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 38 (5%) 746 NA NA NA NA 5e-04 0.0102 9.9999e-06 0.00029 0.81875 1 0.03988 0.284 9.9999e-06 0.00029 9.9999e-06 0.00029 2e-05 0.00056 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 PTEN 28 (4%) 756 NA NA NA NA 0.18769 0.729 0.090259 0.477 0.77227 1 0.66505 1 0.02011 0.184 0.01352 0.144 0.6194 1 0.01209 0.134 0.063209 0.371 0.04472 0.305 SETD2 61 (8%) 723 0.54744 1 0.56616 1 0.00383 0.0564 9.9999e-06 0.00029 0.42454 0.973 0.47251 0.987 0.077729 0.427 9.9999e-06 0.00029 0.10663 0.527 0.0058699 0.0759 0.02789 0.225 0.057719 0.348 PBRM1 143 (18%) 641 0.00168 0.0282 0.0013 0.0223 9.9999e-06 0.00029 9.9999e-06 0.00029 0.02528 0.212 0.00487 0.066 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 NEFH 12 (2%) 772 NA NA NA NA 0.38898 0.953 0.6936 1 0.067339 0.383 0.84362 1 0.52236 1 0.38463 0.945 0.93242 1 0.29932 0.851 0.42907 0.973 0.27488 0.837 VHL 196 (25%) 588 0.00056999 0.0114 0.00095999 0.0175 9.9999e-06 0.00029 9.9999e-06 0.00029 0.0105 0.121 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 9.9999e-06 0.00029 NF2 16 (2%) 768 NA NA NA NA 0.26674 0.837 0.64523 1 0.44024 0.973 0.14079 0.616 0.02292 0.205 0.00239 0.0372 0.21929 0.77 0.094059 0.479 0.058709 0.35 0.40813 0.961 MET 25 (3%) 759 NA NA NA NA 7.9999e-05 0.0021 0.00028 0.00603 0.10227 0.514 0.40956 0.961 9.9999e-06 0.00029 9.9999e-06 0.00029 0.00011 0.0028 9.9999e-06 0.00029 0.00214 0.0346 0.01114 0.125 KDM5C 27 (3%) 757 NA NA NA NA 0.00282 0.0431 0.0079899 0.0959 0.4314 0.973 0.30288 0.851 0.00019 0.00431 0.00019 0.00431 9.9999e-06 0.00029 0.0054899 0.0721 0.31342 0.859 0.50111 0.997 MTOR 34 (4%) 750 NA NA NA NA 0.00014 0.00336 0.00013 0.00321 0.01433 0.149 0.03226 0.249 0.01764 0.166 0.0148 0.15 0.00034 0.00714 5e-05 0.00135 0.13179 0.598 0.00091999 0.0172 ZNF814 14 (2%) 770 NA NA NA NA 0.53704 1 0.067549 0.383 0.80824 1 0.72732 1 0.02472 0.212 0.11486 0.548 0.04631 0.314 0.092099 0.479 0.51706 1 0.58425 1 AR 15 (2%) 769 NA NA NA NA 0.00112 0.02 0.068409 0.386 0.83171 1 0.51264 1 0.00022 0.00486 0.01483 0.15 0.0087599 0.102 0.0075599 0.092 0.064359 0.373 0.1783 0.706 STAG2 15 (2%) 769 NA NA NA NA 0.89255 1 0.03427 0.255 0.51085 1 0.16372 0.665 0.57506 1 0.03037 0.241 0.52438 1 0.42733 0.973 0.2118 0.761 0.44853 0.973 KRAS 6 (1%) 778 NA NA NA NA 0.22639 0.779 0.1917 0.729 0.56884 1 0.45251 0.976 0.04981 0.325 0.30146 0.851 0.12717 0.584 0.4708 0.987 0.11023 0.536 0.00127 0.0222 SLC6A14 4 (1%) 780 NA NA NA NA 0.83973 1 NA NA 0.80589 1 0.071799 0.397 0.23692 0.796 0.36631 0.927 0.03186 0.248 0.37261 0.932 0.02056 0.186 0.37767 0.936 SMARCA4 20 (3%) 764 NA NA NA NA 0.433 0.973 0.54431 1 0.86325 1 0.53604 1 0.24482 0.813 0.57779 1 0.22948 0.782 0.25395 0.826 0.61829 1 0.44374 0.973 NFE2L2 12 (2%) 772 NA NA NA NA 0.13526 0.602 0.093549 0.479 0.66824 1 0.050369 0.325 0.28633 0.843 0.25543 0.826 0.60857 1 0.37038 0.932 0.67562 1 0.75127 1 ARID1A 18 (2%) 766 NA NA NA NA 0.82477 1 0.28707 0.843 0.47459 0.987 0.49754 0.996 0.31027 0.859 0.85039 1 0.58599 1 0.63666 1 0.45719 0.976 0.80337 1 BCLAF1 10 (1%) 774 NA NA NA NA 0.22197 0.77 0.49513 0.996 0.72517 1 0.96983 1 0.1652 0.665 0.81544 1 0.063739 0.372 0.2935 0.851 0.39579 0.954 0.82038 1 ATM 20 (3%) 764 NA NA NA NA 0.51587 1 0.48231 0.988 0.8285 1 0.98425 1 0.41201 0.964 0.054299 0.343 0.37266 0.932 0.21294 0.761 0.83353 1 0.55269 1 CACNA1C 15 (2%) 769 NA NA NA NA 0.46897 0.987 0.055229 0.346 0.86976 1 0.20578 0.748 0.53063 1 0.056359 0.348 0.35147 0.903 0.12052 0.572 0.23967 0.799 0.70267 1 PARD6B 8 (1%) 776 NA NA NA NA 1 1 0.33916 0.883 0.01075 0.122 0.0073699 0.0914 0.093709 0.479 0.02518 0.212 0.21575 0.762 0.04028 0.284 0.48942 0.994 0.1643 0.665 CUL3 16 (2%) 768 NA NA NA NA 1 1 0.01283 0.138 0.87693 1 0.091639 0.479 0.088639 0.471 0.00371 0.0556 0.57946 1 0.19062 0.729 0.32106 0.859 0.73276 1 PIK3CA 15 (2%) 769 NA NA NA NA 0.27518 0.837 0.02349 0.206 0.92784 1 0.78546 1 0.7583 1 0.50808 1 0.63103 1 0.29711 0.851 0.55409 1 0.71414 1 SMARCB1 9 (1%) 775 NA NA NA NA 0.081739 0.443 0.81837 1 0.8636 1 0.73793 1 0.25682 0.826 0.03121 0.245 0.46212 0.98 0.53668 1 0.19985 0.741 0.19815 0.741 PCF11 13 (2%) 771 NA NA NA NA 0.00454 0.0625 0.49576 0.996 0.58864 1 0.00058999 0.0115 0.0061399 0.0781 0.03699 0.271 0.00452 0.0625 0.19947 0.741 0.03298 0.25 0.27457 0.837 WASL 8 (1%) 776 NA NA NA NA 1 1 0.91734 1 0.44075 0.973 0.85086 1 1 1 0.87957 1 0.89025 1 0.90369 1 0.94023 1 0.3946 0.954 DNMT3A 11 (1%) 773 NA NA NA NA 0.45554 0.976 0.66302 1 0.16385 0.665 0.25312 0.826 0.31674 0.859 0.27214 0.837 0.91843 1 0.43088 0.973 0.51735 1 0.2856 0.843 KIAA0922 7 (1%) 777 NA NA NA NA 0.084119 0.45 0.31748 0.859 0.65762 1 0.97407 1 0.13349 0.6 0.41829 0.971 0.057929 0.348 0.32055 0.859 0.4804 0.987 0.4094 0.961 GPR50 5 (1%) 779 NA NA NA NA 0.7403 1 0.694 1 0.03841 0.276 0.34951 0.902 0.43745 0.973 0.74841 1 0.36568 0.927 0.76521 1 NA NA NA NA ACSF2 11 (1%) 773 NA NA NA NA 0.79276 1 0.87046 1 0.19595 0.741 0.15016 0.637 0.78671 1 0.35006 0.902 0.79581 1 0.74231 1 0.46537 0.985 0.39943 0.956 WDR52 9 (1%) 775 NA NA NA NA 1 1 0.3621 0.926 0.96018 1 0.60542 1 0.87765 1 0.91642 1 0.51292 1 0.39757 0.954 0.44614 0.973 0.89435 1 ALMS1 14 (2%) 770 NA NA NA NA 0.37742 0.936 0.94374 1 0.77653 1 0.43288 0.973 0.91239 1 0.81571 1 0.2532 0.826 0.04234 0.292 0.36264 0.926 0.82044 1 TXNIP 8 (1%) 776 NA NA NA NA 0.27798 0.843 0.14949 0.637 0.04965 0.325 0.2 0.741 0.0473 0.318 0.01986 0.183 0.42813 0.973 0.15254 0.644 0.10911 0.536 0.18059 0.712 NUDT11 5 (1%) 779 NA NA NA NA 0.45476 0.976 0.28515 0.843 0.6663 1 0.9041 1 0.70337 1 0.26434 0.837 0.53769 1 0.84234 1 NA NA NA NA PCK1 9 (1%) 775 NA NA NA NA 0.75229 1 0.58917 1 0.6556 1 0.66735 1 0.48037 0.987 0.56546 1 0.75678 1 0.1238 0.575 0.28439 0.843 0.45594 0.976 RAI1 11 (1%) 773 NA NA NA NA 0.060989 0.361 0.70086 1 0.26998 0.837 0.6992 1 0.72162 1 0.31781 0.859 0.4243 0.973 0.52889 1 0.28221 0.843 0.67032 1 PAM 4 (1%) 780 NA NA NA NA 0.23966 0.799 0.14509 0.631 0.1005 0.509 0.093699 0.479 0.052439 0.334 0.52948 1 0.081209 0.443 0.01891 0.176 NA NA NA NA KDM6A 13 (2%) 771 NA NA NA NA 0.00499 0.0665 0.01641 0.158 0.58432 1 0.37106 0.932 0.02415 0.209 0.029 0.232 0.0073999 0.0914 0.01243 0.136 0.31167 0.859 0.20109 0.741 GLS 9 (1%) 775 NA NA NA NA 0.3803 0.94 0.25428 0.826 0.19163 0.729 0.071429 0.397 1 1 0.76266 1 0.34006 0.883 0.92878 1 0.49669 0.996 0.47143 0.987 EPS15L1 10 (1%) 774 NA NA NA NA 0.78647 1 0.55551 1 0.16535 0.665 0.89469 1 0.8668 1 0.46088 0.98 0.050239 0.325 0.77515 1 0.3928 0.954 0.6869 1 NOM1 6 (1%) 778 NA NA NA NA 0.33235 0.88 0.80077 1 0.44964 0.973 0.89095 1 0.94339 1 0.66966 1 0.76027 1 0.93701 1 0.90513 1 0.64441 1 CDK12 8 (1%) 776 NA NA NA NA 0.47875 0.987 0.65563 1 0.53301 1 0.13893 0.611 0.82791 1 0.72644 1 0.73095 1 0.11049 0.536 0.64515 1 0.54578 1 ARHGAP35 7 (1%) 777 NA NA NA NA 0.6228 1 0.02324 0.205 0.7595 1 0.79532 1 0.7036 1 0.48071 0.987 0.0268 0.22 0.22881 0.782 NA NA NA NA RIMBP3 5 (1%) 779 NA NA NA NA 1 1 0.52228 1 0.6069 1 0.78552 1 0.22168 0.77 0.03712 0.271 0.43434 0.973 0.29523 0.851 NA NA NA NA FAT1 20 (3%) 764 NA NA NA NA 0.12707 0.584 0.56839 1 0.95169 1 0.47136 0.987 0.02703 0.22 0.050929 0.327 0.11114 0.537 0.3145 0.859 0.51944 1 0.31876 0.859 FAM178A 8 (1%) 776 NA NA NA NA 0.083669 0.45 1 1 0.57044 1 0.73284 1 0.39769 0.954 0.82253 1 0.81416 1 1 1 NA NA NA NA TCEB1 4 (1%) 780 NA NA NA NA 0.26868 0.837 NA NA 0.14726 0.637 0.30716 0.857 0.26553 0.837 0.00237 0.0372 0.01523 0.152 0.18801 0.729 0.1483 0.637 0.00202 0.0333 PODXL 6 (1%) 778 NA NA NA NA 0.22493 0.778 0.31544 0.859 0.21385 0.761 0.8626 1 1 1 0.237 0.796 1 1 0.68036 1 0.26479 0.837 0.36373 0.926 DNAJA3 3 (0%) 781 NA NA NA NA 1 1 NA NA NA NA NA NA 0.51231 1 0.26996 0.837 0.43761 0.973 0.84277 1 0.86531 1 0.16069 0.665 NASP 5 (1%) 779 NA NA NA NA 0.64607 1 0.30234 0.851 0.15511 0.651 0.62108 1 0.1065 0.527 0.41515 0.969 0.29104 0.849 0.12115 0.572 0.03391 0.254 0.17556 0.702 SLC23A1 6 (1%) 778 NA NA NA NA 0.87733 1 0.61382 1 0.29807 0.851 0.4173 0.971 0.26934 0.837 0.40961 0.961 0.8694 1 0.057099 0.348 NA NA NA NA RILPL1 5 (1%) 779 NA NA NA NA 0.84624 1 0.40953 0.961 0.49024 0.994 0.2485 0.822 0.2796 0.843 0.30566 0.856 0.84778 1 0.2063 0.748 NA NA NA NA NIPBL 15 (2%) 769 NA NA NA NA 0.13345 0.6 0.52054 1 0.6389 1 0.48855 0.994 0.51012 1 0.50473 1 0.16391 0.665 0.44727 0.973 0.81625 1 0.9708 1 FAM47A 6 (1%) 778 NA NA NA NA 0.3331 0.88 0.55609 1 0.30955 0.859 0.94904 1 1 1 0.071829 0.397 0.32103 0.859 0.68046 1 NA NA NA NA RHEB 3 (0%) 781 NA NA NA NA 0.33447 0.881 NA NA 0.23683 0.796 0.20651 0.748 1 1 0.51954 1 0.10645 0.527 0.72731 1 0.14871 0.637 0.52684 1 BRAF 5 (1%) 779 NA NA NA NA 1 1 0.44409 0.973 1 1 0.75319 1 0.18969 0.729 0.47795 0.987 0.84704 1 0.25776 0.826 0.40324 0.96 0.88301 1 MLL3 42 (5%) 742 0.78012 1 0.65831 1 0.16112 0.665 0.42816 0.973 0.29057 0.849 0.91278 1 0.01405 0.148 0.22096 0.77 0.03774 0.273 0.0161 0.157 0.44218 0.973 0.336 0.882 ANK3 22 (3%) 762 0.30178 0.851 0.84247 1 0.284 0.843 0.61749 1 0.76375 1 0.49102 0.994 0.38417 0.945 0.62947 1 0.81705 1 0.87965 1 0.76061 1 0.29654 0.851 EMG1 4 (1%) 780 0.00444 0.0625 0.00428 0.062 0.27305 0.837 NA NA NA NA NA NA 0.0085599 0.101 0.03259 0.249 1 1 0.00089999 0.0172 NA NA NA NA LHX1 4 (1%) 780 NA NA NA NA 1 1 0.37706 0.936 0.9011 1 0.60146 1 0.5689 1 0.61721 1 0.83225 1 0.12266 0.572 NA NA NA NA SCARB2 4 (1%) 780 NA NA NA NA 0.21588 0.762 0.12196 0.572 0.01544 0.153 0.8277 1 0.26522 0.837 0.62619 1 0.04879 0.325 0.47668 0.987 NA NA NA NA C1ORF25 6 (1%) 778 NA NA NA NA 0.5897 1 0.48665 0.994 0.43037 0.973 0.94177 1 0.76217 1 0.13845 0.611 0.87039 1 0.59515 1 0.44854 0.973 0.32663 0.868 KDELR3 7 (1%) 777 NA NA NA NA 0.23 0.782 0.2123 0.761 0.18213 0.715 0.45791 0.976 0.11214 0.538 0.29557 0.851 0.25758 0.826 0.39668 0.954 0.20101 0.741 0.80597 1 TTLL6 4 (1%) 780 NA NA NA NA 0.16461 0.665 0.13555 0.602 0.61143 1 0.39141 0.954 0.04204 0.292 0.33761 0.883 0.83172 1 0.057399 0.348 NA NA NA NA STXBP3 5 (1%) 779 NA NA NA NA 0.64142 1 0.54296 1 NA NA NA NA 0.49908 0.996 0.66674 1 0.849 1 0.49924 0.996 NA NA NA NA FAM20C 5 (1%) 779 NA NA NA NA 0.02647 0.22 0.20349 0.746 0.87921 1 0.78603 1 0.065149 0.375 0.34051 0.883 0.04074 0.285 0.01684 0.161 0.40331 0.96 0.32324 0.862 CCBL2 3 (0%) 781 NA NA NA NA 0.4388 0.973 0.84691 1 NA NA NA NA 0.86065 1 0.79531 1 1 1 0.2822 0.843 NA NA NA NA B3GNT6 3 (0%) 781 NA NA NA NA 0.17691 0.704 0.91693 1 0.71388 1 1 1 0.85959 1 0.66279 1 1 1 1 1 NA NA NA NA HNF1B 4 (1%) 780 NA NA NA NA 0.6855 1 0.74017 1 0.057679 0.348 0.18971 0.729 0.57083 1 0.13055 0.596 0.83446 1 0.59526 1 0.86617 1 0.42452 0.973