Clinical Features CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_CHIERARCHICAL nMutated (%) 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 TP53 196 (50%) 199 9.9999e-06 0.000736 0.00083999 0.0283 3e-04 0.0128 0.02421 0.316 5e-05 0.0027 2e-05 0.00125 0.00155 0.0448 0.14416 0.618 0.0056199 0.126 0.00141 0.0439 RB1 70 (18%) 325 9.9999e-06 0.000736 0.04065 0.397 5e-05 0.0027 0.00021 0.00945 8.9999e-05 0.00456 2e-05 0.00125 0.00011 0.00524 0.3676 0.781 0.00067999 0.025 0.00154 0.0448 ELF3 46 (12%) 349 0.84886 0.975 0.10853 0.541 0.62745 0.911 0.063809 0.46 0.076669 0.474 0.0403 0.397 0.41599 0.806 0.63906 0.911 0.25941 0.713 0.5846 0.88 TSC1 33 (8%) 362 0.21597 0.669 0.93136 0.992 0.31276 0.732 0.20451 0.669 0.32028 0.745 0.23427 0.678 0.52656 0.854 0.072519 0.47 0.59085 0.883 0.85984 0.978 PIK3CA 86 (22%) 309 0.80103 0.966 0.94853 0.992 0.84226 0.974 0.94671 0.992 0.02397 0.316 0.76495 0.95 0.74316 0.945 0.68531 0.924 0.96967 1 0.83897 0.974 RHOB 26 (7%) 369 0.37122 0.781 0.29416 0.727 0.91839 0.987 0.6771 0.919 0.2479 0.702 0.15905 0.638 0.42022 0.807 0.82922 0.97 0.77146 0.953 0.80643 0.966 KDM6A 103 (26%) 292 0.38706 0.795 0.00222 0.0607 0.051719 0.414 0.22193 0.669 0.00446 0.106 0.01129 0.183 0.11704 0.558 0.16925 0.638 0.03729 0.382 0.17013 0.638 CDKN2A 26 (7%) 369 0.85596 0.977 0.03863 0.391 0.68094 0.919 0.02751 0.343 0.28396 0.726 0.4474 0.823 0.0066699 0.14 0.19037 0.664 0.078999 0.478 0.00076999 0.0271 ARID1A 97 (25%) 298 0.24487 0.701 0.48797 0.85 0.76632 0.95 0.52281 0.854 0.14843 0.626 0.78202 0.956 0.0493 0.399 0.066119 0.46 0.11019 0.541 0.6595 0.914 STAG2 56 (14%) 339 0.052989 0.414 0.03001 0.348 0.10609 0.541 0.18971 0.664 0.50806 0.85 0.0067299 0.14 0.10155 0.541 0.22213 0.669 0.04525 0.399 0.03024 0.348 ZFP36L1 25 (6%) 370 0.96098 0.998 0.38447 0.795 0.30724 0.727 0.93157 0.992 0.50945 0.851 0.23453 0.678 0.72299 0.933 0.32664 0.754 0.5674 0.88 0.24643 0.702 CDKN1A 35 (9%) 360 0.95047 0.992 0.16993 0.638 0.30518 0.727 0.03288 0.35 0.72018 0.932 0.35564 0.781 0.17213 0.638 0.087389 0.499 0.29614 0.727 0.50425 0.85 EP300 61 (15%) 334 0.12965 0.587 0.81347 0.966 0.42093 0.807 0.66334 0.914 0.27255 0.717 0.30955 0.727 0.57934 0.88 0.84242 0.974 0.46829 0.843 0.86603 0.98 MLL2 114 (29%) 281 0.15561 0.638 0.60766 0.897 0.90776 0.986 0.10336 0.541 0.67974 0.919 0.93652 0.992 0.44812 0.823 0.34565 0.776 0.5045 0.85 0.068039 0.46 FGFR3 56 (14%) 339 9.9999e-06 0.000736 9.9999e-06 0.000736 9.9999e-06 0.000736 9.9999e-06 0.000736 9.9999e-06 0.000736 9.9999e-06 0.000736 9.9999e-06 0.000736 0.00041 0.0166 9.9999e-06 0.000736 9.9999e-06 0.000736 ERCC2 38 (10%) 357 0.54839 0.871 0.42372 0.807 0.04622 0.399 0.2536 0.711 0.39972 0.795 0.70531 0.928 0.16865 0.638 0.42829 0.807 0.14715 0.624 0.39556 0.795 CREBBP 48 (12%) 347 0.47214 0.848 0.49364 0.85 0.64427 0.914 0.8186 0.967 0.26369 0.714 0.54331 0.866 0.087029 0.499 0.00348 0.0854 0.13925 0.6 0.054209 0.414 HRAS 17 (4%) 378 0.24442 0.701 0.1993 0.669 0.50605 0.85 0.84556 0.975 0.84302 0.974 0.77723 0.956 0.34055 0.773 0.42925 0.807 0.35836 0.781 0.27102 0.717 FOXA1 14 (4%) 381 0.74547 0.945 0.5202 0.854 0.81445 0.966 0.16576 0.638 0.36632 0.781 0.22813 0.672 0.27344 0.717 0.15799 0.638 0.02097 0.288 0.27129 0.717 KRAS 13 (3%) 382 0.071779 0.469 0.62179 0.909 0.58351 0.88 0.15226 0.638 0.10791 0.541 0.17285 0.638 0.63859 0.911 0.56198 0.879 0.7032 0.928 0.58642 0.88 RHOA 18 (5%) 377 0.49576 0.85 0.3529 0.781 0.40308 0.796 0.1782 0.647 0.88552 0.98 0.48047 0.85 0.18071 0.648 0.11087 0.541 0.67611 0.919 0.8158 0.966 KIAA1267 24 (6%) 371 0.4062 0.797 0.04913 0.399 0.95488 0.994 0.64728 0.914 0.33888 0.771 0.21166 0.669 0.25117 0.706 0.78082 0.956 0.056299 0.426 0.52685 0.854 MLL 44 (11%) 351 0.04275 0.399 0.70785 0.928 0.064429 0.46 0.17073 0.638 0.40069 0.795 0.073109 0.47 0.0064599 0.14 0.0109 0.18 0.03221 0.35 0.00471 0.109 FAT1 50 (13%) 345 0.80684 0.966 0.067439 0.46 0.23021 0.676 0.12415 0.575 0.39243 0.795 0.19375 0.665 0.11274 0.547 0.03241 0.35 0.34878 0.78 0.081539 0.486 KLF5 23 (6%) 372 0.66067 0.914 0.95197 0.992 0.04922 0.399 0.6569 0.914 0.58211 0.88 0.70817 0.928 0.24826 0.702 0.062389 0.455 0.15681 0.638 0.084549 0.496 PTEN 14 (4%) 381 0.83372 0.97 0.13507 0.6 0.47782 0.85 0.37144 0.781 0.13833 0.6 0.16203 0.638 0.43393 0.812 1 1 0.93783 0.992 0.66654 0.915 C3ORF70 17 (4%) 378 0.57047 0.88 0.24857 0.702 1 1 0.66758 0.915 0.87165 0.98 0.56887 0.88 0.8754 0.98 0.49372 0.85 0.95139 0.992 0.91444 0.987 PSIP1 20 (5%) 375 0.75039 0.945 0.04815 0.399 0.0178 0.257 0.16727 0.638 0.75198 0.945 0.01628 0.249 0.10683 0.541 0.94219 0.992 0.02803 0.344 0.02571 0.331 MLL3 74 (19%) 321 0.0094899 0.167 0.62805 0.911 0.1158 0.555 0.22462 0.669 0.40152 0.795 0.47931 0.85 0.36916 0.781 0.02885 0.345 0.12428 0.575 0.29701 0.727 ASXL2 36 (9%) 359 0.82034 0.967 0.78473 0.956 0.092479 0.511 0.21696 0.669 0.52174 0.854 0.593 0.883 0.32841 0.756 0.21319 0.669 0.42819 0.807 0.49037 0.85 ZBTB7B 11 (3%) 384 0.90567 0.986 0.87983 0.98 0.78738 0.956 0.53437 0.859 0.42002 0.807 0.39683 0.795 0.52562 0.854 0.21413 0.669 0.67176 0.919 0.40679 0.797 RXRA 24 (6%) 371 0.13465 0.6 0.01036 0.177 0.58255 0.88 0.27695 0.721 0.30975 0.727 0.25757 0.713 0.28655 0.727 0.34545 0.776 0.5407 0.865 0.37075 0.781 FBXW7 30 (8%) 365 0.02189 0.296 0.067029 0.46 0.71056 0.929 0.44073 0.819 0.49044 0.85 0.17081 0.638 0.36506 0.781 0.19819 0.669 0.20914 0.669 0.04687 0.399 RBM10 22 (6%) 373 0.28806 0.727 0.45439 0.828 0.48423 0.85 0.90536 0.986 0.30436 0.727 0.88581 0.98 0.20854 0.669 0.20964 0.669 0.30869 0.727 0.27996 0.724 NFE2L2 24 (6%) 371 0.059369 0.437 0.01449 0.226 0.12006 0.562 0.068719 0.46 0.0084399 0.157 0.0082999 0.157 0.089039 0.5 0.65622 0.914 0.55079 0.873 0.04462 0.399 CUL1 19 (5%) 376 0.81189 0.966 0.6006 0.891 0.10665 0.541 0.2979 0.727 0.78954 0.957 0.45768 0.829 0.8542 0.977 0.83132 0.97 0.80599 0.966 0.3006 0.727 HLA-A 5 (1%) 390 0.48968 0.85 1 1 NA NA NA NA 0.29662 0.727 1 1 0.90692 0.986 0.29099 0.727 0.93006 0.992 0.69325 0.926 GNA13 12 (3%) 383 0.79788 0.963 0.22018 0.669 0.36615 0.781 0.77539 0.956 0.69407 0.926 0.36539 0.781 0.5417 0.865 0.21666 0.669 0.067379 0.46 0.53471 0.859 NUDT11 7 (2%) 388 0.81078 0.966 0.40565 0.797 0.00323 0.0835 0.81239 0.966 0.24369 0.701 0.7164 0.931 0.75845 0.95 0.37042 0.781 0.34441 0.776 0.57845 0.88 MBD1 12 (3%) 383 0.19275 0.664 0.87463 0.98 0.50793 0.85 0.29444 0.727 0.20707 0.669 0.66113 0.914 0.79621 0.963 0.59718 0.888 0.57451 0.88 0.76913 0.951 SCARF2 8 (2%) 387 0.38472 0.795 0.053399 0.414 0.32477 0.754 0.19882 0.669 0.070179 0.462 0.16265 0.638 0.87111 0.98 0.49632 0.85 0.27934 0.724 0.55544 0.874 FOXQ1 14 (4%) 381 0.73691 0.943 0.76673 0.95 0.61843 0.906 0.26793 0.717 0.73296 0.941 0.88671 0.98 0.83096 0.97 0.84131 0.974 1 1 0.96846 1 FAM47C 21 (5%) 374 0.39655 0.795 0.82111 0.967 0.0069799 0.141 0.74313 0.945 0.3887 0.795 0.71817 0.932 0.30517 0.727 0.15466 0.638 0.67702 0.919 0.40753 0.797 METTL3 17 (4%) 378 0.76115 0.95 0.72241 0.933 1 1 0.69134 0.926 0.55815 0.876 0.2184 0.669 0.41232 0.802 0.29926 0.727 0.57479 0.88 0.11002 0.541 ZNF185 5 (1%) 390 0.86851 0.98 0.70762 0.928 0.076269 0.474 0.35634 0.781 0.37835 0.792 0.86384 0.98 0.65675 0.914 0.65167 0.914 0.74458 0.945 0.25756 0.713 ERBB2 48 (12%) 347 0.76208 0.95 0.22297 0.669 0.52955 0.854 0.67878 0.919 0.4493 0.823 0.20688 0.669 0.070059 0.462 0.23288 0.678 0.36151 0.781 0.39306 0.795 ATM 53 (13%) 342 0.48172 0.85 0.17948 0.647 0.17193 0.638 0.01827 0.26 0.63061 0.911 0.65382 0.914 0.26886 0.717 0.20669 0.669 0.27627 0.721 0.097609 0.534 UNC93B1 7 (2%) 388 0.56385 0.88 0.65659 0.914 0.51142 0.852 0.89589 0.982 0.93029 0.992 0.88848 0.98 1 1 1 1 0.67254 0.919 0.66343 0.914 SF1 10 (3%) 385 0.36457 0.781 0.63827 0.911 0.30615 0.727 0.01722 0.254 0.89507 0.982 1 1 0.0033 0.0835 0.01675 0.251 0.092739 0.511 0.49035 0.85 BCL2L1 4 (1%) 391 0.066219 0.46 0.03264 0.35 0.076939 0.474 0.52494 0.854 0.7123 0.929 0.69185 0.926 0.74885 0.945 1 1 0.39603 0.795 0.81573 0.966 DNAH6 16 (4%) 379 0.73384 0.941 0.13907 0.6 0.45195 0.826 0.19104 0.664 0.02053 0.287 0.01235 0.196 0.33035 0.758 0.13663 0.6 0.068539 0.46 0.086129 0.499 HES1 11 (3%) 384 1 1 0.948 0.992 0.58181 0.88 0.1273 0.583 0.91954 0.987 0.63193 0.911 0.35391 0.781 0.30812 0.727 0.87764 0.98 0.49842 0.85 ERBB3 41 (10%) 354 0.47883 0.85 0.35869 0.781 0.9007 0.985 0.26776 0.717 0.52155 0.854 0.21892 0.669 0.8575 0.977 0.85596 0.977 0.94408 0.992 0.30063 0.727 TXNIP 17 (4%) 378 0.72459 0.933 0.49366 0.85 0.12805 0.583 0.74588 0.945 0.30962 0.727 0.0086199 0.157 0.71943 0.932 0.42924 0.807 0.92728 0.992 0.77908 0.956 THRAP3 14 (4%) 381 0.84713 0.975 0.64573 0.914 1 1 1 1 1 1 0.78424 0.956 0.33567 0.766 0.92038 0.987 0.96024 0.998 0.84655 0.975 SPTAN1 45 (11%) 350 0.6518 0.914 0.1575 0.638 0.26156 0.713 0.11983 0.562 0.26737 0.717 0.20289 0.669 0.22423 0.669 0.58583 0.88 0.30863 0.727 0.17234 0.638 ARID1B 23 (6%) 372 0.52878 0.854 0.089469 0.5 0.18657 0.664 0.5852 0.88 0.099179 0.539 0.057859 0.431 0.21031 0.669 0.16255 0.638 0.17541 0.64 0.10883 0.541 NRAS 7 (2%) 388 0.29535 0.727 0.43969 0.819 1 1 0.63788 0.911 0.65844 0.914 0.63831 0.911 0.42298 0.807 0.36754 0.781 0.04343 0.399 0.22475 0.669 RPTN 15 (4%) 380 0.93779 0.992 0.3505 0.781 0.87208 0.98 0.76418 0.95 0.49414 0.85 1 1 0.21441 0.669 0.22008 0.669 0.78641 0.956 0.78217 0.956 RAI1 21 (5%) 374 0.65376 0.914 0.13746 0.6 0.11896 0.562 0.077189 0.474 0.02698 0.341 0.03243 0.35 0.17358 0.638 0.43027 0.807 0.39601 0.795 0.56479 0.88 TMCO4 12 (3%) 383 0.75338 0.945 0.053179 0.414 0.55419 0.874 0.2871 0.727 0.04795 0.399 0.075349 0.474 0.21524 0.669 1 1 0.04922 0.399 0.20347 0.669 CNOT1 21 (5%) 374 0.44169 0.819 0.16202 0.638 0.36274 0.781 0.3888 0.795 0.60548 0.895 0.45502 0.828 0.55482 0.874 0.89504 0.982 0.91046 0.986 0.88131 0.98 PARD3 22 (6%) 373 0.1084 0.541 0.64674 0.914 0.41897 0.807 0.36666 0.781 0.088469 0.5 0.85191 0.977 0.97092 1 0.26075 0.713 0.87603 0.98 0.26132 0.713 EZR 12 (3%) 383 0.44582 0.823 0.48561 0.85 1 1 0.38432 0.795 0.41279 0.802 0.87125 0.98 0.93629 0.992 0.17986 0.647 0.89201 0.982 0.73138 0.94 MOAP1 7 (2%) 388 0.80709 0.966 0.30064 0.727 0.52272 0.854 0.60167 0.891 0.22712 0.672 0.63721 0.911 0.27217 0.717 0.85672 0.977 0.90839 0.986 0.75306 0.945 SF3B1 24 (6%) 371 0.34283 0.776 0.88516 0.98 0.50586 0.85 0.45722 0.829 0.70149 0.928 0.61625 0.904 0.94748 0.992 0.59238 0.883 0.38516 0.795 0.14695 0.624 RUNX1 13 (3%) 382 0.65202 0.914 0.67531 0.919 0.26072 0.713 0.51784 0.854 0.00225 0.0607 0.04647 0.399 0.19221 0.664 0.91672 0.987 0.81333 0.966 0.00109 0.0353 MEGF8 20 (5%) 375 0.6643 0.914 0.44071 0.819 0.68921 0.926 1 1 0.13749 0.6 0.54015 0.865 0.2154 0.669 0.58742 0.88 0.90937 0.986 0.88899 0.98 CASP8 14 (4%) 381 0.49739 0.85 0.48804 0.85 0.082209 0.486 0.10104 0.541 0.87893 0.98 0.57717 0.88 0.16258 0.638 0.40151 0.795 0.54696 0.87 0.28323 0.726 DAZAP1 6 (2%) 389 0.36475 0.781 0.087529 0.499 0.55552 0.874 0.31994 0.745 0.4598 0.831 0.01047 0.177 0.19177 0.664 0.37762 0.792 0.47483 0.85 0.58619 0.88 USP28 13 (3%) 382 0.39652 0.795 0.93878 0.992 0.58345 0.88 0.39722 0.795 0.83318 0.97 1 1 0.75178 0.945 1 1 0.61312 0.901 0.40961 0.799 SETD2 27 (7%) 368 0.70513 0.928 0.71163 0.929 0.50189 0.85 0.82587 0.97 1 1 0.81917 0.967 0.26266 0.714 0.42965 0.807 0.83213 0.97 0.86472 0.98 EME1 5 (1%) 390 0.62845 0.911 0.28694 0.727 0.69665 0.928 0.28211 0.726 0.52293 0.854 0.3351 0.766 0.49324 0.85 0.10458 0.541 0.16012 0.638 0.10874 0.541 ADC 5 (1%) 390 0.081699 0.486 0.9339 0.992 0.69408 0.926 0.70042 0.928 0.9171 0.987 1 1 1 1 0.5262 0.854 0.56911 0.88 0.76159 0.95 CNOT3 10 (3%) 385 0.11018 0.541 0.32673 0.754 0.70202 0.928 0.17411 0.638 0.04831 0.399 0.11553 0.555 0.0087099 0.157 0.44643 0.823 0.0073499 0.145 0.00059999 0.0231 SSH3 15 (4%) 380 0.20742 0.669 0.057969 0.431 0.03417 0.359 0.04379 0.399 0.077889 0.474 0.39455 0.795 0.12543 0.577 0.21983 0.669 0.03693 0.382 0.029 0.345 AHR 22 (6%) 373 0.63147 0.911 0.10268 0.541 0.15703 0.638 0.77785 0.956 0.52137 0.854 0.074089 0.473 0.70469 0.928 0.94798 0.992 0.50412 0.85 0.20593 0.669 EIF4A2 11 (3%) 384 0.51806 0.854 0.71375 0.929 0.3994 0.795 0.61094 0.9 0.73847 0.943 0.26076 0.713 0.42692 0.807 0.1877 0.664 0.62252 0.909 0.054079 0.414 EPHA2 19 (5%) 376 0.94244 0.992 0.0398 0.397 0.64105 0.913 0.49379 0.85 0.90125 0.985 1 1 0.75189 0.945 0.50784 0.85 0.91421 0.987 0.29511 0.727 OGDH 19 (5%) 376 0.21946 0.669 0.13043 0.587 0.88171 0.98 0.56035 0.878 0.82324 0.968 0.86653 0.98 0.46698 0.842 0.23128 0.676 0.43016 0.807 0.27342 0.717 POU3F1 3 (1%) 392 0.57739 0.88 0.18927 0.664 0.03054 0.348 0.63288 0.911 0.04464 0.399 0.79152 0.958 0.28248 0.726 0.16818 0.638 0.04419 0.399 0.22817 0.672