		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
