		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 (15%)	478	0.59684	1	0.30116	1	0.48444	1	0.44319	1	6.3941e-13	4.88e-10	0.9246	1	0.50203	1	0.5886	1	0.33003	1	0.25985	1
1q gain	88 (16%)	472	0.078113	1	0.23435	1	0.13092	1	0.34217	1	1.8255e-16	1.4e-13	0.76209	1	0.57679	1	0.37997	1	0.8182	1	0.36845	1
2p gain	36 (6%)	524	0.4516	1	0.90465	1	0.37897	1	0.72914	1	4.8734e-05	0.0342	0.19597	1	0.57151	1	0.17177	1	1	1	0.18239	1
2q gain	35 (6%)	525	0.64506	1	0.71897	1	0.16627	1	0.71117	1	0.00011127	0.077	0.19597	1	0.91954	1	0.17177	1	0.76976	1	0.0623	1
3p gain	57 (10%)	503	0.00052168	0.35	0.0068105	1	0.66267	1	0.031386	1	5.3581e-08	4e-05	0.13274	1	0.63527	1	0.53871	1	0.78772	1	0.39493	1
3q gain	63 (11%)	497	0.00058149	0.389	0.015309	1	0.88358	1	0.055944	1	6.8919e-07	0.000508	0.062146	1	0.70658	1	0.5289	1	0.52507	1	0.26962	1
4p gain	35 (6%)	525	0.24197	1	0.5309	1	0.49124	1	0.18478	1	0.0035849	1	1	1	0.75747	1	0.4204	1	0.6154	1	0.28089	1
4q gain	33 (6%)	527	0.42882	1	0.21133	1	0.4469	1	0.4426	1	0.012785	1	0.68505	1	0.92647	1	0.63828	1	0.36563	1	0.15064	1
5p gain	48 (9%)	512	0.11757	1	0.2787	1	0.17952	1	0.42764	1	2.1151e-06	0.00154	0.68505	1	0.28178	1	0.34384	1	0.12818	1	0.25906	1
5q gain	40 (7%)	520	0.14265	1	0.42808	1	0.11809	1	0.078418	1	2.9818e-06	0.00217	0.44104	1	0.39034	1	0.09531	1	0.16866	1	0.73883	1
6p gain	23 (4%)	537	0.013797	1	0.11911	1	0.87248	1	0.60953	1	0.15853	1	0.68505	1	0.81179	1	0.31618	1	1	1	0.79667	1
6q gain	22 (4%)	538	0.0021555	1	0.11911	1	0.77021	1	0.50648	1	0.026852	1	0.19597	1	0.93203	1	0.3749	1	0.81243	1	0.79667	1
7p gain	455 (81%)	105	1.8902e-06	0.00138	6.8135e-07	0.000503	0.00043692	0.296	1.3359e-08	1e-05	5.6561e-10	4.28e-07	0.0073146	1	0.0022338	1	0.2944	1	0.016168	1	0.0017742	1
7q gain	460 (82%)	100	8.7227e-07	0.000642	0.00047438	0.32	0.0018585	1	0.00045628	0.308	5.3124e-08	3.97e-05	0.0024016	1	0.10985	1	0.17849	1	0.051264	1	0.0079852	1
8p gain	51 (9%)	509	5.2085e-05	0.0365	0.0031096	1	0.065386	1	0.0056207	1	1.3021e-09	9.83e-07	0.074204	1	0.42691	1	0.077724	1	0.13724	1	0.2715	1
8q gain	58 (10%)	502	5.509e-06	0.00398	0.00026544	0.181	0.041679	1	0.0097244	1	8.9646e-08	6.67e-05	0.16521	1	0.42691	1	0.077724	1	0.11862	1	0.14827	1
9p gain	47 (8%)	513	0.0037862	1	0.13246	1	0.69995	1	0.7107	1	3.496e-05	0.0246	0.19512	1	0.79891	1	0.70547	1	0.45204	1	0.24034	1
9q gain	72 (13%)	488	0.055313	1	0.10667	1	0.5208	1	0.13742	1	3.1244e-05	0.0221	0.062424	1	0.32067	1	0.44136	1	0.67325	1	0.15235	1
10p gain	12 (2%)	548	0.00097254	0.648	0.0074018	1	0.11655	1	0.016567	1	0.0015656	1	NA	NA	0.30734	1	0.38357	1	NA	NA	NA	NA
10q gain	3 (1%)	557	0.55632	1	0.79736	1	0.052608	1	0.66061	1	0.19065	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
11p gain	18 (3%)	542	0.91262	1	0.79949	1	0.59528	1	1	1	0.11578	1	NA	NA	0.86883	1	0.57388	1	0.69559	1	0.42797	1
11q gain	15 (3%)	545	0.12526	1	0.18877	1	0.45518	1	0.64902	1	0.08032	1	NA	NA	0.86883	1	0.57388	1	1	1	1	1
12p gain	58 (10%)	502	0.67282	1	0.69953	1	0.54039	1	0.72116	1	5.245e-05	0.0367	0.19512	1	0.23571	1	0.71053	1	0.0071608	1	0.25647	1
12q gain	48 (9%)	512	0.5234	1	0.30019	1	0.53508	1	0.35454	1	0.00050055	0.336	0.38083	1	0.31369	1	0.51884	1	0.022468	1	0.51653	1
13q gain	9 (2%)	551	0.052994	1	0.50743	1	0.17953	1	0.8458	1	0.0031357	1	NA	NA	0.89429	1	1	1	0.42473	1	1	1
14q gain	22 (4%)	538	0.43735	1	0.55161	1	0.012247	1	0.46265	1	0.72361	1	NA	NA	0.47116	1	0.46071	1	0.42473	1	0.61955	1
15q gain	24 (4%)	536	0.067972	1	0.5407	1	0.56284	1	1	1	6.2844e-05	0.0439	NA	NA	0.53498	1	1	1	0.034698	1	0.22579	1
16p gain	37 (7%)	523	0.0083066	1	0.14706	1	0.41078	1	0.59381	1	2.4294e-05	0.0173	NA	NA	0.61477	1	0.61044	1	1	1	0.7656	1
16q gain	36 (6%)	524	0.019175	1	0.11391	1	0.36025	1	0.10431	1	0.00035183	0.239	NA	NA	0.75747	1	1	1	0.42046	1	0.66872	1
17p gain	45 (8%)	515	0.00049147	0.331	0.048923	1	0.080035	1	0.26286	1	1.6133e-05	0.0116	0.68505	1	0.14996	1	0.12103	1	0.33783	1	0.30688	1
17q gain	56 (10%)	504	0.0011588	0.769	0.10031	1	0.15066	1	0.32265	1	6.4195e-06	0.00463	0.58468	1	0.080075	1	0.029603	1	0.89807	1	0.57213	1
18p gain	58 (10%)	502	4.1258e-07	0.000306	0.00041781	0.284	0.15985	1	0.14233	1	3.5596e-10	2.7e-07	0.53388	1	0.42479	1	0.46537	1	0.018126	1	0.54719	1
18q gain	57 (10%)	503	5.0713e-07	0.000375	0.00072841	0.487	0.17438	1	0.16166	1	9.9036e-11	7.53e-08	0.68239	1	0.47672	1	0.62223	1	0.018126	1	0.27663	1
19p gain	220 (39%)	340	9.8337e-11	7.48e-08	1.4709e-06	0.00108	0.081187	1	0.00015432	0.107	1.5522e-14	1.19e-11	0.0089122	1	0.009218	1	1.5951e-05	0.0114	0.18829	1	0.012876	1
19q gain	193 (34%)	367	2.9328e-12	2.23e-09	6.3577e-09	4.79e-06	0.14389	1	0.0015901	1	3.4881e-16	2.68e-13	0.0060067	1	0.047561	1	6.4699e-05	0.045	0.063728	1	0.018624	1
20p gain	217 (39%)	343	1.4478e-07	0.000107	2.9665e-09	2.24e-06	0.0044304	1	1.0549e-06	0.000775	8.7777e-05	0.0609	0.022551	1	0.053721	1	0.0063961	1	0.77635	1	0.0012274	0.814
20q gain	215 (38%)	345	9.0381e-08	6.72e-05	7.3098e-09	5.5e-06	0.0030277	1	5.4381e-06	0.00394	0.00019234	0.133	0.0045972	1	0.03602	1	0.0051232	1	0.77635	1	0.0012274	0.814
21q gain	62 (11%)	498	0.0013391	0.882	0.0025257	1	0.011963	1	0.0041435	1	0.00022772	0.156	0.7282	1	0.32793	1	0.60154	1	0.017858	1	0.03462	1
22q gain	34 (6%)	526	2.3197e-06	0.00169	0.00022546	0.154	0.47378	1	0.32732	1	6.3896e-05	0.0445	0.25303	1	0.21226	1	0.028574	1	0.24544	1	0.41551	1
xq gain	16 (3%)	544	0.25306	1	0.32074	1	0.98639	1	0.77159	1	0.32121	1	0.50882	1	0.79093	1	1	1	0.039429	1	0.093343	1
1p loss	16 (3%)	544	0.63654	1	0.22562	1	0.93451	1	0.11111	1	0.068217	1	0.069296	1	0.34205	1	0.11583	1	0.11032	1	0.079443	1
1q loss	15 (3%)	545	0.83042	1	0.33809	1	0.85303	1	0.36596	1	0.29301	1	0.069296	1	0.33911	1	0.17327	1	0.51727	1	0.28381	1
2p loss	30 (5%)	530	0.072415	1	0.03427	1	0.38726	1	0.50206	1	3.0619e-05	0.0217	0.0039485	1	0.92647	1	0.44531	1	0.24359	1	0.66872	1
2q loss	30 (5%)	530	0.072415	1	0.03427	1	0.38726	1	0.50206	1	3.0619e-05	0.0217	0.0039485	1	0.84996	1	0.45778	1	0.083621	1	0.42252	1
3p loss	39 (7%)	521	0.89815	1	0.73038	1	0.70396	1	0.6215	1	0.00032966	0.225	0.10938	1	0.23852	1	0.43604	1	0.63843	1	0.054664	1
3q loss	33 (6%)	527	0.23109	1	0.89739	1	0.5127	1	0.76606	1	5.7857e-06	0.00418	0.25303	1	0.78628	1	0.80635	1	0.88785	1	0.042701	1
4p loss	53 (9%)	507	0.082759	1	0.0072304	1	0.034155	1	0.35321	1	0.0092873	1	0.82863	1	0.30076	1	0.22036	1	0.7484	1	0.83836	1
4q loss	54 (10%)	506	0.00045089	0.305	0.003501	1	0.01385	1	0.092083	1	0.0005384	0.361	0.055935	1	0.76748	1	0.35027	1	0.42279	1	0.89332	1
5p loss	42 (8%)	518	1.7646e-05	0.0126	0.0031845	1	0.0020165	1	0.018786	1	0.0012876	0.85	0.077332	1	0.93967	1	0.38811	1	0.32463	1	0.74748	1
5q loss	43 (8%)	517	3.8672e-05	0.0272	0.0098539	1	0.0010935	0.727	0.01871	1	0.00086163	0.575	0.077332	1	0.94352	1	0.26411	1	0.21205	1	0.84969	1
6p loss	84 (15%)	476	0.56501	1	0.39749	1	0.77407	1	0.89247	1	3.4786e-13	2.66e-10	0.28266	1	0.77482	1	0.11788	1	0.85707	1	0.35535	1
6q loss	121 (22%)	439	0.93705	1	0.69793	1	0.56745	1	0.61156	1	1.7784e-10	1.35e-07	0.74876	1	0.95886	1	0.26677	1	0.4942	1	0.78629	1
7p loss	8 (1%)	552	0.022013	1	0.063934	1	0.45597	1	0.079606	1	0.035574	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
7q loss	6 (1%)	554	0.10013	1	0.27933	1	0.94128	1	0.33608	1	0.092654	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
8p loss	58 (10%)	502	0.54109	1	0.43742	1	0.18222	1	0.90577	1	0.030872	1	0.65037	1	0.90477	1	1	1	0.55081	1	0.2453	1
8q loss	42 (8%)	518	0.61096	1	0.2284	1	0.022621	1	0.94347	1	0.0077836	1	0.33135	1	0.85809	1	0.92163	1	0.4599	1	0.051973	1
9p loss	194 (35%)	366	0.0033961	1	0.14302	1	0.52641	1	0.15021	1	0.68473	1	0.71472	1	0.58707	1	0.061703	1	0.018114	1	0.10709	1
9q loss	86 (15%)	474	0.13703	1	0.02149	1	0.17796	1	0.11516	1	0.23236	1	0.17453	1	0.32183	1	0.01549	1	0.61861	1	0.72998	1
10p loss	467 (83%)	93	6.188e-08	4.61e-05	2.8632e-05	0.0203	0.010387	1	1.7644e-06	0.00129	4.8605e-21	3.74e-18	0.074508	1	0.0026906	1	0.028707	1	0.21205	1	0.16781	1
10q loss	478 (85%)	82	4.4803e-08	3.35e-05	1.2759e-06	0.000937	0.0067317	1	8.6766e-05	0.0603	3.7883e-23	2.92e-20	0.036064	1	0.0002068	0.142	0.028707	1	0.24973	1	0.2071	1
11p loss	96 (17%)	464	5.428e-07	0.000401	5.9733e-05	0.0418	0.8462	1	0.005892	1	4.3788e-15	3.36e-12	0.047223	1	0.71855	1	0.12102	1	0.093456	1	0.46635	1
11q loss	90 (16%)	470	1.3124e-05	0.00944	0.0033951	1	0.90892	1	0.11937	1	3.0999e-14	2.37e-11	0.38083	1	0.91396	1	0.30575	1	0.34564	1	0.58371	1
12p loss	59 (11%)	501	0.034911	1	0.023747	1	0.54324	1	0.54879	1	0.001241	0.82	0.81194	1	0.15428	1	0.1999	1	0.88939	1	0.90672	1
12q loss	57 (10%)	503	0.060363	1	0.019625	1	0.54703	1	0.27974	1	2.8206e-05	0.02	0.68239	1	0.17799	1	0.65697	1	0.94113	1	0.6981	1
13q loss	182 (32%)	378	2.3358e-05	0.0166	0.00019576	0.135	0.74534	1	0.20741	1	1.4182e-21	1.09e-18	0.00048404	0.326	0.59398	1	0.074347	1	0.052029	1	0.40509	1
14q loss	141 (25%)	419	1.6146e-06	0.00118	0.0031246	1	0.5077	1	0.77687	1	1.2615e-29	9.75e-27	0.012809	1	0.80253	1	0.14346	1	0.16286	1	0.01404	1
15q loss	99 (18%)	461	3.3825e-05	0.0238	4.2924e-06	0.00312	0.0039645	1	0.0043727	1	2.4653e-08	1.85e-05	1.6366e-05	0.0117	0.034525	1	0.0086479	1	0.0036788	1	0.16136	1
16p loss	62 (11%)	498	0.28626	1	0.34836	1	0.66475	1	0.85614	1	0.0029454	1	0.23085	1	0.44233	1	0.51759	1	0.53213	1	0.53197	1
16q loss	81 (14%)	479	0.061169	1	0.26271	1	0.46126	1	0.84262	1	0.0039324	1	0.58844	1	0.048671	1	0.27554	1	0.66886	1	0.61801	1
17p loss	63 (11%)	497	0.020498	1	0.91192	1	0.6498	1	0.51662	1	1.1887e-09	8.99e-07	0.027889	1	0.21489	1	0.29592	1	0.29185	1	0.25598	1
17q loss	42 (8%)	518	0.0057057	1	0.1228	1	0.25231	1	0.57321	1	4.8906e-06	0.00355	0.074204	1	0.48091	1	0.28761	1	0.14636	1	0.015649	1
18p loss	68 (12%)	492	0.047736	1	0.033758	1	0.35893	1	0.29984	1	0.00018163	0.125	0.38706	1	0.065596	1	0.017854	1	0.12508	1	0.55604	1
18q loss	61 (11%)	499	0.23755	1	0.069547	1	0.62975	1	0.14309	1	0.0066335	1	0.34369	1	0.030192	1	0.0042585	1	0.3948	1	0.30265	1
19p loss	26 (5%)	534	0.0055013	1	0.021531	1	0.18616	1	0.09132	1	0.0055768	1	0.0039485	1	0.036067	1	0.66534	1	0.8388	1	0.22857	1
19q loss	34 (6%)	526	0.0019114	1	0.023045	1	0.51058	1	0.060287	1	0.00022239	0.152	0.074204	1	0.070086	1	0.53871	1	0.78252	1	0.30981	1
20p loss	18 (3%)	542	0.00021397	0.147	0.0062564	1	0.03936	1	0.011363	1	9.12e-06	0.00657	NA	NA	0.41365	1	0.38357	1	0.010425	1	0.079443	1
20q loss	16 (3%)	544	0.0016229	1	0.0099981	1	0.36087	1	0.29417	1	1.3709e-05	0.00984	NA	NA	0.41365	1	0.38357	1	0.039301	1	0.11956	1
21q loss	40 (7%)	520	0.023358	1	0.043098	1	0.035539	1	0.26139	1	9.6636e-05	0.067	0.10212	1	0.012156	1	0.13784	1	0.8234	1	0.21482	1
22q loss	173 (31%)	387	0.65418	1	0.27848	1	0.23685	1	0.30868	1	1.6566e-05	0.0118	0.11692	1	0.89918	1	0.6087	1	0.17508	1	0.67617	1
xq loss	102 (18%)	458	0.011789	1	0.12324	1	0.18552	1	0.36624	1	4.4167e-08	3.31e-05	0.036513	1	0.99009	1	0.77643	1	0.40586	1	0.66638	1
