Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL CN_CNMF METHLYATION_CNMF 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 38 (6%) 630 NA NA NA NA 2e-05 0.000442 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 2e-05 0.000442 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 PBRM1 146 (22%) 522 0.01496 0.0925 0.02198 0.122 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 PTEN 28 (4%) 640 0.31361 0.784 0.78728 1 0.064209 0.277 0.42518 0.932 0.0064799 0.0509 0.00279 0.0253 0.48841 0.999 0.03106 0.162 0.058439 0.259 0.0094199 0.0668 BAP1 49 (7%) 619 0.00032 0.00508 0.00042 0.00626 5e-05 0.000986 3e-05 0.000626 9.9999e-06 0.000243 9.9999e-06 0.000243 5.9999e-05 0.00112 8.9999e-05 0.0016 0.00281 0.0253 0.01014 0.0698 SETD2 58 (9%) 610 0.61729 1 0.66151 1 0.01622 0.0971 0.01166 0.0788 0.12265 0.424 5.9999e-05 0.00112 0.14449 0.465 0.00080999 0.00985 0.03861 0.187 0.063609 0.276 KDM5C 30 (4%) 638 NA NA NA NA 0.02581 0.138 0.01798 0.105 0.01665 0.0988 0.0053999 0.0448 0.00047 0.00686 0.13156 0.441 0.86528 1 0.74004 1 NEFH 15 (2%) 653 NA NA NA NA 0.070529 0.294 0.01361 0.0895 0.00211 0.0211 0.00433 0.0368 0.02344 0.128 5e-05 0.000986 0.35846 0.844 0.25302 0.698 VHL 174 (26%) 494 0.00031 0.00503 0.00072999 0.00969 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 NF2 16 (2%) 652 NA NA NA NA 0.072569 0.301 0.10935 0.389 0.00297 0.0262 0.00035 0.00532 0.070429 0.294 0.17251 0.524 0.00252 0.0236 0.01065 0.0727 HNRNPM 12 (2%) 656 NA NA NA NA 0.0257 0.138 0.00158 0.017 0.00078999 0.00985 0.00173 0.018 0.00122 0.0139 0.01275 0.0854 0.03082 0.162 0.02023 0.116 MET 19 (3%) 649 NA NA NA NA 0.0092299 0.0668 3e-05 0.000626 9.9999e-06 0.000243 9.9999e-06 0.000243 2e-05 0.000442 9.9999e-06 0.000243 0.00079999 0.00985 0.00015 0.00255 MUC5B 30 (4%) 638 NA NA NA NA 0.0060999 0.0489 9.9999e-05 0.00174 7.9999e-05 0.00146 9.9999e-06 0.000243 9.9999e-06 0.000243 9.9999e-06 0.000243 0.02314 0.127 0.00239 0.0227 KDM6A 11 (2%) 657 NA NA NA NA 0.15352 0.481 0.00481 0.0404 0.0093799 0.0668 0.03584 0.177 0.026 0.138 0.0014 0.0153 0.27997 0.732 0.12702 0.433 TDG 5 (1%) 663 NA NA NA NA 0.0327 0.166 0.03767 0.183 0.0351 0.174 0.10783 0.389 0.12076 0.42 0.053449 0.241 0.10134 0.374 0.28045 0.732 NFE2L2 10 (1%) 658 NA NA NA NA 0.52644 1 0.10817 0.389 0.04309 0.2 0.13624 0.448 0.49987 1 0.03373 0.169 0.29442 0.757 0.44064 0.946 ATM 16 (2%) 652 NA NA NA NA 0.7296 1 0.45836 0.959 0.38346 0.88 0.34346 0.827 0.7477 1 0.35368 0.843 0.75632 1 0.48807 0.999 ZNF814 13 (2%) 655 NA NA NA NA 0.0077899 0.0577 0.0068299 0.0525 0.00173 0.018 0.01432 0.09 0.0097699 0.0686 0.01589 0.0959 0.44967 0.951 0.30397 0.773 DNMT3A 10 (1%) 658 NA NA NA NA 1 1 0.34775 0.832 0.03133 0.162 0.097139 0.364 0.76168 1 0.38372 0.88 0.8281 1 0.43797 0.946 CDK12 9 (1%) 659 NA NA NA NA 1 1 0.88449 1 0.96399 1 0.99265 1 0.83293 1 0.53278 1 1 1 0.42511 0.932 CSGALNACT2 8 (1%) 660 NA NA NA NA 0.0039 0.0335 0.24766 0.687 0.0092399 0.0668 0.04761 0.217 0.04594 0.211 0.0429 0.2 0.087349 0.337 0.23493 0.66 PIK3CA 14 (2%) 654 NA NA NA NA 0.13378 0.445 0.63552 1 0.1198 0.42 0.29218 0.754 0.60983 1 0.062759 0.274 NA NA NA NA KIAA1751 8 (1%) 660 NA NA NA NA 0.90279 1 0.51727 1 0.62886 1 0.65188 1 0.215 0.618 0.71283 1 NA NA NA NA MTOR 32 (5%) 636 NA NA NA NA 0.00052999 0.0073 0.0078199 0.0577 0.1458 0.465 0.085119 0.332 0.00134 0.0148 0.00035 0.00532 0.44546 0.947 0.094449 0.357 RIMBP3 5 (1%) 663 NA NA NA NA 0.44607 0.947 0.17289 0.524 0.61992 1 0.01432 0.09 0.44645 0.947 0.47153 0.972 NA NA NA NA ZNF598 11 (2%) 657 NA NA NA NA 0.03189 0.163 0.00222 0.0215 0.00224 0.0215 0.00080999 0.00985 0.00127 0.0143 0.1971 0.578 0.087449 0.337 0.00107 0.0124 GPR50 5 (1%) 663 NA NA NA NA 1 1 0.61456 1 0.41904 0.932 0.55494 1 0.8546 1 0.42451 0.932 NA NA NA NA CCDC120 4 (1%) 664 NA NA NA NA 0.46089 0.959 NA NA 0.52751 1 0.61627 1 0.35522 0.843 1 1 NA NA NA NA SLC6A14 5 (1%) 663 NA NA NA NA 0.8548 1 0.10022 0.371 0.75655 1 0.55529 1 0.52456 1 0.42261 0.932 0.11042 0.391 0.15239 0.479 CYP4F11 5 (1%) 663 NA NA NA NA 0.45063 0.951 0.78474 1 0.37058 0.862 0.82129 1 0.24546 0.684 0.77035 1 NA NA NA NA STAG2 14 (2%) 654 NA NA NA NA 1 1 0.86075 1 0.53918 1 0.0062399 0.0495 0.19728 0.578 0.32616 0.802 0.1346 0.445 0.19075 0.568 SKI 9 (1%) 659 NA NA NA NA 0.00082999 0.00993 0.12821 0.434 3e-04 0.00498 0.00217 0.0214 0.00072999 0.00969 0.0408 0.195 0.02268 0.125 0.061449 0.27 ARID1A 19 (3%) 649 NA NA NA NA 0.95626 1 0.70201 1 0.082759 0.328 0.26129 0.712 0.79327 1 0.28008 0.732 0.01393 0.09 0.16055 0.495 EGFR 7 (1%) 661 NA NA NA NA 0.30629 0.773 0.33914 0.82 0.30852 0.774 0.52767 1 0.13946 0.456 0.65222 1 NA NA NA NA DPCR1 8 (1%) 660 NA NA NA NA 1 1 0.79886 1 0.8286 1 0.89236 1 1 1 1 1 NA NA NA NA GUSB 4 (1%) 664 NA NA NA NA 0.3899 0.887 NA NA 0.63663 1 0.36318 0.85 0.3558 0.843 1 1 NA NA NA NA MED16 4 (1%) 664 NA NA NA NA 0.4608 0.959 0.42186 0.932 0.90591 1 0.04172 0.198 0.82005 1 1 1 0.38475 0.88 0.20705 0.6 PTCH1 8 (1%) 660 NA NA NA NA 0.61077 1 0.71825 1 0.53341 1 0.33448 0.817 0.30514 0.773 0.85051 1 NA NA NA NA AHNAK2 33 (5%) 635 0.27829 0.732 0.02032 0.116 0.54386 1 0.03341 0.168 0.0058799 0.0477 0.00051999 0.0073 0.01702 0.1 0.0067999 0.0525 0.68348 1 0.27507 0.732 RLIM 9 (1%) 659 NA NA NA NA 0.70185 1 0.56581 1 0.58384 1 0.74304 1 0.081009 0.324 1 1 0.90769 1 0.88721 1 SLC23A1 7 (1%) 661 NA NA NA NA 0.80199 1 0.51571 1 0.14773 0.469 0.23301 0.659 0.89443 1 0.68035 1 NA NA NA NA STAM 6 (1%) 662 NA NA NA NA 1 1 0.01406 0.09 0.32953 0.807 0.10599 0.387 0.32024 0.793 0.50756 1 0.00298 0.0262 0.057539 0.256 RHEB 4 (1%) 664 NA NA NA NA 0.56364 1 1 1 1 1 0.17768 0.534 0.21439 0.618 1 1 0.43983 0.946 1 1 SLC4A8 6 (1%) 662 NA NA NA NA 0.15859 0.491 0.3628 0.85 0.15518 0.482 0.42815 0.933 1 1 0.19233 0.571 NA NA NA NA RUFY3 7 (1%) 661 NA NA NA NA 0.21719 0.622 0.42281 0.932 0.24451 0.684 0.12442 0.426 0.076649 0.314 0.02054 0.116 NA NA NA NA PCK1 6 (1%) 662 NA NA NA NA 0.88175 1 0.4273 0.933 0.84489 1 0.58495 1 0.58408 1 1 1 NA NA NA NA TXNIP 8 (1%) 660 NA NA NA NA 0.18109 0.542 0.31925 0.793 0.39107 0.887 0.60957 1 0.30543 0.773 0.40864 0.924 0.58295 1 0.75468 1 RNF128 5 (1%) 663 NA NA NA NA 0.54522 1 0.17546 0.529 0.70463 1 0.67718 1 0.38361 0.88 1 1 NA NA NA NA ZFYVE26 9 (1%) 659 NA NA NA NA 0.91964 1 0.48295 0.993 0.78051 1 0.36628 0.854 0.90955 1 0.6386 1 0.59647 1 0.25947 0.71 FAM160B2 4 (1%) 664 NA NA NA NA 0.84402 1 1 1 0.90492 1 0.85199 1 0.44506 0.947 0.72743 1 NA NA NA NA FAM47A 6 (1%) 662 NA NA NA NA 0.88243 1 1 1 0.89202 1 0.68313 1 0.49653 1 0.80208 1 NA NA NA NA ATP1A1 10 (1%) 658 0.25336 0.698 0.63359 1 0.13983 0.456 1 1 0.12396 0.426 0.78669 1 0.16824 0.514 0.50332 1 NA NA NA NA SH3BP2 4 (1%) 664 NA NA NA NA 0.068029 0.289 0.27521 0.732 0.10922 0.389 0.092229 0.351 0.27415 0.732 0.19331 0.571 NA NA NA NA FAM200A 5 (1%) 663 NA NA NA NA 0.4525 0.952 NA NA 0.057409 0.256 0.0070299 0.0529 0.19931 0.582 0.76911 1 NA NA NA NA RTL1 7 (1%) 661 NA NA NA NA 0.50202 1 0.88456 1 0.078049 0.317 0.3381 0.82 0.49316 0.999 0.081229 0.324 1 1 0.23451 0.66 NASP 4 (1%) 664 NA NA NA NA 0.32027 0.793 0.068039 0.289 0.04073 0.195 0.13426 0.445 0.27341 0.732 0.1028 0.377 0.087709 0.337 0.14539 0.465 RPL7A 3 (0%) 665 NA NA NA NA 1 1 0.098719 0.368 0.085119 0.332 0.075559 0.312 0.23289 0.659 0.10701 0.389 NA NA NA NA UIMC1 5 (1%) 663 NA NA NA NA 0.54782 1 0.33597 0.818 0.93074 1 0.46255 0.959 0.095649 0.36 0.77107 1 NA NA NA NA TCEB1 3 (0%) 665 NA NA NA NA 0.068599 0.289 NA NA 0.868 1 0.63033 1 0.16366 0.502 1 1 NA NA NA NA SFMBT1 3 (0%) 665 NA NA NA NA 0.49019 0.999 NA NA 0.76597 1 0.74532 1 0.80079 1 0.62215 1 NA NA NA NA SLC16A1 3 (0%) 665 NA NA NA NA 1 1 1 1 1 1 1 1 0.80121 1 0.62612 1 NA NA NA NA PAM 4 (1%) 664 NA NA NA NA 0.01941 0.112 0.0058499 0.0477 0.0027 0.0249 0.01539 0.0944 0.01353 0.0895 0.00074999 0.00978 NA NA NA NA TMCO3 7 (1%) 661 NA NA NA NA 0.078189 0.317 0.2726 0.732 0.86688 1 0.080629 0.324 0.38787 0.885 1 1 NA NA NA NA CCDC82 6 (1%) 662 NA NA NA NA 0.02173 0.122 0.30339 0.773 0.089699 0.343 0.01409 0.09 0.27825 0.732 0.50914 1 NA NA NA NA NFAT5 8 (1%) 660 NA NA NA NA 0.68477 1 0.6318 1 0.54772 1 0.67857 1 0.72783 1 1 1 NA NA NA NA HNF1B 3 (0%) 665 NA NA NA NA 0.49357 0.999 0.78595 1 0.43953 0.946 0.49407 0.999 0.8021 1 0.35855 0.844 NA NA NA NA OR2L8 7 (1%) 661 NA NA NA NA 0.70837 1 0.58948 1 0.60211 1 0.084029 0.332 0.43834 0.946 0.67717 1 0.04256 0.2 0.14366 0.464 IDUA 5 (1%) 663 NA NA NA NA 0.54549 1 0.12833 0.434 0.0069299 0.0527 0.01582 0.0959 0.03739 0.183 0.053129 0.241 0.32222 0.795 0.14209 0.461 ZC3H18 6 (1%) 662 NA NA NA NA 0.88155 1 0.42527 0.932 0.80078 1 1 1 0.86917 1 0.37727 0.874 NA NA NA NA GAPDHS 5 (1%) 663 NA NA NA NA 0.64166 1 0.2597 0.71 0.15507 0.482 0.01443 0.09 0.12029 0.42 0.42383 0.932 NA NA NA NA GPR137 4 (1%) 664 NA NA NA NA 0.20442 0.595 0.59822 1 0.28792 0.745 0.34623 0.831 0.11257 0.397 0.30714 0.773 NA NA NA NA GFM1 3 (0%) 665 NA NA NA NA 0.27652 0.732 0.0099699 0.0693 0.00315 0.0274 0.00178 0.0183 0.04564 0.211 0.00098999 0.0117 NA NA NA NA FAT1 22 (3%) 646 NA NA NA NA 0.1507 0.476 0.03144 0.162 0.00049 0.00701 0.00184 0.0187 0.0254 0.137 0.13145 0.441 0.22796 0.65 0.068029 0.289 RRP12 9 (1%) 659 NA NA NA NA 0.84033 1 0.41899 0.932 0.46746 0.967 0.45469 0.954 0.28729 0.745 0.28074 0.732 0.93036 1 0.56 1