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	0.0080499	0.0978	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	3e-05	0.000694	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	3e-05	0.000694	9.9999e-06	0.000256
TP53	296 (30%)	681	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256
GATA3	97 (10%)	880	0.0087599	0.105	8.9999e-05	0.00198	0.00012	0.00253	6.9999e-05	0.00158	0.00023	0.00445	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	0.00024	0.00446	9.9999e-06	0.000256	9.9999e-06	0.000256	0.073579	0.421
MAP3K1	71 (7%)	906	0.00168	0.0275	0.00203	0.0321	3e-05	0.000694	0.02428	0.235	0.00022	0.00434	9.9999e-06	0.000256	0.00022	0.00434	0.00031	0.00565	4e-04	0.00715	0.00013	0.00268	0.00448	0.0616	0.099859	0.504
CDH1	107 (11%)	870	0.00207	0.0322	0.00102	0.0173	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256	9.9999e-06	0.000256
CBFB	22 (2%)	955	0.66232	0.966	0.46757	0.867	0.00068999	0.0119	0.061239	0.403	0.04912	0.364	0.20243	0.64	2e-05	0.000499	0.61342	0.938	0.04956	0.364	0.00011	0.00237	0.0057699	0.076	0.00224	0.0337
PTEN	35 (4%)	942	1	1	0.69529	0.969	0.27613	0.731	0.32107	0.78	0.20554	0.641	0.72639	0.988	0.28856	0.753	0.57315	0.923	0.15	0.586	0.15292	0.587	0.4211	0.837	0.54893	0.915
RUNX1	29 (3%)	948	0.24618	0.701	0.04126	0.324	0.03057	0.276	0.31821	0.777	0.42775	0.837	0.41192	0.835	0.068049	0.414	0.01097	0.125	0.00467	0.0632	0.00362	0.052	0.37384	0.829	0.37278	0.829
MLL3	70 (7%)	907	0.63422	0.951	0.78081	1	0.16795	0.608	0.23583	0.687	0.67449	0.969	0.10871	0.531	0.03057	0.276	0.41463	0.837	0.03891	0.323	0.12132	0.565	0.33588	0.792	0.66149	0.966
CDKN1B	10 (1%)	967	1	1	0.33018	0.789	0.11687	0.565	0.32445	0.785	0.79203	1	0.14784	0.586	0.082059	0.445	0.46387	0.867	0.10724	0.528	0.31647	0.775	0.32843	0.789	0.01698	0.181
MAP2K4	32 (3%)	945	0.065969	0.409	0.069229	0.415	0.052209	0.375	0.0321	0.287	0.03567	0.307	0.0113	0.128	0.0079599	0.0978	0.0037	0.0524	0.00216	0.033	0.00024	0.00446	0.03341	0.293	0.00065999	0.0116
ARID1A	27 (3%)	950	1	1	1	1	0.21028	0.649	0.49359	0.868	0.38427	0.831	0.48537	0.868	0.14057	0.582	0.64351	0.956	0.4407	0.84	0.36343	0.82	0.19594	0.638	0.31092	0.773
FOXA1	23 (2%)	954	0.074769	0.424	0.34105	0.794	0.02335	0.231	0.079489	0.441	0.5691	0.919	0.087309	0.455	0.050479	0.368	0.16017	0.595	0.25797	0.709	0.60004	0.932	0.22593	0.674	0.49113	0.868
GPS2	10 (1%)	967	0.0064299	0.0824	0.60673	0.936	0.0072499	0.0916	0.39156	0.834	0.071969	0.421	0.88556	1	0.4841	0.868	0.066699	0.409	0.33229	0.789	0.59495	0.931	0.32687	0.788	0.03789	0.321
TBX3	27 (3%)	950	0.18735	0.631	0.51773	0.883	0.04282	0.33	0.4243	0.837	0.1398	0.582	0.064759	0.409	0.081029	0.445	0.13352	0.57	0.060189	0.402	0.13289	0.57	0.82997	1	0.59405	0.931
RB1	19 (2%)	958	0.18891	0.631	0.26524	0.712	0.14997	0.586	0.12267	0.565	0.0073799	0.0921	0.15954	0.595	0.21659	0.655	0.26101	0.709	0.28893	0.753	0.11791	0.565	0.02354	0.231	0.26314	0.709
CTCF	16 (2%)	961	0.04791	0.358	0.059559	0.402	0.01084	0.125	0.099579	0.504	0.66676	0.969	0.20208	0.64	0.29545	0.763	0.48922	0.868	0.11764	0.565	0.059809	0.402	0.97246	1	0.75119	1
RBMX	13 (1%)	964	0.77118	1	0.12712	0.568	0.14029	0.582	0.13451	0.571	0.084849	0.451	0.17966	0.626	0.02356	0.231	0.02826	0.264	0.68065	0.969	0.61563	0.94	0.229	0.678	1	1
HRNR	31 (3%)	946	0.87414	1	0.64573	0.956	0.2163	0.655	0.51571	0.882	0.62615	0.947	0.39266	0.835	0.99045	1	0.67672	0.969	0.64327	0.956	0.83536	1	0.62116	0.945	0.74299	0.998
ZMYM3	15 (2%)	962	0.32303	0.783	0.25347	0.709	0.3974	0.835	0.67899	0.969	0.49701	0.869	0.04752	0.358	0.39768	0.835	0.48677	0.868	0.48007	0.868	0.42461	0.837	0.71407	0.98	0.84966	1
NCOR1	40 (4%)	937	0.90729	1	0.947	1	0.8492	1	0.30439	0.772	0.35236	0.81	0.9442	1	0.31252	0.773	0.53229	0.898	0.89594	1	0.02083	0.215	0.42282	0.837	0.71366	0.98
GPRIN2	11 (1%)	966	0.79229	1	0.69018	0.969	0.96066	1	0.60967	0.937	0.93284	1	0.26283	0.709	0.77077	1	0.42499	0.837	0.66965	0.969	0.24791	0.703	0.56007	0.918	1	1
SPEN	32 (3%)	945	0.87663	1	0.53022	0.896	0.50718	0.876	0.42136	0.837	0.94497	1	1	1	0.20869	0.649	0.12049	0.565	0.066599	0.409	0.20434	0.641	0.52612	0.891	0.54148	0.905
NF1	28 (3%)	949	1	1	0.93989	1	0.13885	0.582	0.21642	0.655	0.44063	0.84	0.86614	1	0.12755	0.568	0.41841	0.837	0.28986	0.753	0.55607	0.918	0.91495	1	0.78651	1
TCP11	6 (1%)	971	0.87165	1	1	1	0.46048	0.866	NA	NA	0.78927	1	1	1	0.76245	1	0.37597	0.829	0.64743	0.956	0.39944	0.835	NA	NA	NA	NA
SF3B1	16 (2%)	961	0.72957	0.988	0.45255	0.856	0.50787	0.876	0.17174	0.614	0.17383	0.617	0.2597	0.709	0.64608	0.956	0.35362	0.81	0.33782	0.792	0.19005	0.631	0.62362	0.946	0.18281	0.63
ERBB2	20 (2%)	957	0.19951	0.64	0.16729	0.608	0.38049	0.829	0.15575	0.592	0.01912	0.201	0.3591	0.812	0.068949	0.415	0.13256	0.57	0.055099	0.388	0.056939	0.397	0.9194	1	0.49722	0.869
RAB42	4 (0%)	973	0.81969	1	0.02597	0.249	0.29222	0.757	NA	NA	0.40166	0.835	0.11892	0.565	0.21237	0.654	0.15687	0.592	0.44742	0.848	0.34422	0.798	NA	NA	NA	NA
CDC42EP1	5 (1%)	972	0.82035	1	0.17236	0.614	0.17433	0.617	0.34577	0.799	0.77025	1	0.73906	0.994	0.25879	0.709	0.55922	0.918	0.69246	0.969	0.21829	0.655	NA	NA	NA	NA
KDM6A	15 (2%)	962	0.084119	0.451	0.57324	0.923	0.37134	0.829	0.34802	0.803	0.26049	0.709	0.15289	0.587	0.5403	0.905	0.40521	0.835	0.93086	1	0.98702	1	0.80056	1	0.40064	0.835
AQP12A	6 (1%)	971	0.46697	0.867	1	1	0.56185	0.918	0.77709	1	0.93702	1	0.18544	0.631	0.7766	1	1	1	0.93038	1	0.55862	0.918	0.20247	0.64	1	1
KRAS	6 (1%)	971	0.56546	0.918	0.82596	1	0.17811	0.624	0.35511	0.811	0.63209	0.951	1	1	0.5651	0.918	0.085119	0.451	0.69305	0.969	0.03914	0.323	0.72228	0.987	0.19176	0.631
NBPF9	5 (1%)	972	0.31533	0.775	0.84866	1	0.00409	0.057	NA	NA	0.93655	1	1	1	0.95248	1	0.15497	0.592	0.35274	0.81	0.56068	0.918	NA	NA	NA	NA
MYB	12 (1%)	965	0.38593	0.831	0.58706	0.928	0.1507	0.586	0.55518	0.918	0.15085	0.586	1	1	0.89494	1	0.89886	1	0.24452	0.698	0.31327	0.773	0.086629	0.455	0.00177	0.0284
ZNF362	5 (1%)	972	0.099619	0.504	0.71352	0.98	0.18121	0.627	NA	NA	0.77576	1	0.47334	0.868	0.46227	0.866	0.90869	1	0.17753	0.624	0.070129	0.416	NA	NA	NA	NA
TBL1XR1	9 (1%)	968	0.063089	0.407	0.34028	0.794	0.098349	0.504	NA	NA	0.47388	0.868	1	1	0.04173	0.324	0.56583	0.918	0.42491	0.837	0.2002	0.64	0.90022	1	0.10306	0.512
SP3	7 (1%)	970	1	1	0.30006	0.768	0.4919	0.868	0.94708	1	0.8358	1	0.821	1	0.1943	0.636	0.44187	0.84	0.51872	0.883	0.065179	0.409	0.38009	0.829	1	1
FGFR2	11 (1%)	966	0.49779	0.869	1	1	0.63862	0.953	0.55894	0.918	0.0416	0.324	0.31256	0.773	0.19444	0.636	0.42832	0.837	0.21908	0.655	0.072149	0.421	0.82801	1	0.6734	0.969
ZBTB7C	5 (1%)	972	NA	NA	NA	NA	0.12569	0.565	1	1	0.70421	0.976	1	1	0.88122	1	0.67673	0.969	0.83027	1	0.59721	0.931	NA	NA	NA	NA
NCDN	4 (0%)	973	0.80012	1	0.15662	0.592	0.91578	1	NA	NA	0.95186	1	1	1	0.87976	1	0.91332	1	0.50118	0.87	0.46801	0.867	NA	NA	NA	NA
MUC6	14 (1%)	963	0.63139	0.951	0.9041	1	0.12508	0.565	0.13499	0.571	0.48504	0.868	0.16787	0.608	0.062349	0.405	0.20492	0.641	0.49218	0.868	0.03296	0.292	0.58745	0.928	0.052019	0.375
TGS1	13 (1%)	964	0.21008	0.649	0.26179	0.709	0.62481	0.946	0.28521	0.752	0.83543	1	0.56394	0.918	0.74511	0.999	0.24923	0.703	0.68905	0.969	0.02355	0.231	0.086949	0.455	0.31902	0.777
TFE3	7 (1%)	970	0.1918	0.631	0.14906	0.586	0.40684	0.835	0.69364	0.969	0.35744	0.812	1	1	0.72198	0.987	0.64665	0.956	0.95798	1	0.16464	0.605	1	1	0.31105	0.773
IRS4	11 (1%)	966	0.19105	0.631	0.12545	0.565	0.23149	0.678	0.63753	0.953	0.1656	0.606	0.065169	0.409	0.14597	0.585	0.47033	0.867	0.061409	0.403	0.81537	1	0.70934	0.978	0.81698	1
NLGN3	11 (1%)	966	0.24227	0.695	1	1	0.79121	1	0.87571	1	0.1244	0.565	0.39587	0.835	0.92753	1	0.081929	0.445	0.99422	1	0.99598	1	0.37524	0.829	0.67264	0.969
IL1RAP	9 (1%)	968	NA	NA	NA	NA	0.42681	0.837	0.2986	0.767	0.33688	0.792	0.31242	0.773	0.87332	1	0.64333	0.956	0.5751	0.923	0.30071	0.768	0.83337	1	0.61068	0.937
USP36	8 (1%)	969	0.33586	0.792	0.0059999	0.0779	0.88221	1	0.92662	1	0.45367	0.857	0.49916	0.869	0.40921	0.835	0.075899	0.428	0.59587	0.931	0.74853	1	NA	NA	NA	NA
CASZ1	14 (1%)	963	0.89572	1	0.45754	0.862	0.97234	1	0.46197	0.866	0.49287	0.868	0.097989	0.504	0.9861	1	0.73341	0.99	0.48269	0.868	0.98586	1	0.70654	0.977	0.80901	1
EYS	21 (2%)	956	0.18975	0.631	0.1785	0.624	0.15138	0.586	0.48423	0.868	0.04087	0.324	0.078519	0.438	0.01084	0.125	0.20123	0.64	0.03681	0.314	0.01463	0.159	0.19884	0.64	0.088489	0.458
KCNN3	9 (1%)	968	0.37868	0.829	0.16158	0.598	0.38617	0.831	0.12534	0.565	0.04057	0.324	0.4946	0.868	0.072909	0.421	0.39811	0.835	0.14229	0.584	0.48716	0.868	0.49078	0.868	0.42769	0.837
ZFP36L1	8 (1%)	969	0.20441	0.641	0.58104	0.928	0.00105	0.0175	0.41756	0.837	0.95433	1	0.43426	0.84	0.23855	0.689	0.7315	0.989	0.02062	0.215	0.53797	0.903	0.70951	0.978	0.81831	1
ICOSLG	5 (1%)	972	0.79861	1	0.15748	0.592	0.46962	0.867	1	1	0.10158	0.507	0.38314	0.831	0.83456	1	0.96792	1	0.14112	0.582	0.6816	0.969	NA	NA	NA	NA
ACTL6B	10 (1%)	967	0.67637	0.969	0.39987	0.835	0.0057599	0.076	0.31209	0.773	0.16285	0.601	0.56625	0.918	0.6858	0.969	0.19656	0.638	0.78168	1	0.91328	1	0.5149	0.882	0.84752	1
MYH9	18 (2%)	959	0.47837	0.868	1	1	0.14406	0.584	0.81217	1	0.3897	0.832	0.41189	0.835	0.33829	0.792	0.14287	0.584	0.63309	0.951	0.50351	0.873	0.90598	1	0.17132	0.614
FBXW7	15 (2%)	962	0.76689	1	0.47922	0.868	0.13258	0.57	0.02718	0.258	0.26293	0.709	0.10106	0.507	0.1251	0.565	0.14751	0.586	0.51766	0.883	0.40268	0.835	0.03403	0.296	0.80967	1
FRMPD2	13 (1%)	964	0.44084	0.84	0.12384	0.565	0.23002	0.678	0.13549	0.571	0.13264	0.57	0.26179	0.709	0.57547	0.923	0.054109	0.386	0.43536	0.84	0.2897	0.753	0.55309	0.918	0.5785	0.926
ZFP36L2	7 (1%)	970	0.82046	1	1	1	0.01075	0.125	0.42034	0.837	0.65389	0.96	0.44172	0.84	0.68755	0.969	0.56761	0.918	0.61374	0.938	0.73728	0.993	0.31603	0.775	0.85005	1
TPP2	8 (1%)	969	0.35813	0.812	0.82588	1	0.90762	1	0.63502	0.951	0.93706	1	1	1	0.59825	0.931	0.91577	1	0.59453	0.931	0.88858	1	0.48703	0.868	1	1
C17ORF95	5 (1%)	972	1	1	1	1	1	1	NA	NA	NA	NA	NA	NA	0.9527	1	0.96839	1	0.51276	0.881	0.42893	0.837	NA	NA	NA	NA
RUFY1	6 (1%)	971	1	1	0.29832	0.767	0.37992	0.829	0.72916	0.988	0.069979	0.416	0.73622	0.993	0.87784	1	0.23945	0.69	0.69654	0.969	0.26643	0.713	0.36922	0.829	0.43109	0.839
MED23	14 (1%)	963	0.3883	0.831	0.25104	0.706	0.27368	0.727	0.19753	0.639	0.16975	0.612	0.057679	0.399	0.18422	0.631	0.073659	0.421	0.01643	0.177	0.11655	0.565	0.2671	0.713	0.53412	0.899
PAX2	4 (0%)	973	0.46565	0.867	0.58349	0.928	0.83883	1	NA	NA	0.80478	1	0.48406	0.868	0.37584	0.829	0.28557	0.752	0.3877	0.831	0.33688	0.792	NA	NA	NA	NA
MED12	21 (2%)	956	0.72841	0.988	0.51231	0.881	0.54538	0.91	0.87236	1	0.69653	0.969	0.83223	1	0.66309	0.966	0.40966	0.835	0.70671	0.977	0.91358	1	0.53748	0.903	0.48122	0.868
CHD4	19 (2%)	958	0.75987	1	0.49398	0.868	0.23094	0.678	0.061599	0.403	0.71519	0.98	1	1	0.02974	0.274	0.26873	0.716	0.87339	1	0.066869	0.409	0.81772	1	0.30834	0.773
PFKP	6 (1%)	971	0.12349	0.565	0.058679	0.402	0.69735	0.969	NA	NA	0.30559	0.773	0.68724	0.969	0.58697	0.928	0.30247	0.769	0.42742	0.837	0.13111	0.57	NA	NA	NA	NA
RHBG	4 (0%)	973	NA	NA	NA	NA	1	1	NA	NA	NA	NA	NA	NA	0.21885	0.655	0.10741	0.528	0.67901	0.969	0.28869	0.753	NA	NA	NA	NA
PSIP1	8 (1%)	969	0.69179	0.969	1	1	0.65207	0.96	0.90169	1	0.59241	0.931	0.58492	0.928	0.55617	0.918	0.93475	1	0.41104	0.835	0.90934	1	0.91499	1	0.42932	0.837
LRIG2	7 (1%)	970	0.56372	0.918	0.064289	0.409	0.62357	0.946	0.59012	0.931	0.40645	0.835	0.5837	0.928	0.36812	0.829	0.88451	1	0.33132	0.789	0.92963	1	1	1	1	1
RIBC1	4 (0%)	973	0.35724	0.812	0.65343	0.96	0.70012	0.972	0.03953	0.323	NA	NA	NA	NA	0.68505	0.969	0.60808	0.936	0.38784	0.831	0.4123	0.835	NA	NA	NA	NA
PLK2	9 (1%)	968	0.60642	0.936	0.4422	0.84	1	1	0.92233	1	0.3425	0.796	1	1	0.90797	1	0.79704	1	0.9824	1	0.59604	0.931	0.82939	1	0.67121	0.969
ANKRD20A4	7 (1%)	970	0.60714	0.936	1	1	0.60562	0.936	0.40775	0.835	0.92219	1	0.88247	1	0.072519	0.421	0.3321	0.789	0.84687	1	0.8126	1	0.68775	0.969	0.0236	0.231
PHACTR1	7 (1%)	970	0.12134	0.565	1	1	0.86945	1	0.23697	0.687	0.19109	0.631	0.085139	0.451	0.13177	0.57	0.078439	0.438	0.75689	1	0.04172	0.324	0.89705	1	1	1
DLG1	13 (1%)	964	0.79521	1	0.24894	0.703	0.8718	1	0.13001	0.57	0.63439	0.951	0.82735	1	0.26177	0.709	0.18867	0.631	0.91922	1	0.01167	0.13	0.4359	0.84	1	1
GPRASP2	10 (1%)	967	0.43338	0.84	0.3304	0.789	0.66038	0.966	0.65517	0.96	0.39742	0.835	0.44042	0.84	0.14609	0.585	0.25286	0.709	0.00291	0.0424	0.23074	0.678	0.37885	0.829	0.67196	0.969
CCDC82	6 (1%)	971	0.21692	0.655	0.30249	0.769	0.9101	1	NA	NA	0.01297	0.143	0.5857	0.928	0.41166	0.835	0.00255	0.0378	0.38695	0.831	0.059159	0.402	0.89642	1	1	1
CCDC27	7 (1%)	970	0.21599	0.655	0.40182	0.835	0.1295	0.57	0.02843	0.264	0.081349	0.445	0.14345	0.584	0.03824	0.321	0.26324	0.709	0.21417	0.655	0.055299	0.388	0.23182	0.678	0.31179	0.773
RHOA	6 (1%)	971	0.04592	0.348	0.43922	0.84	0.52595	0.891	0.23625	0.687	0.48132	0.868	0.50823	0.876	0.88942	1	0.26072	0.709	0.72676	0.988	0.37432	0.829	NA	NA	NA	NA
MAMLD1	10 (1%)	967	0.37123	0.829	0.18864	0.631	0.60097	0.932	0.46737	0.867	0.15836	0.593	0.49967	0.869	0.62072	0.945	0.65253	0.96	0.75668	1	0.72733	0.988	0.67128	0.969	1	1
OR8D1	5 (1%)	972	0.69205	0.969	0.04465	0.341	0.76881	1	0.52244	0.888	0.1885	0.631	0.14629	0.585	0.24263	0.695	0.18048	0.627	0.47549	0.868	1	1	NA	NA	NA	NA