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 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 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%) 661 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 0.00144 0.0244 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 TP53 296 (30%) 681 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 GATA3 97 (10%) 880 9.9999e-06 0.000249 9.9999e-06 0.000249 0.00090999 0.0169 0.00082999 0.0157 0.01475 0.163 0.00082999 0.0157 9.9999e-06 0.000249 9.9999e-06 0.000249 0.00214 0.035 9.9999e-06 0.000249 9.9999e-06 0.000249 0.11258 0.542 MAP3K1 71 (7%) 906 4e-05 0.000948 0.00018 0.00416 0.00176 0.0293 0.00347 0.0522 0.00052999 0.0107 9.9999e-06 0.000249 0.00051999 0.0107 0.00026 0.00573 0.00035 0.00754 0.00103 0.0188 0.11039 0.541 0.1303 0.577 CDH1 107 (11%) 870 3e-05 0.000729 0.00371 0.0541 9.9999e-06 0.000249 9.9999e-06 0.000249 0.01011 0.127 0.01358 0.155 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 9.9999e-06 0.000249 CBFB 22 (2%) 955 0.16274 0.64 0.3073 0.826 0.083379 0.47 0.00076999 0.0152 0.14236 0.609 0.27885 0.826 0.071379 0.442 0.61077 0.981 0.02881 0.263 0.00019 0.00429 0.04768 0.374 0.00112 0.02 PTEN 35 (4%) 942 0.3101 0.826 0.90392 1 0.17034 0.654 0.28369 0.826 0.85488 1 0.47452 0.915 1 1 0.57483 0.967 0.13525 0.583 0.66304 0.991 0.6521 0.991 0.82631 1 RUNX1 29 (3%) 948 0.01527 0.164 0.086369 0.472 0.0086399 0.115 0.11119 0.541 0.34341 0.85 0.3295 0.837 0.064899 0.425 0.01154 0.138 0.02234 0.233 0.4044 0.879 0.31294 0.826 0.45434 0.909 MLL3 70 (7%) 907 0.62448 0.986 0.069919 0.436 0.68389 0.994 0.24485 0.771 0.60419 0.981 0.55927 0.964 0.19617 0.707 0.41249 0.879 0.19225 0.707 0.12431 0.564 0.40747 0.879 0.31223 0.826 CDKN1B 10 (1%) 967 0.63877 0.988 0.73909 1 0.069369 0.436 0.22763 0.747 0.74274 1 0.19818 0.712 0.10036 0.513 0.45863 0.909 0.44818 0.902 0.16627 0.643 0.39119 0.879 0.01511 0.164 MAP2K4 32 (3%) 945 0.058139 0.405 0.00437 0.0618 0.063109 0.421 0.0074199 0.102 0.00308 0.0471 0.21117 0.723 0.00274 0.0426 0.00365 0.0541 0.0125 0.145 0.00037 0.00779 0.01183 0.14 0.01221 0.143 ARID1A 27 (3%) 950 0.30265 0.826 0.94125 1 0.03832 0.321 0.084769 0.471 1 1 0.19545 0.707 0.34642 0.85 0.64351 0.988 0.66495 0.991 0.39807 0.879 0.16379 0.64 0.56455 0.965 FOXA1 23 (2%) 954 0.37025 0.865 0.53808 0.952 0.33393 0.841 0.075349 0.452 0.80105 1 0.74857 1 0.057779 0.405 0.15979 0.631 0.02347 0.237 0.02476 0.247 0.18395 0.69 0.52371 0.946 GPS2 10 (1%) 967 0.067929 0.435 0.097629 0.506 0.0369 0.312 0.41701 0.879 0.20245 0.713 0.6307 0.988 0.58302 0.973 0.067209 0.435 0.10967 0.541 0.43621 0.893 0.48129 0.915 0.41833 0.879 TBX3 27 (3%) 950 0.57792 0.968 0.62586 0.986 0.32524 0.837 0.2878 0.826 0.16407 0.64 0.96661 1 0.04387 0.359 0.13285 0.578 0.057859 0.405 0.12495 0.564 0.60336 0.981 0.72153 1 RB1 19 (2%) 958 0.87946 1 0.30461 0.826 0.15913 0.631 0.15311 0.628 0.37057 0.865 0.60747 0.981 0.02717 0.259 0.25987 0.794 0.057029 0.405 0.02755 0.259 0.093629 0.499 0.20903 0.72 CTCF 16 (2%) 961 0.058899 0.408 0.04428 0.359 0.02302 0.235 0.0147 0.163 0.04826 0.375 0.11515 0.546 0.11858 0.556 0.4865 0.917 0.084949 0.471 0.01018 0.127 0.94549 1 0.57617 0.967 RBMX 13 (1%) 964 0.38484 0.879 0.10509 0.532 0.064639 0.425 0.53015 0.946 0.47569 0.915 0.84798 1 0.068619 0.435 0.02851 0.262 0.2416 0.769 0.5733 0.967 0.068819 0.435 1 1 HRNR 31 (3%) 946 0.98793 1 0.78324 1 0.35346 0.85 0.99382 1 0.65473 0.991 0.56838 0.965 0.49413 0.927 0.6819 0.994 0.59581 0.981 0.19477 0.707 0.14777 0.614 0.78557 1 ZMYM3 15 (2%) 962 0.49881 0.927 0.4415 0.898 0.75148 1 0.67144 0.991 0.11408 0.544 0.65421 0.991 0.12328 0.564 0.4858 0.917 0.44287 0.899 0.97034 1 0.22961 0.748 0.8561 1 NCOR1 40 (4%) 937 0.84778 1 0.90312 1 0.92333 1 0.61495 0.981 0.29808 0.826 0.61393 0.981 0.82615 1 0.52972 0.946 0.81078 1 0.12163 0.563 0.71553 1 0.78325 1 GPRIN2 11 (1%) 966 0.6036 0.981 0.62443 0.986 0.97987 1 0.66987 0.991 0.77684 1 0.14377 0.609 0.46659 0.91 0.4204 0.881 0.37064 0.865 0.062789 0.421 0.40134 0.879 0.66551 0.991 SPEN 32 (3%) 945 0.66614 0.991 0.78809 1 0.4835 0.915 0.46436 0.909 0.79088 1 0.0271 0.259 0.20748 0.718 0.11922 0.557 0.2135 0.728 0.0091299 0.119 0.094279 0.499 0.65823 0.991 NF1 28 (3%) 949 0.57005 0.965 0.80456 1 0.56703 0.965 0.22387 0.742 0.54897 0.96 0.23315 0.75 0.38465 0.879 0.41698 0.879 0.32863 0.837 0.6765 0.991 0.94262 1 0.54224 0.954 TCP11 6 (1%) 971 0.7852 1 0.51238 0.938 0.45639 0.909 NA NA 1 1 0.60954 0.981 0.74481 1 0.3743 0.872 0.94642 1 0.76129 1 NA NA NA NA SF3B1 16 (2%) 961 0.84611 1 0.84488 1 0.53929 0.952 0.076489 0.452 0.077589 0.452 0.078819 0.456 0.28829 0.826 0.35622 0.851 0.26195 0.794 0.38724 0.879 0.35311 0.85 0.24677 0.772 ERBB2 20 (2%) 957 0.57527 0.967 0.46498 0.909 0.02714 0.259 0.00238 0.0382 0.30929 0.826 0.95487 1 0.21737 0.731 0.13448 0.582 0.21668 0.731 0.10604 0.532 0.31925 0.835 0.60275 0.981 RAB42 4 (0%) 973 0.40793 0.879 0.067889 0.435 0.04126 0.343 NA NA 0.51518 0.941 0.38809 0.879 0.11697 0.552 0.15607 0.629 0.23163 0.749 0.0099899 0.127 NA NA NA NA CDC42EP1 5 (1%) 972 0.52183 0.946 0.46189 0.909 0.38076 0.879 0.32745 0.837 0.558 0.964 0.47292 0.915 0.84528 1 0.56147 0.965 0.72803 1 0.30634 0.826 NA NA NA NA KDM6A 15 (2%) 962 0.73989 1 0.34459 0.85 0.53512 0.952 0.17616 0.671 0.50826 0.934 0.96478 1 0.30396 0.826 0.40766 0.879 0.67457 0.991 0.6467 0.988 0.75936 1 0.44935 0.902 AQP12A 6 (1%) 971 0.62728 0.986 0.72578 1 0.34641 0.85 0.54271 0.954 0.29637 0.826 0.43489 0.892 1 1 1 1 0.94548 1 0.49727 0.927 0.38473 0.879 1 1 KRAS 6 (1%) 971 0.53923 0.952 0.63225 0.988 0.32505 0.837 0.50637 0.934 0.29614 0.826 0.51246 0.938 0.74567 1 0.084199 0.471 0.85206 1 0.95773 1 0.92236 1 0.12555 0.564 NBPF9 5 (1%) 972 0.61408 0.981 0.62579 0.986 0.80414 1 NA NA 1 1 0.64114 0.988 0.60279 0.981 0.15468 0.629 0.14303 0.609 0.30099 0.826 NA NA NA NA MYB 12 (1%) 965 0.73578 1 0.02851 0.262 0.22635 0.745 0.32286 0.837 0.86933 1 0.6964 1 1 1 0.90091 1 0.097219 0.506 0.12536 0.564 0.28346 0.826 0.00127 0.0223 ZNF362 5 (1%) 972 0.87915 1 0.8701 1 0.090979 0.49 NA NA 0.076059 0.452 0.66188 0.991 0.40958 0.879 0.90957 1 0.085679 0.472 0.41532 0.879 NA NA NA NA TBL1XR1 9 (1%) 968 0.15804 0.629 0.081249 0.461 0.050619 0.387 NA NA 0.35353 0.85 0.15477 0.629 0.54428 0.954 0.56623 0.965 0.47769 0.915 0.55259 0.963 1 1 0.074669 0.452 SP3 7 (1%) 970 0.88209 1 0.55306 0.963 0.55762 0.964 0.90737 1 NA NA NA NA 0.87907 1 0.44139 0.898 0.39828 0.879 0.40901 0.879 0.31859 0.835 1 1 FGFR2 11 (1%) 966 0.91657 1 0.8763 1 0.32892 0.837 0.094019 0.499 0.86828 1 0.79582 1 0.78976 1 0.4306 0.887 0.22566 0.745 0.49751 0.927 0.60772 0.981 0.67315 0.991 ZBTB7C 5 (1%) 972 NA NA NA NA 0.49608 0.927 0.30673 0.826 NA NA NA NA 0.49747 0.927 0.67833 0.991 0.68544 0.994 0.92085 1 NA NA NA NA NCDN 4 (0%) 973 1 1 0.79136 1 1 1 NA NA 0.403 0.879 0.48335 0.915 0.81982 1 0.91303 1 0.84116 1 0.051879 0.39 NA NA NA NA MUC6 14 (1%) 963 0.02061 0.22 0.60789 0.981 0.50637 0.934 0.67401 0.991 0.47933 0.915 0.94128 1 0.061309 0.418 0.20428 0.713 0.62465 0.986 0.11182 0.541 0.28276 0.826 0.051259 0.389 TGS1 13 (1%) 964 0.6366 0.988 0.66559 0.991 0.42082 0.881 0.2364 0.757 0.205 0.713 0.55836 0.964 1 1 0.24457 0.771 0.27003 0.808 0.45967 0.909 0.24783 0.773 0.3538 0.85 TFE3 7 (1%) 970 0.67577 0.991 0.90261 1 0.74128 1 0.32151 0.837 1 1 0.94076 1 0.78565 1 0.64731 0.988 0.75101 1 0.42483 0.881 0.85595 1 0.30137 0.826 IRS4 11 (1%) 966 0.14578 0.609 0.78165 1 0.22297 0.742 0.68337 0.994 0.86891 1 0.84717 1 0.21685 0.731 0.46954 0.912 1 1 0.17433 0.666 0.949 1 0.8241 1 NLGN3 11 (1%) 966 0.54353 0.954 0.56221 0.965 0.24408 0.771 0.15264 0.628 0.054609 0.4 0.25523 0.788 0.78925 1 0.081159 0.461 0.95333 1 0.74741 1 0.60844 0.981 0.6732 0.991 IL1RAP 9 (1%) 968 NA NA NA NA 0.1502 0.622 0.30123 0.826 NA NA NA NA 0.28905 0.826 0.64389 0.988 0.61497 0.981 0.89748 1 0.58697 0.976 0.68583 0.994 USP36 8 (1%) 969 0.83547 1 0.182 0.687 0.96846 1 0.73008 1 0.64212 0.988 0.74444 1 0.45745 0.909 0.077029 0.452 0.67572 0.991 0.34422 0.85 NA NA NA NA CASZ1 14 (1%) 963 0.9357 1 0.85381 1 0.90259 1 0.81349 1 0.20366 0.713 0.93334 1 0.82248 1 0.73304 1 0.5184 0.945 0.73455 1 0.42468 0.881 0.32637 0.837 EYS 21 (2%) 956 0.2621 0.794 0.28547 0.826 0.03254 0.286 0.065069 0.425 0.22333 0.742 0.38253 0.879 0.02196 0.231 0.20188 0.713 0.10039 0.513 0.03245 0.286 0.37052 0.865 0.12647 0.566 KCNN3 9 (1%) 968 0.14391 0.609 0.50746 0.934 0.25152 0.782 0.12182 0.563 0.39119 0.879 0.76808 1 0.28706 0.826 0.39731 0.879 0.30384 0.826 0.71338 1 0.57966 0.969 0.40899 0.879 ZFP36L1 8 (1%) 969 0.40091 0.879 0.897 1 0.00136 0.0234 0.78039 1 0.061299 0.418 0.04895 0.377 0.18412 0.69 0.73094 1 0.89509 1 0.8535 1 0.94878 1 0.82339 1 ICOSLG 5 (1%) 972 0.77178 1 0.13295 0.578 0.04342 0.358 0.83254 1 NA NA NA NA 0.5986 0.981 0.96776 1 0.77196 1 0.46727 0.91 NA NA NA NA ACTL6B 10 (1%) 967 0.3535 0.85 0.29065 0.826 0.02943 0.266 0.35336 0.85 1 1 0.19386 0.707 0.83667 1 0.19434 0.707 0.73868 1 0.71438 1 0.42336 0.881 0.71405 1 MYH9 18 (2%) 959 0.39576 0.879 0.4237 0.881 0.36623 0.864 0.4023 0.879 0.82068 1 0.053779 0.4 0.66303 0.991 0.14561 0.609 0.73609 1 0.40166 0.879 0.5077 0.934 0.26067 0.794 FBXW7 15 (2%) 962 0.81525 1 0.53079 0.946 0.15741 0.629 0.0073199 0.102 0.64366 0.988 0.94024 1 0.22977 0.748 0.14545 0.609 0.35501 0.85 0.10057 0.513 0.062889 0.421 0.89863 1 FRMPD2 13 (1%) 964 0.5293 0.946 0.97816 1 0.46518 0.909 0.44379 0.899 0.55803 0.964 0.93336 1 1 1 0.054789 0.4 0.21581 0.731 0.72958 1 0.18664 0.691 0.75569 1 ZFP36L2 7 (1%) 970 0.39239 0.879 1 1 0.02761 0.259 0.77881 1 1 1 0.88281 1 0.52614 0.946 0.56711 0.965 0.78476 1 0.90268 1 0.36055 0.857 0.85781 1 TPP2 8 (1%) 969 0.086629 0.472 0.94542 1 0.6369 0.988 0.46452 0.909 NA NA NA NA 0.36329 0.859 0.91672 1 0.52973 0.946 0.87964 1 0.87456 1 0.59392 0.981 C17ORF95 5 (1%) 972 0.86616 1 0.85779 1 1 1 NA NA NA NA NA NA 0.84156 1 0.96834 1 0.72715 1 0.751 1 NA NA NA NA RUFY1 6 (1%) 971 0.38729 0.879 0.72724 1 0.31251 0.826 0.29136 0.826 NA NA NA NA 0.65299 0.991 0.23963 0.765 0.85069 1 0.13169 0.578 0.89936 1 0.41066 0.879 MED23 14 (1%) 963 0.097389 0.506 0.2834 0.826 0.35458 0.85 0.076649 0.452 0.075289 0.452 0.22189 0.742 0.04704 0.372 0.073069 0.45 0.3527 0.85 0.3894 0.879 0.28312 0.826 0.41433 0.879 PAX2 4 (0%) 973 0.94558 1 0.33452 0.841 0.29822 0.826 NA NA 0.20395 0.713 0.056669 0.405 0.31606 0.832 0.28666 0.826 0.77572 1 0.47721 0.915 NA NA NA NA MED12 21 (2%) 956 0.83967 1 0.78035 1 0.39816 0.879 0.6778 0.991 0.26312 0.794 0.077679 0.452 0.64364 0.988 0.40996 0.879 0.95235 1 0.8801 1 0.35021 0.85 0.48064 0.915 CHD4 19 (2%) 958 0.23335 0.75 0.35875 0.855 0.8448 1 0.63063 0.988 0.29228 0.826 0.39331 0.879 0.55367 0.963 0.27154 0.809 0.29853 0.826 0.43727 0.893 0.75018 1 0.31155 0.826 PFKP 6 (1%) 971 0.48056 0.915 0.02555 0.252 0.18573 0.691 NA NA 0.39217 0.879 0.79389 1 0.41831 0.879 0.30161 0.826 0.30933 0.826 0.20521 0.713 NA NA NA NA RHBG 4 (0%) 973 NA NA NA NA 0.8953 1 NA NA NA NA NA NA 0.0076999 0.104 0.10609 0.532 0.52436 0.946 0.26518 0.796 NA NA NA NA PSIP1 8 (1%) 969 0.68987 0.998 0.71927 1 0.57026 0.965 0.75566 1 0.83269 1 0.9654 1 0.36202 0.858 0.93573 1 0.20961 0.72 0.45478 0.909 0.85873 1 0.13291 0.578 LRIG2 7 (1%) 970 0.56488 0.965 0.03156 0.282 0.24661 0.772 0.11083 0.541 0.15677 0.629 0.72202 1 0.4606 0.909 0.88587 1 0.62077 0.986 0.60768 0.981 0.85746 1 1 1 RIBC1 4 (0%) 973 0.58985 0.979 0.38258 0.879 0.75686 1 0.50603 0.934 NA NA NA NA 0.52663 0.946 0.60623 0.981 0.44747 0.902 0.32665 0.837 NA NA NA NA PLK2 9 (1%) 968 0.29714 0.826 0.92418 1 0.97455 1 0.892 1 NA NA NA NA 0.91124 1 0.79835 1 0.96968 1 0.52387 0.946 0.82043 1 0.67266 0.991 ANKRD20A4 7 (1%) 970 0.19342 0.707 0.096209 0.506 0.71458 1 0.7076 1 0.64533 0.988 1 1 0.23054 0.748 0.33088 0.839 0.88132 1 0.96672 1 0.4798 0.915 0.03649 0.312 PHACTR1 7 (1%) 970 0.4163 0.879 0.43016 0.887 0.81548 1 0.34138 0.85 0.16594 0.643 0.93658 1 0.20118 0.713 0.079529 0.457 0.41185 0.879 0.0228 0.235 1 1 1 1 DLG1 13 (1%) 964 0.34341 0.85 0.3198 0.835 0.42673 0.883 0.57202 0.967 0.4449 0.899 0.11411 0.544 0.12538 0.564 0.18619 0.691 0.67257 0.991 0.0038 0.0546 0.66968 0.991 0.80498 1 GPRASP2 10 (1%) 967 0.01374 0.155 0.01075 0.132 0.20004 0.713 0.48206 0.915 0.16837 0.649 0.53829 0.952 0.64159 0.988 0.25295 0.784 0.72183 1 0.62655 0.986 0.60623 0.981 0.67198 0.991 CCDC82 6 (1%) 971 0.46096 0.909 0.057659 0.405 0.30347 0.826 NA NA 0.03655 0.312 0.72426 1 0.34884 0.85 0.00243 0.0384 0.30902 0.826 0.8997 1 1 1 1 1 CCDC27 7 (1%) 970 0.088049 0.477 0.13014 0.577 0.04577 0.365 0.04486 0.36 0.11004 0.541 0.94101 1 0.0329 0.286 0.26371 0.794 0.52198 0.946 0.01109 0.135 0.054249 0.4 1 1 RHOA 6 (1%) 971 0.90573 1 0.58653 0.976 0.78077 1 0.93785 1 0.11176 0.541 0.60316 0.981 0.41452 0.879 0.25905 0.794 1 1 0.79608 1 NA NA NA NA MAMLD1 10 (1%) 967 0.91894 1 0.43346 0.891 0.62446 0.986 0.73123 1 0.33213 0.84 0.93699 1 0.70167 1 0.65272 0.991 0.49485 0.927 0.15663 0.629 0.25645 0.789 1 1 OR8D1 5 (1%) 972 0.63897 0.988 0.0090899 0.119 0.64634 0.988 0.87319 1 0.69203 1 0.79298 1 0.3378 0.847 0.18154 0.687 0.77428 1 0.59329 0.981 NA NA NA NA