19q loss 178 (31%) 401 0.6924 1 0.24608 1 0.25042 1 0.01498 1 0.00448 1 0.072849 1 0.060199 1 0.67758 1 0.92494 1 0.71896 1 0.30024 1 0.051959 1 0.0053476 1 0.42669 1 20p loss 50 (9%) 529 0.35261 1 0.72243 1 0.22191 1 0.61966 1 0.11075 1 0.46898 1 0.10311 1 0.19967 1 0.073289 1 0.00338 1 0.00078999 0.817 0.2697 1 0.48052 1 NA NA 20q loss 32 (6%) 547 0.11545 1 0.50035 1 0.03668 1 0.5071 1 0.44248 1 0.63792 1 0.04864 1 0.097179 1 0.13259 1 0.01364 1 0.13558 1 0.37778 1 0.48052 1 NA NA 21q loss 199 (34%) 380 0.81781 1 0.051879 1 0.38551 1 0.18485 1 0.49 1 0.14078 1 0.65211 1 0.43624 1 0.58262 1 0.40808 1 0.68873 1 0.73301 1 0.16188 1 0.58145 1 22q loss 430 (74%) 149 0.00242 1 0.092959 1 0.03689 1 0.12701 1 0.00015 0.159 0.00194 1 0.085479 1 0.02391 1 0.086269 1 0.12921 1 0.04107 1 0.57389 1 0.13534 1 0.10743 1 xq loss 277 (48%) 302 0.052789 1 0.18632 1 0.25331 1 0.90869 1 0.00135 1 0.16219 1 0.32784 1 0.04682 1 0.50823 1 0.89788 1 0.74518 1 0.41486 1 1 1 0.28903 1