		Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		MIR_CNMF		MIR_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL	
	nCNV (%)	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
1p gain	82 (14%)	489	0.59684	1	0.30116	1	0.48444	1	0.44319	1	1.8919e-11	1.45e-08	0.85515	1	0.50203	1	0.5886	1	0.33003	1	0.25985	1
1q gain	89 (16%)	482	0.078113	1	0.23435	1	0.13092	1	0.34217	1	2.5445e-15	1.95e-12	0.51702	1	0.57679	1	0.37997	1	0.8182	1	0.36845	1
2p gain	36 (6%)	535	0.4516	1	0.90465	1	0.37897	1	0.72914	1	9.8673e-05	0.0689	0.19376	1	0.57151	1	0.17177	1	1	1	0.18239	1
2q gain	35 (6%)	536	0.64506	1	0.71897	1	0.16627	1	0.71117	1	0.00023022	0.158	0.19376	1	0.91954	1	0.17177	1	0.76976	1	0.0623	1
3p gain	57 (10%)	514	0.00052168	0.352	0.0068105	1	0.66267	1	0.031386	1	2.0272e-09	1.54e-06	0.12113	1	0.63527	1	0.53871	1	0.78772	1	0.39493	1
3q gain	62 (11%)	509	0.001129	0.75	0.022618	1	0.90823	1	0.075911	1	2.0402e-08	1.53e-05	0.048553	1	0.62781	1	0.15272	1	0.52507	1	0.26962	1
4p gain	36 (6%)	535	0.24197	1	0.5309	1	0.49124	1	0.18478	1	0.0032188	1	0.83128	1	0.75747	1	0.4204	1	0.6154	1	0.28089	1
4q gain	33 (6%)	538	0.31719	1	0.27831	1	0.4914	1	0.47136	1	0.010217	1	0.73455	1	0.92647	1	0.63828	1	0.36563	1	0.15064	1
5p gain	49 (9%)	522	0.11757	1	0.2787	1	0.17952	1	0.42764	1	3.9027e-06	0.00283	0.73455	1	0.28178	1	0.34384	1	0.12818	1	0.25906	1
5q gain	41 (7%)	530	0.14265	1	0.42808	1	0.11809	1	0.078418	1	4.3924e-05	0.0311	0.43861	1	0.39034	1	0.09531	1	0.16866	1	0.73883	1
6p gain	24 (4%)	547	0.013797	1	0.11911	1	0.87248	1	0.60953	1	0.078088	1	0.43907	1	0.81179	1	0.31618	1	1	1	0.79667	1
6q gain	23 (4%)	548	0.0021555	1	0.11911	1	0.77021	1	0.50648	1	0.0069542	1	0.067507	1	0.93203	1	0.3749	1	0.81243	1	0.79667	1
7p gain	463 (81%)	108	2.4223e-06	0.00176	8.591e-07	0.000635	0.00030025	0.205	2.9012e-08	2.17e-05	3.6202e-10	2.76e-07	0.003938	1	0.0022338	1	0.2944	1	0.016168	1	0.0017742	1
7q gain	469 (82%)	102	1.1404e-06	0.000835	0.00056306	0.378	0.0012399	0.817	0.00066921	0.449	9.4049e-08	7e-05	0.00044056	0.298	0.10985	1	0.17849	1	0.051264	1	0.0079852	1
8p gain	52 (9%)	519	5.2085e-05	0.0368	0.0031096	1	0.065386	1	0.0056207	1	2.6296e-08	1.97e-05	0.10514	1	0.42691	1	0.077724	1	0.13724	1	0.2715	1
8q gain	59 (10%)	512	5.509e-06	0.00398	0.00026544	0.182	0.041679	1	0.0097244	1	8.9294e-07	0.000659	0.25196	1	0.42691	1	0.077724	1	0.11862	1	0.14827	1
9p gain	47 (8%)	524	0.0037862	1	0.13246	1	0.69995	1	0.7107	1	4.273e-05	0.0303	0.17908	1	0.79891	1	0.70547	1	0.45204	1	0.24034	1
9q gain	72 (13%)	499	0.087393	1	0.13251	1	0.56112	1	0.18682	1	7.0622e-05	0.0494	0.024198	1	0.32067	1	0.44136	1	0.67325	1	0.15235	1
10p gain	12 (2%)	559	0.00097254	0.649	0.0074018	1	0.11655	1	0.016567	1	0.0028905	1	NA	NA	0.30734	1	0.38357	1	NA	NA	NA	NA
10q gain	3 (1%)	568	0.55632	1	0.79736	1	0.052608	1	0.66061	1	0.19597	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
11p gain	17 (3%)	554	0.9048	1	0.94098	1	0.23863	1	1	1	0.20818	1	NA	NA	0.86883	1	0.57388	1	0.69559	1	0.42797	1
11q gain	14 (2%)	557	0.18868	1	0.33436	1	0.21797	1	0.87815	1	0.12105	1	NA	NA	0.86883	1	0.57388	1	1	1	1	1
12p gain	59 (10%)	512	0.66431	1	0.63779	1	0.64386	1	0.80826	1	2.9725e-05	0.0212	0.17908	1	0.23571	1	0.71053	1	0.0040684	1	0.15974	1
12q gain	48 (8%)	523	0.5234	1	0.30019	1	0.53508	1	0.35454	1	0.00077808	0.52	0.2818	1	0.31369	1	0.51884	1	0.022468	1	0.51653	1
13q gain	10 (2%)	561	0.052994	1	0.50743	1	0.17953	1	0.8458	1	0.017386	1	1	1	0.89429	1	1	1	0.42473	1	1	1
14q gain	22 (4%)	549	0.43735	1	0.55161	1	0.012247	1	0.46265	1	0.79312	1	NA	NA	0.47116	1	0.46071	1	0.42473	1	0.61955	1
15q gain	24 (4%)	547	0.067972	1	0.5407	1	0.56284	1	1	1	0.00015413	0.107	NA	NA	0.53498	1	1	1	0.034698	1	0.22579	1
16p gain	38 (7%)	533	0.0083066	1	0.14706	1	0.41078	1	0.59381	1	1.9623e-05	0.0141	NA	NA	0.61477	1	0.61044	1	1	1	0.7656	1
16q gain	37 (6%)	534	0.019175	1	0.11391	1	0.36025	1	0.10431	1	0.00014986	0.104	NA	NA	0.75747	1	1	1	0.42046	1	0.66872	1
17p gain	48 (8%)	523	0.00049147	0.332	0.048923	1	0.080035	1	0.26286	1	6.3598e-05	0.0448	0.33143	1	0.14996	1	0.12103	1	0.33783	1	0.30688	1
17q gain	59 (10%)	512	0.0011588	0.767	0.10031	1	0.15066	1	0.32265	1	6.2367e-06	0.0045	0.68195	1	0.080075	1	0.029603	1	0.89807	1	0.57213	1
18p gain	58 (10%)	513	4.1258e-07	0.000306	0.00041781	0.283	0.15985	1	0.14233	1	7.9754e-09	6.03e-06	0.47663	1	0.42479	1	0.46537	1	0.018126	1	0.54719	1
18q gain	58 (10%)	513	1.5313e-06	0.00112	0.0021226	1	0.15985	1	0.21405	1	2.1774e-08	1.63e-05	0.62532	1	0.68431	1	0.69052	1	0.018126	1	0.27663	1
19p gain	224 (39%)	347	9.8337e-11	7.49e-08	1.4709e-06	0.00108	0.081187	1	0.00015432	0.107	1.902e-21	1.46e-18	0.0019465	1	0.009218	1	1.5951e-05	0.0115	0.18829	1	0.012876	1
19q gain	197 (35%)	374	9.2932e-12	7.11e-09	1.4144e-08	1.07e-05	0.116	1	0.0011435	0.758	1.0144e-21	7.82e-19	0.0026641	1	0.047561	1	6.4699e-05	0.0455	0.063728	1	0.018624	1
20p gain	220 (39%)	351	1.4478e-07	0.000108	2.9665e-09	2.25e-06	0.0044304	1	1.0549e-06	0.000776	3.8651e-07	0.000287	0.017214	1	0.053721	1	0.0063961	1	0.77635	1	0.0012274	0.811
20q gain	218 (38%)	353	9.0381e-08	6.73e-05	7.3098e-09	5.53e-06	0.0030277	1	5.4381e-06	0.00394	1.0541e-06	0.000776	0.0035042	1	0.03602	1	0.0051232	1	0.77635	1	0.0012274	0.811
21q gain	63 (11%)	508	0.0013391	0.88	0.0025257	1	0.011963	1	0.0041435	1	0.00037022	0.251	0.68195	1	0.32793	1	0.60154	1	0.017858	1	0.03462	1
22q gain	34 (6%)	537	2.3197e-06	0.00169	0.00022546	0.155	0.47378	1	0.32732	1	0.00016811	0.116	0.25608	1	0.21226	1	0.028574	1	0.24544	1	0.41551	1
xq gain	16 (3%)	555	0.25306	1	0.32074	1	0.98639	1	0.77159	1	0.68678	1	0.63467	1	0.79093	1	1	1	0.039429	1	0.093343	1
1p loss	16 (3%)	555	0.63654	1	0.22562	1	0.93451	1	0.11111	1	0.079269	1	0.067507	1	0.34205	1	0.11583	1	0.11032	1	0.079443	1
1q loss	15 (3%)	556	0.83042	1	0.33809	1	0.85303	1	0.36596	1	0.35735	1	0.067507	1	0.33911	1	0.17327	1	0.51727	1	0.28381	1
2p loss	32 (6%)	539	0.036006	1	0.021477	1	0.31288	1	0.37619	1	0.00035164	0.239	0.0081407	1	0.93487	1	0.46642	1	0.24359	1	0.66872	1
2q loss	32 (6%)	539	0.036006	1	0.021477	1	0.31288	1	0.37619	1	0.00035164	0.239	0.0081407	1	0.82591	1	0.44531	1	0.083621	1	0.42252	1
3p loss	40 (7%)	531	0.89815	1	0.73038	1	0.70396	1	0.6215	1	0.00019397	0.134	0.063754	1	0.23852	1	0.43604	1	0.63843	1	0.054664	1
3q loss	34 (6%)	537	0.23109	1	0.89739	1	0.5127	1	0.76606	1	3.2163e-05	0.0229	0.15828	1	0.78628	1	0.80635	1	0.88785	1	0.042701	1
4p loss	54 (9%)	517	0.082759	1	0.0072304	1	0.034155	1	0.35321	1	0.0095665	1	0.64894	1	0.30076	1	0.22036	1	0.7484	1	0.83836	1
4q loss	55 (10%)	516	0.001004	0.669	0.0062655	1	0.019257	1	0.13095	1	0.00048158	0.326	0.007825	1	0.72969	1	0.33104	1	0.55611	1	0.83836	1
5p loss	42 (7%)	529	1.7646e-05	0.0127	0.0031845	1	0.0020165	1	0.018786	1	0.00015196	0.105	0.067333	1	0.93967	1	0.38811	1	0.32463	1	0.74748	1
5q loss	43 (8%)	528	3.8672e-05	0.0274	0.0098539	1	0.0010935	0.727	0.01871	1	0.00010863	0.0757	0.067333	1	0.94352	1	0.26411	1	0.21205	1	0.84969	1
6p loss	86 (15%)	485	0.56501	1	0.39749	1	0.77407	1	0.89247	1	2.1014e-11	1.6e-08	0.2769	1	0.77482	1	0.11788	1	0.85707	1	0.35535	1
6q loss	124 (22%)	447	0.93705	1	0.69793	1	0.56745	1	0.61156	1	9.1846e-09	6.93e-06	0.54953	1	0.95886	1	0.26677	1	0.4942	1	0.78629	1
7p loss	8 (1%)	563	0.022013	1	0.063934	1	0.45597	1	0.079606	1	0.20499	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
7q loss	6 (1%)	565	0.10013	1	0.27933	1	0.94128	1	0.33608	1	0.59159	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
8p loss	58 (10%)	513	0.54109	1	0.43742	1	0.18222	1	0.90577	1	0.069406	1	0.5952	1	0.90477	1	1	1	0.55081	1	0.2453	1
8q loss	42 (7%)	529	0.61096	1	0.2284	1	0.022621	1	0.94347	1	0.015619	1	0.2903	1	0.85809	1	0.92163	1	0.4599	1	0.051973	1
9p loss	200 (35%)	371	0.008542	1	0.15473	1	0.52405	1	0.19017	1	0.68692	1	0.63483	1	0.61548	1	0.09276	1	0.020475	1	0.077524	1
9q loss	91 (16%)	480	0.37065	1	0.027903	1	0.11522	1	0.24826	1	0.33938	1	0.14578	1	0.35583	1	0.024226	1	0.73361	1	0.63472	1
10p loss	477 (84%)	94	6.188e-08	4.62e-05	2.8632e-05	0.0204	0.01193	1	3.1523e-06	0.00229	8.9526e-23	6.91e-20	0.056197	1	0.0028562	1	0.017641	1	0.21205	1	0.16781	1
10q loss	488 (85%)	83	1.2203e-08	9.2e-06	1.1289e-06	0.000827	0.0060201	1	5.3803e-05	0.0379	4.8225e-19	3.71e-16	0.01392	1	0.00013135	0.0914	0.0081834	1	0.24973	1	0.2071	1
11p loss	97 (17%)	474	4.9615e-07	0.000367	3.6132e-05	0.0257	0.8291	1	0.0037675	1	2.6316e-14	2.02e-11	0.03343	1	0.71855	1	0.12102	1	0.093456	1	0.46635	1
11q loss	92 (16%)	479	1.712e-05	0.0123	0.001655	1	0.9303	1	0.075795	1	3.2234e-13	2.47e-10	0.2818	1	0.91396	1	0.30575	1	0.34564	1	0.58371	1
12p loss	59 (10%)	512	0.089227	1	0.023747	1	0.4737	1	0.54879	1	0.0026692	1	0.81451	1	0.15428	1	0.1999	1	1	1	0.89202	1
12q loss	58 (10%)	513	0.10973	1	0.021911	1	0.35475	1	0.21827	1	6.5388e-05	0.0458	0.62532	1	0.17799	1	0.65697	1	1	1	0.62588	1
13q loss	183 (32%)	388	2.3358e-05	0.0167	0.00019576	0.135	0.74534	1	0.20741	1	1.0192e-27	7.88e-25	0.00075907	0.508	0.59398	1	0.074347	1	0.052029	1	0.40509	1
14q loss	146 (26%)	425	1.1127e-06	0.000817	0.0023075	1	0.44429	1	0.72618	1	1.9658e-28	1.52e-25	0.020657	1	0.80253	1	0.14346	1	0.10237	1	0.0093806	1
15q loss	102 (18%)	469	3.3825e-05	0.024	4.2924e-06	0.00311	0.0039645	1	0.0043727	1	1.7587e-08	1.32e-05	0.00054498	0.367	0.034525	1	0.0086479	1	0.0036788	1	0.16136	1
16p loss	63 (11%)	508	0.28626	1	0.34836	1	0.66475	1	0.85614	1	0.020893	1	0.44643	1	0.44233	1	0.51759	1	0.53213	1	0.53197	1
16q loss	83 (15%)	488	0.061169	1	0.26271	1	0.46126	1	0.84262	1	0.010603	1	0.69629	1	0.048671	1	0.27554	1	0.66886	1	0.61801	1
17p loss	64 (11%)	507	0.020498	1	0.91192	1	0.6498	1	0.51662	1	4.6739e-08	3.49e-05	0.039217	1	0.21489	1	0.29592	1	0.29185	1	0.25598	1
17q loss	42 (7%)	529	0.0057057	1	0.1228	1	0.25231	1	0.57321	1	1.6254e-05	0.0117	0.053699	1	0.48091	1	0.28761	1	0.14636	1	0.015649	1
18p loss	69 (12%)	502	0.047736	1	0.033758	1	0.35893	1	0.29984	1	1.5241e-05	0.011	0.19516	1	0.065596	1	0.017854	1	0.12508	1	0.55604	1
18q loss	61 (11%)	510	0.14762	1	0.030751	1	0.61462	1	0.11892	1	9.255e-05	0.0647	0.18342	1	0.01044	1	0.0012915	0.85	0.3948	1	0.30265	1
19p loss	25 (4%)	546	0.002855	1	0.019928	1	0.15634	1	0.071713	1	0.015353	1	0.0035086	1	0.019951	1	0.27693	1	0.8388	1	0.22857	1
19q loss	33 (6%)	538	0.0024343	1	0.03427	1	0.39284	1	0.02605	1	0.00073301	0.491	0.10514	1	0.079903	1	0.19786	1	0.78252	1	0.30981	1
20p loss	18 (3%)	553	0.00021397	0.147	0.0062564	1	0.03936	1	0.011363	1	6.4987e-05	0.0456	NA	NA	0.41365	1	0.38357	1	0.010425	1	0.079443	1
20q loss	16 (3%)	555	0.0016229	1	0.0099981	1	0.36087	1	0.29417	1	0.00018982	0.131	NA	NA	0.41365	1	0.38357	1	0.039301	1	0.11956	1
21q loss	40 (7%)	531	0.023358	1	0.043098	1	0.035539	1	0.26139	1	0.00027602	0.189	0.099415	1	0.012156	1	0.13784	1	0.8234	1	0.21482	1
22q loss	179 (31%)	392	0.71417	1	0.3394	1	0.20805	1	0.3593	1	1.0325e-06	0.000761	0.1088	1	0.89918	1	0.6087	1	0.21421	1	0.69983	1
xq loss	105 (18%)	466	0.020437	1	0.10494	1	0.14658	1	0.29446	1	1.4084e-09	1.07e-06	0.078228	1	0.96607	1	0.86704	1	0.40586	1	0.66638	1
