		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	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
PIK3CA	316 (32%)	659	7.3213e-13	5.87e-10	3.4819e-10	2.78e-07	3.2478e-13	2.61e-10	4.2749e-12	3.42e-09	0.00016969	0.132	5.3753e-06	0.00424	9.7778e-29	7.97e-26	1.6596e-19	1.34e-16	1.3172e-07	0.000104	2.4598e-13	1.98e-10	1.2582e-07	9.97e-05	2.6201e-12	2.1e-09
CBFB	23 (2%)	952	0.13441	1	0.92543	1	0.02276	1	9.1583e-05	0.0718	0.12372	1	0.5135	1	9.4393e-06	0.00743	0.044953	1	0.54119	1	0.0036719	1	0.0035809	1	0.0042736	1
RUNX1	29 (3%)	946	0.014949	1	0.045249	1	0.0017969	1	0.076606	1	1	1	0.28489	1	0.018518	1	0.098414	1	0.038907	1	0.25657	1	0.15671	1	0.036916	1
GATA3	97 (10%)	878	6.0161e-06	0.00474	1.912e-07	0.000151	0.0013877	1	0.0025141	1	0.018438	1	0.00092901	0.715	1.7931e-08	1.42e-05	1.1068e-12	8.87e-10	0.0017814	1	3.9778e-10	3.17e-07	1.1979e-08	9.52e-06	5.6319e-11	4.49e-08
FOXA1	23 (2%)	952	0.35554	1	0.23773	1	0.28899	1	0.03934	1	0.8942	1	0.309	1	0.12683	1	0.053026	1	0.31854	1	0.088201	1	0.067344	1	0.55088	1
SF3B1	16 (2%)	959	0.81451	1	0.29829	1	0.3764	1	0.17243	1	0.4505	1	0.02458	1	0.65487	1	0.24349	1	0.88492	1	0.70441	1	0.61162	1	0.32327	1
MAP3K1	70 (7%)	905	9.8197e-05	0.0769	0.00068883	0.532	0.0028987	1	0.033988	1	0.0006903	0.532	3.812e-05	0.0299	0.00016643	0.13	0.0001777	0.138	0.0083032	1	0.00014004	0.11	0.0002138	0.166	0.0090457	1
TP53	295 (30%)	680	2.3466e-31	1.92e-28	2.139e-29	1.75e-26	4.4916e-56	3.69e-53	1.2585e-32	1.03e-29	4.6324e-23	3.76e-20	2.5759e-23	2.09e-20	5.533e-71	4.56e-68	1.8862e-63	1.55e-60	2.2334e-43	1.83e-40	7.0395e-58	5.79e-55	1.8737e-41	1.54e-38	2.3494e-35	1.92e-32
MAP2K4	32 (3%)	943	0.12266	1	0.0039455	1	0.18854	1	0.020414	1	0.0026164	1	0.029833	1	0.0097678	1	0.00019782	0.154	0.0044841	1	0.00029434	0.228	2.5757e-05	0.0202	0.0012853	0.988
PTEN	35 (4%)	940	0.28021	1	0.65816	1	0.29035	1	0.41921	1	0.92182	1	0.66696	1	0.47362	1	0.66484	1	0.1184	1	0.64803	1	0.48566	1	0.74438	1
CDH1	105 (11%)	870	0.00017383	0.135	0.0033612	1	3.7082e-15	2.99e-12	2.5796e-08	2.05e-05	0.0040434	1	0.01062	1	1.0377e-17	8.37e-15	8.8905e-18	7.18e-15	2.4991e-17	2.01e-14	2.6218e-25	2.13e-22	2.2057e-21	1.79e-18	2.027e-19	1.64e-16
TBX3	27 (3%)	948	0.42752	1	0.30676	1	0.43541	1	0.10753	1	0.082966	1	0.6092	1	0.060446	1	0.040936	1	0.13717	1	0.040081	1	0.27883	1	0.39063	1
MLL3	69 (7%)	906	0.59769	1	0.68788	1	0.60548	1	0.15726	1	0.59668	1	0.86545	1	0.18204	1	0.2339	1	0.061322	1	0.088567	1	0.32017	1	0.7499	1
RB1	19 (2%)	956	0.66565	1	0.40335	1	0.079803	1	0.061508	1	0.48237	1	0.76252	1	0.1495	1	0.056438	1	0.27213	1	0.0028198	1	0.013044	1	0.31778	1
NCOR1	41 (4%)	934	0.57078	1	0.9535	1	0.71019	1	0.94433	1	0.43549	1	0.16749	1	0.39796	1	0.76984	1	0.64043	1	0.57181	1	1	1	0.55424	1
CTCF	17 (2%)	958	0.033075	1	0.32247	1	0.041218	1	0.0093189	1	0.068463	1	0.29653	1	0.57668	1	0.19094	1	0.13004	1	0.047532	1	0.64158	1	0.4427	1
GPS2	11 (1%)	964	0.0013319	1	0.0059227	1	0.12017	1	0.37991	1	0.26774	1	0.31541	1	0.053432	1	0.09457	1	0.13707	1	1	1	0.867	1	0.72087	1
THEM5	11 (1%)	964	0.23079	1	0.44097	1	0.5294	1	0.2796	1	0.20861	1	0.039824	1	0.70054	1	0.56231	1	0.93852	1	1	1	0.33656	1	0.1367	1
RPGR	18 (2%)	957	0.98994	1	0.6639	1	0.86897	1	0.60149	1	0.76744	1	0.69524	1	0.94774	1	0.66854	1	0.78318	1	1	1	0.90892	1	0.45162	1
DNAH12	17 (2%)	958	0.97269	1	0.15798	1	0.47305	1	0.70671	1	0.4505	1	0.62739	1	0.0022397	1	0.38214	1	0.60988	1	0.28019	1	0.40012	1	0.17843	1
CDKN1B	10 (1%)	965	0.63407	1	0.17826	1	0.14164	1	0.10796	1	0.74133	1	0.28049	1	0.23233	1	0.094275	1	0.25217	1	0.11079	1	0.29531	1	0.55727	1
ZFP36L1	9 (1%)	966	0.56989	1	0.44097	1	0.023168	1	0.75837	1	0.026587	1	0.023322	1	0.11856	1	0.29442	1	0.23016	1	0.90647	1	0.867	1	0.72087	1
ASB10	8 (1%)	967	0.86924	1	0.81129	1	0.98108	1	0.7874	1	NA	NA	NA	NA	0.56065	1	0.38617	1	0.6236	1	0.79858	1	0.867	1	1	1
HIST1H3B	11 (1%)	964	0.6378	1	1	1	0.92287	1	0.67728	1	0.63112	1	1	1	0.32397	1	0.13692	1	0.47596	1	0.91832	1	0.77807	1	0.8714	1
FAM86B1	8 (1%)	967	NA	NA	NA	NA	0.73351	1	0.87034	1	NA	NA	NA	NA	0.39973	1	0.53837	1	0.39445	1	0.005431	1	0.89271	1	0.59319	1
PIK3R1	15 (2%)	960	0.026604	1	0.72247	1	0.87297	1	0.077388	1	0.63112	1	0.45223	1	0.51074	1	0.48379	1	0.030701	1	0.1352	1	0.14077	1	0.5659	1
MYH9	19 (2%)	956	0.71129	1	0.18169	1	0.12276	1	0.46489	1	0.82166	1	0.60571	1	0.86881	1	0.28624	1	0.35408	1	0.19169	1	0.66025	1	0.13416	1
CASP8	12 (1%)	963	0.42308	1	0.3584	1	0.066315	1	0.43603	1	0.53088	1	0.73899	1	0.063275	1	1	1	0.43633	1	0.42403	1	0.74099	1	0.45162	1
COL6A5	25 (3%)	950	0.14393	1	0.44035	1	0.79093	1	0.204	1	0.075044	1	0.076018	1	0.20812	1	0.34175	1	0.57815	1	0.038283	1	0.050221	1	0.057654	1
TBL1XR1	10 (1%)	965	0.12343	1	0.23773	1	0.049694	1	0.49246	1	0.45066	1	0.56754	1	0.02278	1	0.14464	1	0.47488	1	0.042022	1	0.57502	1	0.24242	1
ASXL2	16 (2%)	959	0.40257	1	0.097462	1	0.8612	1	0.97149	1	0.28059	1	0.0050502	1	0.51175	1	0.39992	1	0.80324	1	0.18741	1	0.74099	1	0.26019	1
ARID1A	27 (3%)	948	0.13486	1	0.94281	1	0.15163	1	0.0615	1	1	1	0.47473	1	0.092366	1	0.27195	1	0.44301	1	0.093575	1	0.8375	1	0.045623	1
AQP12A	6 (1%)	969	0.71456	1	0.20312	1	0.20671	1	0.024723	1	0.20118	1	0.1152	1	0.69018	1	1	1	0.68865	1	1	1	1	1	1	1
EPDR1	5 (1%)	970	0.37908	1	1	1	0.7904	1	NA	NA	0.55688	1	0.46841	1	0.19109	1	1	1	0.59878	1	1	1	0.29253	1	1	1
ERBB2	21 (2%)	954	0.8865	1	0.34862	1	0.025356	1	0.010142	1	0.54884	1	0.90641	1	0.29561	1	0.6583	1	0.11247	1	0.18328	1	0.58395	1	0.50255	1
MYB	12 (1%)	963	0.63095	1	1	1	0.22983	1	0.51427	1	1	1	0.86234	1	0.76449	1	0.65713	1	0.034389	1	0.17162	1	0.068348	1	0.48911	1
TMEM151B	6 (1%)	969	0.91457	1	0.29719	1	0.11534	1	0.57557	1	0.026587	1	0.19462	1	0.51379	1	0.03134	1	0.27199	1	0.71558	1	0.39672	1	0.19069	1
GALNTL6	5 (1%)	970	0.9212	1	1	1	0.22516	1	0.012448	1	NA	NA	NA	NA	0.42681	1	0.13233	1	0.10957	1	0.65445	1	0.39672	1	0.19069	1
AKD1	18 (2%)	957	0.43967	1	0.59834	1	0.36139	1	0.53246	1	0.23548	1	0.12395	1	0.24229	1	0.080759	1	0.89561	1	0.47362	1	0.08123	1	0.43089	1
AARS	9 (1%)	966	0.40254	1	0.010742	1	0.7375	1	0.42446	1	0.83639	1	0.56319	1	0.0024127	1	0.47226	1	0.7455	1	0.31941	1	0.057313	1	0.071967	1
HLA-C	9 (1%)	966	0.31633	1	0.20312	1	0.58003	1	0.10565	1	0.39944	1	0.63373	1	0.27013	1	0.23622	1	0.18094	1	0.071698	1	0.19894	1	0.026727	1
GPRIN2	11 (1%)	964	0.65545	1	0.46464	1	0.69751	1	0.65535	1	0.87729	1	0.33049	1	0.84522	1	0.43329	1	0.40621	1	0.57806	1	0.7004	1	0.32382	1
TRPM5	11 (1%)	964	0.23713	1	0.61488	1	0.78634	1	0.25108	1	0.77844	1	0.78159	1	0.28761	1	0.062893	1	0.28798	1	0.1048	1	0.022185	1	0.017133	1
ANKRD12	18 (2%)	957	0.17774	1	0.11479	1	0.66005	1	0.8634	1	0.38495	1	0.51771	1	0.41993	1	0.10033	1	0.53702	1	0.64036	1	1	1	0.39886	1
FBXW7	15 (2%)	960	0.818	1	0.63995	1	0.084086	1	0.002505	1	0.77844	1	0.78159	1	0.058183	1	0.13508	1	0.42559	1	0.25636	1	0.48013	1	0.1253	1
PRICKLE3	11 (1%)	964	0.33466	1	0.28151	1	0.9506	1	0.60894	1	0.50889	1	0.89075	1	0.32695	1	0.12613	1	0.49094	1	0.13046	1	0.59767	1	0.26089	1
WDR52	16 (2%)	959	0.76787	1	0.056495	1	0.2201	1	0.16499	1	0.0042406	1	0.13693	1	0.013413	1	0.39992	1	0.30344	1	0.47663	1	0.045501	1	0.547	1
CDC42EP1	5 (1%)	970	0.57864	1	0.45178	1	0.63832	1	0.24153	1	0.83639	1	0.82863	1	0.2762	1	0.53599	1	0.70707	1	0.12382	1	NA	NA	NA	NA
ERBB3	18 (2%)	957	0.41249	1	0.2245	1	0.86719	1	0.52168	1	0.33474	1	0.29835	1	0.030955	1	0.21131	1	0.14347	1	0.81036	1	1	1	0.81661	1
FHOD3	13 (1%)	962	0.0431	1	0.020462	1	0.16211	1	0.026233	1	0.38495	1	0.026144	1	0.12942	1	0.0029597	1	0.16989	1	0.020013	1	0.7004	1	0.040825	1
PTHLH	7 (1%)	968	0.44175	1	0.3584	1	0.0088089	1	0.053291	1	0.68982	1	0.39157	1	0.72136	1	0.34086	1	0.2306	1	0.29043	1	NA	NA	NA	NA
SHISA4	5 (1%)	970	0.021349	1	0.20312	1	0.21824	1	0.26622	1	NA	NA	NA	NA	0.27208	1	0.45449	1	0.34186	1	1	1	NA	NA	NA	NA
KCNN3	9 (1%)	966	0.32125	1	0.8387	1	0.21159	1	0.27041	1	0.32773	1	0.14438	1	0.32629	1	0.23622	1	0.40903	1	0.90647	1	0.16472	1	0.61284	1
FGFR2	11 (1%)	964	0.84052	1	0.87614	1	0.82946	1	0.20774	1	1	1	1	1	0.44261	1	0.79609	1	0.66601	1	1	1	0.80293	1	0.59319	1
HLA-DRB5	6 (1%)	969	0.0072308	1	0.013513	1	0.24773	1	0.87589	1	NA	NA	NA	NA	0.25264	1	0.76969	1	0.22378	1	1	1	0.77994	1	1	1
ICOSLG	6 (1%)	969	0.69284	1	1	1	0.010294	1	0.6227	1	NA	NA	NA	NA	0.10713	1	1	1	0.15593	1	1	1	1	1	0.60738	1
GYG2	8 (1%)	967	0.70324	1	1	1	0.16503	1	0.71371	1	0.15561	1	0.039824	1	0.88512	1	0.90706	1	0.44017	1	1	1	0.39672	1	0.19069	1
PPEF1	11 (1%)	964	0.83986	1	1	1	0.30571	1	0.57527	1	1	1	1	1	0.82254	1	0.63407	1	0.25866	1	0.32973	1	0.80293	1	0.78507	1
MAP4K1	10 (1%)	965	0.82776	1	0.45178	1	0.35791	1	0.57664	1	1	1	0.78159	1	0.43407	1	0.84875	1	0.96293	1	0.32633	1	0.23942	1	0.2073	1
ZNF41	11 (1%)	964	0.80994	1	0.46464	1	0.65645	1	0.20674	1	0.87729	1	0.29104	1	0.69317	1	0.47052	1	0.040139	1	0.84844	1	0.092408	1	0.64478	1
FBXO17	5 (1%)	970	NA	NA	NA	NA	0.82	1	0.39945	1	NA	NA	NA	NA	0.57894	1	0.38034	1	0.00029787	0.23	1	1	1	1	1	1
HRNR	31 (3%)	944	0.89175	1	0.45977	1	0.063615	1	0.97544	1	0.58685	1	0.58809	1	0.93101	1	0.48162	1	0.51649	1	0.87762	1	0.93754	1	0.76312	1
STAG2	13 (1%)	962	0.3573	1	1	1	0.22554	1	0.33686	1	0.87729	1	0.67628	1	0.32321	1	0.72669	1	0.30689	1	0.45343	1	0.50823	1	0.68725	1
CEP57	6 (1%)	969	0.32441	1	1	1	0.11158	1	0.12941	1	NA	NA	NA	NA	0.15399	1	1	1	0.38806	1	0.062156	1	0.29253	1	0.026681	1
SPRR2B	3 (0%)	972	NA	NA	NA	NA	0.73375	1	NA	NA	NA	NA	NA	NA	0.50469	1	0.79472	1	0.90936	1	0.43	1	NA	NA	NA	NA
ZFP36L2	7 (1%)	968	0.43694	1	1	1	0.0095118	1	0.2056	1	1	1	1	1	0.49938	1	0.79821	1	0.66013	1	0.78065	1	1	1	0.83615	1
DMXL2	19 (2%)	956	0.6965	1	0.18169	1	0.05022	1	0.1581	1	0.10691	1	0.072694	1	0.0094671	1	0.069731	1	0.050488	1	0.22136	1	0.085006	1	0.13747	1
ZBTB7C	5 (1%)	970	NA	NA	NA	NA	0.68204	1	0.74617	1	NA	NA	NA	NA	0.81081	1	0.38034	1	0.67531	1	0.49812	1	0.77994	1	1	1
MUC5B	33 (3%)	942	0.69434	1	0.87918	1	0.41392	1	0.28461	1	0.91544	1	0.69524	1	0.37052	1	0.75921	1	0.7795	1	0.20998	1	0.74639	1	0.83032	1
XBP1	4 (0%)	971	NA	NA	NA	NA	0.016381	1	0.36037	1	NA	NA	NA	NA	0.34729	1	1	1	0.39433	1	0.53244	1	0.39341	1	0.81237	1
FXYD5	5 (1%)	970	0.69284	1	0.61488	1	0.33546	1	NA	NA	0.64325	1	1	1	0.30988	1	0.45449	1	0.7564	1	0.49812	1	NA	NA	NA	NA
ATXN2	15 (2%)	960	0.83659	1	0.36588	1	0.39237	1	0.64207	1	0.23413	1	0.076608	1	0.75677	1	0.36431	1	0.53816	1	0.34153	1	0.79285	1	0.9155	1
CCL13	4 (0%)	971	NA	NA	NA	NA	0.00018204	0.141	0.36037	1	NA	NA	NA	NA	0.77842	1	0.56801	1	0.16028	1	0.53244	1	NA	NA	NA	NA
