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 Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square 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 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 Fisher's exact test_P Fisher's exact test_Q PTEN 29 (4%) 742 0.22565 1 0.43675 1 0.60952 1 0.60304 1 0.88203 1 0.2657 1 0.26833 1 0.90051 1 0.37955 1 0.88553 1 0.059701 1 0.34935 1 MLL3 56 (7%) 715 0.27197 1 0.97292 1 0.585 1 0.78898 1 0.74035 1 0.93484 1 0.10714 1 0.85994 1 0.039567 1 0.28112 1 0.15111 1 0.58154 1 ZNF384 14 (2%) 757 NA NA NA NA 0.6096 1 0.15474 1 NA NA NA NA 0.53541 1 1 1 0.88133 1 0.26335 1 0.46638 1 0.30998 1 DCP1B 5 (1%) 766 NA NA NA NA 0.39484 1 0.0047466 1 NA NA NA NA 0.61924 1 0.71884 1 0.60661 1 0.60627 1 1 1 0.66679 1 PIK3CA 261 (34%) 510 8.8999e-15 7.27e-12 3.8799e-10 3.15e-07 1.1263e-12 9.19e-10 1.6672e-09 1.35e-06 1.6388e-05 0.013 1.0648e-06 0.000854 5.1109e-28 4.2e-25 2.61e-12 2.13e-09 8.0222e-08 6.47e-05 1.4866e-11 1.21e-08 6.3973e-05 0.0502 1.8953e-10 1.54e-07 NCOA3 29 (4%) 742 0.54907 1 1 1 0.99322 1 0.38519 1 1 1 1 1 0.26302 1 0.28724 1 0.28079 1 0.096087 1 0.23997 1 0.13218 1 AOAH 19 (2%) 752 NA NA NA NA 0.61198 1 0.65405 1 NA NA NA NA 0.48133 1 0.22789 1 0.10885 1 0.50283 1 0.049802 1 0.89772 1 RBMX 13 (2%) 758 NA NA NA NA 0.0058049 1 0.070635 1 NA NA NA NA 0.49733 1 0.12739 1 0.2758 1 0.4179 1 0.64663 1 0.94849 1 RUNX1 25 (3%) 746 0.0055169 1 0.044232 1 1.8465e-05 0.0146 0.036935 1 1 1 0.25194 1 0.02987 1 0.14114 1 0.0024751 1 0.13304 1 0.10564 1 0.0080311 1 PIK3R1 21 (3%) 750 0.17209 1 0.61649 1 0.68745 1 0.64664 1 0.53782 1 0.29702 1 0.16481 1 0.91342 1 1 1 0.87482 1 0.8033 1 0.78568 1 MEF2A 14 (2%) 757 NA NA NA NA 0.65902 1 0.33538 1 NA NA NA NA 0.63035 1 0.14883 1 0.053096 1 0.012732 1 0.16948 1 0.033172 1 NCOR2 29 (4%) 742 0.67551 1 1 1 0.11101 1 0.3996 1 0.83853 1 0.68963 1 0.695 1 0.54924 1 0.54196 1 0.85918 1 0.41343 1 0.25622 1 AKT1 19 (2%) 752 0.06343 1 0.92454 1 0.0031236 1 0.0003628 0.28 0.16241 1 0.34532 1 3.0929e-05 0.0244 0.28844 1 0.016689 1 0.075601 1 0.081346 1 0.040151 1 GATA3 81 (11%) 690 0.0005751 0.442 0.00010133 0.079 0.0040893 1 0.0088698 1 0.0011529 0.879 0.00040708 0.314 6.2694e-06 0.00498 1.2227e-09 9.92e-07 4.041e-07 0.000325 1.265e-06 0.00101 3.9713e-07 0.00032 1.4562e-06 0.00116 NR1H2 18 (2%) 753 0.32598 1 0.26699 1 0.78925 1 0.048674 1 0.063975 1 0.11594 1 0.56007 1 0.072808 1 0.739 1 0.43998 1 0.48416 1 0.085634 1 MAP3K4 18 (2%) 753 0.10846 1 0.72143 1 0.78841 1 0.02477 1 0.073322 1 0.68963 1 0.46426 1 0.2143 1 0.39762 1 0.20941 1 0.78118 1 0.76456 1 TP53 257 (33%) 514 7.0755e-37 5.84e-34 2.4254e-33 2e-30 3.5347e-49 2.93e-46 6.1766e-23 5.05e-20 1.8749e-27 1.54e-24 1.102e-23 9.03e-21 4.1674e-55 3.46e-52 4.1792e-48 3.46e-45 7.4588e-39 6.16e-36 2.3199e-44 1.92e-41 1.4735e-30 1.21e-27 4.9526e-24 4.06e-21 TPRX1 7 (1%) 764 NA NA NA NA 0.34307 1 0.56062 1 NA NA NA NA 0.98251 1 0.73675 1 0.6937 1 1 1 0.61241 1 0.71235 1 CDH1 55 (7%) 716 1.6718e-07 0.000135 8.2018e-05 0.0641 2.424e-08 1.96e-05 0.00071097 0.545 0.00025549 0.198 0.00057945 0.444 1.2922e-06 0.00103 4.2277e-07 0.000339 1.6686e-06 0.00133 5.9234e-08 4.79e-05 0.00024417 0.19 0.010442 1 ATN1 17 (2%) 754 0.064261 1 0.054511 1 0.064223 1 0.83525 1 0.16884 1 0.29141 1 0.16018 1 0.56919 1 0.85348 1 0.43977 1 0.076673 1 0.35346 1 MAP2K4 32 (4%) 739 0.029235 1 0.0031315 1 0.032318 1 0.0090028 1 0.0023792 1 0.034428 1 0.028129 1 0.00031281 0.242 0.0015556 1 0.0033282 1 0.0010576 0.807 0.094211 1 MAP3K1 57 (7%) 714 4.3258e-06 0.00344 4.3824e-05 0.0344 7.2236e-05 0.0566 0.0011711 0.891 0.00020416 0.159 1.9896e-06 0.00159 1.0792e-05 0.00855 7.5066e-05 0.0587 1.9643e-05 0.0155 4.1587e-05 0.0327 0.00023013 0.179 0.0019527 1 CBFB 16 (2%) 755 0.18352 1 0.64781 1 0.026558 1 0.010661 1 0.34961 1 0.56866 1 0.00047333 0.364 0.58256 1 0.024087 1 0.0040159 1 0.011441 1 0.00073261 0.56 CTCF 18 (2%) 753 0.026496 1 0.31977 1 0.0029681 1 0.0045934 1 0.068249 1 0.36929 1 0.00038582 0.298 0.089065 1 0.20043 1 0.062133 1 0.77764 1 0.53155 1 CCDC144NL 8 (1%) 763 NA NA NA NA 6.2856e-06 0.00499 0.30644 1 NA NA NA NA 0.70488 1 0.34747 1 0.80852 1 0.21646 1 0.24575 1 0.39039 1 AKD1 19 (2%) 752 0.92566 1 0.43682 1 0.11179 1 0.17649 1 0.46668 1 0.24234 1 0.41501 1 0.30499 1 0.32166 1 0.066172 1 0.11379 1 0.2013 1 RB1 14 (2%) 757 0.52273 1 0.1721 1 0.15815 1 0.17085 1 0.48293 1 0.76154 1 0.33908 1 0.23143 1 0.061 1 0.0034669 1 0.13735 1 0.13703 1 PHLDA1 9 (1%) 762 0.32088 1 0.2751 1 0.39475 1 0.60983 1 1 1 0.28034 1 0.89024 1 0.89408 1 0.33083 1 0.43573 1 0.25647 1 0.54794 1 FOXA1 15 (2%) 756 0.7357 1 0.11583 1 0.1745 1 0.033352 1 1 1 0.5168 1 0.63588 1 0.16702 1 0.35916 1 0.22864 1 0.4563 1 0.60005 1 VEZF1 8 (1%) 763 NA NA NA NA 0.47992 1 0.50919 1 NA NA NA NA 0.18282 1 0.87962 1 0.90225 1 0.60501 1 1 1 0.90426 1 ZFP36L1 10 (1%) 761 0.83919 1 0.68646 1 0.011812 1 0.16377 1 0.025798 1 0.39178 1 0.88431 1 0.83148 1 0.84082 1 0.3933 1 0.69507 1 0.12555 1 NCOR1 31 (4%) 740 0.48764 1 0.33042 1 0.26629 1 0.41208 1 0.72317 1 0.72615 1 0.79885 1 0.48369 1 0.094078 1 0.40966 1 0.59269 1 0.45457 1 TBX3 18 (2%) 753 0.61241 1 0.34526 1 0.6018 1 0.056221 1 0.15974 1 0.55094 1 0.18399 1 0.44398 1 0.48866 1 0.48493 1 0.65117 1 1 1 DSPP 26 (3%) 745 0.94455 1 0.4158 1 0.64658 1 0.79242 1 0.098697 1 0.38708 1 0.70327 1 0.052999 1 0.48845 1 0.31114 1 0.13159 1 0.60685 1 AQP7 8 (1%) 763 0.6379 1 0.068244 1 0.039644 1 0.66215 1 NA NA NA NA 0.76833 1 0.34747 1 0.47386 1 0.63156 1 0.61241 1 0.41211 1 BCL6B 8 (1%) 763 NA NA NA NA 0.47613 1 0.69159 1 NA NA NA NA 0.30401 1 1 1 0.80852 1 0.89919 1 0.49039 1 0.53695 1 RPGR 14 (2%) 757 0.60526 1 0.39167 1 0.99538 1 0.62763 1 0.74488 1 0.60567 1 0.3318 1 0.50951 1 0.72451 1 0.28283 1 0.90204 1 0.50119 1 TBL1XR1 9 (1%) 762 0.10865 1 0.29485 1 0.061128 1 NA NA 0.45536 1 0.56866 1 0.021511 1 0.20013 1 0.079369 1 0.48246 1 0.86949 1 0.22898 1 MYB 11 (1%) 760 0.78645 1 1 1 0.085991 1 0.42083 1 1 1 0.68963 1 0.7584 1 0.65567 1 0.78661 1 0.68707 1 0.27798 1 1 1 PABPC3 8 (1%) 763 0.16324 1 0.80139 1 0.70318 1 0.73006 1 NA NA NA NA 0.88844 1 0.39487 1 0.64092 1 0.89919 1 1 1 1 1 GPS2 6 (1%) 765 0.0076799 1 0.02839 1 0.1472 1 0.29336 1 1 1 1 1 0.60413 1 0.18404 1 0.75163 1 1 1 NA NA NA NA E2F4 4 (1%) 767 NA NA NA NA 0.93219 1 NA NA NA NA NA NA 0.8958 1 0.81718 1 0.81691 1 0.49056 1 NA NA NA NA DNAH12 12 (2%) 759 0.96689 1 0.26634 1 0.83584 1 0.67166 1 0.68948 1 0.68963 1 0.30246 1 0.53211 1 0.86336 1 1 1 1 1 0.51991 1 CDKN1B 7 (1%) 764 0.35772 1 0.11035 1 0.0022851 1 0.042808 1 0.33082 1 0.39197 1 0.11395 1 0.30586 1 0.36341 1 0.36774 1 0.45303 1 0.21492 1 HNF1A 9 (1%) 762 NA NA NA NA 0.06612 1 0.62235 1 NA NA NA NA 0.07601 1 0.035277 1 0.40602 1 0.069919 1 0.47124 1 0.27981 1 CRIPAK 6 (1%) 765 NA NA NA NA 0.82085 1 0.11299 1 NA NA NA NA 0.28525 1 0.18404 1 0.2578 1 0.56894 1 0.86949 1 0.73043 1 CASP8 10 (1%) 761 0.35508 1 0.19708 1 0.91923 1 0.56132 1 0.40246 1 1 1 0.23139 1 0.73732 1 0.7723 1 0.16637 1 0.098537 1 0.38772 1 STXBP2 9 (1%) 762 NA NA NA NA 0.9051 1 0.81865 1 NA NA NA NA 0.87632 1 0.48021 1 0.40602 1 0.91679 1 0.90204 1 0.74885 1 CTU2 5 (1%) 766 NA NA NA NA 0.20259 1 0.54198 1 NA NA NA NA 0.74284 1 0.60549 1 0.84742 1 0.070005 1 0.44907 1 0.21252 1 CCDC66 9 (1%) 762 0.36773 1 0.19708 1 0.67481 1 0.67548 1 NA NA NA NA 0.068219 1 0.15665 1 0.090992 1 0.48246 1 0.4836 1 0.12506 1 HIST1H3B 7 (1%) 764 0.38283 1 1 1 0.554 1 0.62332 1 1 1 0.82708 1 0.33857 1 0.40117 1 0.47386 1 0.43028 1 0.6049 1 0.078777 1 TTN 122 (16%) 649 0.12192 1 0.038469 1 1.0151e-05 0.00805 0.039737 1 6.2253e-05 0.0489 0.052035 1 0.0003346 0.259 0.00090047 0.688 0.043402 1 0.019294 1 0.11333 1 0.0035063 1 SLC25A5 3 (0%) 768 NA NA NA NA 0.32891 1 0.71035 1 NA NA NA NA NA NA NA NA 0.78046 1 0.35423 1 0.45638 1 0.22998 1 SELPLG 7 (1%) 764 NA NA NA NA 0.078261 1 0.0037154 1 NA NA NA NA 0.10828 1 0.080144 1 0.47386 1 0.30395 1 1 1 0.092017 1 KRTAP9-9 6 (1%) 765 NA NA NA NA 0.24939 1 0.25343 1 NA NA NA NA 0.14118 1 1 1 0.29814 1 0.25628 1 0.25647 1 0.15597 1 KRTAP4-5 4 (1%) 767 NA NA NA NA 0.47845 1 0.25124 1 NA NA NA NA 0.26016 1 0.053405 1 0.079716 1 0.81408 1 0.15388 1 0.85178 1 SF3B1 14 (2%) 757 0.62869 1 0.094857 1 0.34705 1 0.24046 1 0.25347 1 0.004986 1 0.18599 1 0.02161 1 0.019423 1 0.1855 1 0.36876 1 0.13336 1 HLA-A 4 (1%) 767 0.81613 1 0.54285 1 0.33936 1 NA NA 1 1 0.82708 1 0.016717 1 0.31464 1 0.67074 1 0.2933 1 NA NA NA NA FGFR2 7 (1%) 764 0.60247 1 0.54285 1 0.85664 1 0.18769 1 1 1 0.82708 1 0.30228 1 0.51493 1 0.78505 1 1 1 0.074627 1 0.011131 1 SHROOM4 11 (1%) 760 0.43178 1 0.18175 1 0.031528 1 0.56186 1 0.40246 1 0.63316 1 0.36197 1 0.26908 1 0.6184 1 0.92516 1 0.38563 1 0.90416 1 MED12 20 (3%) 751 0.60328 1 0.32577 1 0.3038 1 0.62272 1 0.45536 1 0.80281 1 0.45212 1 0.95001 1 0.83524 1 0.64695 1 0.33478 1 0.094587 1 DENND4B 8 (1%) 763 NA NA NA NA 0.14752 1 0.015605 1 NA NA NA NA 0.074948 1 0.63103 1 0.4674 1 0.23906 1 0.5865 1 0.19247 1 ODF1 5 (1%) 766 NA NA NA NA 0.93219 1 0.50085 1 NA NA NA NA 0.4543 1 0.51736 1 0.67074 1 0.49056 1 0.69507 1 0.80638 1 AXL 6 (1%) 765 NA NA NA NA 0.2657 1 0.33033 1 NA NA NA NA 0.88681 1 0.25074 1 0.75163 1 0.38443 1 1 1 0.51122 1 RPL18 4 (1%) 767 NA NA NA NA 0.5042 1 0.24093 1 NA NA NA NA 0.11949 1 0.091748 1 0.54246 1 0.12092 1 0.45638 1 0.61526 1 RAI1 7 (1%) 764 NA NA NA NA 0.26858 1 0.87516 1 1 1 0.78219 1 0.7478 1 0.51493 1 0.47386 1 0.79726 1 0.86949 1 0.60024 1 ERBB2 12 (2%) 759 0.28657 1 0.89081 1 0.12105 1 0.012056 1 0.45096 1 0.77302 1 0.74641 1 0.29364 1 0.26937 1 0.06652 1 0.47124 1 0.40222 1 KRT38 4 (1%) 767 0.60247 1 0.8116 1 0.28762 1 0.78568 1 0.40246 1 0.63316 1 0.63301 1 0.81718 1 0.81691 1 1 1 NA NA NA NA TICAM1 5 (1%) 766 NA NA NA NA 0.77376 1 0.86922 1 NA NA NA NA 0.97664 1 0.60549 1 1 1 0.60627 1 1 1 0.60799 1 ASXL2 8 (1%) 763 0.36034 1 0.21437 1 0.79933 1 0.43136 1 NA NA NA NA 0.74886 1 0.30455 1 0.53072 1 0.33561 1 1 1 0.46817 1 ASPHD1 3 (0%) 768 NA NA NA NA 0.71147 1 0.8857 1 NA NA NA NA 0.66094 1 0.59091 1 1 1 0.62612 1 1 1 1 1 FAM171B 8 (1%) 763 0.9247 1 0.29072 1 0.94079 1 0.047031 1 NA NA NA NA 0.19265 1 0.0027711 1 0.31756 1 0.099719 1 0.032175 1 0.18819 1 MUC20 10 (1%) 761 NA NA NA NA 0.10537 1 0.14651 1 NA NA NA NA 0.00053878 0.414 0.19321 1 0.135 1 0.089302 1 0.34242 1 0.10855 1 PPEF1 8 (1%) 763 0.85303 1 1 1 0.35443 1 0.18284 1 1 1 1 1 0.66233 1 0.71053 1 0.25472 1 0.38534 1 0.20259 1 0.241 1 PRRX1 6 (1%) 765 0.57729 1 0.52186 1 0.047191 1 0.05666 1 0.83853 1 0.39197 1 0.55868 1 0.40735 1 0.86591 1 0.43327 1 0.32596 1 0.73033 1 ATP13A4 9 (1%) 762 0.60247 1 0.35582 1 0.15652 1 0.32961 1 NA NA NA NA 0.87337 1 0.42821 1 0.82617 1 0.83471 1 0.78871 1 0.66967 1 MUC2 18 (2%) 753 0.82997 1 0.25866 1 0.3245 1 0.48719 1 0.7782 1 0.88144 1 0.48788 1 0.28799 1 0.95134 1 1 1 1 1 0.30288 1 UBC 8 (1%) 763 0.33635 1 1 1 0.25024 1 0.35008 1 0.55623 1 0.82708 1 0.28977 1 0.89408 1 0.71703 1 0.74094 1 NA NA NA NA KCNN3 6 (1%) 765 0.96764 1 1 1 0.50417 1 0.36047 1 NA NA NA NA 0.14261 1 0.63519 1 0.41493 1 0.76887 1 0.45638 1 0.13839 1 RBM23 6 (1%) 765 NA NA NA NA 0.69345 1 0.40417 1 NA NA NA NA 0.79511 1 0.072164 1 0.41493 1 0.058077 1 0.69507 1 0.19029 1 GNRH2 3 (0%) 768 NA NA NA NA 0.31921 1 NA NA NA NA NA NA 0.95792 1 1 1 0.1245 1 1 1 NA NA NA NA