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 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q TP53 256 (53%) 225 0.084149 0.548 0.14773 0.642 9.9999e-06 0.00054 2e-05 9e-04 0.00015 0.0054 9.9999e-06 0.00054 9.9999e-06 0.00054 9.9999e-06 0.00054 9.9999e-06 0.00054 9.9999e-06 0.00054 9.9999e-06 0.00054 9.9999e-06 0.00054 KRAS 150 (31%) 331 1 1 1 1 9.9999e-06 0.00054 0.00473 0.0984 0.31338 0.801 0.12026 0.582 0.43481 0.905 9.9999e-06 0.00054 0.0077199 0.15 7.9999e-05 0.00309 0.50129 0.962 0.069549 0.501 KEAP1 84 (17%) 397 NA NA NA NA 9.9999e-06 0.00054 9.9999e-06 0.00054 0.00070999 0.0219 0.37005 0.861 9.9999e-06 0.00054 9.9999e-06 0.00054 0.11237 0.582 0.00018 0.00627 0.11902 0.582 0.0084199 0.156 EGFR 67 (14%) 414 NA NA NA NA 9.9999e-06 0.00054 0.41579 0.884 0.00195 0.0516 0.02097 0.302 5.9999e-05 0.00259 2e-05 9e-04 0.02113 0.302 0.00054999 0.018 0.27815 0.772 0.03098 0.376 STK11 77 (16%) 404 NA NA NA NA 9.9999e-06 0.00054 0.00087999 0.0264 2e-05 9e-04 0.097369 0.559 9.9999e-06 0.00054 9.9999e-06 0.00054 0.78749 1 6.9999e-05 0.00291 0.00184 0.051 0.03827 0.401 RBM10 33 (7%) 448 NA NA NA NA 0.073129 0.506 0.10809 0.582 0.28099 0.774 0.45626 0.923 0.17988 0.695 0.77414 1 0.796 1 0.04415 0.432 0.74281 1 0.76615 1 RB1 26 (5%) 455 NA NA NA NA 0.060699 0.473 0.086139 0.548 0.18397 0.699 0.42957 0.901 0.29484 0.78 0.00013 0.00484 0.13156 0.6 0.094849 0.559 0.43415 0.905 0.62207 1 ARID1A 30 (6%) 451 NA NA NA NA 0.90389 1 0.66591 1 0.46711 0.936 0.69899 1 0.66736 1 0.87908 1 0.4641 0.932 0.094859 0.559 0.63481 1 0.33475 0.815 NF1 55 (11%) 426 1 1 0.79249 1 0.0033 0.0775 0.59179 1 0.062269 0.473 0.48132 0.954 0.0455 0.434 0.26061 0.757 0.23328 0.745 0.11486 0.582 0.2445 0.757 0.16114 0.659 SMARCA4 38 (8%) 443 NA NA NA NA 0.00258 0.0648 9.9999e-06 0.00054 0.50913 0.966 0.1082 0.582 7.9999e-05 0.00309 9.9999e-06 0.00054 0.0084999 0.156 0.00135 0.0384 0.11513 0.582 2e-05 9e-04 BRAF 39 (8%) 442 0.77542 1 1 1 0.78471 1 0.04976 0.455 0.57205 1 0.89465 1 0.24088 0.75 0.38283 0.873 0.4574 0.923 0.0472 0.439 0.8701 1 0.061019 0.473 MGA 40 (8%) 441 NA NA NA NA 0.89208 1 0.1557 0.659 0.72291 1 0.10369 0.577 0.11122 0.582 0.15369 0.653 0.02355 0.314 0.11808 0.582 0.41521 0.884 0.18888 0.704 FTSJD1 24 (5%) 457 NA NA NA NA 0.41044 0.881 0.32683 0.815 0.92898 1 0.382 0.873 0.43777 0.909 0.28796 0.779 0.61279 1 0.50571 0.963 0.23064 0.745 0.15311 0.653 MET 21 (4%) 460 NA NA NA NA 0.065699 0.486 0.66872 1 0.45612 0.923 0.267 0.757 0.11856 0.582 0.62903 1 0.1189 0.582 0.20817 0.716 0.72316 1 0.17037 0.684 GAGE2A 8 (2%) 473 NA NA NA NA 0.43273 0.904 0.67558 1 0.71986 1 0.48312 0.956 0.37493 0.866 0.57689 1 0.26805 0.757 0.4942 0.962 0.96247 1 0.72231 1 SETD2 30 (6%) 451 NA NA NA NA 0.61134 1 0.2806 0.774 0.61268 1 0.68017 1 0.6337 1 0.22439 0.745 0.16101 0.659 0.058299 0.473 0.072809 0.506 0.00196 0.0516 U2AF1 11 (2%) 470 NA NA NA NA 0.34615 0.831 0.76185 1 0.058189 0.473 0.68262 1 0.0466 0.438 0.12708 0.593 0.0322 0.384 0.77811 1 0.24106 0.75 0.28714 0.779 ERBB2 11 (2%) 470 NA NA NA NA 0.44502 0.912 0.15934 0.659 0.17369 0.687 1 1 0.30233 0.788 0.13673 0.615 0.67557 1 0.1934 0.71 0.62628 1 0.19776 0.715 CDKN2A 16 (3%) 465 NA NA NA NA 0.31941 0.81 0.6623 1 0.81999 1 0.68893 1 0.03262 0.384 0.20274 0.715 1 1 0.92209 1 0.20242 0.715 0.70972 1 SRPX 14 (3%) 467 NA NA NA NA 0.89764 1 0.22776 0.745 0.63784 1 0.03923 0.407 0.14964 0.642 0.91208 1 0.50231 0.962 0.052389 0.46 0.6868 1 0.35172 0.836 ATM 42 (9%) 439 NA NA NA NA 0.00304 0.073 0.00474 0.0984 0.33076 0.815 0.93365 1 0.070249 0.502 0.00061999 0.0197 0.74389 1 0.03534 0.392 0.11023 0.582 0.73215 1 TCEAL5 13 (3%) 468 NA NA NA NA 0.83735 1 0.50227 0.962 0.33137 0.815 0.92622 1 0.6472 1 0.86776 1 0.47549 0.945 0.50172 0.962 0.99641 1 0.85806 1 PPP3CA 12 (2%) 469 NA NA NA NA 0.39013 0.878 0.40403 0.881 0.63952 1 0.80724 1 0.40585 0.881 0.01589 0.26 0.098299 0.559 0.16979 0.684 0.95681 1 0.70863 1 FCRLA 15 (3%) 466 NA NA NA NA 0.27983 0.774 0.23816 0.75 0.84677 1 0.33326 0.815 0.47158 0.941 0.37524 0.866 1 1 0.89412 1 0.4505 0.92 0.13249 0.6 ARID2 24 (5%) 457 NA NA NA NA 0.17314 0.687 0.057489 0.473 0.82713 1 1 1 0.97545 1 0.090809 0.551 0.083589 0.548 0.11767 0.582 0.23876 0.75 0.088799 0.551 APC 20 (4%) 461 NA NA NA NA 0.56993 1 0.33298 0.815 0.89045 1 0.88229 1 0.18369 0.699 0.22052 0.745 0.04478 0.432 0.061669 0.473 0.69496 1 0.20147 0.715 ZEB1 32 (7%) 449 1 1 1 1 0.075179 0.509 0.43925 0.91 0.76906 1 0.87509 1 0.9655 1 0.47597 0.945 0.42881 0.901 0.15822 0.659 0.88785 1 0.82388 1 SIP1 4 (1%) 477 0.087079 0.548 0.1182 0.582 0.5853 1 NA NA 0.47081 0.941 1 1 0.32352 0.813 0.97741 1 0.83177 1 0.40734 0.881 NA NA NA NA SLC4A3 18 (4%) 463 NA NA NA NA 0.29984 0.788 0.28882 0.779 0.17401 0.687 0.060589 0.473 0.04264 0.432 0.45567 0.923 0.094789 0.559 0.47525 0.945 0.04795 0.443 0.060759 0.473 STK19 5 (1%) 476 NA NA NA NA 1 1 1 1 0.82464 1 0.58383 1 0.69077 1 0.97497 1 0.62158 1 0.70643 1 0.38988 0.878 0.61461 1 NUDT11 5 (1%) 476 NA NA NA NA 0.16305 0.662 1 1 0.62309 1 0.83137 1 0.1121 0.582 0.30506 0.788 0.073079 0.506 0.57696 1 0.83086 1 0.04397 0.432 SLAMF9 12 (2%) 469 NA NA NA NA 0.087259 0.548 0.063299 0.475 0.9331 1 1 1 0.086169 0.548 0.5991 1 0.090869 0.551 0.0167 0.269 0.64272 1 0.63856 1 DNMT3A 19 (4%) 462 NA NA NA NA 0.16082 0.659 0.38758 0.876 0.57711 1 0.29373 0.78 0.20659 0.716 0.55749 1 0.3319 0.815 0.49728 0.962 0.25895 0.757 0.04253 0.432 CTNNB1 19 (4%) 462 NA NA NA NA 0.02152 0.302 0.1259 0.591 0.03589 0.392 0.25323 0.757 0.2224 0.745 0.40637 0.881 0.9129 1 0.81272 1 0.38327 0.873 1 1 PTPRU 18 (4%) 463 NA NA NA NA 0.01996 0.299 0.15754 0.659 0.102 0.574 0.0262 0.337 0.051849 0.46 0.062589 0.473 0.00298 0.073 0.0052699 0.107 0.22597 0.745 0.11035 0.582 PIK3CA 28 (6%) 453 NA NA NA NA 0.53048 0.986 0.20806 0.716 0.14909 0.642 0.1382 0.619 0.01972 0.299 0.02578 0.335 0.82109 1 0.087239 0.548 0.11013 0.582 0.20187 0.715 ZNF608 9 (2%) 472 NA NA NA NA 0.46264 0.932 0.58563 1 0.23237 0.745 1 1 0.46362 0.932 0.0090099 0.16 0.68345 1 0.6898 1 0.03396 0.388 0.23321 0.745 STIM1 9 (2%) 472 NA NA NA NA 0.2573 0.757 0.18141 0.695 0.87674 1 0.86214 1 0.11526 0.582 0.26858 0.757 0.2569 0.757 0.26065 0.757 0.67213 1 0.77913 1 EMG1 5 (1%) 476 0.18448 0.699 0.55468 1 0.29168 0.78 0.49595 0.962 0.74939 1 0.29436 0.78 0.26983 0.757 0.26154 0.757 0.22609 0.745 0.31441 0.801 NA NA NA NA PHKA1 12 (2%) 469 NA NA NA NA 0.03685 0.398 0.1146 0.582 0.69301 1 0.77997 1 0.24862 0.757 0.35315 0.836 0.32595 0.815 0.35382 0.836 0.51579 0.972 0.087269 0.548 PAK1 9 (2%) 472 NA NA NA NA 1 1 0.58325 1 0.29572 0.781 0.8829 1 0.30125 0.788 0.25489 0.757 0.90848 1 0.98243 1 0.87636 1 1 1 NRAS 3 (1%) 478 NA NA NA NA 0.69046 1 NA NA NA NA NA NA 0.11888 0.582 0.89446 1 0.23638 0.75 0.38139 0.873 NA NA NA NA G3BP1 8 (2%) 473 NA NA NA NA 0.21512 0.733 0.68272 1 0.93055 1 0.33587 0.815 0.77079 1 0.83111 1 0.90272 1 0.80355 1 0.25864 0.757 0.43147 0.903 TRERF1 18 (4%) 463 NA NA NA NA 0.067639 0.49 0.40543 0.881 0.29373 0.78 0.6565 1 0.25472 0.757 0.30503 0.788 0.01153 0.201 0.04373 0.432 0.1232 0.589 0.22789 0.745 CACNA1F 27 (6%) 454 NA NA NA NA 0.45691 0.923 0.64843 1 0.20258 0.715 0.81851 1 0.12479 0.591 0.098159 0.559 0.02356 0.314 0.59862 1 0.24065 0.75 0.73866 1 NFE2L2 13 (3%) 468 NA NA NA NA 0.92255 1 0.71063 1 0.26813 0.757 0.24935 0.757 0.34862 0.835 0.03796 0.401 0.74704 1 0.23174 0.745 0.35064 0.836 0.75851 1 RPL5 8 (2%) 473 NA NA NA NA 0.02936 0.36 0.60612 1 0.90148 1 0.12853 0.596 0.79562 1 0.71868 1 0.52476 0.981 0.72123 1 0.56305 1 0.8979 1 STRA8 8 (2%) 473 NA NA NA NA 0.03271 0.384 0.097899 0.559 0.0086899 0.156 0.02329 0.314 0.26725 0.757 0.03417 0.388 0.0083399 0.156 0.17505 0.687 0.33112 0.815 0.21069 0.722 NLRP6 10 (2%) 471 NA NA NA NA 0.13031 0.599 0.29376 0.78 0.0278 0.35 0.16496 0.667 0.11399 0.582 0.01921 0.299 0.14801 0.642 0.061209 0.473 0.80032 1 0.14279 0.629 FAM65C 14 (3%) 467 NA NA NA NA 0.37393 0.866 0.88229 1 0.056389 0.473 0.054549 0.464 0.92995 1 0.68985 1 0.20694 0.716 0.70052 1 0.72204 1 0.087289 0.548 WDR66 14 (3%) 467 NA NA NA NA 0.76483 1 0.25713 0.757 0.00371 0.0835 0.10637 0.582 0.02395 0.315 0.4875 0.957 0.12904 0.596 0.33461 0.815 0.36016 0.844 0.14981 0.642 RIT1 8 (2%) 473 NA NA NA NA 0.1798 0.695 0.33629 0.815 0.35902 0.843 1 1 0.8739 1 0.17484 0.687 0.33588 0.815 0.9534 1 0.69653 1 0.29993 0.788 TGFBR3 14 (3%) 467 NA NA NA NA 0.23682 0.75 0.23114 0.745 0.79685 1 0.14165 0.627 0.5189 0.976 0.22926 0.745 0.02858 0.355 0.10116 0.572 0.26999 0.757 0.01343 0.227 CXCR7 10 (2%) 471 NA NA NA NA 0.40999 0.881 0.095179 0.559 0.65343 1 0.18813 0.704 0.65547 1 0.65621 1 0.24482 0.757 0.69254 1 0.39415 0.881 0.20536 0.716 GAN 10 (2%) 471 NA NA NA NA 0.69161 1 0.81822 1 0.89124 1 0.83772 1 0.39673 0.881 0.40437 0.881 0.49443 0.962 0.67796 1 0.86168 1 0.40727 0.881 TMEM49 5 (1%) 476 NA NA NA NA 0.20728 0.716 0.15922 0.659 0.93298 1 0.090089 0.551 0.68872 1 0.22358 0.745 0.62368 1 0.62452 1 0.63687 1 0.72368 1 HSPA8 9 (2%) 472 NA NA NA NA 0.36464 0.851 0.27174 0.76 0.42629 0.897 1 1 0.75065 1 0.22228 0.745 0.00343 0.0788 0.39402 0.881 0.81522 1 0.78015 1 CD244 12 (2%) 469 NA NA NA NA 0.41841 0.888 0.53545 0.989 0.63057 1 0.77161 1 0.10503 0.579 0.26374 0.757 0.051979 0.46 0.076839 0.515 0.25962 0.757 0.28844 0.779 KIF18B 4 (1%) 477 0.38445 0.874 0.39134 0.879 0.22458 0.745 NA NA 0.36166 0.845 0.12738 0.593 0.66501 1 0.75376 1 0.26795 0.757 0.77054 1 NA NA NA NA PDE6A 16 (3%) 465 NA NA NA NA 0.65945 1 0.71006 1 1 1 0.12007 0.582 0.10435 0.578 0.02785 0.35 0.062469 0.473 0.02151 0.302 0.32192 0.811 0.38769 0.876 CHRND 16 (3%) 465 NA NA NA NA 0.12532 0.591 0.68381 1 0.13284 0.6 0.092379 0.557 0.6647 1 0.20239 0.715 0.38283 0.873 0.26108 0.757 0.81613 1 1 1 KLK1 8 (2%) 473 NA NA NA NA 0.071579 0.506 0.54308 0.996 0.56894 1 0.03824 0.401 0.54918 1 0.64564 1 0.18082 0.695 0.050419 0.456 0.76765 1 0.14607 0.641 KLHL5 14 (3%) 467 NA NA NA NA 0.53462 0.989 0.66051 1 0.75993 1 0.086909 0.548 0.49948 0.962 0.79545 1 0.5633 1 0.79002 1 0.54564 0.999 0.7086 1 DSC2 20 (4%) 461 NA NA NA NA 0.50863 0.966 0.20107 0.715 0.00248 0.0638 0.00444 0.0959 0.58092 1 0.87718 1 0.31552 0.802 0.48654 0.957 0.17813 0.695 0.53803 0.992 RNF160 15 (3%) 466 NA NA NA NA 0.56673 1 0.16273 0.662 0.02066 0.302 0.12564 0.591 0.23129 0.745 0.41327 0.884 0.41398 0.884 0.26285 0.757 0.8581 1 0.28396 0.778 AIFM1 12 (2%) 469 NA NA NA NA 0.58805 1 0.76063 1 0.11734 0.582 0.064369 0.479 0.20396 0.715 0.49258 0.962 0.3512 0.836 0.050639 0.456 0.3222 0.811 0.67832 1 DOT1L 14 (3%) 467 NA NA NA NA 0.30753 0.789 0.23737 0.75 0.060999 0.473 0.2273 0.745 0.19325 0.71 0.0074399 0.149 0.78008 1 0.077769 0.518 0.40968 0.881 0.51978 0.976 MCM9 3 (1%) 478 NA NA NA NA 0.01986 0.299 NA NA NA NA NA NA 0.91845 1 0.7646 1 1 1 0.61277 1 NA NA NA NA NCKAP1L 19 (4%) 462 NA NA NA NA 0.85179 1 0.096229 0.559 0.76997 1 0.62074 1 0.51446 0.971 0.21267 0.727 0.097619 0.559 0.19083 0.708 0.94568 1 0.40331 0.881 ESYT3 8 (2%) 473 NA NA NA NA 0.37967 0.873 1 1 0.23035 0.745 0.25896 0.757 0.67113 1 0.53566 0.989 0.30602 0.788 0.30652 0.788 0.78838 1 0.40804 0.881 MIA2 13 (3%) 468 NA NA NA NA 0.34448 0.829 0.40675 0.881 0.94967 1 0.13907 0.621 0.053559 0.462 0.26565 0.757 0.585 1 0.81977 1 0.44448 0.912 0.51307 0.97 TUBB4 17 (4%) 464 NA NA NA NA 0.6535 1 0.84909 1 0.66553 1 0.45171 0.92 0.67447 1 0.80531 1 0.52894 0.986 0.5871 1 0.39541 0.881 0.20004 0.715 ABHD12B 7 (1%) 474 NA NA NA NA 0.83405 1 0.25036 0.757 0.62477 1 1 1 0.78471 1 0.83386 1 0.057159 0.473 0.29423 0.78 0.24714 0.757 0.48757 0.957 ANTXR1 19 (4%) 462 NA NA NA NA 0.33183 0.815 0.60903 1 0.94392 1 0.91999 1 0.24959 0.757 0.71988 1 0.55094 1 0.76485 1 0.6796 1 0.59121 1 FLCN 9 (2%) 472 NA NA NA NA 0.93381 1 0.48661 0.957 0.23231 0.745 0.85943 1 0.5935 1 0.79967 1 0.56271 1 0.54204 0.996 0.84918 1 1 1 ZNF556 12 (2%) 469 NA NA NA NA 0.25929 0.757 0.26837 0.757 0.73425 1 0.88129 1 0.066679 0.488 0.18538 0.7 0.26168 0.757 0.30633 0.788 0.15632 0.659 0.03338 0.388 ASCL3 7 (1%) 474 NA NA NA NA 0.58591 1 0.45082 0.92 0.33939 0.818 0.39625 0.881 0.66063 1 0.9065 1 0.54337 0.996 0.17755 0.695 0.78172 1 0.83194 1 DSG3 33 (7%) 448 NA NA NA NA 0.13205 0.6 0.30083 0.788 0.20083 0.715 0.85513 1 0.25571 0.757 0.70759 1 0.49523 0.962 0.72048 1 0.5785 1 0.6998 1 C5AR1 6 (1%) 475 NA NA NA NA 0.42265 0.895 0.33727 0.815 0.30377 0.788 0.85072 1 0.52291 0.979 0.58969 1 0.58534 1 0.1967 0.715 0.40976 0.881 0.15957 0.659 ASXL2 18 (4%) 463 NA NA NA NA 0.27322 0.762 0.69418 1 0.53073 0.986 0.075409 0.509 0.35677 0.839 0.7146 1 0.42625 0.897 0.51003 0.966 0.074949 0.509 0.52055 0.976 DLX5 13 (3%) 468 NA NA NA NA 0.31436 0.801 0.87323 1 0.089409 0.551 0.32026 0.81 0.50325 0.962 0.72065 1 0.00423 0.0932 0.33701 0.815 0.28592 0.779 0.17389 0.687 ATAD2 14 (3%) 467 NA NA NA NA 0.86974 1 0.053859 0.462 0.097189 0.559 0.49057 0.96 0.37128 0.862 0.27571 0.767 0.4418 0.91 0.04451 0.432 0.83978 1 0.28282 0.777 RAF1 6 (1%) 475 NA NA NA NA 0.42394 0.896 1 1 0.18051 0.695 0.072089 0.506 0.44245 0.91 0.55388 1 0.86677 1 0.12014 0.582 0.089429 0.551 0.04585 0.434 A2M 20 (4%) 461 NA NA NA NA 0.12096 0.583 0.40881 0.881 0.20347 0.715 0.3878 0.876 0.01534 0.255 0.053199 0.462 3e-04 0.0101 0.03583 0.392 0.63055 1 0.19149 0.708 SND1 16 (3%) 465 NA NA NA NA 0.20272 0.715 0.12187 0.585 0.85256 1 0.01977 0.299 0.059899 0.473 0.02297 0.314 0.03488 0.392 0.14724 0.642 0.10826 0.582 0.0077599 0.15 C7ORF36 6 (1%) 475 NA NA NA NA 0.62339 1 0.56843 1 0.44233 0.91 0.85232 1 0.65265 1 0.35353 0.836 1 1 0.2893 0.779 0.074739 0.509 1 1 HTRA1 10 (2%) 471 NA NA NA NA 0.86567 1 0.61337 1 0.50183 0.962 0.68676 1 0.91827 1 0.76133 1 0.84338 1 0.53127 0.986 0.70571 1 0.75976 1 ADAMTS2 39 (8%) 442 NA NA NA NA 0.10266 0.574 0.00125 0.0365 0.89764 1 0.18771 0.704 0.25429 0.757 0.81631 1 0.1122 0.582 0.01289 0.221 0.64816 1 0.96711 1 TAF1L 50 (10%) 431 1 1 0.79216 1 0.56666 1 0.18911 0.704 0.44215 0.91 0.50431 0.962 0.066839 0.488 0.28445 0.778 0.04287 0.432 0.39786 0.881 0.58007 1 0.26928 0.757 PLEKHB2 6 (1%) 475 NA NA NA NA 1 1 0.33656 0.815 0.69635 1 0.40848 0.881 0.14155 0.627 0.35595 0.839 0.66225 1 0.23501 0.749 0.41164 0.882 0.4903 0.96