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 34 (15%) 191 0.16762 1 0.026897 1 0.35597 1 0.15873 1 0.09957 1 0.24559 1 0.39214 1 0.15338 1 BRAF 115 (51%) 110 9.5946e-08 9.84e-05 0.05716 1 0.017402 1 0.0073078 1 0.0049551 1 4.6664e-05 0.0478 0.083098 1 0.17324 1 C15ORF23 14 (6%) 211 0.10437 1 0.21493 1 0.83814 1 0.81515 1 0.93974 1 0.058114 1 0.82482 1 0.91992 1 CDKN2A 31 (14%) 194 0.15341 1 0.27522 1 0.4169 1 0.77049 1 0.78295 1 0.15053 1 0.82283 1 1 1 NRAS 65 (29%) 160 0.00052961 0.542 0.038322 1 0.089874 1 0.32086 1 0.86672 1 0.47767 1 0.73878 1 0.86299 1 OXA1L 6 (3%) 219 0.28761 1 0.58248 1 0.61661 1 0.47481 1 0.68128 1 0.1824 1 0.11907 1 0.35483 1 STK19 10 (4%) 215 0.92075 1 0.13301 1 0.23766 1 0.99927 1 0.78084 1 0.69494 1 0.83908 1 0.78875 1 PTEN 18 (8%) 207 0.67418 1 0.24327 1 0.14881 1 0.1352 1 1 1 0.12464 1 0.76978 1 0.33327 1 RAC1 16 (7%) 209 0.76275 1 0.9456 1 0.94048 1 0.4504 1 0.46713 1 1 1 0.44121 1 0.11197 1 ACSM2B 36 (16%) 189 0.45378 1 0.43622 1 0.81548 1 0.4015 1 0.37516 1 0.37743 1 0.065931 1 0.66053 1 CADM2 22 (10%) 203 0.66046 1 0.17467 1 0.15346 1 0.35266 1 1 1 0.24617 1 0.43446 1 0.022726 1 OR51S1 26 (12%) 199 0.36561 1 0.64876 1 0.89774 1 0.11298 1 0.54513 1 0.49798 1 0.68734 1 0.90734 1 LCE1B 13 (6%) 212 0.15827 1 0.62646 1 0.22113 1 0.89236 1 0.51723 1 0.56424 1 1 1 0.9153 1 IDH1 11 (5%) 214 0.36724 1 0.17994 1 0.10374 1 0.28059 1 0.5407 1 0.84973 1 0.096421 1 0.13292 1 TAF1A 14 (6%) 211 0.44865 1 0.69178 1 0.44606 1 0.054988 1 0.54642 1 0.19599 1 0.40066 1 0.91992 1 NAP1L2 21 (9%) 204 0.60081 1 0.73965 1 0.78954 1 0.80931 1 0.84384 1 0.54771 1 0.38584 1 1 1 MUC7 19 (8%) 206 1 1 0.46799 1 0.14324 1 0.70607 1 0.50493 1 0.26109 1 0.17049 1 0.075753 1 PPP6C 17 (8%) 208 0.50806 1 0.37064 1 0.095201 1 0.77953 1 0.51549 1 0.36399 1 0.099551 1 0.10796 1 FRG2B 17 (8%) 208 1 1 0.77279 1 0.97516 1 0.99688 1 0.60215 1 0.60385 1 0.84755 1 0.44533 1 USP29 35 (16%) 190 0.91974 1 0.9455 1 0.88257 1 0.7195 1 0.97173 1 1 1 0.70238 1 0.60755 1 PRB4 18 (8%) 207 0.38497 1 0.64303 1 0.13661 1 0.19099 1 0.015215 1 0.18358 1 0.66182 1 0.23804 1 HIST1H2AA 10 (4%) 215 0.3627 1 0.71234 1 0.65519 1 0.72061 1 0.2534 1 0.83739 1 0.15404 1 0.3308 1 RPTN 38 (17%) 187 0.33216 1 0.16719 1 0.37959 1 0.36663 1 0.0271 1 0.38207 1 0.36817 1 0.46941 1 ZNF479 22 (10%) 203 0.72115 1 1 1 0.74139 1 0.11208 1 0.65227 1 0.79378 1 0.055886 1 0.53807 1 C8A 26 (12%) 199 0.70142 1 0.083537 1 0.30192 1 0.39362 1 0.10009 1 0.7636 1 0.057958 1 0.17114 1 FUT9 22 (10%) 203 0.28817 1 0.038679 1 0.48684 1 0.84998 1 0.47706 1 0.096177 1 0.25368 1 0.71073 1 ZNF679 18 (8%) 207 0.5583 1 0.78041 1 0.63207 1 0.67328 1 0.1967 1 0.52655 1 0.34857 1 0.53628 1 NRK 28 (12%) 197 0.90428 1 0.90374 1 0.63199 1 0.30302 1 0.26204 1 1 1 0.54707 1 0.83533 1 CDH9 32 (14%) 193 0.88784 1 0.14053 1 0.25142 1 0.57663 1 0.78928 1 0.63376 1 0.00063419 0.649 0.30143 1 PRAMEF11 21 (9%) 204 0.80797 1 0.058473 1 0.93714 1 0.95985 1 0.14481 1 0.60048 1 0.58194 1 0.79081 1 DDX3X 18 (8%) 207 0.58555 1 0.95308 1 0.22927 1 0.17407 1 0.37545 1 0.52655 1 0.90251 1 0.27429 1 GRXCR1 18 (8%) 207 0.90877 1 0.067023 1 0.41596 1 0.94992 1 0.044334 1 0.94863 1 0.33033 1 0.27429 1 PRB2 29 (13%) 196 0.55476 1 0.57207 1 0.77334 1 0.74067 1 0.010563 1 0.22411 1 0.22302 1 0.21302 1 ELF5 7 (3%) 218 0.71075 1 1 1 0.93308 1 0.52135 1 0.39837 1 0.603 1 0.15359 1 0.19723 1 IL32 9 (4%) 216 0.39171 1 0.11426 1 0.68976 1 0.14866 1 0.76151 1 0.90467 1 0.74763 1 0.88108 1 LUZP2 19 (8%) 206 1 1 0.46799 1 0.20488 1 0.75752 1 1 1 0.32506 1 0.092607 1 0.32726 1 PDE1A 30 (13%) 195 0.49807 1 0.90905 1 0.52333 1 0.38376 1 0.032054 1 0.47062 1 0.71388 1 0.050573 1 RBM11 12 (5%) 213 0.18569 1 0.059947 1 0.79259 1 0.87229 1 0.70426 1 0.081152 1 0.31417 1 0.55973 1 GLRB 22 (10%) 203 0.25537 1 0.5125 1 0.053194 1 0.032994 1 0.38946 1 0.02851 1 0.49613 1 0.16384 1 PRB1 21 (9%) 204 0.50282 1 0.62274 1 0.12694 1 0.089679 1 0.33801 1 0.18308 1 0.72635 1 0.48856 1 KIAA1257 14 (6%) 211 0.42016 1 1 1 0.6373 1 0.77513 1 0.93974 1 0.93668 1 0.2112 1 0.50786 1 USP17L2 18 (8%) 207 0.261 1 0.11013 1 0.18531 1 0.26038 1 0.044334 1 0.14663 1 0.53515 1 0.81741 1 SPAG16 16 (7%) 209 0.48679 1 1 1 0.13249 1 0.28869 1 0.058196 1 0.01767 1 0.11242 1 0.27235 1 OR4M2 22 (10%) 203 1 1 0.95972 1 0.067813 1 0.4546 1 0.35673 1 0.87611 1 0.1911 1 0.63877 1 GFRAL 28 (12%) 197 0.34034 1 0.30492 1 0.681 1 0.76374 1 0.84674 1 0.035524 1 0.7283 1 0.79858 1 UNC119B 6 (3%) 219 0.44842 1 0.39786 1 0.21512 1 0.91489 1 0.37934 1 0.27021 1 1 1 0.44425 1 PHGDH 8 (4%) 217 0.66823 1 1 1 1 1 0.42468 1 0.90361 1 0.89408 1 0.51625 1 0.40591 1 STXBP5L 42 (19%) 183 0.37026 1 0.92963 1 0.83685 1 0.61675 1 0.14536 1 0.42234 1 0.23541 1 0.76775 1 TRAT1 12 (5%) 213 0.93195 1 0.36494 1 0.73237 1 0.6789 1 0.34043 1 0.77999 1 0.47216 1 0.55973 1 ZNF844 9 (4%) 216 1 1 1 1 0.65519 1 0.91489 1 0.90361 1 1 1 0.90955 1 0.77735 1 TTN 171 (76%) 54 0.40255 1 0.019848 1 0.41453 1 0.091227 1 0.077166 1 0.24922 1 0.20356 1 0.13675 1 COPG2 9 (4%) 216 0.31924 1 0.91442 1 0.28667 1 0.25113 1 0.76151 1 1 1 0.74763 1 0.77735 1 DSG3 41 (18%) 184 0.53997 1 0.97578 1 0.78194 1 0.30194 1 0.70999 1 0.85309 1 0.23627 1 0.71509 1 GML 9 (4%) 216 0.17649 1 0.38693 1 0.94036 1 0.41776 1 0.91352 1 0.35795 1 0.24707 1 0.77735 1 HHLA2 14 (6%) 211 0.10437 1 0.4699 1 0.43389 1 0.0037974 1 1 1 0.31754 1 0.19564 1 0.64577 1 LILRB4 27 (12%) 198 0.21397 1 1 1 0.22443 1 0.66839 1 0.46801 1 0.33607 1 0.59852 1 0.46948 1 SLC38A4 25 (11%) 200 0.008452 1 0.77174 1 0.98339 1 0.9622 1 0.048878 1 0.27624 1 0.43859 1 0.60057 1 OR2L3 14 (6%) 211 0.60895 1 0.014789 1 0.7448 1 0.46765 1 0.83878 1 0.36207 1 0.77091 1 0.35996 1 HBD 9 (4%) 216 0.58016 1 1 1 0.83208 1 0.24089 1 0.053919 1 0.096078 1 0.40959 1 1 1 TBC1D3B 5 (2%) 220 0.22606 1 0.74505 1 0.060642 1 0.25787 1 0.8614 1 1 1 0.844 1 0.63804 1 TCEB3C 26 (12%) 199 0.52371 1 0.3127 1 0.34342 1 0.54305 1 0.1818 1 0.13679 1 0.35854 1 0.32136 1 CYLC2 19 (8%) 206 0.35359 1 0.56877 1 0.093435 1 0.12103 1 0.19708 1 0.2503 1 0.28226 1 0.45253 1 HBG2 7 (3%) 218 0.33997 1 0.55836 1 0.23446 1 0.33919 1 0.29878 1 0.78509 1 0.25043 1 0.28923 1 LOC649330 22 (10%) 203 0.24474 1 0.47167 1 0.7912 1 0.75565 1 0.0845 1 0.7331 1 0.84056 1 0.67427 1 FIGLA 3 (1%) 222 0.63189 1 0.62791 1 NA NA NA NA 0.51638 1 0.43363 1 0.42752 1 0.69312 1 PARM1 17 (8%) 208 0.85564 1 1 1 0.72566 1 0.13108 1 0.8631 1 0.60385 1 0.23564 1 0.41698 1 CCK 6 (3%) 219 0.58397 1 0.66194 1 0.32162 1 0.072431 1 0.51737 1 1 1 0.57806 1 0.70209 1 ZFP106 10 (4%) 215 0.84963 1 0.77653 1 0.26377 1 0.26395 1 0.61127 1 0.76131 1 0.13952 1 0.5733 1 UGT2B15 19 (8%) 206 0.33632 1 0.38239 1 0.76688 1 0.73423 1 0.47275 1 0.74008 1 0.34768 1 0.72784 1 FGF16 7 (3%) 218 1 1 0.89714 1 0.0047925 1 0.014242 1 1 1 0.78509 1 0.12717 1 0.86567 1 NUDT4 5 (2%) 220 1 1 0.37488 1 0.36102 1 0.14505 1 1 1 0.84122 1 0.35575 1 0.48925 1 DSG1 37 (16%) 188 0.60359 1 0.52441 1 0.084114 1 0.057477 1 0.39245 1 0.59538 1 0.6927 1 0.23428 1 ARL16 7 (3%) 218 0.18005 1 0.34357 1 0.13983 1 0.6493 1 0.51169 1 0.603 1 0.78922 1 0.86567 1 VEGFC 16 (7%) 209 0.64913 1 0.1435 1 0.34852 1 0.025517 1 0.16667 1 0.3182 1 0.026446 1 0.077519 1 PSG4 23 (10%) 202 0.48903 1 0.96096 1 0.42552 1 0.38712 1 0.55492 1 0.95833 1 0.14944 1 0.11103 1 DEFB119 6 (3%) 219 1 1 0.77077 1 0.49345 1 0.88457 1 0.87545 1 0.64219 1 0.43515 1 1 1 KLHL4 20 (9%) 205 0.79937 1 0.53211 1 0.76225 1 0.86292 1 0.22411 1 0.038636 1 0.90904 1 0.34232 1 EIF3D 4 (2%) 221 0.83167 1 0.83668 1 0.24582 1 0.43577 1 1 1 0.35828 1 0.53777 1 0.43994 1 OR2W1 16 (7%) 209 0.15672 1 0.71898 1 0.24411 1 0.088793 1 0.71095 1 1 1 0.66499 1 0.80038 1 OR4N2 21 (9%) 204 0.3404 1 0.14391 1 0.6395 1 0.36353 1 0.023709 1 0.43343 1 0.16512 1 0.024889 1 CCDC11 17 (8%) 208 0.90315 1 0.064408 1 0.26486 1 0.2116 1 0.10589 1 0.18885 1 0.0042583 1 0.93284 1 LIN7A 10 (4%) 215 0.92075 1 0.26747 1 0.55574 1 0.64788 1 0.17747 1 0.5845 1 0.012651 1 0.3887 1 RAPGEF5 11 (5%) 214 1 1 0.45923 1 0.60379 1 0.49445 1 0.34043 1 0.51797 1 0.12942 1 0.05587 1 CD2 16 (7%) 209 0.39511 1 0.57866 1 0.77572 1 0.51583 1 1 1 0.70194 1 0.46929 1 0.68141 1 C2ORF40 7 (3%) 218 0.23607 1 0.798 1 0.94036 1 0.7248 1 0.51169 1 0.89052 1 0.88496 1 0.73535 1 SGCZ 19 (8%) 206 0.62584 1 0.62524 1 0.86565 1 0.70019 1 0.37428 1 0.27774 1 0.86466 1 0.7761 1 SPANXN2 14 (6%) 211 0.28311 1 0.69178 1 0.58421 1 0.17084 1 0.42697 1 0.083137 1 0.4272 1 0.19954 1 TLL1 42 (19%) 183 0.97605 1 0.018293 1 0.6177 1 0.042055 1 0.060768 1 0.24298 1 0.58477 1 0.43387 1 C9ORF119 7 (3%) 218 1 1 0.1776 1 0.47567 1 0.56303 1 0.39837 1 0.46442 1 0.61012 1 0.86567 1 CCDC54 13 (6%) 212 0.081183 1 0.33374 1 0.29449 1 0.86254 1 0.13032 1 0.082378 1 0.25333 1 0.75844 1 DEFB118 8 (4%) 217 0.19663 1 0.31557 1 0.93308 1 0.26947 1 0.74127 1 0.72737 1 0.72222 1 0.87124 1 HTR3B 16 (7%) 209 0.016933 1 0.13495 1 0.026117 1 0.05977 1 0.00073963 0.756 0.15419 1 0.36834 1 0.11197 1 MARCH11 10 (4%) 215 0.84963 1 1 1 0.37779 1 0.72061 1 0.17747 1 0.1018 1 0.91481 1 0.89306 1 MKX 14 (6%) 211 0.13948 1 0.20003 1 0.58305 1 0.97102 1 0.065626 1 0.15522 1 0.052586 1 0.29366 1 OR5H2 14 (6%) 211 0.78336 1 1 1 0.45805 1 0.51845 1 0.83878 1 0.41503 1 0.6335 1 0.29366 1 SIGLEC14 11 (5%) 214 0.36724 1 0.33836 1 0.035758 1 0.46418 1 0.58184 1 0.92342 1 0.616 1 0.89634 1 TUBB8 12 (5%) 213 0.7037 1 0.86673 1 0.21413 1 0.13784 1 0.5407 1 0.65885 1 0.55195 1 0.10837 1 ZIM3 23 (10%) 202 0.19414 1 0.14008 1 0.67513 1 0.43126 1 0.076062 1 0.17455 1 0.15656 1 0.71731 1 PRC1 13 (6%) 212 0.9377 1 0.41954 1 0.056371 1 0.71626 1 0.22921 1 0.65487 1 0.50164 1 0.6375 1 MUM1L1 25 (11%) 200 0.55488 1 0.80154 1 0.73829 1 0.091809 1 0.64413 1 0.43115 1 0.51743 1 0.81593 1 TRIM58 15 (7%) 210 0.5613 1 0.89082 1 0.81512 1 0.86076 1 0.63692 1 0.73085 1 0.25045 1 1 1 ANKRD20A4 4 (2%) 221 0.38535 1 0.45433 1 0.32162 1 0.13465 1 0.10876 1 0.67884 1 0.53777 1 1 1 OR5J2 13 (6%) 212 0.63308 1 0.55002 1 0.31161 1 0.4999 1 1 1 0.65487 1 0.036594 1 0.6375 1 CLEC14A 18 (8%) 207 0.04246 1 0.49542 1 0.1432 1 0.48327 1 0.21581 1 0.72794 1 0.66182 1 0.93459 1 FAM19A1 8 (4%) 217 0.15606 1 0.38625 1 0.45835 1 0.11246 1 0.48738 1 1 1 0.90352 1 0.56897 1 GK2 28 (12%) 197 0.79191 1 0.60282 1 0.32804 1 0.1868 1 0.37879 1 0.48525 1 0.38176 1 0.87249 1 LONRF2 16 (7%) 209 0.89763 1 0.34259 1 0.94532 1 0.98763 1 0.89866 1 1 1 0.89262 1 0.50419 1 HAPLN1 11 (5%) 214 1 1 0.095855 1 0.77155 1 0.88158 1 0.92594 1 0.77999 1 0.47787 1 0.59449 1 NAP1L4 9 (4%) 216 0.020453 1 0.04602 1 0.035758 1 0.59993 1 0.6335 1 0.32289 1 0.74763 1 0.88108 1 CLCC1 13 (6%) 212 0.9377 1 0.36086 1 0.53285 1 0.1437 1 0.11164 1 0.2336 1 0.043986 1 0.58099 1 OR52J3 13 (6%) 212 0.30101 1 0.27768 1 0.36701 1 0.46386 1 0.51723 1 0.93125 1 1 1 0.17138 1 TMCO5A 8 (4%) 217 0.0088529 1 0.46957 1 0.16386 1 0.095561 1 0.034901 1 0.26124 1 0.90352 1 0.76146 1 C4ORF22 11 (5%) 214 0.63313 1 0.92527 1 0.59267 1 0.28125 1 0.92594 1 0.84973 1 0.045162 1 0.29688 1 MAP2K1 11 (5%) 214 0.15694 1 0.065751 1 0.055753 1 0.12432 1 0.0669 1 0.0056506 1 0.47787 1 0.42362 1 OR7D2 17 (8%) 208 0.5347 1 0.35045 1 0.77805 1 0.83786 1 0.031727 1 1 1 0.46087 1 0.75117 1 CXCR2 11 (5%) 214 0.85951 1 0.49473 1 0.86642 1 0.95232 1 0.5407 1 1 1 0.616 1 0.89634 1 RBM22 7 (3%) 218 0.44156 1 0.1776 1 NA NA NA NA 0.39837 1 0.46442 1 1 1 0.86567 1 CX3CL1 4 (2%) 221 0.14298 1 0.13935 1 NA NA NA NA 1 1 0.67884 1 0.076818 1 0.43994 1 IGF2BP3 6 (3%) 219 0.87926 1 1 1 0.86833 1 0.64558 1 0.51737 1 0.87488 1 0.14718 1 0.8439 1 KLRC3 10 (4%) 215 1 1 0.55826 1 0.51662 1 0.011316 1 0.61127 1 0.11299 1 0.44278 1 1 1 LRRIQ4 19 (8%) 206 0.19982 1 0.095723 1 0.11068 1 0.35677 1 0.86268 1 0.8535 1 0.17049 1 0.0085253 1 NR1H4 11 (5%) 214 0.26348 1 0.33836 1 0.37364 1 0.36239 1 0.92594 1 0.92342 1 0.72915 1 0.42362 1 OR4A15 21 (9%) 204 0.43707 1 0.32096 1 1 1 0.20157 1 0.025852 1 0.29472 1 0.28984 1 0.27835 1 MAGEA4 10 (4%) 215 0.39768 1 0.55826 1 0.01435 1 0.35295 1 0.17747 1 0.26359 1 0.64864 1 0.71119 1 DGAT2L6 10 (4%) 215 0.50849 1 0.71234 1 0.85315 1 0.11049 1 0.30413 1 0.5845 1 0.48388 1 0.3887 1 RGS18 8 (4%) 217 0.35006 1 0.89934 1 0.12159 1 0.40267 1 0.35785 1 0.72737 1 0.41941 1 0.66471 1 TSGA13 9 (4%) 216 0.52999 1 0.57919 1 0.11789 1 0.33261 1 0.6335 1 0.55349 1 0.6157 1 0.68892 1 OPN5 7 (3%) 218 0.20775 1 0.89714 1 1 1 0.34283 1 0.51169 1 0.603 1 1 1 0.86567 1 SPINK13 7 (3%) 218 0.29909 1 0.23271 1 0.89235 1 0.45681 1 0.29878 1 0.68521 1 0.53416 1 0.51601 1