Clinical Features	CN_CNMF		METHLYATION_CNMF		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
SPOP	48 (11%)	377	9.9999e-06	0.000709	9.9999e-06	0.000709	9.9999e-06	0.000709	9.9999e-06	0.000709	0.67982	1	0.03725	0.409	0.33401	0.858	0.19314	0.765
TP53	43 (10%)	382	9.9999e-06	0.000709	0.0062199	0.143	0.00019	0.00857	5e-05	0.00276	0.7725	1	0.057079	0.566	0.15974	0.727	0.04105	0.422
PTEN	14 (3%)	411	0.55718	1	0.16798	0.739	0.099859	0.649	0.0070799	0.146	0.65743	1	0.23591	0.775	0.52677	1	0.14929	0.72
CTNNB1	11 (3%)	414	0.15794	0.725	0.03041	0.359	0.29313	0.822	0.21855	0.768	0.099769	0.649	0.01721	0.259	0.17352	0.748	0.089589	0.612
FOXA1	25 (6%)	400	0.00012	0.00595	9.9999e-06	0.000709	9.9999e-06	0.000709	3e-05	0.00186	0.0057899	0.143	0.0066499	0.143	0.51122	1	0.59297	1
ATM	19 (4%)	406	0.0051199	0.134	0.1666	0.739	0.44534	0.94	0.076499	0.605	0.060269	0.575	0.27784	0.815	0.81119	1	0.38684	0.888
PIK3CA	11 (3%)	414	0.14063	0.712	0.0091599	0.168	0.15575	0.725	0.01298	0.215	0.2302	0.775	0.03219	0.371	0.45757	0.944	0.22135	0.768
BRAF	8 (2%)	417	0.32467	0.852	0.03936	0.415	0.20229	0.765	0.102	0.649	1	1	0.57601	1	0.65244	1	0.38276	0.886
HRAS	5 (1%)	420	0.82879	1	0.53506	1	0.74343	1	1	1	0.74196	1	0.41131	0.9	0.24625	0.788	0.75241	1
KDM6A	9 (2%)	416	0.01054	0.187	0.086859	0.612	0.00158	0.0603	0.069559	0.589	0.54004	1	0.1361	0.7	0.14905	0.72	0.01113	0.19
IDH1	5 (1%)	420	0.00427	0.118	0.0026	0.0921	0.0065799	0.143	0.02936	0.355	0.20085	0.765	0.078039	0.605	1	1	0.076929	0.605
SMG7	7 (2%)	418	0.87394	1	0.30999	0.834	0.074819	0.605	0.00297	0.0921	0.072669	0.601	0.091319	0.612	1	1	0.67973	1
ZMYM3	9 (2%)	416	0.71926	1	0.37116	0.884	0.14515	0.72	0.19999	0.765	0.20199	0.765	0.65215	1	0.15745	0.725	0.091349	0.612
EHHADH	5 (1%)	420	0.47272	0.957	0.86805	1	0.86283	1	1	1	0.63394	1	0.29059	0.822	NA	NA	NA	NA
TP53BP1	7 (2%)	418	0.12904	0.688	0.5144	1	0.89478	1	0.20134	0.765	1	1	0.64782	1	0.52513	1	0.38403	0.886
CNTNAP1	7 (2%)	418	0.20592	0.765	0.31105	0.834	0.34968	0.88	0.70495	1	0.71536	1	0.02537	0.34	NA	NA	NA	NA
BMP2K	6 (1%)	419	0.44052	0.936	0.6926	1	0.78327	1	1	1	0.52064	1	0.6988	1	0.30609	0.834	0.53513	1
RPTN	6 (1%)	419	0.088989	0.612	0.45254	0.943	1	1	1	1	0.87773	1	0.081489	0.612	0.41729	0.9	0.70511	1
TCEB3	4 (1%)	421	0.80703	1	0.55592	1	0.27061	0.812	0.0417	0.422	0.15616	0.725	0.1953	0.765	0.4138	0.9	0.57068	1
NTM	6 (1%)	419	1	1	0.87608	1	0.19489	0.765	0.57958	1	0.77663	1	0.72764	1	0.35871	0.884	0.7546	1
MED12	7 (2%)	418	0.10695	0.651	0.79925	1	0.89625	1	0.23537	0.775	0.63374	1	0.95732	1	0.21158	0.765	0.79611	1
MED15	6 (1%)	419	0.43965	0.936	0.087219	0.612	0.87729	1	0.29347	0.822	0.8784	1	0.69841	1	0.933	1	0.55377	1
ERN1	3 (1%)	422	0.22469	0.771	0.0288	0.355	0.4061	0.895	0.79007	1	0.77846	1	0.91513	1	NA	NA	NA	NA
LMOD2	5 (1%)	420	1	1	1	1	1	1	0.73969	1	0.74256	1	0.73757	1	0.60039	1	0.65261	1
FAM111A	3 (1%)	422	1	1	0.52866	1	0.10941	0.651	0.25687	0.812	0.77858	1	0.10616	0.651	NA	NA	NA	NA
ZNF709	5 (1%)	420	0.22648	0.771	1	1	0.28122	0.82	0.63936	1	0.86212	1	0.26279	0.812	0.63746	1	0.70443	1
MLLT10	4 (1%)	421	0.80828	1	0.16459	0.739	1	1	0.68343	1	0.26913	0.812	0.64849	1	NA	NA	NA	NA
TNRC18	6 (1%)	419	0.85105	1	0.87333	1	0.68865	1	0.39431	0.891	0.6827	1	0.55392	1	0.72084	1	0.75023	1
GAGE2D	3 (1%)	422	0.75354	1	0.067469	0.587	0.02688	0.342	0.061419	0.575	0.64041	1	0.37232	0.884	NA	NA	NA	NA
EMG1	4 (1%)	421	0.493	0.974	0.27359	0.812	0.55351	1	0.23493	0.775	0.03735	0.409	0.00286	0.0921	NA	NA	NA	NA
LAMA3	7 (2%)	418	0.36652	0.884	0.26674	0.812	0.35	0.88	0.70233	1	1	1	1	1	0.87754	1	0.64451	1
RPL11	4 (1%)	421	0.6317	1	1	1	0.55804	1	0.56007	1	1	1	0.8185	1	NA	NA	NA	NA
ZFHX3	13 (3%)	412	0.11395	0.657	0.22122	0.768	0.12787	0.688	0.1076	0.651	0.28848	0.822	0.49199	0.974	0.31732	0.842	0.99045	1
MUC17	25 (6%)	400	0.13626	0.7	0.11742	0.662	0.084049	0.612	0.34072	0.867	0.082499	0.612	0.79505	1	0.95457	1	0.28572	0.822
CDKN1B	5 (1%)	420	1	1	0.86603	1	0.38377	0.886	0.14955	0.72	0.27511	0.812	0.10189	0.649	0.70027	1	0.36903	0.884
POM121	3 (1%)	422	0.75542	1	0.41193	0.9	0.40346	0.895	0.62104	1	0.19957	0.765	0.61719	1	NA	NA	NA	NA
ESCO1	4 (1%)	421	0.63551	1	0.84245	1	0.11339	0.657	0.13247	0.699	0.2685	0.812	0.43271	0.929	NA	NA	NA	NA
MYOT	4 (1%)	421	0.55334	1	0.0089099	0.168	0.21297	0.765	0.45876	0.944	0.46155	0.946	0.12564	0.688	0.21064	0.765	0.19205	0.765
L1CAM	7 (2%)	418	0.578	1	0.02644	0.342	0.40405	0.895	0.2011	0.765	1	1	0.0202	0.295	0.24503	0.788	0.25368	0.807
FAM47C	9 (2%)	416	0.12775	0.688	0.48147	0.964	0.83743	1	0.57998	1	0.5377	1	0.39013	0.891	0.87006	1	0.37483	0.884
CR1L	5 (1%)	420	0.69075	1	0.45495	0.944	0.63043	1	0.15142	0.722	0.63327	1	0.92806	1	NA	NA	NA	NA
FAM120B	3 (1%)	422	0.22689	0.771	1	1	0.64541	1	0.78842	1	0.29341	0.822	0.01653	0.256	NA	NA	NA	NA
EDC4	3 (1%)	422	0.070089	0.589	0.20629	0.765	1	1	0.4675	0.954	0.51223	1	0.00388	0.113	0.16991	0.739	0.64121	1
KIRREL	5 (1%)	420	1	1	0.74175	1	0.44927	0.943	0.37472	0.884	1	1	0.69325	1	0.78154	1	1	1
TCERG1	4 (1%)	421	1	1	0.33091	0.858	0.27238	0.812	0.55994	1	0.83659	1	0.30787	0.834	0.91287	1	0.01638	0.256
SLC16A6	4 (1%)	421	0.80831	1	0.27303	0.812	0.39901	0.891	0.065019	0.587	0.03791	0.409	0.35542	0.884	0.69744	1	0.67937	1
NKX3-1	5 (1%)	420	0.37506	0.884	0.62901	1	1	1	0.74041	1	0.13698	0.7	0.50788	1	NA	NA	NA	NA
RNF17	3 (1%)	422	0.7557	1	0.77661	1	0.11033	0.651	0.18468	0.765	0.63933	1	0.52404	1	NA	NA	NA	NA
KYNU	3 (1%)	422	0.5569	1	0.41555	0.9	0.2031	0.765	0.78786	1	1	1	0.44177	0.936	NA	NA	NA	NA
LARP1	4 (1%)	421	0.63218	1	0.84162	1	0.27017	0.812	0.83395	1	1	1	0.67794	1	NA	NA	NA	NA
CDK12	8 (2%)	417	0.00132	0.0546	0.18008	0.765	0.66802	1	0.1203	0.67	0.3984	0.891	0.45209	0.943	0.31812	0.842	0.70334	1
ACPT	3 (1%)	422	0.37188	0.884	0.65203	1	0.3026	0.832	0.35139	0.88	0.39846	0.891	0.52214	1	0.47888	0.964	0.8759	1
AP4B1	5 (1%)	420	0.36851	0.884	0.24209	0.785	0.33145	0.858	0.84991	1	1	1	0.67397	1	NA	NA	NA	NA
RAG1	9 (2%)	416	0.8021	1	0.48197	0.964	0.53283	1	0.91216	1	0.2723	0.812	0.6133	1	0.20981	0.765	0.30221	0.832
APC	9 (2%)	416	0.065419	0.587	0.20219	0.765	0.48505	0.966	0.23869	0.779	0.02339	0.331	0.34072	0.867	0.16898	0.739	0.7184	1
MSLNL	4 (1%)	421	0.8066	1	0.11726	0.662	0.83976	1	1	1	0.68786	1	0.23189	0.775	NA	NA	NA	NA
GAB2	5 (1%)	420	1	1	0.8666	1	1	1	1	1	0.86325	1	0.29081	0.822	0.64984	1	0.67912	1
DNMT3B	4 (1%)	421	0.8092	1	0.0088899	0.168	0.21467	0.766	0.087699	0.612	1	1	0.85623	1	0.21111	0.765	0.46928	0.954
NCKAP1L	5 (1%)	420	0.68816	1	0.10876	0.651	0.38068	0.886	0.2205	0.768	1	1	0.65207	1	NA	NA	NA	NA
PRTFDC1	3 (1%)	422	0.75395	1	1	1	1	1	0.060649	0.575	0.02406	0.331	0.30376	0.832	NA	NA	NA	NA
PCSK5	6 (1%)	419	0.36936	0.884	0.067139	0.587	0.33203	0.858	0.14313	0.717	0.68036	1	0.97179	1	NA	NA	NA	NA
ITGA2B	4 (1%)	421	0.37587	0.884	1	1	0.39709	0.891	0.29485	0.822	0.21068	0.765	0.31931	0.842	0.87684	1	0.67707	1