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 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 PIK3CA 316 (32%) 659 7.3213e-13 5.87e-10 3.4819e-10 2.78e-07 3.2478e-13 2.61e-10 4.2749e-12 3.42e-09 0.00016969 0.132 5.3753e-06 0.00424 9.7778e-29 7.97e-26 1.6596e-19 1.34e-16 1.3172e-07 0.000104 2.4598e-13 1.98e-10 1.2582e-07 9.97e-05 2.6201e-12 2.1e-09 CBFB 23 (2%) 952 0.13441 1 0.92543 1 0.02276 1 9.1583e-05 0.0718 0.12372 1 0.5135 1 9.4393e-06 0.00743 0.044953 1 0.54119 1 0.0036719 1 0.0035809 1 0.0042736 1 RUNX1 29 (3%) 946 0.014949 1 0.045249 1 0.0017969 1 0.076606 1 1 1 0.28489 1 0.018518 1 0.098414 1 0.038907 1 0.25657 1 0.15671 1 0.036916 1 GATA3 97 (10%) 878 6.0161e-06 0.00474 1.912e-07 0.000151 0.0013877 1 0.0025141 1 0.018438 1 0.00092901 0.715 1.7931e-08 1.42e-05 1.1068e-12 8.87e-10 0.0017814 1 3.9778e-10 3.17e-07 1.1979e-08 9.52e-06 5.6319e-11 4.49e-08 FOXA1 23 (2%) 952 0.35554 1 0.23773 1 0.28899 1 0.03934 1 0.8942 1 0.309 1 0.12683 1 0.053026 1 0.31854 1 0.088201 1 0.067344 1 0.55088 1 SF3B1 16 (2%) 959 0.81451 1 0.29829 1 0.3764 1 0.17243 1 0.4505 1 0.02458 1 0.65487 1 0.24349 1 0.88492 1 0.70441 1 0.61162 1 0.32327 1 MAP3K1 70 (7%) 905 9.8197e-05 0.0769 0.00068883 0.532 0.0028987 1 0.033988 1 0.0006903 0.532 3.812e-05 0.0299 0.00016643 0.13 0.0001777 0.138 0.0083032 1 0.00014004 0.11 0.0002138 0.166 0.0090457 1 TP53 295 (30%) 680 2.3466e-31 1.92e-28 2.139e-29 1.75e-26 4.4916e-56 3.69e-53 1.2585e-32 1.03e-29 4.6324e-23 3.76e-20 2.5759e-23 2.09e-20 5.533e-71 4.56e-68 1.8862e-63 1.55e-60 2.2334e-43 1.83e-40 7.0395e-58 5.79e-55 1.8737e-41 1.54e-38 2.3494e-35 1.92e-32 MAP2K4 32 (3%) 943 0.12266 1 0.0039455 1 0.18854 1 0.020414 1 0.0026164 1 0.029833 1 0.0097678 1 0.00019782 0.154 0.0044841 1 0.00029434 0.228 2.5757e-05 0.0202 0.0012853 0.988 PTEN 35 (4%) 940 0.28021 1 0.65816 1 0.29035 1 0.41921 1 0.92182 1 0.66696 1 0.47362 1 0.66484 1 0.1184 1 0.64803 1 0.48566 1 0.74438 1 CDH1 105 (11%) 870 0.00017383 0.135 0.0033612 1 3.7082e-15 2.99e-12 2.5796e-08 2.05e-05 0.0040434 1 0.01062 1 1.0377e-17 8.37e-15 8.8905e-18 7.18e-15 2.4991e-17 2.01e-14 2.6218e-25 2.13e-22 2.2057e-21 1.79e-18 2.027e-19 1.64e-16 TBX3 27 (3%) 948 0.42752 1 0.30676 1 0.43541 1 0.10753 1 0.082966 1 0.6092 1 0.060446 1 0.040936 1 0.13717 1 0.040081 1 0.27883 1 0.39063 1 MLL3 69 (7%) 906 0.59769 1 0.68788 1 0.60548 1 0.15726 1 0.59668 1 0.86545 1 0.18204 1 0.2339 1 0.061322 1 0.088567 1 0.32017 1 0.7499 1 RB1 19 (2%) 956 0.66565 1 0.40335 1 0.079803 1 0.061508 1 0.48237 1 0.76252 1 0.1495 1 0.056438 1 0.27213 1 0.0028198 1 0.013044 1 0.31778 1 NCOR1 41 (4%) 934 0.57078 1 0.9535 1 0.71019 1 0.94433 1 0.43549 1 0.16749 1 0.39796 1 0.76984 1 0.64043 1 0.57181 1 1 1 0.55424 1 CTCF 17 (2%) 958 0.033075 1 0.32247 1 0.041218 1 0.0093189 1 0.068463 1 0.29653 1 0.57668 1 0.19094 1 0.13004 1 0.047532 1 0.64158 1 0.4427 1 GPS2 11 (1%) 964 0.0013319 1 0.0059227 1 0.12017 1 0.37991 1 0.26774 1 0.31541 1 0.053432 1 0.09457 1 0.13707 1 1 1 0.867 1 0.72087 1 THEM5 11 (1%) 964 0.23079 1 0.44097 1 0.5294 1 0.2796 1 0.20861 1 0.039824 1 0.70054 1 0.56231 1 0.93852 1 1 1 0.33656 1 0.1367 1 RPGR 18 (2%) 957 0.98994 1 0.6639 1 0.86897 1 0.60149 1 0.76744 1 0.69524 1 0.94774 1 0.66854 1 0.78318 1 1 1 0.90892 1 0.45162 1 DNAH12 17 (2%) 958 0.97269 1 0.15798 1 0.47305 1 0.70671 1 0.4505 1 0.62739 1 0.0022397 1 0.38214 1 0.60988 1 0.28019 1 0.40012 1 0.17843 1 CDKN1B 10 (1%) 965 0.63407 1 0.17826 1 0.14164 1 0.10796 1 0.74133 1 0.28049 1 0.23233 1 0.094275 1 0.25217 1 0.11079 1 0.29531 1 0.55727 1 ZFP36L1 9 (1%) 966 0.56989 1 0.44097 1 0.023168 1 0.75837 1 0.026587 1 0.023322 1 0.11856 1 0.29442 1 0.23016 1 0.90647 1 0.867 1 0.72087 1 ASB10 8 (1%) 967 0.86924 1 0.81129 1 0.98108 1 0.7874 1 NA NA NA NA 0.56065 1 0.38617 1 0.6236 1 0.79858 1 0.867 1 1 1 HIST1H3B 11 (1%) 964 0.6378 1 1 1 0.92287 1 0.67728 1 0.63112 1 1 1 0.32397 1 0.13692 1 0.47596 1 0.91832 1 0.77807 1 0.8714 1 FAM86B1 8 (1%) 967 NA NA NA NA 0.73351 1 0.87034 1 NA NA NA NA 0.39973 1 0.53837 1 0.39445 1 0.005431 1 0.89271 1 0.59319 1 PIK3R1 15 (2%) 960 0.026604 1 0.72247 1 0.87297 1 0.077388 1 0.63112 1 0.45223 1 0.51074 1 0.48379 1 0.030701 1 0.1352 1 0.14077 1 0.5659 1 MYH9 19 (2%) 956 0.71129 1 0.18169 1 0.12276 1 0.46489 1 0.82166 1 0.60571 1 0.86881 1 0.28624 1 0.35408 1 0.19169 1 0.66025 1 0.13416 1 CASP8 12 (1%) 963 0.42308 1 0.3584 1 0.066315 1 0.43603 1 0.53088 1 0.73899 1 0.063275 1 1 1 0.43633 1 0.42403 1 0.74099 1 0.45162 1 COL6A5 25 (3%) 950 0.14393 1 0.44035 1 0.79093 1 0.204 1 0.075044 1 0.076018 1 0.20812 1 0.34175 1 0.57815 1 0.038283 1 0.050221 1 0.057654 1 TBL1XR1 10 (1%) 965 0.12343 1 0.23773 1 0.049694 1 0.49246 1 0.45066 1 0.56754 1 0.02278 1 0.14464 1 0.47488 1 0.042022 1 0.57502 1 0.24242 1 ASXL2 16 (2%) 959 0.40257 1 0.097462 1 0.8612 1 0.97149 1 0.28059 1 0.0050502 1 0.51175 1 0.39992 1 0.80324 1 0.18741 1 0.74099 1 0.26019 1 ARID1A 27 (3%) 948 0.13486 1 0.94281 1 0.15163 1 0.0615 1 1 1 0.47473 1 0.092366 1 0.27195 1 0.44301 1 0.093575 1 0.8375 1 0.045623 1 AQP12A 6 (1%) 969 0.71456 1 0.20312 1 0.20671 1 0.024723 1 0.20118 1 0.1152 1 0.69018 1 1 1 0.68865 1 1 1 1 1 1 1 EPDR1 5 (1%) 970 0.37908 1 1 1 0.7904 1 NA NA 0.55688 1 0.46841 1 0.19109 1 1 1 0.59878 1 1 1 0.29253 1 1 1 ERBB2 21 (2%) 954 0.8865 1 0.34862 1 0.025356 1 0.010142 1 0.54884 1 0.90641 1 0.29561 1 0.6583 1 0.11247 1 0.18328 1 0.58395 1 0.50255 1 MYB 12 (1%) 963 0.63095 1 1 1 0.22983 1 0.51427 1 1 1 0.86234 1 0.76449 1 0.65713 1 0.034389 1 0.17162 1 0.068348 1 0.48911 1 TMEM151B 6 (1%) 969 0.91457 1 0.29719 1 0.11534 1 0.57557 1 0.026587 1 0.19462 1 0.51379 1 0.03134 1 0.27199 1 0.71558 1 0.39672 1 0.19069 1 GALNTL6 5 (1%) 970 0.9212 1 1 1 0.22516 1 0.012448 1 NA NA NA NA 0.42681 1 0.13233 1 0.10957 1 0.65445 1 0.39672 1 0.19069 1 AKD1 18 (2%) 957 0.43967 1 0.59834 1 0.36139 1 0.53246 1 0.23548 1 0.12395 1 0.24229 1 0.080759 1 0.89561 1 0.47362 1 0.08123 1 0.43089 1 AARS 9 (1%) 966 0.40254 1 0.010742 1 0.7375 1 0.42446 1 0.83639 1 0.56319 1 0.0024127 1 0.47226 1 0.7455 1 0.31941 1 0.057313 1 0.071967 1 HLA-C 9 (1%) 966 0.31633 1 0.20312 1 0.58003 1 0.10565 1 0.39944 1 0.63373 1 0.27013 1 0.23622 1 0.18094 1 0.071698 1 0.19894 1 0.026727 1 GPRIN2 11 (1%) 964 0.65545 1 0.46464 1 0.69751 1 0.65535 1 0.87729 1 0.33049 1 0.84522 1 0.43329 1 0.40621 1 0.57806 1 0.7004 1 0.32382 1 TRPM5 11 (1%) 964 0.23713 1 0.61488 1 0.78634 1 0.25108 1 0.77844 1 0.78159 1 0.28761 1 0.062893 1 0.28798 1 0.1048 1 0.022185 1 0.017133 1 ANKRD12 18 (2%) 957 0.17774 1 0.11479 1 0.66005 1 0.8634 1 0.38495 1 0.51771 1 0.41993 1 0.10033 1 0.53702 1 0.64036 1 1 1 0.39886 1 FBXW7 15 (2%) 960 0.818 1 0.63995 1 0.084086 1 0.002505 1 0.77844 1 0.78159 1 0.058183 1 0.13508 1 0.42559 1 0.25636 1 0.48013 1 0.1253 1 PRICKLE3 11 (1%) 964 0.33466 1 0.28151 1 0.9506 1 0.60894 1 0.50889 1 0.89075 1 0.32695 1 0.12613 1 0.49094 1 0.13046 1 0.59767 1 0.26089 1 WDR52 16 (2%) 959 0.76787 1 0.056495 1 0.2201 1 0.16499 1 0.0042406 1 0.13693 1 0.013413 1 0.39992 1 0.30344 1 0.47663 1 0.045501 1 0.547 1 CDC42EP1 5 (1%) 970 0.57864 1 0.45178 1 0.63832 1 0.24153 1 0.83639 1 0.82863 1 0.2762 1 0.53599 1 0.70707 1 0.12382 1 NA NA NA NA ERBB3 18 (2%) 957 0.41249 1 0.2245 1 0.86719 1 0.52168 1 0.33474 1 0.29835 1 0.030955 1 0.21131 1 0.14347 1 0.81036 1 1 1 0.81661 1 FHOD3 13 (1%) 962 0.0431 1 0.020462 1 0.16211 1 0.026233 1 0.38495 1 0.026144 1 0.12942 1 0.0029597 1 0.16989 1 0.020013 1 0.7004 1 0.040825 1 PTHLH 7 (1%) 968 0.44175 1 0.3584 1 0.0088089 1 0.053291 1 0.68982 1 0.39157 1 0.72136 1 0.34086 1 0.2306 1 0.29043 1 NA NA NA NA SHISA4 5 (1%) 970 0.021349 1 0.20312 1 0.21824 1 0.26622 1 NA NA NA NA 0.27208 1 0.45449 1 0.34186 1 1 1 NA NA NA NA KCNN3 9 (1%) 966 0.32125 1 0.8387 1 0.21159 1 0.27041 1 0.32773 1 0.14438 1 0.32629 1 0.23622 1 0.40903 1 0.90647 1 0.16472 1 0.61284 1 FGFR2 11 (1%) 964 0.84052 1 0.87614 1 0.82946 1 0.20774 1 1 1 1 1 0.44261 1 0.79609 1 0.66601 1 1 1 0.80293 1 0.59319 1 HLA-DRB5 6 (1%) 969 0.0072308 1 0.013513 1 0.24773 1 0.87589 1 NA NA NA NA 0.25264 1 0.76969 1 0.22378 1 1 1 0.77994 1 1 1 ICOSLG 6 (1%) 969 0.69284 1 1 1 0.010294 1 0.6227 1 NA NA NA NA 0.10713 1 1 1 0.15593 1 1 1 1 1 0.60738 1 GYG2 8 (1%) 967 0.70324 1 1 1 0.16503 1 0.71371 1 0.15561 1 0.039824 1 0.88512 1 0.90706 1 0.44017 1 1 1 0.39672 1 0.19069 1 PPEF1 11 (1%) 964 0.83986 1 1 1 0.30571 1 0.57527 1 1 1 1 1 0.82254 1 0.63407 1 0.25866 1 0.32973 1 0.80293 1 0.78507 1 MAP4K1 10 (1%) 965 0.82776 1 0.45178 1 0.35791 1 0.57664 1 1 1 0.78159 1 0.43407 1 0.84875 1 0.96293 1 0.32633 1 0.23942 1 0.2073 1 ZNF41 11 (1%) 964 0.80994 1 0.46464 1 0.65645 1 0.20674 1 0.87729 1 0.29104 1 0.69317 1 0.47052 1 0.040139 1 0.84844 1 0.092408 1 0.64478 1 FBXO17 5 (1%) 970 NA NA NA NA 0.82 1 0.39945 1 NA NA NA NA 0.57894 1 0.38034 1 0.00029787 0.23 1 1 1 1 1 1 HRNR 31 (3%) 944 0.89175 1 0.45977 1 0.063615 1 0.97544 1 0.58685 1 0.58809 1 0.93101 1 0.48162 1 0.51649 1 0.87762 1 0.93754 1 0.76312 1 STAG2 13 (1%) 962 0.3573 1 1 1 0.22554 1 0.33686 1 0.87729 1 0.67628 1 0.32321 1 0.72669 1 0.30689 1 0.45343 1 0.50823 1 0.68725 1 CEP57 6 (1%) 969 0.32441 1 1 1 0.11158 1 0.12941 1 NA NA NA NA 0.15399 1 1 1 0.38806 1 0.062156 1 0.29253 1 0.026681 1 SPRR2B 3 (0%) 972 NA NA NA NA 0.73375 1 NA NA NA NA NA NA 0.50469 1 0.79472 1 0.90936 1 0.43 1 NA NA NA NA ZFP36L2 7 (1%) 968 0.43694 1 1 1 0.0095118 1 0.2056 1 1 1 1 1 0.49938 1 0.79821 1 0.66013 1 0.78065 1 1 1 0.83615 1 DMXL2 19 (2%) 956 0.6965 1 0.18169 1 0.05022 1 0.1581 1 0.10691 1 0.072694 1 0.0094671 1 0.069731 1 0.050488 1 0.22136 1 0.085006 1 0.13747 1 ZBTB7C 5 (1%) 970 NA NA NA NA 0.68204 1 0.74617 1 NA NA NA NA 0.81081 1 0.38034 1 0.67531 1 0.49812 1 0.77994 1 1 1 MUC5B 33 (3%) 942 0.69434 1 0.87918 1 0.41392 1 0.28461 1 0.91544 1 0.69524 1 0.37052 1 0.75921 1 0.7795 1 0.20998 1 0.74639 1 0.83032 1 XBP1 4 (0%) 971 NA NA NA NA 0.016381 1 0.36037 1 NA NA NA NA 0.34729 1 1 1 0.39433 1 0.53244 1 0.39341 1 0.81237 1 FXYD5 5 (1%) 970 0.69284 1 0.61488 1 0.33546 1 NA NA 0.64325 1 1 1 0.30988 1 0.45449 1 0.7564 1 0.49812 1 NA NA NA NA ATXN2 15 (2%) 960 0.83659 1 0.36588 1 0.39237 1 0.64207 1 0.23413 1 0.076608 1 0.75677 1 0.36431 1 0.53816 1 0.34153 1 0.79285 1 0.9155 1 CCL13 4 (0%) 971 NA NA NA NA 0.00018204 0.141 0.36037 1 NA NA NA NA 0.77842 1 0.56801 1 0.16028 1 0.53244 1 NA NA NA NA