		Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		LINCRNA_CNMF		LINCRNA_CHIERARCHICAL		MIR_MATURE_CNMF		MIR_MATURE_CHIERARCHICAL		CN_CNMF		CN_THRESHOLDED_CNMF		METHYLATION_CNMF		METHYLATION_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
1q gain	10 (12%)	70	0.89522	0.95	0.82465	0.914	0.68839	0.828	0.55517	0.753	0.29369	0.553	0.11745	0.357	0.18044	0.446	0.36974	0.62	0.32225	0.583	0.43669	0.664
2p gain	10 (12%)	70	0.74738	0.866	0.55411	0.753	0.2814	0.546	0.54084	0.741	0.93168	0.976	0.17775	0.442	0.28934	0.553	0.82711	0.915	0.16824	0.427	0.19056	0.461
2q gain	8 (10%)	72	0.5953	0.785	0.25104	0.527	0.12941	0.366	0.27936	0.544	0.60854	0.786	0.080369	0.287	0.50338	0.707	0.64795	0.814	0.10952	0.343	0.13358	0.37
4p gain	8 (10%)	72	0.11309	0.35	0.12501	0.366	0.42055	0.656	0.37463	0.623	0.18952	0.46	0.30842	0.568	0.03858	0.176	0.086569	0.302	0.12853	0.366	0.42832	0.662
4q gain	5 (6%)	75	0.068299	0.262	0.48222	0.687	0.60628	0.786	0.66551	0.815	0.46891	0.683	0.64369	0.814	0.1096	0.343	0.0066699	0.0472	0.17461	0.437	0.26156	0.531
5p gain	4 (5%)	76	0.60442	0.786	0.75681	0.873	0.53278	0.74	0.4681	0.683	0.21719	0.482	0.81172	0.91	0.4732	0.686	0.72127	0.851	0.2603	0.531	0.39621	0.632
5q gain	4 (5%)	76	0.60504	0.786	0.75859	0.873	0.53364	0.74	0.468	0.683	0.21899	0.483	0.81072	0.91	0.47328	0.686	0.72411	0.851	0.26004	0.531	0.39855	0.632
6p gain	40 (50%)	40	0.0086399	0.0572	0.00015	0.00174	0.00089999	0.00883	5e-05	0.000671	9.9999e-06	0.000165	9.9999e-06	0.000165	2e-05	0.000309	3e-05	0.000437	0.00093999	0.00905	9.9999e-06	0.000165
6q gain	20 (25%)	60	0.1358	0.372	0.00056999	0.00593	0.0070099	0.049	6.9999e-05	0.000892	0.00022	0.00244	5e-05	0.000671	0.00019	0.00215	0.00026	0.00282	0.0032	0.0268	8.9999e-05	0.00109
7p gain	8 (10%)	72	0.21544	0.482	0.19252	0.461	0.15972	0.413	0.4451	0.671	0.74309	0.866	0.91155	0.957	0.86905	0.95	0.35726	0.609	0.56108	0.757	0.54332	0.743
7q gain	7 (9%)	73	0.42797	0.662	0.097169	0.325	0.29495	0.553	0.31528	0.578	0.71706	0.848	0.63402	0.804	0.66457	0.815	0.20675	0.481	0.15856	0.413	0.13915	0.379
8p gain	32 (40%)	48	0.070829	0.264	0.0028	0.0238	0.098699	0.325	0.02463	0.134	0.25719	0.531	0.04123	0.181	0.00381	0.0308	0.075659	0.276	0.02679	0.135	0.02349	0.13
8q gain	54 (68%)	26	0.0054099	0.0411	4e-05	0.000567	2e-05	0.000309	9.9999e-06	0.000165	7.9999e-05	0.000995	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	3e-05	0.000437	9.9999e-06	0.000165
9p gain	4 (5%)	76	0.8829	0.95	0.63012	0.801	0.47633	0.687	0.36155	0.613	0.23289	0.505	1	1	0.3971	0.632	0.96211	1	0.20509	0.48	0.65605	0.815
9q gain	3 (4%)	77	0.59981	0.786	0.77418	0.887	0.10374	0.335	0.62065	0.797	0.18845	0.46	0.84185	0.928	0.65928	0.815	0.88758	0.95	0.37495	0.623	0.57923	0.768
11p gain	9 (11%)	71	0.74541	0.866	0.70414	0.839	0.35979	0.612	0.19387	0.461	0.14124	0.383	0.40587	0.637	0.58776	0.777	0.68689	0.828	0.49248	0.698	0.90222	0.95
11q gain	9 (11%)	71	0.82176	0.913	0.44798	0.672	0.31981	0.583	0.12111	0.365	0.24837	0.523	0.04189	0.183	0.56379	0.757	0.69119	0.829	0.67822	0.822	0.45735	0.679
12p gain	3 (4%)	77	0.27148	0.531	0.071339	0.264	0.90296	0.95	0.01944	0.113	0.39817	0.632	0.54025	0.741	0.20984	0.481	0.43903	0.664	0.26719	0.531	0.29175	0.553
12q gain	3 (4%)	77	0.27086	0.531	0.071419	0.264	0.90186	0.95	0.02039	0.116	0.39916	0.632	0.53771	0.741	0.20923	0.481	0.43528	0.664	0.26693	0.531	0.29319	0.553
13q gain	6 (8%)	74	0.7357	0.863	0.02513	0.134	0.2118	0.481	0.35335	0.608	0.38303	0.63	0.38282	0.63	0.56715	0.757	0.15428	0.406	0.64457	0.814	0.64756	0.814
14q gain	3 (4%)	77	0.27165	0.531	0.069839	0.264	0.90167	0.95	0.01888	0.112	0.67037	0.817	0.84419	0.928	0.051519	0.219	0.065099	0.258	1	1	1	1
16p gain	3 (4%)	77	0.2147	0.482	1	1	0.61546	0.793	1	1	1	1	0.4642	0.683	1	1	0.12608	0.366	0.2706	0.531	0.43457	0.664
17p gain	9 (11%)	71	0.14674	0.39	0.18678	0.458	0.30663	0.567	0.01947	0.113	0.80457	0.91	0.44625	0.671	0.20795	0.481	0.23687	0.512	0.29124	0.553	0.71558	0.848
17q gain	10 (12%)	70	0.32731	0.584	0.14197	0.383	0.37146	0.621	0.060939	0.252	0.62371	0.797	0.2437	0.518	0.25884	0.531	0.22328	0.491	0.16932	0.427	0.43892	0.664
20p gain	8 (10%)	72	0.70347	0.839	0.0057899	0.0428	0.087389	0.303	0.04103	0.181	1	1	0.35088	0.608	0.061529	0.252	0.40182	0.632	0.33823	0.595	0.38031	0.63
20q gain	9 (11%)	71	0.36637	0.617	0.00401	0.0315	0.12447	0.366	0.02013	0.115	0.97636	1	0.48926	0.695	0.02507	0.134	0.35436	0.608	0.67797	0.822	0.51053	0.715
21q gain	14 (18%)	66	0.10583	0.337	0.0054799	0.0411	0.10506	0.337	0.0039	0.0311	0.098589	0.325	0.65581	0.815	0.03889	0.176	0.495	0.699	0.26705	0.531	0.42716	0.662
22q gain	6 (8%)	74	0.22664	0.496	0.36466	0.616	0.03659	0.17	0.13585	0.372	0.88272	0.95	0.2833	0.547	0.56391	0.757	0.061729	0.252	0.24457	0.518	0.46901	0.683
xp gain	10 (12%)	70	0.89593	0.95	0.32061	0.583	0.65193	0.815	0.40165	0.632	0.0092299	0.0603	0.45286	0.677	0.687	0.828	0.87671	0.95	0.0061099	0.0439	0.60088	0.786
xq gain	9 (11%)	71	0.95917	1	0.40002	0.632	0.39684	0.632	0.1147	0.352	0.0019	0.0176	0.13196	0.368	0.71418	0.848	0.79439	0.9	0.02507	0.134	0.45787	0.679
1p loss	18 (22%)	62	0.10895	0.343	0.10137	0.329	0.41691	0.652	0.32113	0.583	0.96248	1	0.01434	0.0892	0.00073999	0.0074	9.9999e-06	0.000165	0.068049	0.262	0.35121	0.608
1q loss	4 (5%)	76	0.095789	0.325	0.13062	0.366	0.19453	0.461	0.21656	0.482	0.26282	0.531	0.02818	0.141	0.26023	0.531	0.15872	0.413	0.38419	0.63	0.18092	0.446
3p loss	42 (52%)	38	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165
3q loss	44 (55%)	36	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165	9.9999e-06	0.000165
4q loss	3 (4%)	77	0.89683	0.95	0.38825	0.632	1	1	0.70161	0.839	0.67087	0.817	0.49757	0.701	1	1	0.12516	0.366	0.87695	0.95	1	1
5q loss	3 (4%)	77	0.89445	0.95	1	1	0.56681	0.757	0.78469	0.893	0.60887	0.786	0.46725	0.683	0.3255	0.584	0.88881	0.95	0.14673	0.39	0.76205	0.875
6q loss	14 (18%)	66	0.065859	0.258	0.00043	0.00457	0.03217	0.156	0.00226	0.0199	0.00064999	0.00663	0.074989	0.275	5.9999e-05	0.000785	9.9999e-06	0.000165	0.00013	0.00154	0.01218	0.0767
8p loss	7 (9%)	73	0.161	0.413	0.0059399	0.0433	0.058299	0.244	0.02875	0.142	0.01726	0.105	0.11176	0.348	0.01533	0.0942	0.00223	0.0199	0.04687	0.203	0.17175	0.431
9p loss	8 (10%)	72	0.02599	0.134	0.33953	0.595	0.21218	0.481	0.082889	0.292	0.19422	0.461	0.33743	0.595	0.070909	0.264	0.04063	0.181	0.14853	0.392	0.10046	0.328
9q loss	7 (9%)	73	0.00365	0.03	0.16109	0.413	0.48127	0.687	0.23156	0.505	0.35403	0.608	0.51214	0.716	0.24305	0.518	0.063319	0.256	0.065679	0.258	0.11768	0.357
11p loss	3 (4%)	77	0.30203	0.56	0.33029	0.585	0.74399	0.866	0.26532	0.531	0.16444	0.419	0.7244	0.851	0.050729	0.217	0.54006	0.741	0.57939	0.768	0.29345	0.553
12p loss	3 (4%)	77	1	1	1	1	0.81959	0.913	0.78664	0.894	0.2574	0.531	0.29158	0.553	0.66332	0.815	0.89025	0.95	0.66662	0.815	0.57747	0.768
13q loss	3 (4%)	77	0.097059	0.325	1	1	0.74278	0.866	0.4819	0.687	0.35545	0.608	0.62251	0.797	1	1	0.12578	0.366	0.26896	0.531	0.43488	0.664
15q loss	5 (6%)	75	0.45716	0.679	0.48052	0.687	0.20006	0.472	0.66652	0.815	0.2148	0.482	1	1	0.03217	0.156	0.0076199	0.0519	0.6563	0.815	0.48223	0.687
16p loss	7 (9%)	73	0.39114	0.632	0.23978	0.514	0.62471	0.797	0.3302	0.585	0.75201	0.87	0.85682	0.94	0.84338	0.928	0.26041	0.531	0.60751	0.786	0.87017	0.95
16q loss	16 (20%)	64	0.12808	0.366	0.090249	0.311	0.56256	0.757	0.35283	0.608	0.23842	0.513	0.38714	0.632	0.21179	0.481	9.9999e-06	0.000165	0.03827	0.176	0.29954	0.56
17p loss	3 (4%)	77	0.30207	0.56	0.38926	0.632	0.51501	0.718	1	1	0.5496	0.749	0.14588	0.39	1	1	0.66142	0.815	0.87355	0.95	0.43534	0.664
19p loss	3 (4%)	77	0.89681	0.95	0.13007	0.366	0.81808	0.913	0.78387	0.893	0.80992	0.91	0.12919	0.366	0.32703	0.584	0.01042	0.0664	0.065239	0.258	0.03352	0.161
19q loss	3 (4%)	77	0.89686	0.95	0.12778	0.366	0.81898	0.913	0.78445	0.893	0.80928	0.91	0.1269	0.366	0.324	0.584	0.01009	0.0651	0.066769	0.26	0.03421	0.163
xp loss	11 (14%)	69	0.03467	0.164	0.0079999	0.0537	0.00434	0.0335	0.092219	0.316	0.20484	0.48	0.078829	0.283	0.078789	0.283	0.057959	0.244	0.0076299	0.0519	0.02606	0.134
xq loss	12 (15%)	68	0.02122	0.119	0.00259	0.0224	0.00104	0.00982	0.082919	0.292	0.097549	0.325	0.02678	0.135	0.03558	0.166	0.02589	0.134	0.00202	0.0184	0.0183	0.11
