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	0.00412	0.573	0.26529	1	0.18652	1	0.58729	1	0.092519	1	0.091939	1
4p gain	4 (2%)	187	0.02859	1	0.04852	1	NA	NA	NA	NA	0.34084	1	0.83526	1
4q gain	4 (2%)	187	0.028	1	0.04946	1	NA	NA	NA	NA	0.3455	1	0.83419	1
8p gain	22 (12%)	169	0.00083999	0.131	0.00049	0.0784	0.02832	1	0.00073999	0.117	0.01028	1	0.01616	1
8q gain	23 (12%)	168	0.00145	0.219	0.00152	0.226	0.01312	1	0.00157	0.232	0.0071899	0.942	0.015	1
10q gain	3 (2%)	188	0.01476	1	0.26566	1	0.18524	1	0.58863	1	0.55355	1	0.091289	1
11p gain	4 (2%)	187	0.00070999	0.113	0.14651	1	0.4675	1	0.36557	1	0.52721	1	0.02258	1
11q gain	7 (4%)	184	2e-05	0.00338	0.01256	1	0.066439	1	0.074369	1	0.29271	1	0.01605	1
13q gain	6 (3%)	185	0.04176	1	0.02928	1	0.12379	1	0.083239	1	0.80189	1	0.074039	1
17q gain	3 (2%)	188	0.0062099	0.834	0.30173	1	1	1	0.58952	1	0.48216	1	0.30707	1
19p gain	5 (3%)	186	0.01267	1	0.64266	1	1	1	0.86394	1	0.57816	1	1	1
19q gain	5 (3%)	186	0.01266	1	0.64484	1	1	1	0.86524	1	0.58087	1	1	1
21q gain	8 (4%)	183	9.9999e-06	0.00174	0.23053	1	0.12581	1	0.52526	1	0.081839	1	0.41071	1
22q gain	9 (5%)	182	0.00104	0.16	0.0179	1	0.13392	1	0.01632	1	0.054979	1	0.01272	1
xq gain	3 (2%)	188	0.00174	0.256	0.88154	1	NA	NA	NA	NA	0.89149	1	0.04524	1
3p loss	3 (2%)	188	0.0070699	0.933	0.26377	1	0.78666	1	1	1	0.061539	1	0.091849	1
3q loss	3 (2%)	188	0.0066999	0.891	0.26639	1	0.78572	1	1	1	0.061729	1	0.093759	1
5q loss	6 (3%)	185	2e-05	0.00338	0.0304	1	0.22469	1	0.63122	1	0.0316	1	0.03273	1
7p loss	17 (9%)	174	4e-05	0.00664	0.00012	0.0196	0.00095999	0.149	9.9999e-06	0.00174	0.00351	0.495	0.00357	0.5
7q loss	20 (10%)	171	9.9999e-06	0.00174	4e-05	0.00664	0.0061799	0.834	9.9999e-06	0.00174	0.00151	0.226	0.00075999	0.119
12p loss	4 (2%)	187	0.0059899	0.815	0.095179	1	0.375	1	0.39023	1	0.48383	1	0.18456	1
15q loss	4 (2%)	187	0.00045	0.0724	0.57101	1	0.066489	1	0.3684	1	0.02298	1	0.18371	1
16q loss	4 (2%)	187	0.00126	0.193	0.14703	1	0.78489	1	1	1	0.01437	1	0.02207	1
17p loss	13 (7%)	178	9.9999e-06	0.00174	0.00449	0.62	0.15668	1	0.00191	0.279	0.16014	1	0.00343	0.487
17q loss	7 (4%)	184	2e-05	0.00338	0.2137	1	0.065019	1	0.23312	1	0.03906	1	0.0485	1
18p loss	5 (3%)	186	0.00033	0.0535	0.068459	1	1	1	0.86576	1	0.24662	1	0.18619	1
18q loss	4 (2%)	187	0.00134	0.204	0.14519	1	0.46725	1	0.86538	1	0.10083	1	0.1843	1
19p loss	4 (2%)	187	0.00307	0.442	0.53635	1	0.46472	1	0.86544	1	0.31182	1	0.24829	1
19q loss	4 (2%)	187	0.00298	0.432	0.53618	1	0.46772	1	0.86432	1	0.31398	1	0.25105	1
xq loss	5 (3%)	186	5.9999e-05	0.00984	0.14521	1	0.22117	1	0.63076	1	0.00331	0.473	0.00462	0.633