		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	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square 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
PTEN	29 (4%)	742	0.22565	1	0.43675	1	0.60952	1	0.60304	1	0.88203	1	0.2657	1	0.26833	1	0.90051	1	0.37955	1	0.88553	1	0.059701	1	0.34935	1
MLL3	56 (7%)	715	0.27197	1	0.97292	1	0.585	1	0.78898	1	0.74035	1	0.93484	1	0.10714	1	0.85994	1	0.039567	1	0.28112	1	0.15111	1	0.58154	1
ZNF384	14 (2%)	757	NA	NA	NA	NA	0.6096	1	0.15474	1	NA	NA	NA	NA	0.53541	1	1	1	0.88133	1	0.26335	1	0.46638	1	0.30998	1
DCP1B	5 (1%)	766	NA	NA	NA	NA	0.39484	1	0.0047466	1	NA	NA	NA	NA	0.61924	1	0.71884	1	0.60661	1	0.60627	1	1	1	0.66679	1
PIK3CA	261 (34%)	510	8.8999e-15	7.27e-12	3.8799e-10	3.15e-07	1.1263e-12	9.19e-10	1.6672e-09	1.35e-06	1.6388e-05	0.013	1.0648e-06	0.000854	5.1109e-28	4.2e-25	2.61e-12	2.13e-09	8.0222e-08	6.47e-05	1.4866e-11	1.21e-08	6.3973e-05	0.0502	1.8953e-10	1.54e-07
NCOA3	29 (4%)	742	0.54907	1	1	1	0.99322	1	0.38519	1	1	1	1	1	0.26302	1	0.28724	1	0.28079	1	0.096087	1	0.23997	1	0.13218	1
AOAH	19 (2%)	752	NA	NA	NA	NA	0.61198	1	0.65405	1	NA	NA	NA	NA	0.48133	1	0.22789	1	0.10885	1	0.50283	1	0.049802	1	0.89772	1
RBMX	13 (2%)	758	NA	NA	NA	NA	0.0058049	1	0.070635	1	NA	NA	NA	NA	0.49733	1	0.12739	1	0.2758	1	0.4179	1	0.64663	1	0.94849	1
RUNX1	25 (3%)	746	0.0055169	1	0.044232	1	1.8465e-05	0.0146	0.036935	1	1	1	0.25194	1	0.02987	1	0.14114	1	0.0024751	1	0.13304	1	0.10564	1	0.0080311	1
PIK3R1	21 (3%)	750	0.17209	1	0.61649	1	0.68745	1	0.64664	1	0.53782	1	0.29702	1	0.16481	1	0.91342	1	1	1	0.87482	1	0.8033	1	0.78568	1
MEF2A	14 (2%)	757	NA	NA	NA	NA	0.65902	1	0.33538	1	NA	NA	NA	NA	0.63035	1	0.14883	1	0.053096	1	0.012732	1	0.16948	1	0.033172	1
NCOR2	29 (4%)	742	0.67551	1	1	1	0.11101	1	0.3996	1	0.83853	1	0.68963	1	0.695	1	0.54924	1	0.54196	1	0.85918	1	0.41343	1	0.25622	1
AKT1	19 (2%)	752	0.06343	1	0.92454	1	0.0031236	1	0.0003628	0.28	0.16241	1	0.34532	1	3.0929e-05	0.0244	0.28844	1	0.016689	1	0.075601	1	0.081346	1	0.040151	1
GATA3	81 (11%)	690	0.0005751	0.442	0.00010133	0.079	0.0040893	1	0.0088698	1	0.0011529	0.879	0.00040708	0.314	6.2694e-06	0.00498	1.2227e-09	9.92e-07	4.041e-07	0.000325	1.265e-06	0.00101	3.9713e-07	0.00032	1.4562e-06	0.00116
NR1H2	18 (2%)	753	0.32598	1	0.26699	1	0.78925	1	0.048674	1	0.063975	1	0.11594	1	0.56007	1	0.072808	1	0.739	1	0.43998	1	0.48416	1	0.085634	1
MAP3K4	18 (2%)	753	0.10846	1	0.72143	1	0.78841	1	0.02477	1	0.073322	1	0.68963	1	0.46426	1	0.2143	1	0.39762	1	0.20941	1	0.78118	1	0.76456	1
TP53	257 (33%)	514	7.0755e-37	5.84e-34	2.4254e-33	2e-30	3.5347e-49	2.93e-46	6.1766e-23	5.05e-20	1.8749e-27	1.54e-24	1.102e-23	9.03e-21	4.1674e-55	3.46e-52	4.1792e-48	3.46e-45	7.4588e-39	6.16e-36	2.3199e-44	1.92e-41	1.4735e-30	1.21e-27	4.9526e-24	4.06e-21
TPRX1	7 (1%)	764	NA	NA	NA	NA	0.34307	1	0.56062	1	NA	NA	NA	NA	0.98251	1	0.73675	1	0.6937	1	1	1	0.61241	1	0.71235	1
CDH1	55 (7%)	716	1.6718e-07	0.000135	8.2018e-05	0.0641	2.424e-08	1.96e-05	0.00071097	0.545	0.00025549	0.198	0.00057945	0.444	1.2922e-06	0.00103	4.2277e-07	0.000339	1.6686e-06	0.00133	5.9234e-08	4.79e-05	0.00024417	0.19	0.010442	1
ATN1	17 (2%)	754	0.064261	1	0.054511	1	0.064223	1	0.83525	1	0.16884	1	0.29141	1	0.16018	1	0.56919	1	0.85348	1	0.43977	1	0.076673	1	0.35346	1
MAP2K4	32 (4%)	739	0.029235	1	0.0031315	1	0.032318	1	0.0090028	1	0.0023792	1	0.034428	1	0.028129	1	0.00031281	0.242	0.0015556	1	0.0033282	1	0.0010576	0.807	0.094211	1
MAP3K1	57 (7%)	714	4.3258e-06	0.00344	4.3824e-05	0.0344	7.2236e-05	0.0566	0.0011711	0.891	0.00020416	0.159	1.9896e-06	0.00159	1.0792e-05	0.00855	7.5066e-05	0.0587	1.9643e-05	0.0155	4.1587e-05	0.0327	0.00023013	0.179	0.0019527	1
CBFB	16 (2%)	755	0.18352	1	0.64781	1	0.026558	1	0.010661	1	0.34961	1	0.56866	1	0.00047333	0.364	0.58256	1	0.024087	1	0.0040159	1	0.011441	1	0.00073261	0.56
CTCF	18 (2%)	753	0.026496	1	0.31977	1	0.0029681	1	0.0045934	1	0.068249	1	0.36929	1	0.00038582	0.298	0.089065	1	0.20043	1	0.062133	1	0.77764	1	0.53155	1
CCDC144NL	8 (1%)	763	NA	NA	NA	NA	6.2856e-06	0.00499	0.30644	1	NA	NA	NA	NA	0.70488	1	0.34747	1	0.80852	1	0.21646	1	0.24575	1	0.39039	1
AKD1	19 (2%)	752	0.92566	1	0.43682	1	0.11179	1	0.17649	1	0.46668	1	0.24234	1	0.41501	1	0.30499	1	0.32166	1	0.066172	1	0.11379	1	0.2013	1
RB1	14 (2%)	757	0.52273	1	0.1721	1	0.15815	1	0.17085	1	0.48293	1	0.76154	1	0.33908	1	0.23143	1	0.061	1	0.0034669	1	0.13735	1	0.13703	1
PHLDA1	9 (1%)	762	0.32088	1	0.2751	1	0.39475	1	0.60983	1	1	1	0.28034	1	0.89024	1	0.89408	1	0.33083	1	0.43573	1	0.25647	1	0.54794	1
FOXA1	15 (2%)	756	0.7357	1	0.11583	1	0.1745	1	0.033352	1	1	1	0.5168	1	0.63588	1	0.16702	1	0.35916	1	0.22864	1	0.4563	1	0.60005	1
VEZF1	8 (1%)	763	NA	NA	NA	NA	0.47992	1	0.50919	1	NA	NA	NA	NA	0.18282	1	0.87962	1	0.90225	1	0.60501	1	1	1	0.90426	1
ZFP36L1	10 (1%)	761	0.83919	1	0.68646	1	0.011812	1	0.16377	1	0.025798	1	0.39178	1	0.88431	1	0.83148	1	0.84082	1	0.3933	1	0.69507	1	0.12555	1
NCOR1	31 (4%)	740	0.48764	1	0.33042	1	0.26629	1	0.41208	1	0.72317	1	0.72615	1	0.79885	1	0.48369	1	0.094078	1	0.40966	1	0.59269	1	0.45457	1
TBX3	18 (2%)	753	0.61241	1	0.34526	1	0.6018	1	0.056221	1	0.15974	1	0.55094	1	0.18399	1	0.44398	1	0.48866	1	0.48493	1	0.65117	1	1	1
DSPP	26 (3%)	745	0.94455	1	0.4158	1	0.64658	1	0.79242	1	0.098697	1	0.38708	1	0.70327	1	0.052999	1	0.48845	1	0.31114	1	0.13159	1	0.60685	1
AQP7	8 (1%)	763	0.6379	1	0.068244	1	0.039644	1	0.66215	1	NA	NA	NA	NA	0.76833	1	0.34747	1	0.47386	1	0.63156	1	0.61241	1	0.41211	1
BCL6B	8 (1%)	763	NA	NA	NA	NA	0.47613	1	0.69159	1	NA	NA	NA	NA	0.30401	1	1	1	0.80852	1	0.89919	1	0.49039	1	0.53695	1
RPGR	14 (2%)	757	0.60526	1	0.39167	1	0.99538	1	0.62763	1	0.74488	1	0.60567	1	0.3318	1	0.50951	1	0.72451	1	0.28283	1	0.90204	1	0.50119	1
TBL1XR1	9 (1%)	762	0.10865	1	0.29485	1	0.061128	1	NA	NA	0.45536	1	0.56866	1	0.021511	1	0.20013	1	0.079369	1	0.48246	1	0.86949	1	0.22898	1
MYB	11 (1%)	760	0.78645	1	1	1	0.085991	1	0.42083	1	1	1	0.68963	1	0.7584	1	0.65567	1	0.78661	1	0.68707	1	0.27798	1	1	1
PABPC3	8 (1%)	763	0.16324	1	0.80139	1	0.70318	1	0.73006	1	NA	NA	NA	NA	0.88844	1	0.39487	1	0.64092	1	0.89919	1	1	1	1	1
GPS2	6 (1%)	765	0.0076799	1	0.02839	1	0.1472	1	0.29336	1	1	1	1	1	0.60413	1	0.18404	1	0.75163	1	1	1	NA	NA	NA	NA
E2F4	4 (1%)	767	NA	NA	NA	NA	0.93219	1	NA	NA	NA	NA	NA	NA	0.8958	1	0.81718	1	0.81691	1	0.49056	1	NA	NA	NA	NA
DNAH12	12 (2%)	759	0.96689	1	0.26634	1	0.83584	1	0.67166	1	0.68948	1	0.68963	1	0.30246	1	0.53211	1	0.86336	1	1	1	1	1	0.51991	1
CDKN1B	7 (1%)	764	0.35772	1	0.11035	1	0.0022851	1	0.042808	1	0.33082	1	0.39197	1	0.11395	1	0.30586	1	0.36341	1	0.36774	1	0.45303	1	0.21492	1
HNF1A	9 (1%)	762	NA	NA	NA	NA	0.06612	1	0.62235	1	NA	NA	NA	NA	0.07601	1	0.035277	1	0.40602	1	0.069919	1	0.47124	1	0.27981	1
CRIPAK	6 (1%)	765	NA	NA	NA	NA	0.82085	1	0.11299	1	NA	NA	NA	NA	0.28525	1	0.18404	1	0.2578	1	0.56894	1	0.86949	1	0.73043	1
CASP8	10 (1%)	761	0.35508	1	0.19708	1	0.91923	1	0.56132	1	0.40246	1	1	1	0.23139	1	0.73732	1	0.7723	1	0.16637	1	0.098537	1	0.38772	1
STXBP2	9 (1%)	762	NA	NA	NA	NA	0.9051	1	0.81865	1	NA	NA	NA	NA	0.87632	1	0.48021	1	0.40602	1	0.91679	1	0.90204	1	0.74885	1
CTU2	5 (1%)	766	NA	NA	NA	NA	0.20259	1	0.54198	1	NA	NA	NA	NA	0.74284	1	0.60549	1	0.84742	1	0.070005	1	0.44907	1	0.21252	1
CCDC66	9 (1%)	762	0.36773	1	0.19708	1	0.67481	1	0.67548	1	NA	NA	NA	NA	0.068219	1	0.15665	1	0.090992	1	0.48246	1	0.4836	1	0.12506	1
HIST1H3B	7 (1%)	764	0.38283	1	1	1	0.554	1	0.62332	1	1	1	0.82708	1	0.33857	1	0.40117	1	0.47386	1	0.43028	1	0.6049	1	0.078777	1
TTN	122 (16%)	649	0.12192	1	0.038469	1	1.0151e-05	0.00805	0.039737	1	6.2253e-05	0.0489	0.052035	1	0.0003346	0.259	0.00090047	0.688	0.043402	1	0.019294	1	0.11333	1	0.0035063	1
SLC25A5	3 (0%)	768	NA	NA	NA	NA	0.32891	1	0.71035	1	NA	NA	NA	NA	NA	NA	NA	NA	0.78046	1	0.35423	1	0.45638	1	0.22998	1
SELPLG	7 (1%)	764	NA	NA	NA	NA	0.078261	1	0.0037154	1	NA	NA	NA	NA	0.10828	1	0.080144	1	0.47386	1	0.30395	1	1	1	0.092017	1
KRTAP9-9	6 (1%)	765	NA	NA	NA	NA	0.24939	1	0.25343	1	NA	NA	NA	NA	0.14118	1	1	1	0.29814	1	0.25628	1	0.25647	1	0.15597	1
KRTAP4-5	4 (1%)	767	NA	NA	NA	NA	0.47845	1	0.25124	1	NA	NA	NA	NA	0.26016	1	0.053405	1	0.079716	1	0.81408	1	0.15388	1	0.85178	1
SF3B1	14 (2%)	757	0.62869	1	0.094857	1	0.34705	1	0.24046	1	0.25347	1	0.004986	1	0.18599	1	0.02161	1	0.019423	1	0.1855	1	0.36876	1	0.13336	1
HLA-A	4 (1%)	767	0.81613	1	0.54285	1	0.33936	1	NA	NA	1	1	0.82708	1	0.016717	1	0.31464	1	0.67074	1	0.2933	1	NA	NA	NA	NA
FGFR2	7 (1%)	764	0.60247	1	0.54285	1	0.85664	1	0.18769	1	1	1	0.82708	1	0.30228	1	0.51493	1	0.78505	1	1	1	0.074627	1	0.011131	1
SHROOM4	11 (1%)	760	0.43178	1	0.18175	1	0.031528	1	0.56186	1	0.40246	1	0.63316	1	0.36197	1	0.26908	1	0.6184	1	0.92516	1	0.38563	1	0.90416	1
MED12	20 (3%)	751	0.60328	1	0.32577	1	0.3038	1	0.62272	1	0.45536	1	0.80281	1	0.45212	1	0.95001	1	0.83524	1	0.64695	1	0.33478	1	0.094587	1
DENND4B	8 (1%)	763	NA	NA	NA	NA	0.14752	1	0.015605	1	NA	NA	NA	NA	0.074948	1	0.63103	1	0.4674	1	0.23906	1	0.5865	1	0.19247	1
ODF1	5 (1%)	766	NA	NA	NA	NA	0.93219	1	0.50085	1	NA	NA	NA	NA	0.4543	1	0.51736	1	0.67074	1	0.49056	1	0.69507	1	0.80638	1
AXL	6 (1%)	765	NA	NA	NA	NA	0.2657	1	0.33033	1	NA	NA	NA	NA	0.88681	1	0.25074	1	0.75163	1	0.38443	1	1	1	0.51122	1
RPL18	4 (1%)	767	NA	NA	NA	NA	0.5042	1	0.24093	1	NA	NA	NA	NA	0.11949	1	0.091748	1	0.54246	1	0.12092	1	0.45638	1	0.61526	1
RAI1	7 (1%)	764	NA	NA	NA	NA	0.26858	1	0.87516	1	1	1	0.78219	1	0.7478	1	0.51493	1	0.47386	1	0.79726	1	0.86949	1	0.60024	1
ERBB2	12 (2%)	759	0.28657	1	0.89081	1	0.12105	1	0.012056	1	0.45096	1	0.77302	1	0.74641	1	0.29364	1	0.26937	1	0.06652	1	0.47124	1	0.40222	1
KRT38	4 (1%)	767	0.60247	1	0.8116	1	0.28762	1	0.78568	1	0.40246	1	0.63316	1	0.63301	1	0.81718	1	0.81691	1	1	1	NA	NA	NA	NA
TICAM1	5 (1%)	766	NA	NA	NA	NA	0.77376	1	0.86922	1	NA	NA	NA	NA	0.97664	1	0.60549	1	1	1	0.60627	1	1	1	0.60799	1
ASXL2	8 (1%)	763	0.36034	1	0.21437	1	0.79933	1	0.43136	1	NA	NA	NA	NA	0.74886	1	0.30455	1	0.53072	1	0.33561	1	1	1	0.46817	1
ASPHD1	3 (0%)	768	NA	NA	NA	NA	0.71147	1	0.8857	1	NA	NA	NA	NA	0.66094	1	0.59091	1	1	1	0.62612	1	1	1	1	1
FAM171B	8 (1%)	763	0.9247	1	0.29072	1	0.94079	1	0.047031	1	NA	NA	NA	NA	0.19265	1	0.0027711	1	0.31756	1	0.099719	1	0.032175	1	0.18819	1
MUC20	10 (1%)	761	NA	NA	NA	NA	0.10537	1	0.14651	1	NA	NA	NA	NA	0.00053878	0.414	0.19321	1	0.135	1	0.089302	1	0.34242	1	0.10855	1
PPEF1	8 (1%)	763	0.85303	1	1	1	0.35443	1	0.18284	1	1	1	1	1	0.66233	1	0.71053	1	0.25472	1	0.38534	1	0.20259	1	0.241	1
PRRX1	6 (1%)	765	0.57729	1	0.52186	1	0.047191	1	0.05666	1	0.83853	1	0.39197	1	0.55868	1	0.40735	1	0.86591	1	0.43327	1	0.32596	1	0.73033	1
ATP13A4	9 (1%)	762	0.60247	1	0.35582	1	0.15652	1	0.32961	1	NA	NA	NA	NA	0.87337	1	0.42821	1	0.82617	1	0.83471	1	0.78871	1	0.66967	1
MUC2	18 (2%)	753	0.82997	1	0.25866	1	0.3245	1	0.48719	1	0.7782	1	0.88144	1	0.48788	1	0.28799	1	0.95134	1	1	1	1	1	0.30288	1
UBC	8 (1%)	763	0.33635	1	1	1	0.25024	1	0.35008	1	0.55623	1	0.82708	1	0.28977	1	0.89408	1	0.71703	1	0.74094	1	NA	NA	NA	NA
KCNN3	6 (1%)	765	0.96764	1	1	1	0.50417	1	0.36047	1	NA	NA	NA	NA	0.14261	1	0.63519	1	0.41493	1	0.76887	1	0.45638	1	0.13839	1
RBM23	6 (1%)	765	NA	NA	NA	NA	0.69345	1	0.40417	1	NA	NA	NA	NA	0.79511	1	0.072164	1	0.41493	1	0.058077	1	0.69507	1	0.19029	1
GNRH2	3 (0%)	768	NA	NA	NA	NA	0.31921	1	NA	NA	NA	NA	NA	NA	0.95792	1	1	1	0.1245	1	1	1	NA	NA	NA	NA
