Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_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
1p gain	3 (2%)	188	0.0055199	0.745	0.26603	1	0.18537	1	0.58809	1	0.090649	1	0.093579	1
4p gain	4 (2%)	187	0.02656	1	0.04833	1	NA	NA	NA	NA	0.34059	1	0.83504	1
4q gain	4 (2%)	187	0.02562	1	0.050049	1	NA	NA	NA	NA	0.34229	1	0.83267	1
8p gain	22 (12%)	169	0.00099999	0.153	0.00047	0.0757	0.02871	1	0.00081999	0.128	0.01003	1	0.01598	1
8q gain	23 (12%)	168	0.0017	0.25	0.0016	0.237	0.01337	1	0.00173	0.253	0.0072099	0.956	0.01457	1
10q gain	3 (2%)	188	0.01187	1	0.27001	1	0.18704	1	0.58843	1	0.55355	1	0.094899	1
11p gain	4 (2%)	187	0.00065999	0.105	0.147	1	0.46732	1	0.36505	1	0.51948	1	0.02196	1
11q gain	7 (4%)	184	2e-05	0.00338	0.01207	1	0.065489	1	0.073739	1	0.29072	1	0.01539	1
13q gain	6 (3%)	185	0.03304	1	0.03027	1	0.12521	1	0.083699	1	0.79896	1	0.072879	1
17q gain	3 (2%)	188	0.0085599	1	0.302	1	1	1	0.58939	1	0.48404	1	0.30493	1
19p gain	5 (3%)	186	0.00077999	0.122	0.64543	1	1	1	0.86435	1	0.57924	1	1	1
19q gain	5 (3%)	186	0.00070999	0.112	0.64571	1	1	1	0.86479	1	0.57781	1	1	1
21q gain	8 (4%)	183	9.9999e-06	0.00174	0.22966	1	0.12551	1	0.52425	1	0.081319	1	0.40886	1
22q gain	9 (5%)	182	0.00124	0.188	0.01776	1	0.13645	1	0.01624	1	0.056659	1	0.01318	1
xq gain	3 (2%)	188	0.00296	0.425	0.87995	1	NA	NA	NA	NA	0.89279	1	0.04588	1
3p loss	3 (2%)	188	0.0071899	0.956	0.26834	1	0.78466	1	1	1	0.060679	1	0.092599	1
3q loss	3 (2%)	188	0.0074999	0.982	0.2643	1	0.78583	1	1	1	0.062039	1	0.091969	1
5q loss	6 (3%)	185	5.9999e-05	0.00996	0.03018	1	0.22425	1	0.63209	1	0.03138	1	0.03293	1
7p loss	17 (9%)	174	0.00013	0.0214	0.00029	0.047	0.00096999	0.149	9.9999e-06	0.00174	0.00382	0.535	0.00295	0.425
7q loss	20 (10%)	171	9.9999e-06	0.00174	3e-05	0.00504	0.0060099	0.805	9.9999e-06	0.00174	0.00142	0.214	0.00087999	0.136
12p loss	4 (2%)	187	0.0083999	1	0.094889	1	0.3735	1	0.39287	1	0.48443	1	0.18497	1
15q loss	4 (2%)	187	0.00051999	0.0832	0.57028	1	0.065729	1	0.36616	1	0.02358	1	0.18629	1
16q loss	4 (2%)	187	0.00159	0.237	0.14859	1	0.7851	1	1	1	0.0147	1	0.02174	1
17p loss	13 (7%)	178	9.9999e-06	0.00174	0.00418	0.574	0.15555	1	0.00192	0.278	0.16241	1	0.00345	0.49
17q loss	7 (4%)	184	3e-05	0.00504	0.21564	1	0.068479	1	0.23341	1	0.04	1	0.04752	1
18p loss	5 (3%)	186	0.00021	0.0342	0.068749	1	1	1	0.86479	1	0.24754	1	0.18457	1
18q loss	4 (2%)	187	0.00157	0.235	0.14791	1	0.46802	1	0.86392	1	0.10059	1	0.18563	1
19p loss	4 (2%)	187	0.00416	0.574	0.53555	1	0.46794	1	0.86567	1	0.31164	1	0.24744	1
19q loss	4 (2%)	187	0.00406	0.564	0.53416	1	0.4654	1	0.86487	1	0.31143	1	0.24758	1
xq loss	5 (3%)	186	0.00013	0.0214	0.14477	1	0.22372	1	0.63221	1	0.00347	0.49	0.00482	0.656