		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
TP53	38 (5%)	746	NA	NA	NA	NA	5e-04	0.0102	9.9999e-06	0.00029	0.81875	1	0.03988	0.284	9.9999e-06	0.00029	9.9999e-06	0.00029	2e-05	0.00056	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029
PTEN	28 (4%)	756	NA	NA	NA	NA	0.18769	0.729	0.090259	0.477	0.77227	1	0.66505	1	0.02011	0.184	0.01352	0.144	0.6194	1	0.01209	0.134	0.063209	0.371	0.04472	0.305
SETD2	61 (8%)	723	0.54744	1	0.56616	1	0.00383	0.0564	9.9999e-06	0.00029	0.42454	0.973	0.47251	0.987	0.077729	0.427	9.9999e-06	0.00029	0.10663	0.527	0.0058699	0.0759	0.02789	0.225	0.057719	0.348
PBRM1	143 (18%)	641	0.00168	0.0282	0.0013	0.0223	9.9999e-06	0.00029	9.9999e-06	0.00029	0.02528	0.212	0.00487	0.066	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029
NEFH	12 (2%)	772	NA	NA	NA	NA	0.38898	0.953	0.6936	1	0.067339	0.383	0.84362	1	0.52236	1	0.38463	0.945	0.93242	1	0.29932	0.851	0.42907	0.973	0.27488	0.837
VHL	196 (25%)	588	0.00056999	0.0114	0.00095999	0.0175	9.9999e-06	0.00029	9.9999e-06	0.00029	0.0105	0.121	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029	9.9999e-06	0.00029
NF2	16 (2%)	768	NA	NA	NA	NA	0.26674	0.837	0.64523	1	0.44024	0.973	0.14079	0.616	0.02292	0.205	0.00239	0.0372	0.21929	0.77	0.094059	0.479	0.058709	0.35	0.40813	0.961
MET	25 (3%)	759	NA	NA	NA	NA	7.9999e-05	0.0021	0.00028	0.00603	0.10227	0.514	0.40956	0.961	9.9999e-06	0.00029	9.9999e-06	0.00029	0.00011	0.0028	9.9999e-06	0.00029	0.00214	0.0346	0.01114	0.125
KDM5C	27 (3%)	757	NA	NA	NA	NA	0.00282	0.0431	0.0079899	0.0959	0.4314	0.973	0.30288	0.851	0.00019	0.00431	0.00019	0.00431	9.9999e-06	0.00029	0.0054899	0.0721	0.31342	0.859	0.50111	0.997
MTOR	34 (4%)	750	NA	NA	NA	NA	0.00014	0.00336	0.00013	0.00321	0.01433	0.149	0.03226	0.249	0.01764	0.166	0.0148	0.15	0.00034	0.00714	5e-05	0.00135	0.13179	0.598	0.00091999	0.0172
ZNF814	14 (2%)	770	NA	NA	NA	NA	0.53704	1	0.067549	0.383	0.80824	1	0.72732	1	0.02472	0.212	0.11486	0.548	0.04631	0.314	0.092099	0.479	0.51706	1	0.58425	1
AR	15 (2%)	769	NA	NA	NA	NA	0.00112	0.02	0.068409	0.386	0.83171	1	0.51264	1	0.00022	0.00486	0.01483	0.15	0.0087599	0.102	0.0075599	0.092	0.064359	0.373	0.1783	0.706
STAG2	15 (2%)	769	NA	NA	NA	NA	0.89255	1	0.03427	0.255	0.51085	1	0.16372	0.665	0.57506	1	0.03037	0.241	0.52438	1	0.42733	0.973	0.2118	0.761	0.44853	0.973
KRAS	6 (1%)	778	NA	NA	NA	NA	0.22639	0.779	0.1917	0.729	0.56884	1	0.45251	0.976	0.04981	0.325	0.30146	0.851	0.12717	0.584	0.4708	0.987	0.11023	0.536	0.00127	0.0222
SLC6A14	4 (1%)	780	NA	NA	NA	NA	0.83973	1	NA	NA	0.80589	1	0.071799	0.397	0.23692	0.796	0.36631	0.927	0.03186	0.248	0.37261	0.932	0.02056	0.186	0.37767	0.936
SMARCA4	20 (3%)	764	NA	NA	NA	NA	0.433	0.973	0.54431	1	0.86325	1	0.53604	1	0.24482	0.813	0.57779	1	0.22948	0.782	0.25395	0.826	0.61829	1	0.44374	0.973
NFE2L2	12 (2%)	772	NA	NA	NA	NA	0.13526	0.602	0.093549	0.479	0.66824	1	0.050369	0.325	0.28633	0.843	0.25543	0.826	0.60857	1	0.37038	0.932	0.67562	1	0.75127	1
ARID1A	18 (2%)	766	NA	NA	NA	NA	0.82477	1	0.28707	0.843	0.47459	0.987	0.49754	0.996	0.31027	0.859	0.85039	1	0.58599	1	0.63666	1	0.45719	0.976	0.80337	1
BCLAF1	10 (1%)	774	NA	NA	NA	NA	0.22197	0.77	0.49513	0.996	0.72517	1	0.96983	1	0.1652	0.665	0.81544	1	0.063739	0.372	0.2935	0.851	0.39579	0.954	0.82038	1
ATM	20 (3%)	764	NA	NA	NA	NA	0.51587	1	0.48231	0.988	0.8285	1	0.98425	1	0.41201	0.964	0.054299	0.343	0.37266	0.932	0.21294	0.761	0.83353	1	0.55269	1
CACNA1C	15 (2%)	769	NA	NA	NA	NA	0.46897	0.987	0.055229	0.346	0.86976	1	0.20578	0.748	0.53063	1	0.056359	0.348	0.35147	0.903	0.12052	0.572	0.23967	0.799	0.70267	1
PARD6B	8 (1%)	776	NA	NA	NA	NA	1	1	0.33916	0.883	0.01075	0.122	0.0073699	0.0914	0.093709	0.479	0.02518	0.212	0.21575	0.762	0.04028	0.284	0.48942	0.994	0.1643	0.665
CUL3	16 (2%)	768	NA	NA	NA	NA	1	1	0.01283	0.138	0.87693	1	0.091639	0.479	0.088639	0.471	0.00371	0.0556	0.57946	1	0.19062	0.729	0.32106	0.859	0.73276	1
PIK3CA	15 (2%)	769	NA	NA	NA	NA	0.27518	0.837	0.02349	0.206	0.92784	1	0.78546	1	0.7583	1	0.50808	1	0.63103	1	0.29711	0.851	0.55409	1	0.71414	1
SMARCB1	9 (1%)	775	NA	NA	NA	NA	0.081739	0.443	0.81837	1	0.8636	1	0.73793	1	0.25682	0.826	0.03121	0.245	0.46212	0.98	0.53668	1	0.19985	0.741	0.19815	0.741
PCF11	13 (2%)	771	NA	NA	NA	NA	0.00454	0.0625	0.49576	0.996	0.58864	1	0.00058999	0.0115	0.0061399	0.0781	0.03699	0.271	0.00452	0.0625	0.19947	0.741	0.03298	0.25	0.27457	0.837
WASL	8 (1%)	776	NA	NA	NA	NA	1	1	0.91734	1	0.44075	0.973	0.85086	1	1	1	0.87957	1	0.89025	1	0.90369	1	0.94023	1	0.3946	0.954
DNMT3A	11 (1%)	773	NA	NA	NA	NA	0.45554	0.976	0.66302	1	0.16385	0.665	0.25312	0.826	0.31674	0.859	0.27214	0.837	0.91843	1	0.43088	0.973	0.51735	1	0.2856	0.843
KIAA0922	7 (1%)	777	NA	NA	NA	NA	0.084119	0.45	0.31748	0.859	0.65762	1	0.97407	1	0.13349	0.6	0.41829	0.971	0.057929	0.348	0.32055	0.859	0.4804	0.987	0.4094	0.961
GPR50	5 (1%)	779	NA	NA	NA	NA	0.7403	1	0.694	1	0.03841	0.276	0.34951	0.902	0.43745	0.973	0.74841	1	0.36568	0.927	0.76521	1	NA	NA	NA	NA
ACSF2	11 (1%)	773	NA	NA	NA	NA	0.79276	1	0.87046	1	0.19595	0.741	0.15016	0.637	0.78671	1	0.35006	0.902	0.79581	1	0.74231	1	0.46537	0.985	0.39943	0.956
WDR52	9 (1%)	775	NA	NA	NA	NA	1	1	0.3621	0.926	0.96018	1	0.60542	1	0.87765	1	0.91642	1	0.51292	1	0.39757	0.954	0.44614	0.973	0.89435	1
ALMS1	14 (2%)	770	NA	NA	NA	NA	0.37742	0.936	0.94374	1	0.77653	1	0.43288	0.973	0.91239	1	0.81571	1	0.2532	0.826	0.04234	0.292	0.36264	0.926	0.82044	1
TXNIP	8 (1%)	776	NA	NA	NA	NA	0.27798	0.843	0.14949	0.637	0.04965	0.325	0.2	0.741	0.0473	0.318	0.01986	0.183	0.42813	0.973	0.15254	0.644	0.10911	0.536	0.18059	0.712
NUDT11	5 (1%)	779	NA	NA	NA	NA	0.45476	0.976	0.28515	0.843	0.6663	1	0.9041	1	0.70337	1	0.26434	0.837	0.53769	1	0.84234	1	NA	NA	NA	NA
PCK1	9 (1%)	775	NA	NA	NA	NA	0.75229	1	0.58917	1	0.6556	1	0.66735	1	0.48037	0.987	0.56546	1	0.75678	1	0.1238	0.575	0.28439	0.843	0.45594	0.976
RAI1	11 (1%)	773	NA	NA	NA	NA	0.060989	0.361	0.70086	1	0.26998	0.837	0.6992	1	0.72162	1	0.31781	0.859	0.4243	0.973	0.52889	1	0.28221	0.843	0.67032	1
PAM	4 (1%)	780	NA	NA	NA	NA	0.23966	0.799	0.14509	0.631	0.1005	0.509	0.093699	0.479	0.052439	0.334	0.52948	1	0.081209	0.443	0.01891	0.176	NA	NA	NA	NA
KDM6A	13 (2%)	771	NA	NA	NA	NA	0.00499	0.0665	0.01641	0.158	0.58432	1	0.37106	0.932	0.02415	0.209	0.029	0.232	0.0073999	0.0914	0.01243	0.136	0.31167	0.859	0.20109	0.741
GLS	9 (1%)	775	NA	NA	NA	NA	0.3803	0.94	0.25428	0.826	0.19163	0.729	0.071429	0.397	1	1	0.76266	1	0.34006	0.883	0.92878	1	0.49669	0.996	0.47143	0.987
EPS15L1	10 (1%)	774	NA	NA	NA	NA	0.78647	1	0.55551	1	0.16535	0.665	0.89469	1	0.8668	1	0.46088	0.98	0.050239	0.325	0.77515	1	0.3928	0.954	0.6869	1
NOM1	6 (1%)	778	NA	NA	NA	NA	0.33235	0.88	0.80077	1	0.44964	0.973	0.89095	1	0.94339	1	0.66966	1	0.76027	1	0.93701	1	0.90513	1	0.64441	1
CDK12	8 (1%)	776	NA	NA	NA	NA	0.47875	0.987	0.65563	1	0.53301	1	0.13893	0.611	0.82791	1	0.72644	1	0.73095	1	0.11049	0.536	0.64515	1	0.54578	1
ARHGAP35	7 (1%)	777	NA	NA	NA	NA	0.6228	1	0.02324	0.205	0.7595	1	0.79532	1	0.7036	1	0.48071	0.987	0.0268	0.22	0.22881	0.782	NA	NA	NA	NA
RIMBP3	5 (1%)	779	NA	NA	NA	NA	1	1	0.52228	1	0.6069	1	0.78552	1	0.22168	0.77	0.03712	0.271	0.43434	0.973	0.29523	0.851	NA	NA	NA	NA
FAT1	20 (3%)	764	NA	NA	NA	NA	0.12707	0.584	0.56839	1	0.95169	1	0.47136	0.987	0.02703	0.22	0.050929	0.327	0.11114	0.537	0.3145	0.859	0.51944	1	0.31876	0.859
FAM178A	8 (1%)	776	NA	NA	NA	NA	0.083669	0.45	1	1	0.57044	1	0.73284	1	0.39769	0.954	0.82253	1	0.81416	1	1	1	NA	NA	NA	NA
TCEB1	4 (1%)	780	NA	NA	NA	NA	0.26868	0.837	NA	NA	0.14726	0.637	0.30716	0.857	0.26553	0.837	0.00237	0.0372	0.01523	0.152	0.18801	0.729	0.1483	0.637	0.00202	0.0333
PODXL	6 (1%)	778	NA	NA	NA	NA	0.22493	0.778	0.31544	0.859	0.21385	0.761	0.8626	1	1	1	0.237	0.796	1	1	0.68036	1	0.26479	0.837	0.36373	0.926
DNAJA3	3 (0%)	781	NA	NA	NA	NA	1	1	NA	NA	NA	NA	NA	NA	0.51231	1	0.26996	0.837	0.43761	0.973	0.84277	1	0.86531	1	0.16069	0.665
NASP	5 (1%)	779	NA	NA	NA	NA	0.64607	1	0.30234	0.851	0.15511	0.651	0.62108	1	0.1065	0.527	0.41515	0.969	0.29104	0.849	0.12115	0.572	0.03391	0.254	0.17556	0.702
SLC23A1	6 (1%)	778	NA	NA	NA	NA	0.87733	1	0.61382	1	0.29807	0.851	0.4173	0.971	0.26934	0.837	0.40961	0.961	0.8694	1	0.057099	0.348	NA	NA	NA	NA
RILPL1	5 (1%)	779	NA	NA	NA	NA	0.84624	1	0.40953	0.961	0.49024	0.994	0.2485	0.822	0.2796	0.843	0.30566	0.856	0.84778	1	0.2063	0.748	NA	NA	NA	NA
NIPBL	15 (2%)	769	NA	NA	NA	NA	0.13345	0.6	0.52054	1	0.6389	1	0.48855	0.994	0.51012	1	0.50473	1	0.16391	0.665	0.44727	0.973	0.81625	1	0.9708	1
FAM47A	6 (1%)	778	NA	NA	NA	NA	0.3331	0.88	0.55609	1	0.30955	0.859	0.94904	1	1	1	0.071829	0.397	0.32103	0.859	0.68046	1	NA	NA	NA	NA
RHEB	3 (0%)	781	NA	NA	NA	NA	0.33447	0.881	NA	NA	0.23683	0.796	0.20651	0.748	1	1	0.51954	1	0.10645	0.527	0.72731	1	0.14871	0.637	0.52684	1
BRAF	5 (1%)	779	NA	NA	NA	NA	1	1	0.44409	0.973	1	1	0.75319	1	0.18969	0.729	0.47795	0.987	0.84704	1	0.25776	0.826	0.40324	0.96	0.88301	1
MLL3	42 (5%)	742	0.78012	1	0.65831	1	0.16112	0.665	0.42816	0.973	0.29057	0.849	0.91278	1	0.01405	0.148	0.22096	0.77	0.03774	0.273	0.0161	0.157	0.44218	0.973	0.336	0.882
ANK3	22 (3%)	762	0.30178	0.851	0.84247	1	0.284	0.843	0.61749	1	0.76375	1	0.49102	0.994	0.38417	0.945	0.62947	1	0.81705	1	0.87965	1	0.76061	1	0.29654	0.851
EMG1	4 (1%)	780	0.00444	0.0625	0.00428	0.062	0.27305	0.837	NA	NA	NA	NA	NA	NA	0.0085599	0.101	0.03259	0.249	1	1	0.00089999	0.0172	NA	NA	NA	NA
LHX1	4 (1%)	780	NA	NA	NA	NA	1	1	0.37706	0.936	0.9011	1	0.60146	1	0.5689	1	0.61721	1	0.83225	1	0.12266	0.572	NA	NA	NA	NA
SCARB2	4 (1%)	780	NA	NA	NA	NA	0.21588	0.762	0.12196	0.572	0.01544	0.153	0.8277	1	0.26522	0.837	0.62619	1	0.04879	0.325	0.47668	0.987	NA	NA	NA	NA
C1ORF25	6 (1%)	778	NA	NA	NA	NA	0.5897	1	0.48665	0.994	0.43037	0.973	0.94177	1	0.76217	1	0.13845	0.611	0.87039	1	0.59515	1	0.44854	0.973	0.32663	0.868
KDELR3	7 (1%)	777	NA	NA	NA	NA	0.23	0.782	0.2123	0.761	0.18213	0.715	0.45791	0.976	0.11214	0.538	0.29557	0.851	0.25758	0.826	0.39668	0.954	0.20101	0.741	0.80597	1
TTLL6	4 (1%)	780	NA	NA	NA	NA	0.16461	0.665	0.13555	0.602	0.61143	1	0.39141	0.954	0.04204	0.292	0.33761	0.883	0.83172	1	0.057399	0.348	NA	NA	NA	NA
STXBP3	5 (1%)	779	NA	NA	NA	NA	0.64142	1	0.54296	1	NA	NA	NA	NA	0.49908	0.996	0.66674	1	0.849	1	0.49924	0.996	NA	NA	NA	NA
FAM20C	5 (1%)	779	NA	NA	NA	NA	0.02647	0.22	0.20349	0.746	0.87921	1	0.78603	1	0.065149	0.375	0.34051	0.883	0.04074	0.285	0.01684	0.161	0.40331	0.96	0.32324	0.862
CCBL2	3 (0%)	781	NA	NA	NA	NA	0.4388	0.973	0.84691	1	NA	NA	NA	NA	0.86065	1	0.79531	1	1	1	0.2822	0.843	NA	NA	NA	NA
B3GNT6	3 (0%)	781	NA	NA	NA	NA	0.17691	0.704	0.91693	1	0.71388	1	1	1	0.85959	1	0.66279	1	1	1	1	1	NA	NA	NA	NA
HNF1B	4 (1%)	780	NA	NA	NA	NA	0.6855	1	0.74017	1	0.057679	0.348	0.18971	0.729	0.57083	1	0.13055	0.596	0.83446	1	0.59526	1	0.86617	1	0.42452	0.973
