Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL MIR_CNMF MIR_CHIERARCHICAL CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_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 1p gain 82 (14%) 489 0.60653 1 0.13113 1 0.48353 1 0.24709 1 9.9999e-06 0.00774 0.67464 1 0.50128 1 0.084299 1 0.34189 1 0.27295 1 1q gain 89 (16%) 482 0.076749 1 0.088649 1 0.12892 1 0.62659 1 9.9999e-06 0.00774 0.26047 1 0.5787 1 0.25671 1 0.82565 1 0.50498 1 2p gain 36 (6%) 535 0.45688 1 0.68159 1 0.37568 1 0.1582 1 0.00016 0.109 0.18775 1 0.57765 1 0.41527 1 1 1 0.53608 1 2q gain 35 (6%) 536 0.63975 1 0.86369 1 0.16217 1 0.20152 1 2e-04 0.136 0.18925 1 0.92145 1 0.41342 1 0.77094 1 0.17715 1 3p gain 57 (10%) 514 0.00046 0.307 0.02824 1 0.66788 1 0.02634 1 9.9999e-06 0.00774 0.04096 1 0.63484 1 0.34102 1 0.81164 1 0.2553 1 3q gain 62 (11%) 509 0.00089999 0.595 0.096429 1 0.9226 1 0.076469 1 9.9999e-06 0.00774 0.01643 1 0.62526 1 0.30419 1 0.51629 1 0.15098 1 4p gain 36 (6%) 535 0.24129 1 0.6135 1 0.48565 1 0.51895 1 0.00298 1 0.82594 1 0.75837 1 0.55121 1 0.61599 1 0.79101 1 4q gain 33 (6%) 538 0.31166 1 0.31862 1 0.4946 1 0.54115 1 0.01089 1 0.62242 1 0.92651 1 0.6871 1 0.36638 1 0.66283 1 5p gain 49 (9%) 522 0.11473 1 0.15568 1 0.17599 1 0.34437 1 9.9999e-06 0.00774 0.62116 1 0.28054 1 0.52621 1 0.12803 1 0.23052 1 5q gain 41 (7%) 530 0.14135 1 0.23223 1 0.11777 1 0.054999 1 5e-05 0.0351 0.38116 1 0.38975 1 0.29601 1 0.16852 1 0.39884 1 6p gain 24 (4%) 547 0.01214 1 0.11802 1 0.87796 1 0.16011 1 0.077319 1 0.31888 1 0.81217 1 0.58325 1 1 1 1 1 6q gain 23 (4%) 548 0.00174 1 0.03701 1 0.78414 1 0.10295 1 0.0067399 1 0.064779 1 0.93185 1 0.52904 1 0.81032 1 1 1 7p gain 463 (81%) 108 9.9999e-06 0.00774 9.9999e-06 0.00774 0.00039 0.262 9.9999e-06 0.00774 9.9999e-06 0.00774 0.00172 1 0.00207 1 0.0025 1 0.01453 1 3e-05 0.0215 7q gain 469 (82%) 102 9.9999e-06 0.00774 9.9999e-06 0.00774 0.00106 0.694 0.00012 0.0829 9.9999e-06 0.00774 0.00016 0.109 0.10438 1 0.04404 1 0.054959 1 0.00166 1 8p gain 52 (9%) 519 4e-05 0.0284 0.00064999 0.432 0.063059 1 0.55702 1 9.9999e-06 0.00774 0.088739 1 0.43286 1 0.7573 1 0.13927 1 0.67366 1 8q gain 59 (10%) 512 9.9999e-06 0.00774 2e-05 0.0144 0.04054 1 0.45174 1 9.9999e-06 0.00774 0.19818 1 0.43466 1 0.75433 1 0.12461 1 0.51524 1 9p gain 47 (8%) 524 0.00334 1 0.03046 1 0.702 1 0.4336 1 5e-05 0.0351 0.15807 1 0.79812 1 0.36594 1 0.42898 1 0.11333 1 9q gain 72 (13%) 499 0.088349 1 0.050629 1 0.56077 1 0.12745 1 6.9999e-05 0.0489 0.03575 1 0.32036 1 0.38532 1 0.66897 1 0.078419 1 10p gain 12 (2%) 559 0.00106 0.694 8.9999e-05 0.0625 0.11798 1 0.058919 1 0.0029 1 NA NA 0.3085 1 0.56189 1 NA NA NA NA 10q gain 3 (1%) 568 0.5572 1 1 1 0.051539 1 0.796 1 0.19567 1 NA NA NA NA NA NA NA NA NA NA 11p gain 17 (3%) 554 0.90351 1 0.87951 1 0.24303 1 0.94317 1 0.22043 1 NA NA 0.86946 1 0.53217 1 0.69492 1 1 1 11q gain 14 (2%) 557 0.18546 1 0.065139 1 0.21621 1 0.36214 1 0.12345 1 NA NA 0.86977 1 1 1 1 1 1 1 12p gain 59 (10%) 512 0.67147 1 0.79411 1 0.64429 1 0.16481 1 4e-05 0.0284 0.5916 1 0.23406 1 0.66389 1 0.00413 1 0.075869 1 12q gain 48 (8%) 523 0.5225 1 0.95443 1 0.53771 1 0.0099299 1 0.00073999 0.49 0.75102 1 0.31181 1 0.29914 1 0.02219 1 0.12377 1 13q gain 10 (2%) 561 0.053159 1 0.49721 1 0.18135 1 0.82237 1 0.01697 1 0.36715 1 0.8934 1 1 1 0.42277 1 1 1 14q gain 22 (4%) 549 0.43059 1 0.77816 1 0.01017 1 0.80604 1 0.82843 1 NA NA 0.47035 1 0.85769 1 0.42584 1 0.32785 1 15q gain 24 (4%) 547 0.060919 1 0.11034 1 0.56806 1 0.13353 1 8.9999e-05 0.0625 NA NA 0.53608 1 0.34066 1 0.03502 1 0.38548 1 16p gain 38 (7%) 533 0.0077699 1 0.064819 1 0.41273 1 0.27022 1 2e-05 0.0144 NA NA 0.6171 1 0.47574 1 1 1 1 1 16q gain 37 (6%) 534 0.01884 1 0.0055099 1 0.35807 1 0.066709 1 0.00016 0.109 NA NA 0.75436 1 0.41845 1 0.42271 1 0.73583 1 17p gain 48 (8%) 523 0.00037 0.249 0.02001 1 0.079699 1 0.03996 1 7.9999e-05 0.0557 0.057289 1 0.1498 1 0.23721 1 0.33753 1 0.39143 1 17q gain 59 (10%) 512 0.00101 0.665 0.04412 1 0.14953 1 0.04366 1 9.9999e-06 0.00774 0.17872 1 0.078659 1 0.1613 1 0.9446 1 0.61679 1 18p gain 58 (10%) 513 9.9999e-06 0.00774 0.00039 0.262 0.1574 1 0.36741 1 9.9999e-06 0.00774 0.37722 1 0.42317 1 0.14999 1 0.01896 1 0.097449 1 18q gain 58 (10%) 513 9.9999e-06 0.00774 0.00072999 0.485 0.15892 1 0.4322 1 9.9999e-06 0.00774 0.51508 1 0.69198 1 0.47947 1 0.01859 1 0.11185 1 19p gain 224 (39%) 347 9.9999e-06 0.00774 3e-05 0.0215 0.080929 1 0.00043 0.287 9.9999e-06 0.00774 0.00246 1 0.0090799 1 3e-05 0.0215 0.18959 1 0.65473 1 19q gain 197 (35%) 374 9.9999e-06 0.00774 9.9999e-06 0.00774 0.11596 1 0.00425 1 9.9999e-06 0.00774 0.01871 1 0.04669 1 0.00098999 0.652 0.062819 1 0.3407 1 20p gain 220 (39%) 351 9.9999e-06 0.00774 9.9999e-06 0.00774 0.00437 1 9.9999e-06 0.00774 9.9999e-06 0.00774 0.10066 1 0.053059 1 0.00192 1 0.79612 1 0.11679 1 20q gain 218 (38%) 353 9.9999e-06 0.00774 9.9999e-06 0.00774 0.00286 1 9.9999e-06 0.00774 2e-05 0.0144 0.02916 1 0.03579 1 0.00102 0.67 0.79721 1 0.12092 1 21q gain 63 (11%) 508 0.00127 0.827 0.0072799 1 0.01179 1 0.00389 1 0.00034 0.229 0.16612 1 0.31815 1 0.02668 1 0.0187 1 0.33281 1 22q gain 34 (6%) 537 9.9999e-06 0.00774 0.00308 1 0.46895 1 0.21587 1 2e-04 0.136 0.18611 1 0.21149 1 0.0353 1 0.24361 1 0.19284 1 xq gain 16 (3%) 555 0.25223 1 0.94771 1 0.98471 1 0.36125 1 0.66042 1 0.62372 1 0.78958 1 1 1 0.03876 1 0.25879 1 1p loss 16 (3%) 555 0.63935 1 0.82838 1 0.94043 1 0.19467 1 0.087739 1 0.67707 1 0.34058 1 0.17973 1 0.10957 1 0.01839 1 1q loss 15 (3%) 556 0.83075 1 0.97769 1 0.85429 1 0.36322 1 0.3678 1 0.67816 1 0.33989 1 0.20855 1 0.51773 1 0.083529 1 2p loss 32 (6%) 539 0.03412 1 0.03407 1 0.31176 1 0.66346 1 0.00036 0.242 0.0050499 1 0.93515 1 0.21801 1 0.2409 1 0.22642 1 2q loss 32 (6%) 539 0.03369 1 0.03457 1 0.31194 1 0.66267 1 0.00034 0.229 0.0053699 1 0.82694 1 0.13268 1 0.082989 1 0.074799 1 3p loss 40 (7%) 531 0.91004 1 0.78892 1 0.71682 1 0.14855 1 0.00018 0.122 0.057439 1 0.23646 1 0.90073 1 0.63929 1 0.23067 1 3q loss 34 (6%) 537 0.23037 1 0.12912 1 0.50919 1 0.67765 1 4e-05 0.0284 0.11776 1 0.78751 1 0.32089 1 0.88938 1 0.18266 1 4p loss 54 (9%) 517 0.079439 1 0.00331 1 0.03374 1 0.22472 1 0.0094899 1 1 1 0.29407 1 0.12129 1 0.74648 1 1 1 4q loss 55 (10%) 516 0.00097999 0.647 0.00063999 0.426 0.01911 1 0.15221 1 4e-04 0.268 0.01057 1 0.73327 1 0.4821 1 0.55962 1 1 1 5p loss 42 (7%) 529 9.9999e-06 0.00774 3e-05 0.0215 0.00182 1 0.095729 1 0.00016 0.109 0.03537 1 0.93908 1 0.54442 1 0.34195 1 0.052139 1 5q loss 43 (8%) 528 5e-05 0.0351 4e-05 0.0284 0.00104 0.682 0.18553 1 0.00014 0.0963 0.03501 1 0.94253 1 0.6259 1 0.22187 1 0.04285 1 6p loss 86 (15%) 485 0.56669 1 0.334 1 0.77156 1 0.70622 1 9.9999e-06 0.00774 0.30557 1 0.79434 1 0.30073 1 0.87095 1 0.59619 1 6q loss 124 (22%) 447 0.94005 1 0.57834 1 0.56756 1 0.94065 1 9.9999e-06 0.00774 0.1899 1 0.96939 1 0.64583 1 0.4984 1 0.29318 1 7p loss 8 (1%) 563 0.02212 1 0.03408 1 0.45692 1 0.04105 1 0.20541 1 NA NA NA NA NA NA NA NA NA NA 7q loss 6 (1%) 565 0.099479 1 0.30375 1 0.94052 1 0.12505 1 0.59113 1 NA NA NA NA NA NA NA NA NA NA 8p loss 58 (10%) 513 0.5458 1 0.44086 1 0.18014 1 0.77713 1 0.067839 1 0.59071 1 0.9059 1 0.95007 1 0.57544 1 0.3911 1 8q loss 42 (7%) 529 0.61765 1 0.1502 1 0.02189 1 0.80779 1 0.01422 1 0.25757 1 0.85866 1 0.65528 1 0.45707 1 0.14681 1 9p loss 200 (35%) 371 0.0091699 1 0.13448 1 0.52668 1 0.44598 1 0.6875 1 0.56871 1 0.6179 1 0.04669 1 0.02201 1 0.0088499 1 9q loss 91 (16%) 480 0.37348 1 0.069179 1 0.11469 1 0.20571 1 0.33343 1 0.32371 1 0.36599 1 0.11809 1 0.75269 1 0.17899 1 10p loss 477 (84%) 94 9.9999e-06 0.00774 9.9999e-06 0.00774 0.01139 1 0.00014 0.0963 9.9999e-06 0.00774 0.03413 1 0.00216 1 0.0167 1 0.22313 1 0.01315 1 10q loss 488 (85%) 83 9.9999e-06 0.00774 9.9999e-06 0.00774 0.0056999 1 0.00012 0.0829 9.9999e-06 0.00774 0.00238 1 0.00012 0.0829 0.00442 1 0.25981 1 0.02178 1 11p loss 97 (17%) 474 9.9999e-06 0.00774 9.9999e-06 0.00774 0.82983 1 0.0142 1 9.9999e-06 0.00774 0.02577 1 0.7298 1 0.15887 1 0.091719 1 0.085709 1 11q loss 92 (16%) 479 9.9999e-06 0.00774 8.9999e-05 0.0625 0.93355 1 0.060879 1 9.9999e-06 0.00774 0.27616 1 0.9354 1 0.56947 1 0.34495 1 0.53606 1 12p loss 59 (10%) 512 0.088389 1 0.065299 1 0.47291 1 0.80912 1 0.00274 1 0.89976 1 0.15548 1 0.057929 1 1 1 0.66164 1 12q loss 58 (10%) 513 0.10739 1 0.062419 1 0.35179 1 0.59027 1 4e-05 0.0284 0.51653 1 0.18149 1 0.3949 1 1 1 0.66171 1 13q loss 183 (32%) 388 4e-05 0.0284 0.00165 1 0.75032 1 0.58932 1 9.9999e-06 0.00774 0.00119 0.776 0.59534 1 0.01702 1 0.04955 1 0.40149 1 14q loss 146 (26%) 425 9.9999e-06 0.00774 7.9999e-05 0.0557 0.44735 1 0.48269 1 9.9999e-06 0.00774 0.01352 1 0.81276 1 0.093079 1 0.10567 1 0.60136 1 15q loss 102 (18%) 469 5e-05 0.0351 2e-05 0.0144 0.00378 1 0.0038 1 9.9999e-06 0.00774 0.00222 1 0.03197 1 0.01166 1 0.00336 1 0.02198 1 16p loss 63 (11%) 508 0.28722 1 0.85269 1 0.65984 1 0.73519 1 0.02014 1 0.42986 1 0.45389 1 0.18893 1 0.56511 1 0.64679 1 16q loss 83 (15%) 488 0.061809 1 0.42953 1 0.46316 1 0.89751 1 0.01016 1 0.82242 1 0.04785 1 0.01823 1 0.66286 1 0.59775 1 17p loss 64 (11%) 507 0.0201 1 0.02121 1 0.65271 1 0.58321 1 9.9999e-06 0.00774 0.090189 1 0.21193 1 0.34976 1 0.30183 1 0.70536 1 17q loss 42 (7%) 529 0.005 1 0.059679 1 0.25279 1 0.04253 1 3e-05 0.0215 0.25368 1 0.48123 1 0.34002 1 0.14496 1 0.10915 1 18p loss 69 (12%) 502 0.04793 1 0.0318 1 0.35855 1 0.21956 1 3e-05 0.0215 0.27032 1 0.063219 1 0.0065999 1 0.13471 1 0.59937 1 18q loss 61 (11%) 510 0.1449 1 0.0069499 1 0.62108 1 0.23839 1 6.9999e-05 0.0489 0.2596 1 0.0095799 1 0.00334 1 0.41559 1 0.12011 1 19p loss 25 (4%) 546 0.00207 1 0.0071899 1 0.14872 1 0.41007 1 0.01397 1 0.00203 1 0.01992 1 0.01075 1 0.83925 1 0.80174 1 19q loss 33 (6%) 538 0.00211 1 0.01042 1 0.39199 1 0.10429 1 0.00072999 0.485 0.090369 1 0.080409 1 0.33745 1 0.7823 1 0.48515 1 20p loss 18 (3%) 553 0.00021 0.142 3e-05 0.0215 0.03612 1 0.094859 1 5e-05 0.0351 NA NA 0.41309 1 0.46009 1 0.01038 1 0.00207 1 20q loss 16 (3%) 555 0.00154 1 0.00015 0.103 0.36394 1 0.26602 1 0.00015 0.103 NA NA 0.41478 1 0.45943 1 0.03867 1 0.01269 1 21q loss 40 (7%) 531 0.02131 1 0.00112 0.731 0.03455 1 0.31874 1 0.00025 0.169 0.067229 1 0.01186 1 0.083799 1 0.82418 1 1 1 22q loss 179 (31%) 392 0.72076 1 0.60598 1 0.20853 1 0.93317 1 9.9999e-06 0.00774 0.15924 1 0.9081 1 0.137 1 0.20091 1 0.092719 1 xq loss 105 (18%) 466 0.02059 1 0.02429 1 0.14739 1 0.1605 1 9.9999e-06 0.00774 0.12402 1 0.96002 1 0.55441 1 0.41497 1 0.95976 1