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 0.02528 0.297 0.14935 0.61 9.9999e-06 0.000568 0.00053999 0.0188 0.00015 0.00648 9.9999e-06 0.000568 9.9999e-06 0.000568 9.9999e-06 0.000568 9.9999e-06 0.000568 9.9999e-06 0.000568 0.88519 1 9.9999e-06 0.000568 KRAS 150 (31%) 331 0.89862 1 1 1 0.00184 0.0523 0.00227 0.0597 0.30989 0.822 0.11866 0.552 0.01027 0.17 9.9999e-06 0.000568 0.00155 0.0452 5.9999e-05 0.00282 0.44001 0.949 0.15648 0.62 KEAP1 84 (17%) 397 NA NA NA NA 2e-05 0.00103 9.9999e-06 0.000568 0.00080999 0.026 0.36976 0.901 9.9999e-06 0.000568 9.9999e-06 0.000568 0.12142 0.558 0.00018 0.00748 0.054689 0.427 0.00081999 0.026 EGFR 67 (14%) 414 NA NA NA NA 0.00039 0.0145 0.43368 0.947 0.00189 0.0523 0.02124 0.276 2e-05 0.00103 9.9999e-06 0.000568 0.0050499 0.105 0.03123 0.331 0.071419 0.467 0.00282 0.0708 STK11 77 (16%) 404 NA NA NA NA 9.9999e-06 0.000568 0.00057999 0.0196 9.9999e-06 0.000568 0.095739 0.513 9.9999e-06 0.000568 9.9999e-06 0.000568 0.44516 0.952 0.01037 0.17 0.20763 0.703 0.11683 0.552 RBM10 33 (7%) 448 NA NA NA NA 0.63954 1 0.056969 0.429 0.28432 0.802 0.45031 0.959 0.92319 1 0.77372 1 0.89274 1 0.053499 0.427 0.42868 0.943 0.65049 1 RB1 26 (5%) 455 NA NA NA NA 0.43688 0.947 0.082939 0.482 0.18285 0.676 0.43239 0.947 0.072989 0.474 6.9999e-05 0.00315 0.15074 0.611 0.02763 0.304 0.057709 0.429 0.96018 1 ARID1A 30 (6%) 451 NA NA NA NA 0.72037 1 0.7799 1 0.46694 0.97 0.70004 1 0.44026 0.949 0.87729 1 0.24228 0.75 0.077949 0.476 0.053059 0.427 0.11245 0.547 NF1 55 (11%) 426 0.63894 1 0.79157 1 0.53752 1 0.93066 1 0.061599 0.434 0.48073 0.98 0.062919 0.434 0.26059 0.778 0.109 0.54 0.35152 0.884 0.10718 0.54 0.088379 0.493 SMARCA4 38 (8%) 443 NA NA NA NA 0.49164 0.989 9.9999e-06 0.000568 0.50875 1 0.10845 0.54 9.9999e-06 0.000568 9.9999e-06 0.000568 0.0053899 0.106 0.00036 0.0139 0.04939 0.427 5e-05 0.00245 BRAF 39 (8%) 442 0.14717 0.604 1 1 0.62967 1 0.078259 0.476 0.57357 1 0.89342 1 0.27251 0.787 0.38491 0.91 0.59052 1 0.03295 0.342 0.91861 1 0.51431 1 MGA 40 (8%) 441 NA NA NA NA 0.26619 0.781 0.055749 0.427 0.72269 1 0.10313 0.532 0.00232 0.0597 0.15327 0.618 0.03108 0.331 0.065829 0.447 0.32769 0.855 0.080609 0.481 FTSJD1 24 (5%) 457 NA NA NA NA 0.26767 0.783 0.34107 0.873 0.92977 1 0.38403 0.91 0.22325 0.728 0.28919 0.807 0.62638 1 0.66788 1 0.089489 0.495 0.19916 0.697 MET 21 (4%) 460 NA NA NA NA 0.084879 0.483 0.73035 1 0.45724 0.962 0.26629 0.781 0.52149 1 0.62636 1 0.084939 0.483 0.20995 0.704 0.46961 0.97 0.16909 0.652 GAGE2A 8 (2%) 473 NA NA NA NA 0.43631 0.947 0.59761 1 0.72064 1 0.4818 0.98 0.36057 0.891 0.5742 1 0.068889 0.456 0.73754 1 0.52522 1 0.31732 0.836 SETD2 30 (6%) 451 NA NA NA NA 0.20842 0.703 0.37707 0.901 0.61059 1 0.68142 1 0.10151 0.529 0.22826 0.73 0.55451 1 0.9698 1 0.013 0.195 0.053989 0.427 U2AF1 11 (2%) 470 NA NA NA NA 0.7171 1 0.84081 1 0.058019 0.429 0.68643 1 0.04818 0.427 0.12596 0.571 0.0086599 0.153 0.64754 1 0.098639 0.522 0.52908 1 ERBB2 11 (2%) 470 NA NA NA NA 0.6833 1 0.096009 0.513 0.17183 0.655 1 1 0.51521 1 0.13871 0.59 0.73385 1 0.24076 0.749 0.50141 1 0.22223 0.728 CDKN2A 16 (3%) 465 NA NA NA NA 0.76893 1 0.93648 1 0.82126 1 0.68859 1 0.060259 0.431 0.20706 0.703 1 1 0.85801 1 0.53084 1 0.91695 1 SRPX 14 (3%) 467 NA NA NA NA 0.88566 1 0.79822 1 0.63789 1 0.03885 0.375 0.58625 1 0.91114 1 0.45633 0.962 0.5886 1 0.77482 1 0.30369 0.816 ATM 42 (9%) 439 NA NA NA NA 0.00019 0.0076 0.00099999 0.0309 0.33247 0.859 0.93268 1 0.00206 0.0556 0.00047 0.0169 0.89021 1 0.053289 0.427 0.50928 1 0.91497 1 TCEAL5 13 (3%) 468 NA NA NA NA 0.56384 1 0.66282 1 0.33079 0.859 0.92614 1 0.93557 1 0.86628 1 0.93333 1 0.62531 1 0.74635 1 0.57551 1 PPP3CA 12 (2%) 469 NA NA NA NA 0.92618 1 0.30022 0.816 0.6398 1 0.80557 1 0.46985 0.97 0.01536 0.218 0.14184 0.596 0.24201 0.75 0.45806 0.962 0.2526 0.768 FCRLA 15 (3%) 466 NA NA NA NA 0.17375 0.656 0.79946 1 0.84534 1 0.33236 0.859 0.8477 1 0.37459 0.901 1 1 0.84434 1 0.64254 1 0.19898 0.697 ARID2 24 (5%) 457 NA NA NA NA 0.79171 1 0.6411 1 0.82648 1 1 1 0.13838 0.59 0.091809 0.498 0.079069 0.477 0.2861 0.803 0.12637 0.571 0.38464 0.91 APC 20 (4%) 461 NA NA NA NA 0.88217 1 0.64246 1 0.88911 1 0.88421 1 0.086099 0.485 0.22159 0.728 0.063029 0.434 0.051599 0.427 0.82995 1 0.27646 0.79 ZEB1 32 (7%) 449 0.63899 1 1 1 0.65679 1 0.68935 1 0.76812 1 0.87703 1 0.46153 0.968 0.47634 0.976 0.50558 1 0.04397 0.413 0.96448 1 0.66404 1 SIP1 4 (1%) 477 0.11428 0.552 0.1195 0.552 0.066239 0.447 NA NA 0.47073 0.97 1 1 1 1 0.97817 1 0.40751 0.921 0.14366 0.599 NA NA NA NA SLC4A3 18 (4%) 463 NA NA NA NA 1 1 0.37392 0.901 0.17613 0.66 0.058339 0.429 0.12955 0.576 0.45369 0.959 0.14647 0.604 0.75179 1 0.34429 0.873 0.00348 0.0783 STK19 5 (1%) 476 NA NA NA NA 0.66963 1 1 1 0.82294 1 0.58829 1 0.39037 0.913 0.97609 1 0.84824 1 0.65289 1 0.055469 0.427 0.828 1 NUDT11 5 (1%) 476 NA NA NA NA 0.79967 1 1 1 0.62339 1 0.83231 1 0.82999 1 0.30672 0.816 0.066999 0.447 0.22971 0.73 1 1 0.14592 0.604 SLAMF9 12 (2%) 469 NA NA NA NA 0.0089899 0.154 0.04039 0.386 0.93373 1 1 1 0.19952 0.697 0.60096 1 0.082369 0.482 0.01223 0.189 0.60555 1 0.62496 1 DNMT3A 19 (4%) 462 NA NA NA NA 0.60314 1 0.48643 0.984 0.57637 1 0.2947 0.808 0.587 1 0.56283 1 0.33768 0.866 0.11051 0.545 0.0091299 0.154 0.0083099 0.152 CTNNB1 19 (4%) 462 NA NA NA NA 0.43484 0.947 0.27798 0.79 0.03471 0.35 0.252 0.768 0.26982 0.784 0.40773 0.921 0.02688 0.302 0.79055 1 0.26358 0.781 0.76904 1 PTPRU 18 (4%) 463 NA NA NA NA 0.01376 0.204 0.10793 0.54 0.10338 0.532 0.02607 0.302 0.01117 0.177 0.061039 0.434 0.00296 0.0727 0.0073899 0.14 1 1 0.18903 0.691 PIK3CA 28 (6%) 453 NA NA NA NA 0.3678 0.899 0.30551 0.816 0.14965 0.61 0.13489 0.583 0.050399 0.427 0.02492 0.296 0.87445 1 0.56178 1 0.15942 0.622 0.16364 0.636 ZNF608 9 (2%) 472 NA NA NA NA 0.18349 0.676 0.64067 1 0.23253 0.73 1 1 0.19944 0.697 0.0088899 0.154 0.50412 1 0.53315 1 0.56403 1 0.37374 0.901 STIM1 9 (2%) 472 NA NA NA NA 0.01536 0.218 1 1 0.87554 1 0.86182 1 0.69889 1 0.26476 0.781 0.11865 0.552 0.19081 0.691 0.43532 0.947 0.88189 1 EMG1 5 (1%) 476 1 1 0.55757 1 0.6097 1 0.4007 0.92 0.75033 1 0.29457 0.808 0.074739 0.474 0.26167 0.779 0.21219 0.705 0.37285 0.901 NA NA NA NA PHKA1 12 (2%) 469 NA NA NA NA 0.00124 0.0372 0.34498 0.873 0.69266 1 0.78127 1 0.13466 0.583 0.3553 0.886 0.39832 0.92 0.27905 0.791 0.41847 0.93 0.050529 0.427 PAK1 9 (2%) 472 NA NA NA NA 0.35314 0.884 0.641 1 0.29212 0.808 0.88425 1 0.30038 0.816 0.2548 0.771 0.91231 1 0.84039 1 1 1 1 1 NRAS 3 (1%) 478 NA NA NA NA 0.076529 0.476 NA NA NA NA NA NA 0.1154 0.552 0.8951 1 0.30466 0.816 0.34982 0.883 NA NA NA NA G3BP1 8 (2%) 473 NA NA NA NA 0.17578 0.66 0.69418 1 0.93069 1 0.33417 0.861 0.49884 0.999 0.83302 1 0.89812 1 0.81974 1 0.68714 1 0.65307 1 TRERF1 18 (4%) 463 NA NA NA NA 0.15666 0.62 0.059819 0.431 0.29217 0.808 0.65425 1 0.01115 0.177 0.30692 0.816 0.069229 0.456 0.29827 0.816 0.55395 1 0.19549 0.697 CACNA1F 27 (6%) 454 NA NA NA NA 1 1 0.9365 1 0.20179 0.7 0.81904 1 0.56145 1 0.10013 0.525 0.0078399 0.146 0.99155 1 0.58866 1 0.67689 1 NFE2L2 13 (3%) 468 NA NA NA NA 0.60627 1 0.58074 1 0.27096 0.785 0.25016 0.768 0.074579 0.474 0.03832 0.375 1 1 0.19619 0.697 0.65732 1 0.75821 1 RPL5 8 (2%) 473 NA NA NA NA 1 1 0.74267 1 0.90235 1 0.12937 0.576 0.73828 1 0.71892 1 0.42043 0.93 0.36749 0.899 0.46888 0.97 1 1 STRA8 8 (2%) 473 NA NA NA NA 0.0047 0.0995 0.076609 0.476 0.0085099 0.153 0.02289 0.284 0.10499 0.535 0.03383 0.348 0.01281 0.195 0.11808 0.552 0.52768 1 0.23973 0.748 NLRP6 10 (2%) 471 NA NA NA NA 0.1315 0.579 0.44338 0.952 0.02635 0.302 0.16513 0.639 0.73371 1 0.01871 0.253 0.13685 0.586 0.077839 0.476 0.56143 1 0.090709 0.495 FAM65C 14 (3%) 467 NA NA NA NA 0.56676 1 0.83246 1 0.057299 0.429 0.054209 0.427 0.94493 1 0.68805 1 0.10736 0.54 0.48038 0.98 0.7957 1 0.13191 0.579 WDR66 14 (3%) 467 NA NA NA NA 0.054689 0.427 0.0454 0.416 0.00342 0.0783 0.10398 0.532 0.55134 1 0.49114 0.989 0.15466 0.619 0.51081 1 0.12824 0.575 0.15878 0.622 RIT1 8 (2%) 473 NA NA NA NA 0.03154 0.331 0.87706 1 0.36348 0.892 1 1 0.90723 1 0.17254 0.655 0.26903 0.784 1 1 0.49963 0.999 0.26993 0.784 TGFBR3 14 (3%) 467 NA NA NA NA 0.60094 1 0.66477 1 0.79895 1 0.13942 0.59 0.3876 0.91 0.22793 0.73 0.0448 0.414 0.20349 0.7 0.19766 0.697 0.02236 0.284 CXCR7 10 (2%) 471 NA NA NA NA 0.75064 1 0.78899 1 0.6551 1 0.19039 0.691 0.66946 1 0.65726 1 0.33719 0.866 0.65732 1 1 1 0.58956 1 GAN 10 (2%) 471 NA NA NA NA 0.47858 0.979 0.90841 1 0.88849 1 0.83782 1 0.73176 1 0.40464 0.92 0.53748 1 0.79183 1 1 1 0.76728 1 TMEM49 5 (1%) 476 NA NA NA NA 0.51656 1 0.2362 0.739 0.93405 1 0.090659 0.495 0.28104 0.795 0.21964 0.728 0.42629 0.94 0.46724 0.97 0.6174 1 0.40879 0.922 HSPA8 9 (2%) 472 NA NA NA NA 0.15556 0.62 0.20643 0.703 0.42587 0.94 1 1 0.69915 1 0.22284 0.728 0.0053499 0.106 0.15722 0.62 0.29391 0.808 0.88583 1 CD244 12 (2%) 469 NA NA NA NA 0.2604 0.778 0.66088 1 0.63024 1 0.77151 1 0.37807 0.901 0.26054 0.778 0.074709 0.474 0.01416 0.207 1 1 0.59408 1 KIF18B 4 (1%) 477 0.28927 0.807 0.39082 0.913 0.04607 0.418 NA NA 0.36107 0.891 0.12576 0.571 0.4723 0.972 0.75345 1 1 1 0.45352 0.959 NA NA NA NA PDE6A 16 (3%) 465 NA NA NA NA 0.32563 0.852 0.40504 0.92 1 1 0.11945 0.552 0.02464 0.296 0.02676 0.302 0.01848 0.253 0.02975 0.325 0.69514 1 0.574 1 CHRND 16 (3%) 465 NA NA NA NA 0.15942 0.622 0.5346 1 0.13256 0.58 0.092989 0.502 0.4055 0.92 0.20444 0.701 0.3982 0.92 0.11798 0.552 0.60584 1 0.57245 1 KLK1 8 (2%) 473 NA NA NA NA 0.03749 0.371 0.079449 0.477 0.56776 1 0.03853 0.375 0.55411 1 0.64823 1 0.19552 0.697 0.22497 0.73 0.20607 0.703 0.23037 0.73 KLHL5 14 (3%) 467 NA NA NA NA 0.41796 0.93 0.93665 1 0.7584 1 0.086229 0.485 0.43326 0.947 0.7969 1 0.93903 1 0.65217 1 0.67441 1 0.76803 1 DSC2 20 (4%) 461 NA NA NA NA 0.57815 1 0.075529 0.474 0.00317 0.0761 0.00444 0.0959 0.62672 1 0.8782 1 0.19134 0.691 0.34361 0.873 0.062439 0.434 0.1729 0.655 RNF160 15 (3%) 466 NA NA NA NA 0.15486 0.619 0.10197 0.529 0.02172 0.279 0.12763 0.574 0.02104 0.276 0.41362 0.925 0.37587 0.901 0.20902 0.703 1 1 0.40402 0.92 AIFM1 12 (2%) 469 NA NA NA NA 0.65569 1 0.32905 0.856 0.11926 0.552 0.065259 0.446 0.7623 1 0.49253 0.989 0.31716 0.836 0.085019 0.483 0.066729 0.447 0.85654 1 DOT1L 14 (3%) 467 NA NA NA NA 0.65476 1 0.56302 1 0.062179 0.434 0.22808 0.73 0.78668 1 0.0070599 0.136 0.77357 1 0.082479 0.482 0.58528 1 0.29095 0.808 MCM9 3 (1%) 478 NA NA NA NA 1 1 NA NA NA NA NA NA 0.63861 1 0.76515 1 1 1 0.48435 0.983 NA NA NA NA NCKAP1L 19 (4%) 462 NA NA NA NA 0.30321 0.816 0.24878 0.765 0.77014 1 0.62505 1 0.04414 0.413 0.21181 0.705 0.03595 0.359 0.059179 0.431 0.46268 0.968 0.7717 1 ESYT3 8 (2%) 473 NA NA NA NA 0.84307 1 0.35233 0.884 0.23157 0.73 0.2608 0.778 0.40302 0.92 0.53722 1 0.46577 0.97 0.32502 0.852 0.25104 0.768 0.39746 0.92 MIA2 13 (3%) 468 NA NA NA NA 0.01191 0.186 0.31532 0.835 0.95068 1 0.14136 0.596 0.30417 0.816 0.26575 0.781 0.87466 1 0.67912 1 1 1 0.76872 1 TUBB4 17 (4%) 464 NA NA NA NA 0.57056 1 0.71844 1 0.66432 1 0.45176 0.959 0.74671 1 0.8065 1 0.80821 1 0.45108 0.959 0.5991 1 0.1167 0.552 ABHD12B 7 (1%) 474 NA NA NA NA 0.22179 0.728 0.22871 0.73 0.62477 1 1 1 1 1 0.83554 1 0.082109 0.482 0.76291 1 0.76588 1 0.40097 0.92 ANTXR1 19 (4%) 462 NA NA NA NA 0.77168 1 0.64086 1 0.94286 1 0.92032 1 0.69876 1 0.71862 1 0.48548 0.984 0.73398 1 0.72136 1 0.44516 0.952 FLCN 9 (2%) 472 NA NA NA NA 0.36244 0.892 0.36118 0.891 0.23238 0.73 0.86085 1 0.83773 1 0.80233 1 0.60919 1 0.47638 0.976 0.30694 0.816 0.89327 1 ZNF556 12 (2%) 469 NA NA NA NA 0.27786 0.79 0.59751 1 0.73142 1 0.88276 1 0.16993 0.653 0.18433 0.677 0.23248 0.73 0.58135 1 0.92354 1 0.051949 0.427 ASCL3 7 (1%) 474 NA NA NA NA 0.3924 0.913 0.38282 0.91 0.34288 0.873 0.39158 0.913 0.27682 0.79 0.90731 1 0.04959 0.427 0.124 0.567 0.85209 1 0.50198 1 DSG3 33 (7%) 448 NA NA NA NA 0.084489 0.483 0.38681 0.91 0.19747 0.697 0.85699 1 0.17275 0.655 0.70804 1 0.41978 0.93 0.40129 0.92 0.76504 1 0.41354 0.925 C5AR1 6 (1%) 475 NA NA NA NA 0.64707 1 0.29241 0.808 0.30439 0.816 0.85029 1 0.22866 0.73 0.59044 1 0.11524 0.552 0.20109 0.7 1 1 0.11193 0.547 ASXL2 18 (4%) 463 NA NA NA NA 0.54935 1 0.51064 1 0.53296 1 0.074029 0.474 0.41007 0.923 0.71644 1 0.37663 0.901 0.41987 0.93 0.14547 0.604 0.78152 1 DLX5 13 (3%) 468 NA NA NA NA 0.75362 1 1 1 0.090149 0.495 0.32213 0.846 0.35906 0.891 0.71773 1 0.00412 0.0908 0.13495 0.583 0.15104 0.611 0.25959 0.778 ATAD2 14 (3%) 467 NA NA NA NA 0.02475 0.296 0.02711 0.302 0.096929 0.516 0.49027 0.989 0.055199 0.427 0.27729 0.79 0.37412 0.901 0.01617 0.224 0.76094 1 0.40366 0.92 RAF1 6 (1%) 475 NA NA NA NA 1 1 1 1 0.18104 0.674 0.074999 0.474 0.77692 1 0.55203 1 1 1 0.21133 0.705 0.04436 0.413 0.02461 0.296 A2M 20 (4%) 461 NA NA NA NA 0.099079 0.522 0.62404 1 0.20362 0.7 0.38718 0.91 0.050409 0.427 0.051079 0.427 0.0052499 0.106 0.13545 0.583 0.20231 0.7 0.13172 0.579 SND1 16 (3%) 465 NA NA NA NA 0.052119 0.427 0.059419 0.431 0.85244 1 0.0197 0.263 0.056399 0.429 0.02289 0.284 0.03426 0.349 0.088569 0.493 0.27381 0.789 0.01594 0.224 C7ORF36 6 (1%) 475 NA NA NA NA 0.4514 0.959 0.55607 1 0.44346 0.952 0.85153 1 0.22903 0.73 0.35376 0.884 1 1 0.25348 0.769 1 1 1 1 HTRA1 10 (2%) 471 NA NA NA NA 0.24768 0.764 0.18032 0.674 0.5053 1 0.68363 1 1 1 0.76342 1 0.84135 1 0.078499 0.476 1 1 0.75963 1 ADAMTS2 39 (8%) 442 NA NA NA NA 0.19733 0.697 0.00339 0.0783 0.89834 1 0.1893 0.691 0.46828 0.97 0.81896 1 0.081799 0.482 0.050189 0.427 0.10888 0.54 0.79278 1 TAF1L 50 (10%) 431 0.63826 1 0.79358 1 0.3431 0.873 0.37219 0.901 0.44025 0.949 0.5067 1 0.04736 0.426 0.28563 0.803 0.03079 0.331 0.92385 1 0.76787 1 0.62652 1 PLEKHB2 6 (1%) 475 NA NA NA NA 0.18225 0.676 0.87709 1 0.69889 1 0.41105 0.923 0.77631 1 0.35659 0.887 0.58143 1 0.11227 0.547 0.58513 1 0.1432 0.599