Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_CHIERARCHICAL	
	nCNV (%)	nWild-Type	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	Fisher's exact test_P	Fisher's exact test_Q
1p gain	33 (22%)	117	0.00044167	0.273	0.00042152	0.262	0.14573	1	0.67056	1	0.39134	1	0.6263	1	0.7719	1	0.78052	1
1q gain	35 (23%)	115	0.0016441	0.985	0.01779	1	0.038728	1	0.038178	1	0.41524	1	0.20552	1	0.16239	1	0.11591	1
2p gain	16 (11%)	134	0.001211	0.734	0.0034398	1	0.17431	1	0.079016	1	0.0034463	1	0.020792	1	0.0059833	1	0.020792	1
2q gain	13 (9%)	137	0.010714	1	0.096003	1	0.48402	1	0.2045	1	0.028773	1	0.063442	1	0.038032	1	0.063442	1
3p gain	16 (11%)	134	0.07481	1	0.021275	1	0.060781	1	0.14601	1	0.87759	1	0.67707	1	0.51217	1	0.44383	1
3q gain	15 (10%)	135	0.12322	1	0.083438	1	0.094255	1	0.37961	1	1	1	1	1	0.56566	1	0.54746	1
4p gain	34 (23%)	116	0.0034756	1	0.0015453	0.932	0.67047	1	0.85782	1	0.028489	1	0.080706	1	0.038082	1	0.01821	1
4q gain	27 (18%)	123	0.19876	1	0.074429	1	0.86337	1	1	1	0.25714	1	0.51302	1	0.088934	1	0.24699	1
5p gain	52 (35%)	98	0.00046917	0.289	0.01102	1	0.069468	1	1	1	0.78182	1	0.52002	1	0.2901	1	0.69472	1
5q gain	43 (29%)	107	0.0031283	1	0.028814	1	0.42717	1	1	1	0.29894	1	1	1	0.059288	1	0.84962	1
6p gain	33 (22%)	117	0.0004487	0.277	0.001077	0.657	0.014859	1	0.0057725	1	0.014079	1	0.0077849	1	0.0034402	1	0.030963	1
6q gain	31 (21%)	119	0.006854	1	0.00084976	0.521	0.02328	1	0.0087889	1	0.007179	1	0.005286	1	0.0016004	0.96	0.022897	1
7p gain	46 (31%)	104	0.0022045	1	0.029848	1	0.072697	1	0.3531	1	0.28267	1	0.18025	1	0.095653	1	0.26735	1
7q gain	38 (25%)	112	0.0017786	1	0.125	1	0.55399	1	0.18891	1	0.28997	1	0.13541	1	0.087839	1	0.21068	1
8p gain	34 (23%)	116	0.010298	1	0.51383	1	0.33553	1	1	1	1	1	0.81201	1	0.54897	1	0.81201	1
8q gain	39 (26%)	111	0.039152	1	0.024086	1	0.035714	1	0.79014	1	0.97409	1	0.422	1	0.82357	1	0.422	1
9p gain	30 (20%)	120	0.003396	1	0.061991	1	0.23024	1	0.2493	1	0.11165	1	0.10823	1	0.16347	1	0.10823	1
9q gain	38 (25%)	112	0.00033636	0.21	0.065487	1	0.27372	1	0.092475	1	0.11191	1	0.13541	1	0.042925	1	0.13541	1
10p gain	13 (9%)	137	0.06123	1	0.014606	1	0.8274	1	0.42718	1	0.78359	1	0.68934	1	0.52527	1	0.68934	1
10q gain	5 (3%)	145	0.85273	1	0.01108	1	0.62907	1	0.1131	1	0.80034	1	1	1	0.20883	1	1	1
11p gain	14 (9%)	136	0.10987	1	0.35672	1	0.14998	1	1	1	0.61847	1	0.5982	1	0.28767	1	0.5982	1
11q gain	13 (9%)	137	0.66652	1	0.33666	1	0.22845	1	0.61581	1	0.87471	1	1	1	0.87334	1	1	1
12p gain	20 (13%)	130	0.50188	1	0.042043	1	0.70313	1	0.16519	1	0.4054	1	0.38234	1	0.49305	1	0.38234	1
12q gain	14 (9%)	136	0.59913	1	0.35766	1	0.3837	1	0.79902	1	0.26887	1	0.26272	1	0.32349	1	0.26272	1
13q gain	7 (5%)	143	0.26199	1	0.052139	1	0.041915	1	0.026624	1	0.6207	1	0.16006	1	0.52787	1	0.45309	1
14q gain	31 (21%)	119	0.27905	1	0.087457	1	0.21894	1	0.54256	1	0.27307	1	0.11765	1	0.39486	1	0.11765	1
15q gain	39 (26%)	111	0.081794	1	0.0032667	1	0.00057472	0.353	0.0061028	1	0.33523	1	0.79797	1	0.48195	1	0.79797	1
16p gain	25 (17%)	125	0.015102	1	0.02857	1	1	1	1	1	0.57001	1	1	1	0.72774	1	1	1
16q gain	10 (7%)	140	0.13802	1	0.075658	1	0.86062	1	0.48408	1	0.059824	1	0.57635	1	0.092948	1	0.57635	1
17p gain	37 (25%)	113	0.013999	1	0.018044	1	0.51312	1	0.44418	1	0.038556	1	0.008868	1	0.083737	1	0.008868	1
17q gain	34 (23%)	116	0.20004	1	0.054071	1	0.17326	1	0.61642	1	0.01284	1	0.0017333	1	0.038475	1	0.0017333	1
18p gain	26 (17%)	124	0.017471	1	0.014614	1	0.95208	1	0.74834	1	0.61756	1	1	1	0.93262	1	0.67352	1
18q gain	22 (15%)	128	0.39324	1	0.10226	1	0.63067	1	1	1	0.69345	1	1	1	0.76031	1	0.80167	1
19p gain	50 (33%)	100	5.188e-07	0.00033	0.056472	1	0.53974	1	0.21151	1	0.3966	1	0.20297	1	0.31985	1	0.20297	1
19q gain	36 (24%)	114	1.0539e-05	0.00669	0.0090371	1	0.43209	1	0.1095	1	0.21623	1	0.12728	1	0.13141	1	0.12728	1
20p gain	41 (27%)	109	0.066732	1	0.16582	1	0.73156	1	0.53901	1	0.5473	1	0.69929	1	0.2867	1	0.69929	1
20q gain	52 (35%)	98	0.0056742	1	0.047009	1	1	1	0.21151	1	0.15143	1	0.22605	1	0.14483	1	0.22605	1
21q gain	39 (26%)	111	0.00024607	0.154	0.0054225	1	0.25126	1	0.18891	1	0.54188	1	0.42985	1	0.79927	1	0.42985	1
22q gain	37 (25%)	113	0.07777	1	0.195	1	0.4284	1	0.39155	1	0.85072	1	0.54699	1	0.92411	1	0.54699	1
xq gain	19 (13%)	131	0.025067	1	0.048765	1	1	1	1	1	0.30401	1	0.33569	1	0.33711	1	0.48391	1
1p loss	22 (15%)	128	0.91939	1	0.1507	1	0.11332	1	0.76032	1	0.67992	1	0.02193	1	0.79865	1	0.02193	1
1q loss	20 (13%)	130	0.23474	1	0.15218	1	0.68321	1	0.81807	1	0.52053	1	0.53698	1	0.23001	1	0.53698	1
2p loss	47 (31%)	103	0.00030714	0.192	5.4044e-05	0.0341	0.00029154	0.182	0.0010944	0.665	0.022293	1	0.0015901	0.957	0.0088424	1	0.0015901	0.957
2q loss	40 (27%)	110	0.00053988	0.332	0.04429	1	0.70936	1	0.72116	1	0.88348	1	1	1	1	1	1	1
3p loss	30 (20%)	120	0.0019405	1	3.7231e-05	0.0236	0.0052913	1	0.0030825	1	0.013328	1	0.016431	1	0.0043588	1	0.016431	1
3q loss	34 (23%)	116	0.0017094	1	0.0021893	1	0.010267	1	0.0025156	1	0.024693	1	0.0097399	1	0.013776	1	0.0097399	1
4p loss	25 (17%)	125	0.32871	1	0.0051264	1	0.11313	1	0.48602	1	0.22713	1	0.16649	1	0.20636	1	0.16649	1
4q loss	27 (18%)	123	0.012349	1	0.0017126	1	0.077929	1	0.85472	1	0.56253	1	0.17765	1	0.51031	1	0.17765	1
5p loss	14 (9%)	136	0.51415	1	0.43821	1	0.20687	1	0.33162	1	0.12209	1	0.04298	1	0.14572	1	0.04298	1
5q loss	18 (12%)	132	0.15455	1	0.38872	1	0.10153	1	0.38302	1	0.33493	1	0.088588	1	0.38983	1	0.088588	1
6p loss	35 (23%)	115	0.47061	1	0.60007	1	0.079917	1	0.0516	1	0.71463	1	0.33452	1	0.64665	1	0.33452	1
6q loss	25 (17%)	125	0.19453	1	0.046715	1	0.041064	1	0.17539	1	0.21706	1	0.43062	1	0.23632	1	0.43062	1
7p loss	23 (15%)	127	0.10645	1	0.0010829	0.66	0.057031	1	0.29807	1	0.63137	1	0.56837	1	0.31921	1	0.56837	1
7q loss	19 (13%)	131	0.64135	1	0.22903	1	0.13478	1	0.39095	1	0.47528	1	0.55818	1	0.47458	1	0.55818	1
8p loss	31 (21%)	119	0.39164	1	0.024158	1	0.24523	1	0.35655	1	0.10808	1	0.0062883	1	0.057928	1	0.0022837	1
8q loss	21 (14%)	129	0.10059	1	0.399	1	0.73026	1	0.7798	1	0.27658	1	0.47437	1	0.18661	1	0.2692	1
9p loss	47 (31%)	103	0.0032594	1	0.011517	1	0.87615	1	0.098379	1	0.51112	1	0.20354	1	0.47345	1	0.30013	1
9q loss	31 (21%)	119	0.067772	1	0.017985	1	0.43245	1	0.37861	1	0.59455	1	0.54684	1	0.83612	1	0.68188	1
10p loss	68 (45%)	82	0.030159	1	0.002318	1	0.00025656	0.161	0.023382	1	0.27521	1	0.061947	1	0.46977	1	0.061947	1
10q loss	78 (52%)	72	2.616e-07	0.000167	1.7166e-07	0.00011	3.0254e-07	0.000193	3.5186e-05	0.0223	0.0023896	1	0.00043915	0.272	0.0021145	1	0.00043915	0.272
11p loss	56 (37%)	94	0.00021589	0.136	0.00022193	0.139	0.54901	1	0.14361	1	0.45281	1	0.31323	1	0.54071	1	0.45607	1
11q loss	48 (32%)	102	8.304e-06	0.00528	0.0041143	1	0.63154	1	0.064812	1	0.077024	1	0.065792	1	0.21654	1	0.18257	1
12p loss	40 (27%)	110	0.0011268	0.684	0.021491	1	0.44058	1	0.63421	1	0.69308	1	0.88588	1	0.57963	1	0.74982	1
12q loss	33 (22%)	117	0.0087311	1	0.40274	1	0.9429	1	0.77233	1	0.86638	1	1	1	0.75475	1	0.87846	1
13q loss	75 (50%)	75	0.0030877	1	0.0010605	0.648	0.69769	1	0.12461	1	0.25179	1	0.099061	1	0.24902	1	0.21357	1
14q loss	44 (29%)	106	0.48773	1	0.0055937	1	0.0068279	1	0.36668	1	0.83556	1	0.2888	1	0.47918	1	0.45469	1
15q loss	25 (17%)	125	0.39494	1	0.045076	1	0.019928	1	0.066788	1	0.21511	1	0.1509	1	0.19777	1	0.083098	1
16p loss	42 (28%)	108	0.0015161	0.916	0.066394	1	0.37466	1	0.3531	1	0.39543	1	0.085563	1	0.62695	1	0.056026	1
16q loss	74 (49%)	76	0.00041112	0.256	0.00021753	0.137	0.0022298	1	0.0023995	1	0.002524	1	0.0016993	1	0.0029206	1	0.0016993	1
17p loss	29 (19%)	121	0.81873	1	0.11109	1	0.31675	1	0.73198	1	0.66804	1	0.35167	1	0.60743	1	0.23384	1
17q loss	27 (18%)	123	0.080511	1	0.031444	1	0.0042746	1	0.11015	1	0.39473	1	0.5061	1	0.65722	1	0.24135	1
18p loss	36 (24%)	114	0.22394	1	0.31731	1	0.26833	1	0.61133	1	0.82848	1	0.54699	1	0.77545	1	0.40962	1
18q loss	38 (25%)	112	0.099885	1	0.042372	1	0.83483	1	0.59875	1	0.80177	1	0.47142	1	0.65319	1	0.65985	1
19p loss	11 (7%)	139	0.088654	1	0.032094	1	0.48402	1	1	1	0.23416	1	0.79032	1	0.24419	1	0.79032	1
19q loss	22 (15%)	128	0.29931	1	0.14119	1	0.72442	1	0.54256	1	0.067073	1	1	1	0.078024	1	1	1
20p loss	25 (17%)	125	0.72445	1	0.026089	1	0.23436	1	0.85782	1	0.59556	1	1	1	0.65034	1	0.75204	1
20q loss	10 (7%)	140	0.26797	1	0.039757	1	0.27466	1	0.65347	1	0.26411	1	0.57635	1	0.29611	1	0.29187	1
21q loss	26 (17%)	124	0.032622	1	0.19948	1	0.51936	1	0.4652	1	0.17737	1	0.51302	1	0.21573	1	0.51302	1
22q loss	43 (29%)	107	0.010624	1	0.095307	1	0.031217	1	0.26968	1	0.4224	1	0.67633	1	0.36872	1	0.67633	1
xq loss	58 (39%)	92	0.086415	1	4.9394e-05	0.0312	0.062311	1	0.0049578	1	0.0075307	1	0.0013038	0.789	0.0010238	0.627	0.004258	1