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%) 495 0.60302 1 0.12977 1 0.4869 1 0.25075 1 9.9999e-06 0.00784 0.82743 1 0.5008 1 0.084459 1 0.34022 1 0.27281 1 1q gain 89 (15%) 488 0.078149 1 0.088749 1 0.13246 1 0.62765 1 9.9999e-06 0.00784 0.52785 1 0.582 1 0.25801 1 0.82559 1 0.50606 1 2p gain 37 (6%) 540 0.46687 1 0.73396 1 0.25209 1 0.22469 1 0.0024 1 0.39171 1 0.80802 1 0.60958 1 1 1 0.53985 1 2q gain 36 (6%) 541 0.64891 1 0.91191 1 0.098119 1 0.27837 1 0.00154 0.986 0.38986 1 0.98462 1 0.6105 1 0.76623 1 0.17928 1 3p gain 58 (10%) 519 0.00062999 0.418 0.02888 1 0.66811 1 0.0267 1 9.9999e-06 0.00784 0.13035 1 0.63692 1 0.3417 1 0.81501 1 0.25474 1 3q gain 64 (11%) 513 0.00061999 0.412 0.061809 1 0.89857 1 0.063989 1 9.9999e-06 0.00784 0.065829 1 0.71441 1 0.20302 1 0.51643 1 0.15034 1 4p gain 36 (6%) 541 0.24148 1 0.61464 1 0.48558 1 0.52149 1 0.00065999 0.436 0.4576 1 0.75677 1 0.55003 1 0.61429 1 0.79178 1 4q gain 33 (6%) 544 0.30852 1 0.31772 1 0.49604 1 0.54092 1 0.0055199 1 0.26562 1 0.9259 1 0.68399 1 0.36371 1 0.65689 1 5p gain 49 (8%) 528 0.11395 1 0.15656 1 0.17773 1 0.34465 1 5e-05 0.0351 0.23295 1 0.28032 1 0.5308 1 0.12807 1 0.22747 1 5q gain 41 (7%) 536 0.14051 1 0.23428 1 0.11631 1 0.054939 1 0.00014 0.0953 0.11684 1 0.39018 1 0.29621 1 0.16919 1 0.40508 1 6p gain 24 (4%) 553 0.01212 1 0.11709 1 0.87525 1 0.16152 1 0.15809 1 0.082449 1 0.81116 1 0.58307 1 1 1 1 1 6q gain 23 (4%) 554 0.00141 0.908 0.03623 1 0.78696 1 0.10359 1 0.02492 1 0.0057499 1 0.93115 1 0.52876 1 0.81321 1 1 1 7p gain 468 (81%) 109 9.9999e-06 0.00784 9.9999e-06 0.00784 0.00029 0.196 9.9999e-06 0.00784 9.9999e-06 0.00784 9.9999e-06 0.00784 0.00189 1 0.00285 1 0.01527 1 6.9999e-05 0.0486 7q gain 474 (82%) 103 2e-05 0.0144 9.9999e-06 0.00784 0.00146 0.936 0.00017 0.115 9.9999e-06 0.00784 4e-05 0.0282 0.10492 1 0.04467 1 0.054459 1 0.00143 0.919 8p gain 52 (9%) 525 2e-05 0.0144 0.00064999 0.43 0.063659 1 0.55894 1 9.9999e-06 0.00784 0.00409 1 0.43627 1 0.75533 1 0.13946 1 0.67569 1 8q gain 59 (10%) 518 9.9999e-06 0.00784 9.9999e-06 0.00784 0.04018 1 0.45463 1 9.9999e-06 0.00784 0.00048 0.322 0.43406 1 0.75768 1 0.12278 1 0.51089 1 9p gain 47 (8%) 530 0.00359 1 0.03132 1 0.70213 1 0.43224 1 2e-05 0.0144 0.54548 1 0.80003 1 0.3668 1 0.42865 1 0.1135 1 9q gain 71 (12%) 506 0.080219 1 0.070929 1 0.57764 1 0.16719 1 3e-05 0.0213 0.19768 1 0.31785 1 0.38652 1 0.6703 1 0.077379 1 10p gain 13 (2%) 564 0.00091999 0.603 0.00011 0.0756 0.11693 1 0.058609 1 0.00103 0.669 0.00036 0.242 0.30775 1 0.56124 1 NA NA NA NA 10q gain 3 (1%) 574 0.55543 1 1 1 0.052779 1 0.79408 1 0.19571 1 0.18959 1 NA NA NA NA NA NA NA NA 11p gain 17 (3%) 560 0.90648 1 0.88121 1 0.24732 1 0.94483 1 0.19694 1 0.085699 1 0.86811 1 0.52886 1 0.69691 1 1 1 11q gain 14 (2%) 563 0.18728 1 0.064669 1 0.2159 1 0.36021 1 0.15032 1 0.00056999 0.38 0.86849 1 1 1 1 1 1 1 12p gain 60 (10%) 517 0.67002 1 0.7929 1 0.64107 1 0.16449 1 7.9999e-05 0.0551 0.89981 1 0.23568 1 0.66209 1 0.00392 1 0.075179 1 12q gain 49 (8%) 528 0.51748 1 0.95508 1 0.53788 1 0.0098599 1 0.0016 1 0.59066 1 0.31229 1 0.29979 1 0.02206 1 0.12421 1 13q gain 10 (2%) 567 0.053059 1 0.49388 1 0.1791 1 0.82614 1 0.056759 1 1 1 0.89345 1 1 1 0.42634 1 1 1 14q gain 22 (4%) 555 0.42941 1 0.78174 1 0.01031 1 0.80585 1 0.39012 1 0.50826 1 0.47258 1 0.8571 1 0.42516 1 0.32574 1 15q gain 24 (4%) 553 0.060859 1 0.10816 1 0.56624 1 0.1331 1 5.9999e-05 0.0419 0.27901 1 0.53421 1 0.33909 1 0.03428 1 0.38666 1 16p gain 38 (7%) 539 0.0082599 1 0.065909 1 0.41247 1 0.27275 1 9.9999e-06 0.00784 0.03116 1 0.61196 1 0.47416 1 1 1 1 1 16q gain 37 (6%) 540 0.01818 1 0.0058099 1 0.35758 1 0.066379 1 5.9999e-05 0.0419 0.02596 1 0.75785 1 0.41784 1 0.41883 1 0.73622 1 17p gain 48 (8%) 529 0.00048 0.322 0.02045 1 0.078319 1 0.04002 1 5e-05 0.0351 0.03275 1 0.149 1 0.23843 1 0.33644 1 0.38995 1 17q gain 60 (10%) 517 0.00112 0.726 0.04511 1 0.12905 1 0.070339 1 9.9999e-06 0.00784 0.03787 1 0.087969 1 0.10797 1 0.94514 1 0.61473 1 18p gain 58 (10%) 519 9.9999e-06 0.00784 0.00047 0.315 0.157 1 0.36479 1 9.9999e-06 0.00784 0.00485 1 0.42164 1 0.14936 1 0.01826 1 0.096449 1 18q gain 58 (10%) 519 9.9999e-06 0.00784 0.00071999 0.475 0.15698 1 0.43082 1 9.9999e-06 0.00784 0.0055699 1 0.69217 1 0.47907 1 0.01844 1 0.11422 1 19p gain 226 (39%) 351 9.9999e-06 0.00784 2e-05 0.0144 0.090369 1 3e-04 0.202 9.9999e-06 0.00784 9.9999e-06 0.00784 0.0091599 1 9.9999e-06 0.00784 0.18838 1 0.65525 1 19q gain 199 (34%) 378 9.9999e-06 0.00784 9.9999e-06 0.00784 0.14339 1 0.0033 1 9.9999e-06 0.00784 9.9999e-06 0.00784 0.04613 1 0.00099999 0.651 0.062869 1 0.34284 1 20p gain 222 (38%) 355 9.9999e-06 0.00784 9.9999e-06 0.00784 0.00432 1 9.9999e-06 0.00784 2e-05 0.0144 8.9999e-05 0.0619 0.053929 1 0.00185 1 0.79382 1 0.11831 1 20q gain 220 (38%) 357 9.9999e-06 0.00784 9.9999e-06 0.00784 0.0032 1 9.9999e-06 0.00784 9.9999e-06 0.00784 6.9999e-05 0.0486 0.03433 1 0.00089999 0.59 0.7952 1 0.11885 1 21q gain 64 (11%) 513 0.00121 0.783 0.0073599 1 0.01083 1 0.00422 1 0.00019 0.129 0.00182 1 0.31506 1 0.02606 1 0.0178 1 0.33388 1 22q gain 34 (6%) 543 2e-05 0.0144 0.00329 1 0.46863 1 0.21849 1 6.9999e-05 0.0486 0.14323 1 0.21406 1 0.03529 1 0.24594 1 0.19412 1 xq gain 16 (3%) 561 0.25495 1 0.94719 1 0.98471 1 0.36157 1 0.95182 1 0.71846 1 0.79025 1 1 1 0.03982 1 0.26317 1 1p loss 16 (3%) 561 0.63609 1 0.82698 1 0.94052 1 0.19766 1 0.02176 1 0.58208 1 0.33884 1 0.18086 1 0.11091 1 0.018 1 1q loss 15 (3%) 562 0.83057 1 0.97766 1 0.85726 1 0.36346 1 0.13418 1 1 1 0.33914 1 0.20836 1 0.51464 1 0.083909 1 2p loss 32 (6%) 545 0.03073 1 0.02821 1 0.26317 1 0.77145 1 9.9999e-06 0.00784 0.61817 1 1 1 0.42807 1 0.24438 1 0.22621 1 2q loss 32 (6%) 545 0.02985 1 0.02838 1 0.26184 1 0.76962 1 9.9999e-06 0.00784 0.61559 1 0.89643 1 0.24899 1 0.082319 1 0.073259 1 3p loss 40 (7%) 537 0.91039 1 0.78848 1 0.7181 1 0.15109 1 5.9999e-05 0.0419 0.20228 1 0.23561 1 0.90085 1 0.63753 1 0.231 1 3q loss 34 (6%) 543 0.22909 1 0.1291 1 0.51351 1 0.67773 1 9.9999e-06 0.00784 0.03437 1 0.7846 1 0.32078 1 0.88848 1 0.18034 1 4p loss 55 (10%) 522 0.079599 1 0.00323 1 0.03287 1 0.22634 1 0.00274 1 0.00199 1 0.29437 1 0.12239 1 0.7443 1 1 1 4q loss 56 (10%) 521 0.00097999 0.639 0.00057999 0.386 0.01886 1 0.15352 1 0.00019 0.129 0.00091999 0.603 0.73236 1 0.479 1 0.56112 1 1 1 5p loss 43 (7%) 534 3e-05 0.0213 2e-05 0.0144 0.00193 1 0.096689 1 5.9999e-05 0.0419 3e-05 0.0213 0.93954 1 0.54609 1 0.34302 1 0.051639 1 5q loss 44 (8%) 533 4e-05 0.0282 4e-05 0.0282 0.00085999 0.565 0.18779 1 5e-05 0.0351 9.9999e-06 0.00784 0.94346 1 0.625 1 0.22341 1 0.04303 1 6p loss 86 (15%) 491 0.5693 1 0.33184 1 0.7726 1 0.70557 1 9.9999e-06 0.00784 0.57227 1 0.79455 1 0.30035 1 0.86863 1 0.59457 1 6q loss 125 (22%) 452 0.93913 1 0.57916 1 0.56307 1 0.94107 1 9.9999e-06 0.00784 0.65313 1 0.96941 1 0.64691 1 0.4955 1 0.29347 1 7p loss 8 (1%) 569 0.02233 1 0.03441 1 0.45821 1 0.04222 1 0.01581 1 NA NA NA NA NA NA NA NA NA NA 7q loss 6 (1%) 571 0.10058 1 0.29926 1 0.94162 1 0.12543 1 0.098699 1 NA NA NA NA NA NA NA NA NA NA 8p loss 58 (10%) 519 0.544 1 0.4411 1 0.18067 1 0.78043 1 0.26076 1 0.64985 1 0.90629 1 0.95013 1 0.5749 1 0.39202 1 8q loss 42 (7%) 535 0.62114 1 0.15238 1 0.02241 1 0.80816 1 0.10329 1 0.13664 1 0.85774 1 0.65546 1 0.46142 1 0.14587 1 9p loss 202 (35%) 375 0.0073999 1 0.10823 1 0.55105 1 0.48433 1 0.59904 1 0.47973 1 0.6206 1 0.04677 1 0.02219 1 0.0087299 1 9q loss 94 (16%) 483 0.37022 1 0.098499 1 0.073059 1 0.27558 1 0.54803 1 0.57396 1 0.36178 1 0.11656 1 0.75076 1 0.18083 1 10p loss 483 (84%) 94 9.9999e-06 0.00784 9.9999e-06 0.00784 0.01041 1 6.9999e-05 0.0486 9.9999e-06 0.00784 9.9999e-06 0.00784 0.00232 1 0.02743 1 0.22314 1 0.01279 1 10q loss 494 (86%) 83 9.9999e-06 0.00784 9.9999e-06 0.00784 0.0061199 1 0.00011 0.0756 9.9999e-06 0.00784 5e-05 0.0351 6.9999e-05 0.0486 0.00429 1 0.26019 1 0.02178 1 11p loss 99 (17%) 478 9.9999e-06 0.00784 9.9999e-06 0.00784 0.83076 1 0.01405 1 9.9999e-06 0.00784 0.00283 1 0.72937 1 0.15865 1 0.093019 1 0.086689 1 11q loss 93 (16%) 484 2e-05 0.0144 0.00014 0.0953 0.93414 1 0.060169 1 9.9999e-06 0.00784 0.41582 1 0.93632 1 0.56795 1 0.34315 1 0.53628 1 12p loss 58 (10%) 519 0.096079 1 0.095379 1 0.55904 1 0.83194 1 0.0061599 1 0.5994 1 0.15445 1 0.058109 1 1 1 0.66183 1 12q loss 57 (10%) 520 0.14007 1 0.098309 1 0.44385 1 0.65335 1 3e-04 0.202 0.55258 1 0.18162 1 0.39073 1 1 1 0.66306 1 13q loss 186 (32%) 391 2e-05 0.0144 0.00137 0.884 0.75102 1 0.58832 1 9.9999e-06 0.00784 0.01104 1 0.59409 1 0.01697 1 0.04922 1 0.40021 1 14q loss 146 (25%) 431 9.9999e-06 0.00784 0.00016 0.109 0.51161 1 0.53934 1 9.9999e-06 0.00784 0.02481 1 0.81332 1 0.092159 1 0.16594 1 0.70134 1 15q loss 106 (18%) 471 2e-05 0.0144 9.9999e-06 0.00784 0.00385 1 0.00382 1 9.9999e-06 0.00784 0.075469 1 0.03212 1 0.01154 1 0.00356 1 0.02344 1 16p loss 63 (11%) 514 0.28681 1 0.85172 1 0.66147 1 0.73464 1 0.03426 1 0.059279 1 0.45091 1 0.18998 1 0.56473 1 0.64943 1 16q loss 83 (14%) 494 0.060309 1 0.42751 1 0.46725 1 0.89774 1 0.01281 1 0.36711 1 0.04892 1 0.01829 1 0.66213 1 0.59951 1 17p loss 65 (11%) 512 0.01941 1 0.02022 1 0.65 1 0.58108 1 9.9999e-06 0.00784 0.12874 1 0.21376 1 0.35112 1 0.29968 1 0.70426 1 17q loss 41 (7%) 536 0.0050399 1 0.060219 1 0.21203 1 0.04716 1 9.9999e-06 0.00784 0.03626 1 0.68694 1 0.48019 1 0.1467 1 0.10677 1 18p loss 71 (12%) 506 0.04732 1 0.03183 1 0.36088 1 0.22111 1 9.9999e-06 0.00784 0.50631 1 0.063749 1 0.0058999 1 0.13409 1 0.59749 1 18q loss 62 (11%) 515 0.14689 1 0.0073199 1 0.62045 1 0.23927 1 0.00013 0.0888 0.47903 1 0.0091599 1 0.00351 1 0.41762 1 0.1204 1 19p loss 27 (5%) 550 0.00061999 0.412 0.00091999 0.603 0.058409 1 0.43469 1 0.0134 1 0.00012 0.0822 0.01977 1 0.01085 1 0.85277 1 0.66847 1 19q loss 35 (6%) 542 0.00055999 0.374 0.00497 1 0.41315 1 0.15205 1 0.00106 0.688 0.00078999 0.521 0.080149 1 0.33707 1 0.93013 1 0.51328 1 20p loss 19 (3%) 558 0.00013 0.0888 5e-05 0.0351 0.03663 1 0.093699 1 9.9999e-06 0.00784 0.30816 1 0.41317 1 0.45575 1 0.01043 1 0.00206 1 20q loss 17 (3%) 560 0.00145 0.931 0.00012 0.0822 0.36545 1 0.26589 1 9.9999e-06 0.00784 0.30917 1 0.41481 1 0.45878 1 0.03947 1 0.01171 1 21q loss 42 (7%) 535 0.02149 1 0.00134 0.866 0.053109 1 0.26322 1 0.00079999 0.526 0.00177 1 0.01214 1 0.083749 1 0.82714 1 1 1 22q loss 181 (31%) 396 0.65061 1 0.56167 1 0.19772 1 0.87549 1 9.9999e-06 0.00784 0.073609 1 0.90916 1 0.13537 1 0.20166 1 0.092469 1 xq loss 106 (18%) 471 0.01887 1 0.01566 1 0.11209 1 0.10631 1 9.9999e-06 0.00784 0.0058699 1 0.90252 1 0.68255 1 0.41449 1 0.96119 1