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 0.16217 1 0.38935 1 0.88203 1 0.2657 1 0.17711 1 0.96766 1 0.67393 1 0.69111 1 0.10154 1 0.13953 1 MLL3 61 (8%) 710 0.27852 1 0.9223 1 0.83388 1 0.70393 1 0.70239 1 0.96821 1 0.27509 1 0.92176 1 0.13684 1 0.22145 1 0.6044 1 0.92584 1 NUDT11 8 (1%) 763 NA NA NA NA 0.70169 1 0.17941 1 NA NA NA NA 0.17226 1 0.89651 1 0.80029 1 0.27542 1 0.70069 1 0.27245 1 GIGYF2 13 (2%) 758 NA NA NA NA 0.45394 1 0.68534 1 NA NA NA NA 0.54601 1 0.43713 1 0.87066 1 1 1 0.6724 1 0.81676 1 ZNF384 14 (2%) 757 NA NA NA NA 0.48734 1 0.43662 1 NA NA NA NA 0.50968 1 0.67004 1 0.81957 1 0.39649 1 0.40121 1 0.70999 1 DCP1B 5 (1%) 766 NA NA NA NA 0.36455 1 0.12612 1 NA NA NA NA 0.77164 1 0.72323 1 1 1 0.52742 1 0.58821 1 0.79467 1 PIK3CA 261 (34%) 510 8.8999e-15 7.81e-12 3.8799e-10 3.38e-07 1.6772e-13 1.47e-10 7.3072e-11 6.39e-08 1.6388e-05 0.014 1.0648e-06 0.000919 3.8326e-29 3.39e-26 6.8439e-11 5.99e-08 2.315e-10 2.02e-07 3.1598e-18 2.78e-15 0.00018427 0.155 4.1293e-07 0.000358 NCOA3 29 (4%) 742 0.54907 1 1 1 0.97473 1 0.5047 1 1 1 1 1 0.61132 1 0.74609 1 0.49649 1 0.22984 1 0.062202 1 0.77251 1 AOAH 19 (2%) 752 NA NA NA NA 0.42582 1 0.73637 1 NA NA NA NA 0.64636 1 0.17461 1 0.086127 1 0.87102 1 0.14956 1 0.72067 1 RBMX 13 (2%) 758 NA NA NA NA 0.0015106 1 0.23588 1 NA NA NA NA 0.56305 1 0.18262 1 0.53198 1 0.34475 1 1 1 0.49978 1 RUNX1 25 (3%) 746 0.0055169 1 0.044232 1 0.00093052 0.769 0.056316 1 1 1 0.25194 1 0.022186 1 0.57998 1 0.06663 1 0.30514 1 0.059349 1 0.93353 1 PIK3R1 21 (3%) 750 0.17209 1 0.61649 1 0.49248 1 0.70872 1 0.53782 1 0.29702 1 0.12021 1 0.38466 1 0.38666 1 0.87102 1 0.6724 1 0.61693 1 MEF2A 14 (2%) 757 NA NA NA NA 0.57671 1 0.37665 1 NA NA NA NA 0.55297 1 0.27116 1 0.035238 1 0.038617 1 0.060584 1 0.2104 1 NCOR2 29 (4%) 742 0.67551 1 1 1 0.11209 1 0.48268 1 0.83853 1 0.68963 1 0.83808 1 0.59336 1 0.76738 1 0.46152 1 0.88739 1 0.77656 1 AKT1 19 (2%) 752 0.06343 1 0.92454 1 0.0033259 1 0.00021616 0.181 0.16241 1 0.34532 1 0.00021017 0.176 0.34782 1 0.063322 1 0.016691 1 0.21555 1 0.12484 1 GATA3 81 (11%) 690 0.0005751 0.477 0.00010133 0.0856 0.0040369 1 0.010043 1 0.0011529 0.949 0.00040708 0.34 4.6522e-05 0.0396 2.7512e-09 2.39e-06 3.5036e-06 0.00301 1.0567e-06 0.000913 1.1812e-06 0.00102 0.00010159 0.0857 NR1H2 18 (2%) 753 0.32598 1 0.26699 1 0.94048 1 0.16341 1 0.063975 1 0.11594 1 0.40117 1 0.24559 1 0.21476 1 0.29185 1 0.77994 1 0.038503 1 MAP3K4 18 (2%) 753 0.10846 1 0.72143 1 0.76841 1 0.17162 1 0.073322 1 0.68963 1 0.22325 1 0.40757 1 0.50865 1 0.41346 1 0.2723 1 0.15476 1 TP53 257 (33%) 514 7.0755e-37 6.28e-34 2.4254e-33 2.15e-30 8.753e-53 7.8e-50 6.9452e-21 6.11e-18 1.8749e-27 1.66e-24 1.102e-23 9.71e-21 3.3096e-56 2.95e-53 1.1394e-48 1.01e-45 2.6519e-38 2.35e-35 4.0047e-43 3.56e-40 2.8788e-27 2.54e-24 1.0741e-27 9.5e-25 TPRX1 7 (1%) 764 NA NA NA NA 0.20542 1 0.50354 1 NA NA NA NA 0.95837 1 1 1 0.74212 1 1 1 1 1 1 1 CDH1 55 (7%) 716 1.6718e-07 0.000145 8.2018e-05 0.0695 2.1968e-08 1.91e-05 0.0010338 0.852 0.00025549 0.214 0.00057945 0.48 3.3691e-06 0.0029 5.1525e-08 4.47e-05 7.6951e-11 6.72e-08 7.415e-12 6.5e-09 6.5448e-05 0.0555 8.5596e-05 0.0724 ATN1 17 (2%) 754 0.064261 1 0.054511 1 0.063086 1 0.89559 1 0.16884 1 0.29141 1 0.077561 1 0.85491 1 0.80239 1 0.25678 1 0.3213 1 0.11539 1 MAP2K4 32 (4%) 739 0.029235 1 0.0031315 1 0.050696 1 0.010517 1 0.0023792 1 0.034428 1 0.0055447 1 0.00046889 0.39 0.004306 1 0.00099684 0.822 0.0016355 1 0.026351 1 MAP3K1 57 (7%) 714 4.3258e-06 0.00371 4.3824e-05 0.0373 2.0756e-05 0.0177 0.018539 1 0.00020416 0.171 1.9896e-06 0.00171 0.00011847 0.0999 1.994e-05 0.017 4.2353e-07 0.000366 1.7299e-05 0.0148 2.4827e-05 0.0212 0.00028358 0.237 CBFB 16 (2%) 755 0.18352 1 0.64781 1 0.024527 1 0.0008626 0.714 0.34961 1 0.56866 1 0.00056344 0.468 0.12368 1 0.032708 1 6.1215e-05 0.052 0.070835 1 0.034001 1 CTCF 18 (2%) 753 0.026496 1 0.31977 1 0.0092394 1 0.020587 1 0.068249 1 0.36929 1 0.0045047 1 0.42782 1 0.085153 1 0.1836 1 0.83052 1 0.42634 1 CCDC144NL 8 (1%) 763 NA NA NA NA 0.00091566 0.757 0.40791 1 NA NA NA NA 0.66354 1 0.19095 1 0.27283 1 0.47799 1 0.44269 1 0.3963 1 AKD1 19 (2%) 752 0.92566 1 0.43682 1 0.29985 1 0.2303 1 0.46668 1 0.24234 1 0.67169 1 0.041243 1 0.12929 1 0.35775 1 0.077309 1 0.1461 1 RB1 14 (2%) 757 0.52273 1 0.1721 1 0.072745 1 0.13844 1 0.48293 1 0.76154 1 0.32912 1 0.29732 1 0.33287 1 0.037457 1 0.17895 1 0.084215 1 FOXA1 15 (2%) 756 0.7357 1 0.11583 1 0.13534 1 0.026194 1 1 1 0.5168 1 0.89156 1 0.1575 1 0.47827 1 0.53254 1 0.53182 1 0.32867 1 PHLDA1 9 (1%) 762 0.32088 1 0.2751 1 0.32491 1 0.69105 1 1 1 0.28034 1 0.67986 1 0.81417 1 0.32006 1 0.90902 1 0.38932 1 0.38219 1 VEZF1 8 (1%) 763 NA NA NA NA 0.40909 1 0.54832 1 NA NA NA NA 0.19199 1 0.89554 1 1 1 0.81765 1 1 1 0.85198 1 ZFP36L1 10 (1%) 761 0.83919 1 0.68646 1 0.028024 1 0.13784 1 0.025798 1 0.39178 1 0.84007 1 0.59866 1 0.83422 1 0.41659 1 0.64309 1 0.73502 1 NCOR1 31 (4%) 740 0.48764 1 0.33042 1 0.35421 1 0.7453 1 0.72317 1 0.72615 1 0.52793 1 0.15393 1 0.44644 1 0.28089 1 0.52819 1 0.74718 1 AQP7 9 (1%) 762 0.6379 1 0.068244 1 0.75221 1 0.71871 1 NA NA NA NA 0.72071 1 0.50927 1 0.31602 1 0.65716 1 0.73479 1 0.43413 1 TBX3 18 (2%) 753 0.61241 1 0.34526 1 0.79141 1 0.17976 1 0.15974 1 0.55094 1 0.39478 1 0.40757 1 0.90233 1 0.90959 1 0.79112 1 1 1 DSPP 26 (3%) 745 0.94455 1 0.4158 1 0.56107 1 0.93901 1 0.098697 1 0.38708 1 0.71045 1 0.054405 1 0.099238 1 0.7355 1 0.26141 1 0.6751 1 RPGR 16 (2%) 755 0.29663 1 0.20509 1 0.99925 1 0.72434 1 0.61624 1 0.37325 1 0.28458 1 0.26891 1 0.62607 1 0.14756 1 0.64906 1 0.50961 1 BCL6B 8 (1%) 763 NA NA NA NA 0.47779 1 0.63016 1 NA NA NA NA 0.24909 1 0.79136 1 1 1 0.81765 1 0.73479 1 0.54856 1 TBL1XR1 9 (1%) 762 0.10865 1 0.29485 1 0.15624 1 NA NA 0.45536 1 0.56866 1 0.043173 1 0.15173 1 0.44597 1 0.16819 1 0.86441 1 0.27675 1 CRIPAK 13 (2%) 758 NA NA NA NA 0.39803 1 0.45922 1 NA NA NA NA 0.45343 1 0.29214 1 0.65662 1 0.55049 1 0.14018 1 0.13206 1 MYB 11 (1%) 760 0.78645 1 1 1 0.26898 1 0.35474 1 1 1 0.68963 1 0.79751 1 0.57354 1 0.72574 1 0.73192 1 0.5474 1 1 1 GPS2 6 (1%) 765 0.0076799 1 0.02839 1 0.12836 1 0.28289 1 1 1 1 1 0.49013 1 0.55892 1 0.19798 1 0.27764 1 NA NA NA NA PABPC3 8 (1%) 763 0.16324 1 0.80139 1 0.74083 1 0.98057 1 NA NA NA NA 0.67986 1 0.89651 1 0.71277 1 0.90878 1 1 1 1 1 E2F4 4 (1%) 767 NA NA NA NA 0.92851 1 NA NA NA NA NA NA 0.86779 1 0.68673 1 0.81639 1 1 1 NA NA NA NA DNAH12 12 (2%) 759 0.96689 1 0.26634 1 0.84945 1 0.54081 1 0.68948 1 0.68963 1 0.07991 1 0.75339 1 0.86042 1 1 1 0.79112 1 0.32358 1 CDKN1B 7 (1%) 764 0.35772 1 0.11035 1 0.0027083 1 0.031152 1 0.33082 1 0.39197 1 0.26761 1 0.36716 1 0.040976 1 0.2541 1 0.50191 1 0.5587 1 HNF1A 9 (1%) 762 NA NA NA NA 0.19414 1 0.66005 1 NA NA NA NA 0.33624 1 0.10716 1 0.12995 1 0.16819 1 0.63003 1 0.15643 1 CCDC66 14 (2%) 757 0.36696 1 0.4455 1 0.2681 1 0.8655 1 1 1 0.63316 1 0.051439 1 0.27863 1 0.51636 1 0.18966 1 0.37105 1 0.099176 1 CASP8 10 (1%) 761 0.35508 1 0.19708 1 0.60767 1 0.47331 1 0.40246 1 1 1 0.26583 1 0.55042 1 0.059332 1 0.032962 1 0.18898 1 0.22668 1 STXBP2 10 (1%) 761 NA NA NA NA 0.9235 1 0.95417 1 NA NA NA NA 0.8074 1 0.50313 1 0.47464 1 0.50533 1 0.8143 1 0.88442 1 HIST1H3B 7 (1%) 764 0.38283 1 1 1 0.55331 1 0.70532 1 1 1 0.82708 1 0.21455 1 0.69146 1 1 1 0.79627 1 0.42904 1 0.29977 1 CTU2 5 (1%) 766 NA NA NA NA 0.26011 1 0.53442 1 NA NA NA NA 0.71726 1 0.72323 1 1 1 0.075431 1 0.46606 1 0.030434 1 TTN 122 (16%) 649 0.12192 1 0.038469 1 0.00017024 0.143 0.032938 1 6.2253e-05 0.0529 0.052035 1 0.00038205 0.319 0.0046546 1 0.06148 1 0.0068111 1 0.068656 1 0.045491 1 SHROOM4 12 (2%) 759 0.64041 1 0.18326 1 0.1066 1 0.43456 1 0.15759 1 0.31381 1 0.24497 1 0.41863 1 0.73982 1 0.70111 1 0.91417 1 0.48585 1 HLA-A 4 (1%) 767 0.81613 1 0.54285 1 0.26393 1 NA NA 1 1 0.82708 1 0.011559 1 0.27736 1 0.65878 1 0.21369 1 NA NA NA NA SLC25A5 3 (0%) 768 NA NA NA NA 0.24272 1 0.70019 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SELPLG 7 (1%) 764 NA NA NA NA 0.27842 1 0.10011 1 NA NA NA NA 0.078972 1 0.16647 1 0.31026 1 0.12762 1 1 1 0.22899 1 KRTAP9-9 6 (1%) 765 NA NA NA NA 0.26164 1 0.22848 1 NA NA NA NA 0.13768 1 1 1 0.86864 1 0.49835 1 1 1 0.073146 1 KRTAP4-5 4 (1%) 767 NA NA NA NA 0.44794 1 0.28186 1 NA NA NA NA 0.14604 1 0.12849 1 0.24838 1 0.69082 1 0.094929 1 1 1 SF3B1 14 (2%) 757 0.62869 1 0.094857 1 0.37821 1 0.22359 1 0.25347 1 0.004986 1 0.2535 1 0.1575 1 0.11922 1 0.47539 1 0.63092 1 0.067048 1 FGFR2 7 (1%) 764 0.60247 1 0.54285 1 0.8479 1 0.30201 1 1 1 0.82708 1 0.24909 1 0.79136 1 0.60298 1 0.49407 1 0.39004 1 0.068751 1 MUC2 22 (3%) 749 0.82997 1 0.25866 1 0.32807 1 0.30884 1 0.7782 1 0.88144 1 0.50001 1 0.42241 1 0.59842 1 0.72542 1 0.75192 1 0.287 1 MED12 20 (3%) 751 0.60328 1 0.32577 1 0.35219 1 0.72296 1 0.45536 1 0.80281 1 0.70119 1 1 1 0.42926 1 0.80283 1 0.29363 1 0.23039 1 USP36 13 (2%) 758 0.66846 1 0.42948 1 0.65266 1 0.38843 1 NA NA NA NA 0.77823 1 0.27116 1 1 1 0.82253 1 0.92246 1 0.81676 1 DENND4B 8 (1%) 763 NA NA NA NA 0.20938 1 0.034578 1 NA NA NA NA 0.077266 1 0.45725 1 0.10729 1 0.14746 1 0.16494 1 0.08534 1 RAI1 7 (1%) 764 NA NA NA NA 0.37462 1 0.89945 1 1 1 0.78219 1 0.82565 1 0.32593 1 0.5198 1 0.16314 1 0.63092 1 0.82959 1 ODF1 5 (1%) 766 NA NA NA NA 0.92851 1 0.4445 1 NA NA NA NA 0.68869 1 0.27736 1 0.81639 1 0.35632 1 0.64309 1 1 1 AXL 6 (1%) 765 NA NA NA NA 0.37654 1 0.20999 1 NA NA NA NA 0.82568 1 0.081587 1 0.71439 1 1 1 0.50191 1 0.27816 1 RPL18 4 (1%) 767 NA NA NA NA 0.50065 1 0.19195 1 NA NA NA NA 0.12087 1 0.094382 1 0.10966 1 0.04957 1 0.27417 1 0.44128 1 KRT38 4 (1%) 767 0.60247 1 0.8116 1 0.23754 1 0.75452 1 0.40246 1 0.63316 1 0.62545 1 1 1 0.81639 1 0.082309 1 NA NA NA NA ASXL2 8 (1%) 763 0.36034 1 0.21437 1 0.78093 1 0.42025 1 NA NA NA NA 0.81206 1 0.52305 1 0.60298 1 0.44064 1 0.74982 1 0.18004 1 TICAM1 5 (1%) 766 NA NA NA NA 0.7551 1 0.87267 1 NA NA NA NA 0.94862 1 0.44917 1 1 1 0.52742 1 0.81929 1 1 1 RBM5 12 (2%) 759 NA NA NA NA 0.75847 1 0.77222 1 NA NA NA NA 0.75019 1 0.80916 1 0.3076 1 0.20725 1 0.051367 1 0.52291 1 ASPHD1 3 (0%) 768 NA NA NA NA 0.68605 1 0.87636 1 NA NA NA NA 0.56391 1 0.80988 1 1 1 1 1 1 1 1 1 PPEF1 8 (1%) 763 0.85303 1 1 1 0.35467 1 0.47219 1 1 1 1 1 0.43223 1 0.59186 1 0.27283 1 0.38352 1 0.10282 1 0.12029 1 MUC20 10 (1%) 761 NA NA NA NA 0.014858 1 0.1776 1 NA NA NA NA 0.00043008 0.358 0.054636 1 0.36004 1 0.12483 1 0.64906 1 0.14048 1 TMEM184A 4 (1%) 767 NA NA NA NA 0.5432 1 0.0060914 1 NA NA NA NA 0.9577 1 0.68673 1 1 1 0.27801 1 0.0067701 1 0.0012482 1 FAM171B 8 (1%) 763 0.9247 1 0.29072 1 0.55199 1 0.056486 1 NA NA NA NA 0.1999 1 0.0017518 1 0.60298 1 0.037408 1 0.17256 1 0.12797 1 PRRX1 6 (1%) 765 0.57729 1 0.52186 1 0.39848 1 0.093932 1 0.83853 1 0.39197 1 0.48891 1 0.4965 1 0.29328 1 0.43499 1 0.58788 1 0.67986 1 ATP13A4 9 (1%) 762 0.60247 1 0.35582 1 0.13358 1 0.36178 1 NA NA NA NA 0.86502 1 0.33516 1 0.90702 1 0.63096 1 0.44269 1 0.50564 1 MUC21 6 (1%) 765 0.31688 1 0.42948 1 0.12836 1 0.2773 1 NA NA NA NA 0.64894 1 0.4965 1 0.86864 1 0.24158 1 1 1 0.29977 1 HLA-B 4 (1%) 767 NA NA NA NA 0.61152 1 0.69956 1 NA NA NA NA 0.38146 1 1 1 0.81639 1 0.35632 1 1 1 1 1 RBM23 6 (1%) 765 NA NA NA NA 0.66715 1 0.32805 1 NA NA NA NA 0.78941 1 0.035799 1 0.35137 1 0.087158 1 0.64309 1 0.73502 1 UBC 8 (1%) 763 0.33635 1 1 1 0.74395 1 0.30902 1 0.55623 1 0.82708 1 0.21452 1 1 1 0.89859 1 0.27542 1 NA NA NA NA SPRED3 4 (1%) 767 NA NA NA NA 0.84468 1 0.7513 1 NA NA NA NA 0.9577 1 0.46897 1 0.53638 1 0.27801 1 0.42904 1 0.29977 1 KCNN3 6 (1%) 765 0.96764 1 1 1 0.070738 1 0.31109 1 NA NA NA NA 0.10152 1 0.37941 1 0.35137 1 0.67321 1 0.27417 1 0.18004 1 GNRH2 3 (0%) 768 NA NA NA NA 0.24718 1 NA NA NA NA NA NA 0.82169 1 1 1 0.77469 1 0.80052 1 NA NA NA NA MED15 7 (1%) 764 NA NA NA NA 0.43695 1 0.12429 1 NA NA NA NA 0.52357 1 0.28801 1 0.23492 1 0.2541 1 0.17869 1 0.22899 1