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 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 BRAF 140 (53%) 124 0.035979 1 0.055172 1 0.6685 1 0.89834 1 0.043213 1 0.073025 1 0.70495 1 0.2515 1 C15ORF23 14 (5%) 250 0.9119 1 0.32125 1 1 1 0.59614 1 0.71773 1 0.61086 1 0.57436 1 0.5768 1 CDKN2A 34 (13%) 230 0.43712 1 0.31103 1 1 1 0.54441 1 0.63862 1 0.7137 1 0.50666 1 1 1 NRAS 73 (28%) 191 0.098058 1 0.20067 1 0.49853 1 0.070235 1 0.55335 1 0.8109 1 0.81227 1 0.88745 1 OXA1L 8 (3%) 256 0.61835 1 0.20117 1 1 1 0.56259 1 0.29581 1 0.38677 1 0.38421 1 0.71423 1 STK19 11 (4%) 253 0.86509 1 0.12978 1 0.87767 1 1 1 0.14836 1 0.28261 1 0.79216 1 0.54011 1 TP53 39 (15%) 225 0.32786 1 0.054178 1 0.26294 1 0.36365 1 0.022033 1 0.20448 1 0.9039 1 0.1072 1 TTN 204 (77%) 60 0.91773 1 0.0077772 1 0.17941 1 0.15461 1 0.36457 1 0.33213 1 0.023493 1 0.22303 1 UGT2B15 24 (9%) 240 0.093603 1 0.38042 1 0.3423 1 0.6095 1 0.38392 1 1 1 0.3132 1 1 1 PTEN 23 (9%) 241 0.81417 1 0.28831 1 0.010724 1 0.39415 1 0.41654 1 0.32879 1 0.92404 1 0.65491 1 RAC1 17 (6%) 247 0.29448 1 0.8586 1 0.70408 1 0.91731 1 0.23786 1 0.62973 1 0.33309 1 0.076958 1 PPP6C 23 (9%) 241 0.27892 1 0.64614 1 0.76764 1 0.11609 1 0.47543 1 0.24715 1 0.086688 1 0.072335 1 PRB2 39 (15%) 225 0.34939 1 1 1 1 1 0.91555 1 0.032978 1 0.28782 1 0.65156 1 0.21127 1 IDH1 15 (6%) 249 0.036175 1 0.34494 1 0.56287 1 0.8305 1 0.27976 1 0.30237 1 0.39211 1 0.7895 1 NAP1L2 26 (10%) 238 0.15077 1 0.96557 1 0.74885 1 0.70454 1 0.70938 1 0.70206 1 0.93186 1 1 1 FIGLA 4 (2%) 260 0.65549 1 0.36708 1 NA NA NA NA 0.35902 1 0.37734 1 0.37251 1 0.30106 1 RBM11 16 (6%) 248 0.30716 1 0.026656 1 0.79213 1 0.85295 1 0.39886 1 0.023745 1 0.068028 1 0.42619 1 HBG2 9 (3%) 255 0.53673 1 0.19524 1 0.44726 1 0.44419 1 0.3827 1 0.43109 1 0.1038 1 0.30874 1 LCE1B 12 (5%) 252 0.081147 1 0.65072 1 0.91958 1 0.91731 1 0.45027 1 0.75675 1 0.93003 1 1 1 MUC7 19 (7%) 245 0.80639 1 0.44608 1 0.37601 1 0.49532 1 0.39887 1 0.64268 1 0.40246 1 0.048277 1 DDX3X 20 (8%) 244 0.95457 1 0.44048 1 0.53615 1 0.27826 1 0.1304 1 0.40745 1 0.87384 1 1 1 CDH9 37 (14%) 227 0.82355 1 0.060664 1 0.6422 1 0.88897 1 0.763 1 0.6984 1 0.0091006 1 0.19808 1 HIST1H2AA 10 (4%) 254 0.80359 1 0.71104 1 0.65874 1 0.57351 1 0.10527 1 0.84748 1 0.29786 1 0.74604 1 GFRAL 33 (12%) 231 0.76256 1 0.40491 1 0.60899 1 0.76088 1 0.12405 1 0.77118 1 0.66397 1 0.24979 1 TBC1D3B 6 (2%) 258 0.097465 1 0.66114 1 0.48038 1 0.084183 1 0.029784 1 0.85816 1 0.57812 1 1 1 HHLA2 18 (7%) 246 0.22901 1 0.7096 1 0.2837 1 0.011699 1 0.38746 1 0.26668 1 0.00070522 0.611 0.13482 1 COPG2 10 (4%) 254 0.97239 1 0.77651 1 0.20158 1 0.28303 1 0.89288 1 0.84748 1 0.29786 1 0.74604 1 FGF16 8 (3%) 256 0.67727 1 0.53411 1 0.012799 1 0.027857 1 0.10996 1 0.33991 1 0.27254 1 1 1 IL32 10 (4%) 254 0.74722 1 0.053827 1 1 1 0.14038 1 0.89288 1 0.46716 1 0.65504 1 1 1 PRB4 19 (7%) 245 0.86775 1 0.51515 1 0.030269 1 0.072937 1 0.10082 1 0.040866 1 0.29083 1 0.085709 1 NBPF7 16 (6%) 248 0.050207 1 0.20778 1 0.86121 1 1 1 0.44859 1 0.9435 1 0.15763 1 1 1 POM121 18 (7%) 246 1 1 0.25521 1 0.72997 1 0.78543 1 0.82876 1 0.58127 1 0.24502 1 0.45392 1 ARID2 38 (14%) 226 0.28991 1 0.42567 1 0.67897 1 0.026646 1 0.073387 1 1 1 0.36309 1 0.37266 1 MAP2K1 13 (5%) 251 0.85932 1 0.58704 1 0.002344 1 0.023687 1 0.20472 1 0.1715 1 0.8772 1 1 1 DEFB118 10 (4%) 254 0.80359 1 0.097812 1 1 1 1 1 0.89288 1 0.46716 1 1 1 0.74604 1 HBD 10 (4%) 254 0.91835 1 0.84711 1 0.88601 1 0.14038 1 0.28162 1 0.037849 1 0.9219 1 0.74604 1 ANKRD20A4 5 (2%) 259 0.18932 1 0.45236 1 0.20081 1 0.27791 1 0.047115 1 0.18021 1 0.52784 1 1 1 GLRB 26 (10%) 238 0.76523 1 0.45483 1 0.10813 1 0.024209 1 0.36265 1 0.56658 1 0.3521 1 0.13538 1 NR1H4 14 (5%) 250 0.98163 1 0.15238 1 0.22791 1 0.47066 1 0.74331 1 0.87686 1 0.81898 1 0.25273 1 OR51S1 30 (11%) 234 0.10543 1 0.93953 1 0.74209 1 0.038987 1 0.23328 1 0.16303 1 0.93939 1 1 1 TFEC 16 (6%) 248 0.34986 1 0.43851 1 0.083606 1 0.24698 1 0.59563 1 0.9435 1 0.80721 1 1 1 UNC119B 6 (2%) 258 0.14021 1 0.44691 1 0.42437 1 0.66793 1 0.80491 1 0.15344 1 1 1 0.67729 1 ZNF479 27 (10%) 237 0.53216 1 0.84154 1 0.27901 1 0.34765 1 0.8914 1 0.48542 1 0.15659 1 0.67418 1 FAM19A1 10 (4%) 254 0.056021 1 0.60473 1 0.17254 1 0.013259 1 0.074394 1 1 1 0.84663 1 0.51265 1 GIMAP7 24 (9%) 240 0.0015335 1 0.48322 1 0.1815 1 0.23868 1 0.23815 1 0.79024 1 0.52127 1 0.27029 1 KLHL4 23 (9%) 241 0.69306 1 0.38255 1 0.93994 1 0.73332 1 0.63315 1 0.063956 1 0.53749 1 0.49644 1 NOTCH2NL 13 (5%) 251 0.6947 1 0.34247 1 0.37413 1 0.066896 1 0.016991 1 0.0056382 1 0.32014 1 0.085883 1 PRC1 15 (6%) 249 0.29539 1 0.36656 1 0.25671 1 0.37779 1 0.36761 1 0.62534 1 0.21388 1 0.42089 1 ZMAT4 10 (4%) 254 0.3248 1 0.078288 1 0.7027 1 0.24861 1 0.94389 1 0.84748 1 0.38516 1 0.51265 1 PDE1A 34 (13%) 230 0.83128 1 0.9453 1 0.66265 1 0.39959 1 0.056979 1 0.20753 1 0.45299 1 0.34431 1 GML 10 (4%) 254 0.84371 1 0.42869 1 0.20158 1 0.32649 1 0.60435 1 0.46716 1 0.12393 1 1 1 OR4N2 25 (9%) 239 0.3179 1 0.3023 1 0.36353 1 0.44537 1 0.0023067 1 0.098639 1 0.57379 1 0.053554 1 ACSM2B 40 (15%) 224 0.37793 1 0.5797 1 0.69 1 0.719 1 0.31358 1 0.33564 1 0.22915 1 0.4822 1 USP17L2 19 (7%) 245 0.26475 1 0.04887 1 0.24216 1 0.45007 1 0.0051397 1 0.23918 1 0.33395 1 0.46401 1 TAF1A 13 (5%) 251 0.47947 1 0.87611 1 0.67011 1 0.78543 1 0.78342 1 0.44484 1 0.81898 1 0.77153 1 OR5H2 19 (7%) 245 0.34236 1 0.75484 1 0.79213 1 0.66571 1 0.82876 1 0.74504 1 0.75375 1 1 1 PHGDH 9 (3%) 255 0.93638 1 0.91088 1 0.79009 1 0.48257 1 0.39375 1 0.35759 1 0.91018 1 0.30874 1 BAGE2 14 (5%) 250 1 1 1 1 1 1 0.90415 1 0.5784 1 0.81952 1 0.40998 1 0.78019 1 FUT9 25 (9%) 239 0.63869 1 0.0056769 1 0.46962 1 0.32777 1 0.27269 1 0.56244 1 0.32642 1 0.83209 1 MPP7 29 (11%) 235 0.38829 1 0.74646 1 0.9178 1 0.74198 1 0.11957 1 0.49682 1 0.74098 1 1 1 TSPAN9 4 (2%) 260 0.47309 1 1 1 0.1638 1 0.60607 1 0.83428 1 0.57201 1 0.68562 1 1 1 TRAT1 13 (5%) 251 0.53165 1 0.2563 1 0.49675 1 0.7654 1 0.18274 1 0.45671 1 0.63023 1 0.77153 1 C9ORF119 8 (3%) 256 0.67727 1 0.66805 1 0.61685 1 0.60607 1 0.38516 1 1 1 0.27254 1 0.26602 1 TUBB8 15 (6%) 249 0.29218 1 0.74722 1 0.41078 1 0.65089 1 0.83895 1 0.94108 1 0.52723 1 0.42089 1 ACD 10 (4%) 254 0.91835 1 0.42869 1 0.65674 1 0.23856 1 0.66023 1 0.38848 1 0.17085 1 0.18788 1 NUDT4 5 (2%) 259 0.13427 1 0.37271 1 0.21836 1 0.040932 1 1 1 0.61651 1 0.22352 1 0.373 1 C8A 30 (11%) 234 0.21456 1 0.20181 1 0.26761 1 0.067287 1 0.029298 1 0.28855 1 0.60452 1 0.32363 1 KIAA1257 15 (6%) 249 0.91962 1 0.74722 1 0.67011 1 0.28219 1 0.80168 1 0.47186 1 0.70693 1 0.42089 1 SNAP91 28 (11%) 236 0.31256 1 0.87581 1 0.17639 1 0.46909 1 0.86057 1 1 1 0.27455 1 0.29784 1 CCK 7 (3%) 257 1 1 0.70306 1 0.041483 1 0.15999 1 0.60854 1 0.8016 1 0.37911 1 0.71174 1 SPINK13 9 (3%) 255 0.15269 1 0.57491 1 0.62115 1 0.6124 1 0.068317 1 0.11671 1 0.20271 1 0.73504 1 ANXA10 14 (5%) 250 0.19844 1 0.014546 1 0.25766 1 0.44999 1 0.097698 1 0.027561 1 0.34344 1 0.16086 1 LIN7A 11 (4%) 253 0.41603 1 0.17939 1 0.20158 1 0.28303 1 0.027788 1 0.11726 1 0.39005 1 0.54011 1 C2 14 (5%) 250 0.15136 1 0.41363 1 0.91071 1 0.8305 1 0.0037429 1 0.11683 1 0.29878 1 0.77153 1 DGAT2L6 12 (5%) 252 0.3452 1 0.60352 1 0.61851 1 0.34335 1 0.74719 1 0.93044 1 0.8134 1 1 1 RAPGEF5 13 (5%) 251 0.33929 1 0.62762 1 0.7027 1 0.54051 1 0.070187 1 0.76731 1 0.17728 1 0.25273 1 OR2L3 17 (6%) 247 0.884 1 0.063734 1 0.41032 1 0.52668 1 0.76028 1 0.5965 1 0.90249 1 0.44885 1 ZNF679 20 (8%) 244 0.51173 1 0.51062 1 0.73622 1 0.65295 1 0.14563 1 0.80165 1 0.15871 1 0.48315 1 NAP1L4 10 (4%) 254 0.058702 1 0.029481 1 0.87767 1 0.43066 1 0.12991 1 0.12357 1 0.9219 1 0.51265 1 PARM1 18 (7%) 246 0.027564 1 1 1 0.81411 1 0.21991 1 0.92379 1 0.86207 1 0.1776 1 0.045801 1 DEFB119 6 (2%) 258 0.53149 1 0.76827 1 0.8122 1 0.81851 1 0.94639 1 1 1 0.33604 1 1 1 RGS18 10 (4%) 254 0.36883 1 0.22293 1 0.21836 1 0.15999 1 0.39375 1 1 1 0.32309 1 1 1 VEGFC 17 (6%) 247 0.058783 1 0.40833 1 1 1 0.27272 1 0.29532 1 0.048894 1 0.18928 1 0.11872 1 ARL16 7 (3%) 257 0.68668 1 0.79607 1 0.15924 1 0.68437 1 0.51912 1 0.18133 1 1 1 1 1 CACNA1H 24 (9%) 240 0.4358 1 0.091067 1 0.89665 1 0.64478 1 0.414 1 0.76743 1 0.54225 1 0.82602 1 CCNE2 13 (5%) 251 0.30284 1 0.76966 1 0.11604 1 0.10182 1 0.43579 1 0.72138 1 0.041685 1 0.3812 1 FRG2B 17 (6%) 247 0.77075 1 0.50814 1 0.92929 1 0.79992 1 0.37235 1 0.73591 1 0.15429 1 0.2066 1 SPAG16 17 (6%) 247 0.22209 1 0.73221 1 0.61851 1 0.37893 1 0.14876 1 0.14713 1 0.19985 1 0.44885 1 USP29 40 (15%) 224 0.85823 1 1 1 0.75777 1 0.6196 1 0.7011 1 0.77768 1 0.31858 1 0.21683 1 GH2 10 (4%) 254 0.17628 1 0.55639 1 0.58854 1 0.58536 1 0.066376 1 0.42507 1 0.60685 1 0.51265 1 ST18 47 (18%) 217 0.30021 1 0.62013 1 0.36891 1 0.19171 1 0.54961 1 0.15916 1 0.87748 1 0.40778 1 CCDC102B 22 (8%) 242 0.91378 1 0.88464 1 0.32381 1 0.30283 1 0.6708 1 0.91871 1 1 1 0.49644 1 B2M 6 (2%) 258 0.94606 1 1 1 0.76622 1 0.86985 1 0.49509 1 0.22639 1 0.022681 1 0.67729 1 CD2 17 (6%) 247 0.9196 1 0.59622 1 0.41032 1 0.41123 1 0.4162 1 0.90259 1 0.69748 1 0.60717 1 SLC38A4 30 (11%) 234 0.5452 1 0.58417 1 0.69271 1 0.94807 1 0.060157 1 0.55715 1 0.77366 1 1 1 OR8D4 11 (4%) 253 0.11407 1 0.53676 1 0.15924 1 0.21334 1 0.17113 1 0.28261 1 0.85868 1 1 1 MKX 16 (6%) 248 0.31325 1 0.34665 1 0.84075 1 0.84058 1 0.31721 1 0.074133 1 0.21828 1 1 1 SPATA8 11 (4%) 253 0.41603 1 0.46141 1 NA NA NA NA 0.34206 1 0.55633 1 0.30634 1 0.21393 1 GPR137 10 (4%) 254 0.27544 1 0.39159 1 1 1 0.86985 1 0.94389 1 0.71603 1 1 1 0.51265 1 GRXCR2 15 (6%) 249 0.68254 1 0.94439 1 0.09373 1 0.8305 1 0.016148 1 0.30359 1 0.6655 1 0.58609 1 C2ORF40 7 (3%) 257 0.44055 1 0.89587 1 0.28701 1 0.43066 1 0.36228 1 1 1 1 1 0.71174 1 CADM2 23 (9%) 241 0.97034 1 0.073828 1 0.34583 1 0.34787 1 0.79437 1 0.7284 1 0.46882 1 0.0026473 1 OR5J2 16 (6%) 248 0.81612 1 0.76149 1 1 1 0.17569 1 0.1963 1 0.51821 1 0.046261 1 0.30179 1 SIGLEC14 12 (5%) 252 0.11961 1 0.60352 1 1 1 0.44419 1 0.34445 1 0.7038 1 1 1 1 1 CX3CL1 4 (2%) 260 0.51272 1 0.13098 1 NA NA NA NA 1 1 0.37734 1 0.095063 1 0.30106 1 GNAI2 4 (2%) 260 0.33377 1 0.36708 1 0.79236 1 1 1 0.17252 1 0.57201 1 0.17022 1 0.15696 1 OR52J3 17 (6%) 247 0.64177 1 0.28212 1 0.3423 1 0.6095 1 0.83783 1 0.94632 1 0.39299 1 0.80078 1 AREG 6 (2%) 258 1 1 0.5786 1 0.58471 1 0.68437 1 0.66978 1 0.33498 1 0.44084 1 0.20607 1 RUNDC3B 15 (6%) 249 0.49387 1 0.011051 1 0.89719 1 0.90415 1 0.91246 1 1 1 0.52723 1 0.7895 1