Clinical Features CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_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 Chi-square test_P Chi-square 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 35 (15%) 193 0.14268 1 0.027085 1 0.31446 1 0.13834 1 0.22544 1 0.45799 1 0.3756 1 0.12067 1 BRAF 117 (51%) 111 2.222e-07 0.000201 0.058578 1 0.031116 1 0.0098264 1 0.031391 1 8.8803e-05 0.0804 0.23133 1 0.15416 1 C15ORF23 14 (6%) 214 0.12845 1 0.2629 1 0.86034 1 0.82559 1 0.78415 1 1 1 0.7757 1 0.77911 1 CDKN2A 33 (14%) 195 0.11048 1 0.25999 1 0.37395 1 0.78937 1 0.89011 1 0.47865 1 0.73995 1 0.7308 1 NRAS 67 (29%) 161 0.0005311 0.48 0.083969 1 0.092324 1 0.32888 1 0.96562 1 0.85837 1 0.85029 1 0.82882 1 OXA1L 7 (3%) 221 0.43712 1 0.43413 1 0.61495 1 0.47172 1 0.50301 1 0.27586 1 0.61758 1 0.62738 1 STK19 11 (5%) 217 0.7369 1 0.14733 1 0.22397 1 0.99881 1 0.86136 1 0.36214 1 0.5773 1 0.6046 1 PTEN 18 (8%) 210 0.6428 1 0.21372 1 0.14937 1 0.13056 1 0.90814 1 0.062529 1 0.81862 1 0.32341 1 RAC1 17 (7%) 211 0.63124 1 0.77159 1 0.94006 1 0.46967 1 0.51222 1 0.84872 1 0.58235 1 0.32079 1 IDH1 12 (5%) 216 0.31122 1 0.33604 1 0.089075 1 0.2525 1 0.31708 1 0.79481 1 0.15989 1 0.11542 1 ACSM2B 38 (17%) 190 0.65763 1 0.44964 1 0.79211 1 0.43767 1 0.37073 1 0.58303 1 0.29564 1 0.70427 1 PPP6C 18 (8%) 210 0.55793 1 0.25358 1 0.099245 1 0.79008 1 0.55766 1 0.65317 1 0.34522 1 0.11301 1 LCE1B 12 (5%) 216 0.14641 1 0.60549 1 0.3173 1 0.85812 1 0.57116 1 0.79481 1 0.92949 1 0.91004 1 MUC7 19 (8%) 209 0.95484 1 0.48733 1 0.13051 1 0.71322 1 0.50324 1 0.037731 1 0.087017 1 0.049653 1 OR51S1 27 (12%) 201 0.31584 1 0.83975 1 0.88427 1 0.10846 1 0.38292 1 0.68998 1 0.63031 1 0.87135 1 NAP1L2 23 (10%) 205 0.70028 1 1 1 0.80156 1 0.82878 1 0.59838 1 1 1 0.92227 1 1 1 PRB2 31 (14%) 197 0.50856 1 0.53532 1 0.73346 1 0.76656 1 0.016145 1 0.038057 1 0.19551 1 0.19334 1 TAF1A 13 (6%) 215 0.67642 1 0.87741 1 0.54602 1 0.083809 1 0.82345 1 0.38811 1 0.4099 1 0.91364 1 HIST1H2AA 10 (4%) 218 0.36277 1 0.7115 1 0.65164 1 0.70851 1 0.39859 1 0.91706 1 0.31469 1 0.22852 1 FRG2B 16 (7%) 212 0.89814 1 0.71657 1 0.97542 1 0.99498 1 0.2503 1 0.83704 1 0.6026 1 0.18722 1 CDH9 33 (14%) 195 0.83929 1 0.13683 1 0.21565 1 0.56212 1 0.81651 1 0.58079 1 0.003658 1 0.41869 1 PRAMEF11 21 (9%) 207 0.77312 1 0.063101 1 0.93732 1 0.95167 1 0.21669 1 0.49664 1 0.80438 1 0.63058 1 HBG2 8 (4%) 220 0.60129 1 0.42077 1 0.25787 1 0.34399 1 0.35439 1 0.89387 1 0.11435 1 0.20636 1 DDX3X 18 (8%) 210 0.61444 1 0.95143 1 0.23055 1 0.17631 1 0.67589 1 0.9489 1 0.86179 1 0.20807 1 PRB4 19 (8%) 209 0.41029 1 0.56417 1 0.12903 1 0.17412 1 0.029854 1 0.14945 1 0.36097 1 0.26002 1 GRXCR1 18 (8%) 210 0.86682 1 0.072901 1 0.39102 1 0.95545 1 0.039199 1 1 1 0.63576 1 0.20807 1 HHLA2 17 (7%) 211 0.051862 1 0.77159 1 0.45585 1 0.0044067 1 0.89812 1 0.079456 1 0.014979 1 0.49272 1 RBM11 13 (6%) 215 0.24241 1 0.03939 1 0.77063 1 0.88126 1 0.77054 1 0.051919 1 0.21335 1 0.45354 1 FUT9 22 (10%) 206 0.41775 1 0.025842 1 0.50487 1 0.86053 1 0.44155 1 0.25411 1 0.2751 1 0.67775 1 TTN 176 (77%) 52 0.4098 1 0.013727 1 0.49483 1 0.11376 1 0.19811 1 0.21998 1 0.11917 1 0.3143 1 HBD 10 (4%) 218 0.29953 1 0.77863 1 0.83228 1 0.25229 1 0.035177 1 0.16637 1 0.55085 1 0.89081 1 KIAA1257 14 (6%) 214 0.41959 1 0.94078 1 0.58218 1 0.74693 1 0.78415 1 0.76529 1 0.56778 1 0.51481 1 USP17L2 19 (8%) 209 0.22897 1 0.1545 1 0.16726 1 0.25012 1 0.23992 1 0.35961 1 0.27936 1 0.46226 1 CADM2 23 (10%) 205 0.72881 1 0.11171 1 0.16917 1 0.37056 1 0.67533 1 0.71053 1 0.27555 1 0.0059113 1 GFRAL 31 (14%) 197 0.16388 1 0.21195 1 0.69878 1 0.74051 1 0.85892 1 0.87374 1 0.51456 1 0.95974 1 OR4N2 22 (10%) 206 0.2987 1 0.17405 1 0.61417 1 0.37033 1 0.022162 1 0.22989 1 0.60006 1 0.18452 1 UGT2B15 21 (9%) 207 0.43871 1 0.37969 1 0.81502 1 0.73987 1 0.43859 1 0.8728 1 0.15091 1 0.34473 1 UNC119B 6 (3%) 222 0.44999 1 0.44971 1 0.21258 1 0.91979 1 0.59009 1 0.55071 1 1 1 0.46189 1 RAPGEF5 12 (5%) 216 1 1 0.60549 1 0.62719 1 0.50272 1 0.49083 1 0.6855 1 0.23841 1 0.062404 1 C8A 27 (12%) 201 0.61526 1 0.080069 1 0.25593 1 0.36372 1 0.11238 1 0.68998 1 0.34043 1 0.16307 1 ANKRD20A4 5 (2%) 223 0.27021 1 0.45027 1 0.31977 1 0.14289 1 0.23011 1 0.60444 1 0.61552 1 1 1 ELF5 6 (3%) 222 1 1 1 1 0.93438 1 0.5189 1 0.59009 1 1 1 0.2044 1 0.15658 1 SPAG16 16 (7%) 212 0.8474 1 0.84911 1 0.14438 1 0.30564 1 0.10975 1 0.12319 1 0.072475 1 0.10588 1 PHGDH 9 (4%) 219 0.47988 1 0.91249 1 1 1 0.43302 1 0.76257 1 0.74674 1 0.7657 1 0.3496 1 COPG2 9 (4%) 219 0.32099 1 0.91249 1 0.27075 1 0.25968 1 0.69183 1 0.61403 1 0.90742 1 0.77943 1 GML 9 (4%) 219 0.17449 1 0.37826 1 0.94065 1 0.42935 1 0.8343 1 0.90228 1 0.18112 1 0.77943 1 TBC1D3B 5 (2%) 223 0.22507 1 0.84789 1 0.059099 1 0.24109 1 0.86106 1 1 1 0.85305 1 0.64053 1 TFEC 15 (7%) 213 1 1 0.5924 1 0.056842 1 0.074215 1 0.29459 1 1 1 0.58763 1 0.72791 1 TRAT1 13 (6%) 215 1 1 0.29009 1 0.73139 1 0.69735 1 0.31708 1 0.92573 1 0.31241 1 0.58723 1 PRR23B 15 (7%) 213 0.39209 1 0.037131 1 0.0068491 1 0.12465 1 0.53063 1 0.16168 1 0.090015 1 0.0010898 0.984 C9ORF119 8 (4%) 220 0.48257 1 0.59807 1 0.47592 1 0.5596 1 0.66474 1 0.38725 1 0.24689 1 0.30408 1 LIN7A 11 (5%) 217 0.85842 1 0.17947 1 0.55169 1 0.64417 1 0.16077 1 0.60541 1 0.12689 1 0.81023 1 PARM1 18 (8%) 210 0.86682 1 1 1 0.75013 1 0.14174 1 0.95197 1 0.85057 1 0.16103 1 0.39024 1 CCK 6 (3%) 222 0.58164 1 0.65826 1 0.31977 1 0.077061 1 0.44687 1 0.87588 1 0.57635 1 0.71353 1 FIGLA 3 (1%) 225 0.62875 1 0.62272 1 NA NA NA NA 0.51401 1 0.42936 1 0.47226 1 0.68966 1 TCEB3C 26 (11%) 202 0.50626 1 0.30897 1 0.3631 1 0.55651 1 0.30832 1 0.042814 1 0.66648 1 0.25162 1 DEFB118 9 (4%) 219 0.39093 1 0.21607 1 0.93438 1 0.2836 1 0.8343 1 0.61403 1 0.69684 1 0.77943 1 VEGFC 17 (7%) 211 0.59818 1 0.12003 1 0.3342 1 0.027575 1 0.19735 1 0.29935 1 0.018162 1 0.14769 1 MARCH11 11 (5%) 217 1 1 0.85792 1 0.37425 1 0.70851 1 0.16077 1 0.14203 1 1 1 1 1 ZFP106 10 (4%) 218 0.84896 1 0.77863 1 0.23403 1 0.25731 1 0.50932 1 0.91706 1 0.55085 1 0.44694 1 PDE1A 32 (14%) 196 0.33711 1 0.91279 1 0.4751 1 0.40562 1 0.036085 1 0.22813 1 0.52296 1 0.29864 1 NUDT4 5 (2%) 223 1 1 0.3724 1 0.35693 1 0.15084 1 1 1 0.83746 1 0.53002 1 0.49838 1 FGF16 7 (3%) 221 1 1 0.79715 1 0.004686 1 0.01568 1 1 1 0.14833 1 0.093997 1 0.52376 1 OR4F6 15 (7%) 213 0.94276 1 0.43331 1 0.4326 1 0.44972 1 0.040032 1 0.16168 1 0.13026 1 0.39196 1 CD2 17 (7%) 211 0.41074 1 0.40952 1 0.75598 1 0.53952 1 0.95019 1 0.75788 1 0.76946 1 0.70329 1 EIF3D 4 (2%) 224 0.82902 1 0.83579 1 0.2405 1 0.4188 1 1 1 0.36076 1 0.56615 1 0.4292 1 MKX 15 (7%) 213 0.11989 1 0.20999 1 0.55123 1 0.97739 1 0.079515 1 0.29513 1 0.31401 1 0.49209 1 ARL16 7 (3%) 221 0.18037 1 0.34484 1 0.13778 1 0.63649 1 0.39107 1 1 1 1 1 1 1 OR2L3 15 (7%) 213 0.53126 1 0.010843 1 0.74391 1 0.48818 1 0.89211 1 0.35699 1 0.88857 1 0.42354 1 DEFB119 6 (3%) 222 1 1 0.77012 1 0.49204 1 0.88029 1 0.87685 1 0.87588 1 0.43819 1 1 1 KLHL4 21 (9%) 207 0.80747 1 0.54369 1 0.78791 1 0.85856 1 0.20761 1 0.22958 1 0.84091 1 0.34473 1 NR1H4 12 (5%) 216 0.42667 1 0.24615 1 0.34134 1 0.37525 1 0.93415 1 0.58018 1 1 1 0.37123 1 IL32 9 (4%) 219 0.39093 1 0.12612 1 0.68761 1 0.14582 1 0.52776 1 1 1 0.62869 1 1 1 DGAT2L6 11 (5%) 217 0.33856 1 0.53553 1 0.88467 1 0.11987 1 0.24283 1 0.60541 1 0.78915 1 0.81023 1 OR8D4 11 (5%) 217 0.58476 1 0.42064 1 0.07232 1 0.015148 1 0.20685 1 0.070748 1 0.5773 1 0.66689 1 GRXCR2 15 (7%) 213 0.39209 1 0.945 1 0.13384 1 0.65316 1 0.47026 1 0.46784 1 0.88857 1 0.79057 1 OR5H2 15 (7%) 213 0.70685 1 0.89034 1 0.43167 1 0.50958 1 0.89211 1 0.77451 1 0.48751 1 0.49209 1 SIGLEC14 12 (5%) 216 0.31122 1 0.24615 1 0.034959 1 0.44476 1 0.65965 1 0.79481 1 0.86763 1 0.91004 1 ZNF479 24 (11%) 204 0.65654 1 1 1 0.73933 1 0.11482 1 0.53252 1 0.42355 1 0.074008 1 0.63274 1 C2 12 (5%) 216 0.032855 1 0.28849 1 0.054874 1 0.39523 1 0.0989 1 0.58018 1 0.45023 1 0.41483 1 GH2 10 (4%) 218 0.098703 1 0.60114 1 0.85233 1 0.87971 1 0.66046 1 0.58505 1 0.46058 1 0.57342 1 GK2 29 (13%) 199 0.77072 1 0.5332 1 0.35659 1 0.2091 1 0.70073 1 0.6348 1 0.15024 1 0.80714 1 C2ORF40 7 (3%) 221 0.2361 1 0.89827 1 0.94065 1 0.72573 1 0.8924 1 0.78577 1 0.38065 1 0.62738 1 CXCR2 13 (6%) 215 0.59373 1 0.33581 1 0.86613 1 0.9544 1 0.55473 1 0.55803 1 0.81881 1 0.91364 1 RPTN 39 (17%) 189 0.31502 1 0.24347 1 0.32928 1 0.39568 1 0.029629 1 0.32884 1 0.56268 1 0.45223 1 PRIM2 13 (6%) 215 0.36632 1 0.062478 1 0.11595 1 0.45637 1 0.17366 1 0.017701 1 0.50332 1 0.41169 1 MUM1L1 26 (11%) 202 0.62907 1 0.77696 1 0.79861 1 0.098813 1 0.58661 1 0.15519 1 0.49845 1 0.58748 1 TLL1 44 (19%) 184 0.93261 1 0.018726 1 0.67045 1 0.050845 1 0.11731 1 0.10323 1 0.88696 1 0.4557 1 PRC1 13 (6%) 215 0.93779 1 0.44806 1 0.059666 1 0.7173 1 0.32043 1 0.52173 1 0.31241 1 0.54073 1 GLRB 23 (10%) 205 0.28593 1 0.4637 1 0.059756 1 0.034615 1 0.4023 1 0.26648 1 0.40774 1 0.49956 1 AREG 6 (3%) 222 0.76895 1 0.58051 1 0.38473 1 0.28688 1 0.77327 1 0.21638 1 0.76568 1 0.46189 1 SPINK13 8 (4%) 220 0.13967 1 0.46857 1 0.89288 1 0.46861 1 0.43986 1 0.44651 1 0.21961 1 0.4846 1 ACD 9 (4%) 219 0.28895 1 0.69055 1 0.47 1 0.54089 1 0.39436 1 0.13765 1 0.086231 1 0.058432 1 C2ORF39 9 (4%) 219 0.39093 1 0.21607 1 0.86613 1 0.26974 1 0.032245 1 0.017989 1 0.50336 1 0.88929 1 RERG 9 (4%) 219 0.47988 1 0.57914 1 0.29154 1 0.22821 1 0.52776 1 0.43708 1 0.18112 1 0.68787 1 TUBB8 13 (6%) 215 0.63485 1 0.82297 1 0.21176 1 0.13689 1 0.42519 1 0.37082 1 0.47147 1 0.37296 1 AGXT2 18 (8%) 210 0.7447 1 1 1 0.095928 1 0.54124 1 0.74598 1 0.80839 1 0.73803 1 0.34466 1 C9 16 (7%) 212 0.94902 1 0.515 1 0.87396 1 0.58259 1 0.72272 1 0.65962 1 0.89642 1 0.68794 1 CX3CL1 4 (2%) 224 0.13954 1 0.13435 1 NA NA NA NA 1 1 0.54803 1 0.12235 1 0.4292 1 DEFB112 8 (4%) 220 0.17749 1 0.42077 1 0.39258 1 0.61598 1 0.35439 1 0.44651 1 0.90514 1 0.42084 1 FAM19A1 8 (4%) 220 0.15791 1 0.37939 1 0.45621 1 0.11744 1 0.48839 1 1 1 1 1 0.87566 1 LONRF2 16 (7%) 212 1 1 0.34133 1 0.94426 1 0.98728 1 0.94751 1 0.83704 1 0.4299 1 0.68794 1 NAP1L4 9 (4%) 219 0.025919 1 0.043846 1 0.034959 1 0.60504 1 0.63584 1 0.060586 1 0.62869 1 1 1 OR5J2 14 (6%) 214 0.57394 1 0.77864 1 0.31875 1 0.49191 1 1 1 1 1 0.055671 1 0.37024 1 POM121 14 (6%) 214 0.47384 1 0.36343 1 0.29935 1 0.2653 1 0.69418 1 0.35694 1 0.88266 1 0.55314 1 RBM22 7 (3%) 221 0.43712 1 0.12768 1 NA NA NA NA 0.34183 1 0.45923 1 1 1 0.52376 1 SLC10A2 20 (9%) 208 0.42579 1 0.15348 1 0.74751 1 0.32811 1 0.16043 1 0.61529 1 0.47811 1 0.14493 1 C4ORF22 11 (5%) 217 0.63385 1 0.92651 1 0.62125 1 0.27399 1 0.86136 1 0.85006 1 0.13772 1 0.26672 1 CLEC14A 19 (8%) 209 0.027035 1 0.34738 1 0.13675 1 0.47823 1 0.26372 1 0.60353 1 0.36097 1 1 1 GNAI2 4 (2%) 224 1 1 0.36957 1 0.69591 1 0.7965 1 0.83402 1 0.80927 1 0.21855 1 0.14388 1 IGF2BP3 6 (3%) 222 0.88062 1 0.88267 1 0.86573 1 0.65943 1 0.51788 1 1 1 0.17364 1 0.71353 1 RBM46 15 (7%) 213 0.7521 1 0.17209 1 0.087177 1 0.15499 1 0.94444 1 0.68663 1 0.45761 1 0.17724 1 SERPINB4 30 (13%) 198 0.75245 1 0.90837 1 0.39478 1 0.15632 1 0.2184 1 0.37956 1 0.63496 1 0.31492 1 SORT1 10 (4%) 218 0.9204 1 0.77863 1 1 1 0.49761 1 0.25294 1 0.16637 1 1 1 0.50993 1