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 133 (27%) 360 0.38747 1 1 1 9.9999e-06 0.00946 0.38721 1 0.074189 1 0.00447 1 0.12854 1 0.03138 1 0.071509 1 0.04963 1 0.31032 1 0.82583 1 1q gain 297 (60%) 196 0.12052 1 1 1 0.0019 1 0.00469 1 0.00076999 0.553 0.03918 1 0.12743 1 0.00015 0.115 0.51917 1 3e-04 0.225 0.01514 1 0.16935 1 2p gain 148 (30%) 345 0.30198 1 0.24258 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.45399 1 0.22306 1 0.00014 0.108 5.9999e-05 0.0479 9.9999e-06 0.00946 0.00024 0.182 0.00193 1 9.9999e-06 0.00946 2q gain 135 (27%) 358 0.1257 1 0.28828 1 2e-05 0.0167 9.9999e-06 0.00946 0.70036 1 0.79328 1 0.078979 1 0.01461 1 0.00184 1 0.01983 1 0.02964 1 0.00247 1 3p gain 40 (8%) 453 NA NA NA NA 0.00344 1 0.01863 1 0.10977 1 0.02873 1 4e-05 0.0323 0.00022 0.167 0.068359 1 0.47479 1 0.17373 1 0.34315 1 3q gain 86 (17%) 407 0.080699 1 0.12628 1 0.0012 0.838 3e-05 0.0244 0.02712 1 0.0347 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.01669 1 0.058629 1 0.0095699 1 0.03836 1 4p gain 80 (16%) 413 0.87648 1 1 1 9.9999e-06 0.00946 0.26934 1 0.29871 1 0.04605 1 0.04357 1 0.28372 1 0.090559 1 0.43542 1 0.43912 1 0.19384 1 4q gain 46 (9%) 447 0.33251 1 0.58458 1 0.01132 1 0.67854 1 0.39994 1 0.13332 1 0.0074399 1 0.00358 1 0.01728 1 0.04917 1 0.16282 1 0.24686 1 5p gain 267 (54%) 226 0.79987 1 0.36289 1 9.9999e-06 0.00946 0.29683 1 0.16216 1 0.84478 1 0.02387 1 9.9999e-06 0.00946 0.0435 1 0.30529 1 0.092139 1 0.0042 1 5q gain 124 (25%) 369 0.19412 1 0.28493 1 0.0057099 1 0.00031 0.231 0.028 1 0.28103 1 0.0058799 1 0.02798 1 0.14622 1 0.00042 0.309 0.03648 1 0.0085099 1 6p gain 141 (29%) 352 0.35257 1 0.088529 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.03011 1 0.64741 1 0.10802 1 0.01216 1 0.02684 1 0.068079 1 0.065999 1 0.0061799 1 6q gain 60 (12%) 433 1 1 1 1 0.01253 1 0.0053899 1 0.16847 1 0.90273 1 0.21684 1 0.0199 1 0.00218 1 0.01609 1 0.28367 1 0.0054499 1 7p gain 251 (51%) 242 0.85595 1 0.53607 1 9.9999e-06 0.00946 0.00317 1 0.00047 0.345 0.00082999 0.592 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00058999 0.429 0.00038 0.28 9.9999e-06 0.00946 7q gain 207 (42%) 286 0.48099 1 0.31077 1 9.9999e-06 0.00946 0.02875 1 0.13054 1 0.11388 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00275 1 0.0069499 1 0.01223 1 6.9999e-05 0.0556 8p gain 123 (25%) 370 0.15171 1 0.25398 1 9.9999e-06 0.00946 0.093689 1 0.43494 1 0.51104 1 0.00167 1 0.00026 0.196 0.45657 1 0.73481 1 0.84515 1 0.2886 1 8q gain 235 (48%) 258 0.02407 1 0.04669 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.28485 1 0.0052599 1 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00076999 0.553 3e-04 0.225 9.9999e-06 0.00946 9p gain 42 (9%) 451 NA NA NA NA 0.01404 1 0.072169 1 0.44016 1 0.21633 1 0.00019 0.145 0.0050899 1 0.21962 1 0.34538 1 0.20628 1 0.28431 1 9q gain 30 (6%) 463 NA NA NA NA 0.26812 1 0.5469 1 0.5723 1 0.62913 1 0.077469 1 0.066619 1 0.4815 1 0.93343 1 0.4455 1 0.34962 1 10p gain 105 (21%) 388 0.2368 1 0.29484 1 0.00070999 0.511 9.9999e-06 0.00946 0.01843 1 0.00117 0.82 5.9999e-05 0.0479 9.9999e-06 0.00946 0.0092399 1 0.0018 1 0.03786 1 5.9999e-05 0.0479 10q gain 76 (15%) 417 NA NA NA NA 0.03788 1 9.9999e-06 0.00946 0.28478 1 0.097329 1 0.00028 0.21 9.9999e-06 0.00946 0.37288 1 0.03394 1 0.21821 1 0.077009 1 11p gain 92 (19%) 401 0.0092399 1 0.0099099 1 2e-05 0.0167 0.34225 1 0.5211 1 0.31922 1 0.21483 1 0.00045 0.331 0.00053999 0.394 9.9999e-06 0.00946 0.00054999 0.401 2e-05 0.0167 11q gain 112 (23%) 381 0.0098999 1 0.01684 1 9.9999e-06 0.00946 0.059539 1 0.26937 1 0.12258 1 0.00451 1 0.00033 0.246 4e-05 0.0323 0.0012 0.838 0.00035 0.26 2e-05 0.0167 12p gain 131 (27%) 362 0.22201 1 0.04708 1 9.9999e-06 0.00946 2e-05 0.0167 0.01569 1 0.0082999 1 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 12q gain 126 (26%) 367 0.22225 1 0.13643 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.16358 1 0.0166 1 9.9999e-06 0.00946 9.9999e-06 0.00946 2e-05 0.0167 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 13q gain 43 (9%) 450 0.41336 1 0.54273 1 0.75821 1 0.01525 1 0.051199 1 0.50006 1 0.060539 1 0.12806 1 0.9755 1 0.13081 1 0.79615 1 0.66422 1 14q gain 120 (24%) 373 0.80351 1 0.84394 1 9.9999e-06 0.00946 0.00419 1 0.23635 1 0.074109 1 0.00012 0.0938 2e-05 0.0167 3e-05 0.0244 0.00133 0.918 0.00078999 0.565 0.00102 0.723 15q gain 35 (7%) 458 0.19248 1 0.14925 1 0.3879 1 0.30554 1 0.55856 1 0.46424 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.78795 1 0.50446 1 0.18751 1 0.86412 1 16p gain 127 (26%) 366 0.53442 1 0.33605 1 0.00307 1 0.061859 1 0.31156 1 0.12346 1 0.1755 1 0.0069099 1 0.01018 1 0.071459 1 0.04724 1 0.0303 1 16q gain 94 (19%) 399 0.43559 1 0.15309 1 0.00265 1 0.089779 1 0.070649 1 0.02266 1 0.42375 1 0.02494 1 0.00201 1 0.01293 1 0.02075 1 0.02821 1 17p gain 83 (17%) 410 0.45203 1 0.68732 1 7.9999e-05 0.063 0.01301 1 0.86926 1 0.075649 1 0.0083799 1 0.02263 1 9.9999e-06 0.00946 0.00047 0.345 0.23082 1 0.0072999 1 17q gain 186 (38%) 307 0.30459 1 0.87592 1 9.9999e-06 0.00946 4e-05 0.0323 0.61296 1 0.01814 1 6.9999e-05 0.0556 9.9999e-06 0.00946 2e-05 0.0167 0.00018 0.138 0.057019 1 0.00024 0.182 18p gain 91 (18%) 402 0.87479 1 0.63333 1 6.9999e-05 0.0556 9.9999e-06 0.00946 0.23955 1 0.59515 1 0.02141 1 0.00309 1 0.01511 1 0.00194 1 0.0057899 1 0.00041 0.302 18q gain 66 (13%) 427 0.59507 1 0.147 1 0.00018 0.138 9.9999e-06 0.00946 0.02026 1 0.03042 1 0.00012 0.0938 0.00118 0.826 0.01045 1 0.00070999 0.511 0.00236 1 0.00122 0.848 19p gain 32 (6%) 461 0.1917 1 0.03985 1 0.18809 1 0.76551 1 1 1 0.85184 1 0.99366 1 0.74267 1 0.45252 1 0.88588 1 0.01953 1 0.71045 1 19q gain 71 (14%) 422 0.051329 1 0.04146 1 0.00313 1 0.0146 1 0.94148 1 0.61415 1 0.18238 1 0.01621 1 0.36794 1 0.092159 1 0.071649 1 0.02409 1 20p gain 164 (33%) 329 0.082219 1 0.14193 1 0.00012 0.0938 0.00018 0.138 0.42616 1 0.04377 1 0.00026 0.196 9.9999e-06 0.00946 5e-05 0.04 0.00372 1 0.00018 0.138 4e-05 0.0323 20q gain 189 (38%) 304 0.01012 1 0.02487 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.22428 1 0.03447 1 9.9999e-06 0.00946 9.9999e-06 0.00946 2e-05 0.0167 0.00022 0.167 5e-05 0.04 9.9999e-06 0.00946 21q gain 94 (19%) 399 0.53954 1 0.26466 1 8.9999e-05 0.0707 0.40393 1 0.33536 1 0.072759 1 0.02982 1 6.9999e-05 0.0556 0.34245 1 0.30816 1 0.64355 1 0.58771 1 22q gain 61 (12%) 432 0.10677 1 0.12084 1 0.00333 1 0.76372 1 0.23591 1 0.18995 1 0.17834 1 0.096429 1 0.60748 1 0.77981 1 0.47729 1 0.29784 1 xq gain 68 (14%) 425 0.65622 1 0.24823 1 0.00066999 0.485 0.30964 1 0.27301 1 0.40294 1 0.02877 1 0.0063899 1 0.11712 1 0.42143 1 0.2168 1 0.076309 1 1p loss 79 (16%) 414 0.080639 1 0.12622 1 2e-05 0.0167 0.00116 0.817 0.88764 1 0.24969 1 0.00016 0.123 9.9999e-06 0.00946 0.53042 1 0.00102 0.723 0.4517 1 0.10164 1 1q loss 28 (6%) 465 NA NA NA NA 0.1801 1 0.01284 1 0.19422 1 0.1562 1 0.04783 1 0.1656 1 0.74749 1 0.32322 1 0.30491 1 0.16229 1 2p loss 24 (5%) 469 0.75002 1 0.58104 1 0.12377 1 0.33935 1 0.61006 1 0.92966 1 0.97846 1 0.90212 1 0.083019 1 0.78856 1 0.071949 1 0.35471 1 2q loss 23 (5%) 470 NA NA NA NA 0.00136 0.934 0.11089 1 0.42715 1 1 1 0.29203 1 0.38843 1 0.35304 1 0.38821 1 0.44716 1 0.16561 1 3p loss 205 (42%) 288 0.34208 1 0.11438 1 4e-05 0.0323 0.00112 0.79 0.26187 1 0.30286 1 0.03237 1 9.9999e-06 0.00946 0.02132 1 0.0078599 1 0.12565 1 0.0088399 1 3q loss 140 (28%) 353 0.5536 1 0.14134 1 0.01512 1 0.0071899 1 0.91767 1 0.91353 1 0.066269 1 0.00077999 0.558 0.68858 1 0.065629 1 0.85502 1 0.49792 1 4p loss 116 (24%) 377 0.18401 1 0.37957 1 6.9999e-05 0.0556 9.9999e-06 0.00946 0.19629 1 0.0155 1 8.9999e-05 0.0707 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 0.0058099 1 0.00052999 0.387 4q loss 132 (27%) 361 0.00057999 0.422 0.0076699 1 2e-05 0.0167 9.9999e-06 0.00946 0.27661 1 0.00133 0.918 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00027 0.203 9.9999e-06 0.00946 5p loss 40 (8%) 453 0.59302 1 0.30918 1 0.69535 1 0.02249 1 0.40645 1 0.099429 1 0.01343 1 0.0012 0.838 0.064929 1 0.081319 1 0.01637 1 0.0079499 1 5q loss 137 (28%) 356 0.063589 1 0.03579 1 9.9999e-06 0.00946 2e-05 0.0167 0.00126 0.874 0.00082999 0.592 9.9999e-06 0.00946 0.00014 0.108 9.9999e-06 0.00946 9.9999e-06 0.00946 2e-05 0.0167 9.9999e-06 0.00946 6p loss 101 (20%) 392 0.01225 1 0.00439 1 0.051139 1 0.12584 1 0.53364 1 0.47703 1 0.18796 1 0.27694 1 0.54192 1 0.18266 1 0.49847 1 0.70583 1 6q loss 208 (42%) 285 0.24603 1 0.53986 1 0.03003 1 0.00014 0.108 0.83925 1 0.30274 1 0.080669 1 5e-05 0.04 0.34196 1 0.02993 1 0.74232 1 0.059399 1 7p loss 33 (7%) 460 1 1 1 1 3e-05 0.0244 0.04303 1 0.32947 1 0.94454 1 0.0058799 1 0.00278 1 0.27322 1 0.19699 1 0.89858 1 0.32304 1 7q loss 39 (8%) 454 0.80155 1 0.25567 1 0.0071499 1 0.073999 1 0.90485 1 0.15512 1 0.10427 1 0.03321 1 0.37501 1 0.055869 1 0.27348 1 0.84023 1 8p loss 191 (39%) 302 0.13359 1 0.078069 1 9.9999e-06 0.00946 0.0139 1 0.051609 1 0.0078999 1 0.00013 0.101 3e-05 0.0244 0.00243 1 0.0052099 1 0.0055199 1 0.0082699 1 8q loss 54 (11%) 439 NA NA NA NA 0.00025 0.188 0.93014 1 0.297 1 0.49513 1 0.1739 1 0.063729 1 0.21047 1 0.82843 1 0.42007 1 0.53846 1 9p loss 254 (52%) 239 0.051219 1 0.59782 1 0.00199 1 0.12276 1 0.21665 1 0.02507 1 0.00089999 0.64 7.9999e-05 0.063 0.061659 1 0.01058 1 0.34987 1 0.51515 1 9q loss 238 (48%) 255 0.49867 1 0.90367 1 4e-05 0.0323 0.00224 1 0.41782 1 0.0066599 1 0.1403 1 0.00031 0.231 0.0061599 1 3e-05 0.0244 0.02399 1 0.0089099 1 10p loss 108 (22%) 385 0.8168 1 0.78769 1 2e-05 0.0167 0.12898 1 0.03988 1 0.0042 1 3e-05 0.0244 9.9999e-06 0.00946 0.00414 1 0.00263 1 0.00173 1 0.0073699 1 10q loss 128 (26%) 365 0.81732 1 0.7842 1 2e-05 0.0167 0.065549 1 0.055939 1 0.02716 1 0.00133 0.918 9.9999e-06 0.00946 0.0052899 1 0.00013 0.101 0.00131 0.907 0.00116 0.817 11p loss 108 (22%) 385 0.14451 1 0.070339 1 0.00012 0.0938 0.0099099 1 0.03648 1 0.13537 1 0.00214 1 0.00406 1 0.02632 1 0.03493 1 0.0271 1 0.00432 1 11q loss 88 (18%) 405 0.84013 1 0.4837 1 0.0064499 1 0.00435 1 0.00334 1 0.27666 1 0.00092999 0.66 0.0060199 1 0.055739 1 0.10334 1 0.02928 1 0.03321 1 12p loss 106 (22%) 387 0.63116 1 0.88161 1 0.0063799 1 0.26161 1 0.04571 1 0.058929 1 0.00442 1 0.00035 0.26 0.26371 1 0.11314 1 0.61279 1 0.81236 1 12q loss 93 (19%) 400 0.55564 1 0.42585 1 9.9999e-06 0.00946 0.077229 1 0.095569 1 0.0186 1 0.00067999 0.491 8.9999e-05 0.0707 0.20248 1 0.00453 1 0.55765 1 0.476 1 13q loss 243 (49%) 250 0.10538 1 0.6245 1 9.9999e-06 0.00946 0.01194 1 0.00048 0.351 2e-05 0.0167 9.9999e-06 0.00946 9.9999e-06 0.00946 0.01359 1 0.03806 1 0.04241 1 0.058789 1 14q loss 111 (23%) 382 0.93055 1 0.4081 1 0.060059 1 0.14168 1 0.17402 1 0.28157 1 0.0318 1 0.00486 1 0.073419 1 0.0062299 1 0.00079999 0.571 0.0056499 1 15q loss 233 (47%) 260 0.10108 1 0.28162 1 9.9999e-06 0.00946 2e-05 0.0167 0.12401 1 0.00246 1 9.9999e-06 0.00946 9.9999e-06 0.00946 9.9999e-06 0.00946 0.01757 1 0.01716 1 0.00103 0.728 16p loss 108 (22%) 385 0.45536 1 0.48188 1 2e-05 0.0167 2e-05 0.0167 0.2354 1 0.14333 1 9.9999e-06 0.00946 0.00126 0.874 0.0083399 1 0.0070599 1 0.0080399 1 0.00388 1 16q loss 137 (28%) 356 0.54737 1 0.62343 1 2e-05 0.0167 9.9999e-06 0.00946 0.081909 1 0.03222 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.0066799 1 0.00438 1 0.00159 1 8.9999e-05 0.0707 17p loss 206 (42%) 287 0.54868 1 0.36135 1 9.9999e-06 0.00946 0.00017 0.131 0.13711 1 0.0256 1 0.0011 0.777 0.00118 0.826 0.50107 1 0.18234 1 0.60824 1 0.28874 1 17q loss 55 (11%) 438 0.29628 1 0.47307 1 0.00013 0.101 0.0163 1 0.01013 1 0.02474 1 0.13901 1 0.50849 1 0.4169 1 0.30773 1 0.082079 1 0.076399 1 18p loss 169 (34%) 324 0.43746 1 0.45499 1 3e-05 0.0244 0.71424 1 0.03729 1 0.0084099 1 0.02286 1 0.00152 1 0.029 1 0.79826 1 0.14928 1 0.50377 1 18q loss 207 (42%) 286 0.52029 1 0.42397 1 9.9999e-06 0.00946 0.50799 1 0.0039 1 0.00139 0.954 3e-04 0.225 0.00017 0.131 0.02361 1 0.94299 1 0.69031 1 0.8619 1 19p loss 235 (48%) 258 0.8146 1 1 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.33714 1 0.27617 1 9.9999e-06 0.00946 9.9999e-06 0.00946 5.9999e-05 0.0479 3e-05 0.0244 0.0060599 1 6.9999e-05 0.0556 19q loss 153 (31%) 340 0.34492 1 0.46526 1 9.9999e-06 0.00946 2e-05 0.0167 0.27176 1 0.45482 1 0.00024 0.182 2e-05 0.0167 0.00058999 0.429 0.00141 0.966 0.02519 1 0.00021 0.16 20p loss 114 (23%) 379 0.33542 1 0.45352 1 0.00037 0.274 0.00116 0.817 0.00058999 0.429 0.00187 1 0.01586 1 0.0052999 1 0.96742 1 0.73202 1 0.12937 1 0.85679 1 20q loss 67 (14%) 426 0.51333 1 0.87597 1 0.39632 1 0.51506 1 0.26003 1 0.40361 1 0.6628 1 0.73464 1 0.60825 1 0.72044 1 0.13195 1 0.66892 1 21q loss 157 (32%) 336 0.18431 1 0.14337 1 9.9999e-06 0.00946 0.00066999 0.485 0.03141 1 0.00132 0.912 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00037 0.274 0.00012 0.0938 0.0074699 1 0.00248 1 22q loss 212 (43%) 281 0.12906 1 0.16744 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.80617 1 0.04899 1 9.9999e-06 0.00946 9.9999e-06 0.00946 0.00021 0.16 0.00012 0.0938 0.00035 0.26 9.9999e-06 0.00946 xq loss 64 (13%) 429 0.27229 1 0.054109 1 0.00069999 0.505 0.0082999 1 0.43432 1 0.64337 1 0.42528 1 0.57226 1 0.34892 1 0.47299 1 0.50613 1 0.59702 1