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 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 PIK3CA 316 (32%) 659 7.3213e-13 5.87e-10 3.4819e-10 2.78e-07 2.645e-12 2.11e-09 2.4604e-14 1.98e-11 0.00016969 0.132 5.3753e-06 0.00424 1.3599e-14 1.09e-11 8.7063e-19 7.04e-16 1.0999e-12 8.8e-10 4.2188e-20 3.42e-17 5.3762e-09 4.27e-06 1.2872e-12 1.03e-09 CBFB 23 (2%) 952 0.13441 1 0.92543 1 0.039004 1 0.00015956 0.124 0.12372 1 0.5135 1 0.090424 1 0.14882 1 0.064896 1 1.7311e-05 0.0136 0.0039533 1 0.0048085 1 GATA3 77 (8%) 898 4.4184e-06 0.00349 1.1563e-06 0.000915 0.0005203 0.402 0.0034112 1 0.21784 1 0.038833 1 7.8764e-10 6.27e-07 9.9595e-13 7.98e-10 3.3422e-05 0.0263 3.1471e-07 0.000249 5.9136e-05 0.0463 5.391e-08 4.28e-05 FOXA1 23 (2%) 952 0.35554 1 0.23773 1 0.24783 1 0.044781 1 0.8942 1 0.309 1 0.015531 1 0.048076 1 0.12562 1 0.041109 1 0.070473 1 0.57976 1 SF3B1 16 (2%) 959 0.81451 1 0.29829 1 0.43348 1 0.15456 1 0.4505 1 0.02458 1 0.12455 1 0.26457 1 0.049717 1 0.90101 1 0.66952 1 0.20042 1 TP53 295 (30%) 680 2.3466e-31 1.92e-28 2.139e-29 1.75e-26 6.9443e-52 5.71e-49 3.9073e-31 3.19e-28 4.6324e-23 3.77e-20 2.5759e-23 2.1e-20 1.6178e-64 1.33e-61 2.8593e-61 2.36e-58 1.9855e-49 1.63e-46 1.4497e-59 1.19e-56 1.3208e-41 1.08e-38 1.6264e-34 1.33e-31 CDH1 105 (11%) 870 0.00017383 0.135 0.0033612 1 6.8705e-14 5.52e-11 5.8934e-09 4.68e-06 0.0040434 1 0.01062 1 8.3584e-15 6.74e-12 3.6969e-18 2.98e-15 6.4202e-25 5.23e-22 3.0393e-22 2.47e-19 4.9983e-21 4.05e-18 2.0636e-18 1.67e-15 RUNX1 29 (3%) 946 0.014949 1 0.045249 1 0.0090456 1 0.034625 1 1 1 0.28489 1 0.062115 1 0.0049317 1 0.0057018 1 0.0021253 1 0.18284 1 0.05935 1 PTEN 35 (4%) 940 0.28021 1 0.65816 1 0.16967 1 0.32714 1 0.92182 1 0.66696 1 0.96724 1 0.96867 1 0.65472 1 0.81019 1 0.43789 1 0.71969 1 TBX3 27 (3%) 948 0.42752 1 0.30676 1 0.44612 1 0.057841 1 0.082966 1 0.6092 1 0.05061 1 0.089064 1 0.15873 1 0.096252 1 0.31474 1 0.30048 1 MAP2K4 32 (3%) 943 0.12266 1 0.0039455 1 0.072194 1 0.016884 1 0.0026164 1 0.029833 1 0.00068125 0.525 0.0003078 0.238 0.00023682 0.184 0.0022805 1 2.8252e-05 0.0222 0.013714 1 MLL3 69 (7%) 906 0.59769 1 0.68788 1 0.59624 1 0.29165 1 0.59668 1 0.86545 1 0.056831 1 0.1275 1 0.085948 1 0.071574 1 0.46247 1 0.56611 1 MAP3K1 70 (7%) 905 9.8197e-05 0.0768 0.00068883 0.53 0.0078231 1 0.018398 1 0.0006903 0.531 3.812e-05 0.0299 0.0003039 0.236 0.00031891 0.247 5.8372e-05 0.0458 0.00072492 0.557 0.00028108 0.218 0.018787 1 NCOR1 41 (4%) 934 0.57078 1 0.9535 1 0.9338 1 0.82308 1 0.43549 1 0.16749 1 0.84736 1 0.88344 1 0.69869 1 0.66637 1 0.7941 1 0.67725 1 RB1 19 (2%) 956 0.66565 1 0.40335 1 0.15325 1 0.063942 1 0.48237 1 0.76252 1 0.023272 1 0.070698 1 0.059062 1 0.075557 1 0.011564 1 0.28723 1 CTCF 17 (2%) 958 0.033075 1 0.32247 1 0.014476 1 0.0041324 1 0.068463 1 0.29653 1 0.11895 1 0.19535 1 0.042839 1 0.062952 1 0.69851 1 0.44393 1 THEM5 11 (1%) 964 0.23079 1 0.44097 1 0.23056 1 0.48761 1 0.20861 1 0.039824 1 0.63124 1 0.55936 1 1 1 0.56198 1 1 1 0.18598 1 GPS2 10 (1%) 965 0.0013319 1 0.0059227 1 0.068238 1 0.37481 1 0.26774 1 0.31541 1 0.17205 1 0.25265 1 0.37891 1 0.0083012 1 1 1 0.25871 1 RPGR 18 (2%) 957 0.98994 1 0.6639 1 0.8721 1 0.6672 1 0.76744 1 0.69524 1 0.80447 1 0.9002 1 0.91709 1 0.57355 1 0.90766 1 0.45146 1 DNAH12 17 (2%) 958 0.97269 1 0.15798 1 0.57381 1 0.63142 1 0.4505 1 0.62739 1 0.94631 1 0.37659 1 0.28326 1 0.79766 1 0.40017 1 0.16389 1 CDKN1B 10 (1%) 965 0.63407 1 0.17826 1 0.0061977 1 0.07241 1 0.74133 1 0.28049 1 0.096597 1 0.19265 1 0.02942 1 0.10718 1 0.33128 1 0.56142 1 ZFP36L1 9 (1%) 966 0.56989 1 0.44097 1 0.020838 1 0.24436 1 0.026587 1 0.023322 1 0.28222 1 0.32416 1 0.53446 1 0.91239 1 0.86462 1 0.71625 1 ASB10 8 (1%) 967 0.86924 1 0.81129 1 0.97844 1 0.7381 1 NA NA NA NA 0.50111 1 0.90822 1 0.092578 1 0.74013 1 0.86462 1 1 1 HIST1H3B 11 (1%) 964 0.6378 1 1 1 0.91747 1 0.73295 1 0.63112 1 1 1 0.91776 1 0.46683 1 0.69372 1 0.58752 1 0.87992 1 0.87172 1 FAM86B1 8 (1%) 967 NA NA NA NA 0.73845 1 0.89118 1 NA NA NA NA 0.89365 1 0.53335 1 0.22728 1 0.60031 1 0.89227 1 0.5963 1 PIK3R1 15 (2%) 960 0.026604 1 0.72247 1 0.88044 1 0.086842 1 0.63112 1 0.45223 1 0.14165 1 0.53014 1 0.05482 1 1 1 0.13955 1 0.43632 1 MYH9 19 (2%) 956 0.71129 1 0.18169 1 0.2277 1 0.43662 1 0.82166 1 0.60571 1 0.87321 1 0.50711 1 0.61439 1 0.066769 1 0.65163 1 0.13651 1 CASP8 12 (1%) 963 0.42308 1 0.3584 1 0.38677 1 0.37155 1 0.53088 1 0.73899 1 1 1 1 1 0.40171 1 0.45833 1 0.74026 1 0.45146 1 COL6A5 25 (3%) 950 0.14393 1 0.44035 1 0.63074 1 0.34247 1 0.075044 1 0.076018 1 0.21749 1 0.11176 1 0.034698 1 0.2965 1 0.044794 1 0.024419 1 TBL1XR1 10 (1%) 965 0.12343 1 0.23773 1 0.04456 1 0.43976 1 0.45066 1 0.56754 1 0.42568 1 0.14324 1 0.17522 1 0.0499 1 0.64197 1 0.23929 1 ASXL2 16 (2%) 959 0.40257 1 0.097462 1 0.89419 1 0.86753 1 0.28059 1 0.0050502 1 0.33435 1 0.40813 1 1 1 0.14427 1 0.74026 1 0.25162 1 ARID1A 27 (3%) 948 0.13486 1 0.94281 1 0.055199 1 0.10362 1 1 1 0.47473 1 0.20623 1 0.29461 1 0.20139 1 0.12959 1 0.30729 1 0.87698 1 AQP12A 6 (1%) 969 0.71456 1 0.20312 1 0.23009 1 0.031676 1 0.20118 1 0.1152 1 0.86707 1 0.5838 1 0.77657 1 1 1 1 1 1 1 EPDR1 5 (1%) 970 0.37908 1 1 1 0.71924 1 NA NA 0.55688 1 0.46841 1 0.71525 1 1 1 0.82275 1 1 1 0.28926 1 1 1 ERBB2 21 (2%) 954 0.8865 1 0.34862 1 0.10944 1 0.013403 1 0.54884 1 0.90641 1 0.25628 1 0.37705 1 0.015527 1 0.00078762 0.604 0.66587 1 0.39621 1 MYB 12 (1%) 963 0.63095 1 1 1 0.20797 1 0.51234 1 1 1 0.86234 1 1 1 0.87016 1 0.46876 1 0.86997 1 0.45409 1 0.36007 1 TMEM151B 6 (1%) 969 0.91457 1 0.29719 1 0.30619 1 0.52004 1 0.026587 1 0.19462 1 0.34304 1 0.0298 1 0.28251 1 0.13211 1 0.38941 1 0.7847 1 GALNTL6 5 (1%) 970 0.9212 1 1 1 0.21114 1 0.012448 1 NA NA NA NA 0.0402 1 0.10219 1 0.57234 1 0.16536 1 0.38941 1 0.17909 1 AKD1 18 (2%) 957 0.43967 1 0.59834 1 0.32172 1 0.54521 1 0.23548 1 0.12395 1 0.2818 1 0.076892 1 0.21584 1 0.58157 1 0.11111 1 0.3392 1 AARS 9 (1%) 966 0.40254 1 0.010742 1 0.74175 1 0.50896 1 0.83639 1 0.56319 1 0.057123 1 0.1094 1 0.24163 1 0.35892 1 0.039847 1 0.83704 1 HLA-C 9 (1%) 966 0.31633 1 0.20312 1 0.5508 1 0.092617 1 0.39944 1 0.63373 1 0.080603 1 0.39179 1 0.26655 1 0.14265 1 0.16749 1 0.024685 1 GPRIN2 11 (1%) 964 0.65545 1 0.46464 1 0.92734 1 0.65485 1 0.87729 1 0.33049 1 0.46128 1 0.39523 1 0.66987 1 0.33082 1 0.6416 1 0.2879 1 TRPM5 11 (1%) 964 0.23713 1 0.61488 1 0.60638 1 0.033047 1 0.77844 1 0.78159 1 0.040848 1 0.06027 1 0.093321 1 0.09375 1 0.021554 1 0.038314 1 ANKRD12 18 (2%) 957 0.17774 1 0.11479 1 0.6031 1 0.89703 1 0.38495 1 0.51771 1 0.46398 1 0.034278 1 0.53921 1 0.33225 1 1 1 0.4909 1 FBXW7 15 (2%) 960 0.818 1 0.63995 1 0.064232 1 0.0029613 1 0.77844 1 0.78159 1 0.22246 1 0.13007 1 0.39827 1 0.14427 1 0.41089 1 0.096829 1 PRICKLE3 11 (1%) 964 0.33466 1 0.28151 1 0.94145 1 0.6452 1 0.50889 1 0.89075 1 0.17012 1 0.431 1 0.80118 1 0.086352 1 0.59376 1 0.63939 1 WDR52 16 (2%) 959 0.76787 1 0.056495 1 0.31838 1 0.165 1 0.0042406 1 0.13693 1 0.011861 1 0.36613 1 0.0095824 1 0.36944 1 0.04484 1 1 1 CDC42EP1 5 (1%) 970 0.57864 1 0.45178 1 0.60676 1 0.25157 1 0.83639 1 0.82863 1 0.83942 1 0.53101 1 0.618 1 0.13211 1 NA NA NA NA ERBB3 18 (2%) 957 0.41249 1 0.2245 1 0.80267 1 0.19246 1 0.33474 1 0.29835 1 0.16814 1 0.098587 1 0.925 1 0.77675 1 1 1 1 1 FHOD3 13 (1%) 962 0.0431 1 0.020462 1 0.064893 1 0.09072 1 0.38495 1 0.026144 1 0.021512 1 0.0020774 1 0.08291 1 0.0031311 1 0.6416 1 0.23493 1 PTHLH 7 (1%) 968 0.44175 1 0.3584 1 0.027646 1 0.004115 1 0.68982 1 0.39157 1 0.16354 1 0.29521 1 0.11395 1 0.2136 1 NA NA NA NA SHISA4 5 (1%) 970 0.021349 1 0.20312 1 0.1882 1 0.41349 1 NA NA NA NA 0.83942 1 0.45341 1 0.34171 1 1 1 NA NA NA NA KCNN3 9 (1%) 966 0.32125 1 0.8387 1 0.20741 1 0.28884 1 0.32773 1 0.14438 1 0.24837 1 0.21311 1 0.24163 1 0.76293 1 0.16219 1 0.61632 1 FGFR2 11 (1%) 964 0.84052 1 0.87614 1 0.32309 1 0.23972 1 1 1 1 1 0.84966 1 0.79671 1 0.54789 1 0.86309 1 0.80235 1 0.36341 1 HLA-DRB5 6 (1%) 969 0.0072308 1 0.013513 1 0.12657 1 0.65367 1 NA NA NA NA 0.64537 1 0.77012 1 0.25956 1 0.12682 1 0.78082 1 1 1 ICOSLG 6 (1%) 969 0.69284 1 1 1 0.16095 1 0.65367 1 NA NA NA NA 0.55392 1 1 1 0.88572 1 0.77226 1 1 1 1 1 GYG2 8 (1%) 967 0.70324 1 1 1 0.18929 1 0.71942 1 0.15561 1 0.039824 1 1 1 0.43309 1 0.4031 1 0.9042 1 0.38941 1 0.17909 1 PPEF1 11 (1%) 964 0.83986 1 1 1 0.07714 1 0.36027 1 1 1 1 1 0.24937 1 0.92827 1 0.80118 1 0.50533 1 1 1 0.31691 1 MAP4K1 10 (1%) 965 0.82776 1 0.45178 1 0.2321 1 0.59864 1 1 1 0.78159 1 0.3575 1 0.048784 1 0.4427 1 0.66153 1 0.27381 1 0.20153 1 ZNF41 11 (1%) 964 0.80994 1 0.46464 1 0.60161 1 0.24368 1 0.87729 1 0.29104 1 0.18708 1 0.431 1 0.37046 1 0.86309 1 0.091757 1 0.10948 1 FBXO17 5 (1%) 970 NA NA NA NA 0.83105 1 0.43335 1 NA NA NA NA 0.40138 1 0.62182 1 0.74026 1 1 1 1 1 1 1 HRNR 31 (3%) 944 0.89175 1 0.45977 1 0.22488 1 0.94421 1 0.58685 1 0.58809 1 0.57686 1 0.43609 1 0.30036 1 0.67693 1 0.69337 1 1 1 STAG2 13 (1%) 962 0.3573 1 1 1 0.29449 1 0.37294 1 0.87729 1 0.67628 1 0.52587 1 0.93636 1 0.19385 1 0.59524 1 0.50671 1 0.88306 1 CEP57 6 (1%) 969 0.32441 1 1 1 0.40589 1 0.14452 1 NA NA NA NA 0.55392 1 1 1 0.073139 1 0.77226 1 0.058139 1 0.027044 1 SPRR2B 3 (0%) 972 NA NA NA NA 0.73408 1 NA NA NA NA NA NA 0.43218 1 0.7978 1 0.63316 1 0.79337 1 NA NA NA NA ZFP36L2 7 (1%) 968 0.43694 1 1 1 0.010789 1 0.78702 1 1 1 1 1 0.34544 1 0.44158 1 0.65433 1 0.89073 1 1 1 0.83704 1 DMXL2 19 (2%) 956 0.6965 1 0.18169 1 0.037617 1 0.26308 1 0.10691 1 0.072694 1 0.046416 1 0.056612 1 0.016827 1 0.19235 1 0.071305 1 0.10168 1 ZBTB7C 5 (1%) 970 NA NA NA NA 0.67347 1 0.75175 1 NA NA NA NA 0.26434 1 0.38053 1 0.86827 1 1 1 0.78082 1 1 1 MUC5B 33 (3%) 942 0.69434 1 0.87918 1 0.44446 1 0.3709 1 0.91544 1 0.69524 1 0.32913 1 0.77132 1 0.53254 1 0.72907 1 0.81797 1 0.8597 1 XBP1 4 (0%) 971 NA NA NA NA 0.019942 1 0.38558 1 NA NA NA NA 1 1 0.82291 1 0.48147 1 0.69299 1 0.39343 1 0.81394 1 FXYD5 5 (1%) 970 0.69284 1 0.61488 1 0.25884 1 NA NA 0.64325 1 1 1 0.079658 1 0.45341 1 0.4009 1 0.86196 1 NA NA NA NA ATXN2 15 (2%) 960 0.83659 1 0.36588 1 0.37967 1 0.70144 1 0.23413 1 0.076608 1 0.60274 1 0.34483 1 0.8458 1 1 1 0.8556 1 0.91643 1 CCL13 4 (0%) 971 NA NA NA NA 0.00015071 0.118 0.30632 1 NA NA NA NA 0.31234 1 0.5652 1 0.3113 1 0.47991 1 NA NA NA NA