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	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	4 (4%)	86	0.11869	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
1q gain	8 (9%)	82	0.11957	1	0.65445	1	0.04674	1	0.077619	1	0.064679	1	0.24228	1	0.29843	1	0.22964	1
2p gain	13 (14%)	77	0.00026	0.143	0.00112	0.594	0.01179	1	0.00014	0.0784	0.37295	1	0.0185	1	0.079909	1	0.04682	1
2q gain	12 (13%)	78	0.0037	1	0.00225	1	0.01805	1	0.00263	1	0.055579	1	0.00431	1	0.01963	1	0.00352	1
3p gain	13 (14%)	77	0.092479	1	0.068729	1	0.32923	1	0.36239	1	0.40859	1	0.10653	1	0.30973	1	0.60105	1
3q gain	15 (17%)	75	0.059869	1	0.051779	1	0.052069	1	0.79322	1	0.65172	1	0.24577	1	0.56035	1	0.85565	1
4p gain	37 (41%)	53	3e-05	0.0174	0.0438	1	5e-05	0.0287	5e-05	0.0287	0.2951	1	0.00193	0.998	0.68817	1	0.14597	1
4q gain	33 (37%)	57	6.9999e-05	0.0399	0.03628	1	3e-05	0.0174	9.9999e-06	0.00598	0.55874	1	0.00081999	0.44	0.58787	1	0.089239	1
5p gain	57 (63%)	33	9.9999e-06	0.00598	0.03649	1	0.00057999	0.314	9.9999e-06	0.00598	0.25105	1	0.22748	1	0.067379	1	0.34236	1
5q gain	53 (59%)	37	3e-05	0.0174	0.0088599	1	0.00070999	0.383	3e-05	0.0174	0.33374	1	0.13491	1	0.36973	1	0.38766	1
6p gain	18 (20%)	72	0.061659	1	0.68281	1	0.067129	1	0.47174	1	0.16181	1	0.054949	1	0.20853	1	0.02529	1
6q gain	16 (18%)	74	0.00232	1	0.45836	1	0.19892	1	0.2944	1	0.29812	1	0.19629	1	0.25974	1	0.16146	1
7p gain	48 (53%)	42	0.00042	0.23	0.11826	1	0.00012	0.0676	0.00133	0.698	0.91369	1	0.54961	1	0.87356	1	0.31418	1
7q gain	48 (53%)	42	2e-05	0.0117	0.11574	1	9.9999e-06	0.00598	9.9999e-05	0.0565	0.91482	1	0.33066	1	1	1	0.17987	1
8p gain	32 (36%)	58	0.00177	0.917	0.13921	1	0.16745	1	0.14466	1	0.11304	1	0.17417	1	0.02613	1	0.060529	1
8q gain	38 (42%)	52	0.01872	1	0.29113	1	0.41558	1	0.23139	1	0.49603	1	0.26134	1	0.096299	1	0.12078	1
9p gain	20 (22%)	70	6.9999e-05	0.0399	0.0023	1	0.0093199	1	0.01123	1	0.38474	1	0.54999	1	0.23664	1	0.62979	1
9q gain	29 (32%)	61	0.00019	0.106	0.00121	0.639	0.02301	1	0.00169	0.879	0.0342	1	0.35384	1	0.01719	1	0.36025	1
10p gain	25 (28%)	65	0.00078999	0.424	0.058819	1	3e-05	0.0174	0.00019	0.106	0.03372	1	0.51103	1	0.10373	1	0.66735	1
10q gain	26 (29%)	64	0.00056999	0.309	0.071169	1	4e-05	0.023	0.00045	0.246	0.02032	1	0.34045	1	0.069829	1	0.65132	1
11p gain	5 (6%)	85	0.11085	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
11q gain	6 (7%)	84	0.17449	1	0.17553	1	0.04428	1	0.078719	1	0.18735	1	0.37121	1	0.44496	1	0.15979	1
12p gain	64 (71%)	26	2e-05	0.0117	0.20878	1	0.00022	0.122	5e-05	0.0287	0.2459	1	0.20937	1	0.069769	1	0.12018	1
12q gain	64 (71%)	26	9.9999e-06	0.00598	0.31127	1	0.00067999	0.367	0.00014	0.0784	0.23566	1	0.45508	1	0.04255	1	0.20737	1
13q gain	6 (7%)	84	1	1	0.46358	1	0.03846	1	0.63872	1	0.13953	1	0.91305	1	0.29986	1	0.3943	1
14q gain	21 (23%)	69	0.01412	1	0.055719	1	0.00038	0.208	0.00081999	0.44	2e-05	0.0117	0.00014	0.0784	2e-05	0.0117	2e-05	0.0117
15q gain	11 (12%)	79	0.2146	1	0.04544	1	0.01048	1	0.00482	1	0.36103	1	0.00072999	0.393	0.24764	1	0.0058299	1
16p gain	49 (54%)	41	9.9999e-06	0.00598	0.01075	1	9.9999e-06	0.00598	9.9999e-06	0.00598	0.04662	1	0.02624	1	0.01224	1	0.1688	1
16q gain	47 (52%)	43	9.9999e-06	0.00598	0.0082499	1	0.00012	0.0676	9.9999e-06	0.00598	0.02405	1	0.01306	1	0.01177	1	0.14389	1
17p gain	5 (6%)	85	0.088269	1	0.33742	1	0.6847	1	0.14366	1	0.205	1	0.794	1	0.14095	1	0.9286	1
17q gain	7 (8%)	83	0.01452	1	0.33825	1	0.68854	1	0.14433	1	0.21077	1	0.79312	1	0.1402	1	0.92799	1
18p gain	6 (7%)	84	0.49291	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
18q gain	5 (6%)	85	0.6596	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
19p gain	56 (62%)	34	0.0075699	1	0.054929	1	0.00133	0.698	0.00045	0.246	0.46587	1	0.47055	1	0.3699	1	0.62581	1
19q gain	52 (58%)	38	0.00050999	0.277	0.04982	1	0.00036	0.198	0.00114	0.603	0.14338	1	0.10969	1	0.10121	1	0.19248	1
20p gain	46 (51%)	44	9.9999e-06	0.00598	0.23649	1	8.9999e-05	0.0509	0.00014	0.0784	0.00495	1	0.091179	1	0.00013	0.0729	0.00372	1
20q gain	49 (54%)	41	2e-05	0.0117	0.064919	1	6.9999e-05	0.0399	0.00025	0.138	0.01945	1	0.27476	1	0.00097999	0.522	0.03338	1
21q gain	31 (34%)	59	0.03712	1	0.0088799	1	0.0195	1	0.00090999	0.486	0.01315	1	0.0205	1	0.02594	1	0.15439	1
22q gain	3 (3%)	87	0.37526	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
xq gain	40 (44%)	50	9.9999e-06	0.00598	0.16855	1	0.00166	0.865	0.0084999	1	0.79748	1	0.15129	1	0.61125	1	0.061749	1
1p loss	29 (32%)	61	0.20206	1	0.14068	1	0.43818	1	0.065029	1	0.4687	1	0.41011	1	0.78448	1	0.40598	1
1q loss	20 (22%)	70	0.58414	1	0.089109	1	0.962	1	0.60081	1	0.36741	1	0.84144	1	0.59433	1	0.60933	1
2p loss	17 (19%)	73	0.00055999	0.304	0.02717	1	0.61158	1	0.26652	1	0.03775	1	0.76852	1	0.12678	1	0.7601	1
2q loss	15 (17%)	75	9.9999e-05	0.0565	0.00106	0.564	0.11327	1	0.053519	1	0.0313	1	0.72864	1	0.1151	1	0.83524	1
3p loss	20 (22%)	70	0.059729	1	0.14324	1	0.11151	1	0.13505	1	0.52343	1	0.39058	1	0.19548	1	0.30601	1
3q loss	20 (22%)	70	0.01637	1	0.16634	1	0.02216	1	0.0292	1	0.19262	1	0.33838	1	0.04031	1	0.18517	1
4p loss	10 (11%)	80	0.01678	1	0.23382	1	0.02342	1	0.080979	1	0.30767	1	0.93065	1	0.42356	1	0.90328	1
4q loss	11 (12%)	79	0.04693	1	0.097479	1	0.0074999	1	0.02766	1	0.25236	1	0.80981	1	0.38276	1	0.76118	1
5p loss	8 (9%)	82	0.275	1	0.050009	1	0.22972	1	0.01041	1	0.77376	1	0.29785	1	0.45487	1	0.9621	1
5q loss	7 (8%)	83	0.8628	1	0.65609	1	0.2784	1	0.13611	1	0.65851	1	0.1278	1	0.86337	1	0.33275	1
6p loss	19 (21%)	71	0.03028	1	0.85039	1	0.62223	1	0.69169	1	0.62411	1	0.099269	1	0.81547	1	0.16204	1
6q loss	22 (24%)	68	0.0073799	1	0.86165	1	0.63424	1	0.69201	1	0.72946	1	0.17682	1	0.73985	1	0.068669	1
7p loss	5 (6%)	85	0.27546	1	0.58452	1	0.91037	1	0.89101	1	0.81611	1	0.41643	1	0.68404	1	0.12954	1
7q loss	6 (7%)	84	0.1922	1	0.3045	1	0.61983	1	0.65797	1	1	1	0.23264	1	0.59551	1	0.071179	1
8p loss	16 (18%)	74	0.00308	1	0.22435	1	0.18097	1	0.14105	1	0.18056	1	0.02263	1	0.01706	1	0.0069599	1
8q loss	12 (13%)	78	0.00147	0.769	0.086949	1	0.03191	1	0.12426	1	0.078239	1	0.03523	1	0.03322	1	0.11561	1
9p loss	20 (22%)	70	0.00127	0.668	0.04787	1	5.9999e-05	0.0343	0.00125	0.659	0.0091999	1	0.13708	1	0.058719	1	0.204	1
9q loss	11 (12%)	79	0.14222	1	0.93411	1	0.082119	1	0.32179	1	0.55731	1	0.49546	1	0.82986	1	0.28202	1
10p loss	12 (13%)	78	0.73587	1	0.42801	1	0.26396	1	1	1	0.68329	1	0.70958	1	0.61753	1	0.74864	1
10q loss	10 (11%)	80	0.38954	1	0.62444	1	0.5341	1	1	1	1	1	0.70905	1	0.89194	1	0.82419	1
11p loss	24 (27%)	66	0.00173	0.898	0.01739	1	0.22062	1	0.18699	1	0.27985	1	0.89075	1	0.44707	1	0.92538	1
11q loss	23 (26%)	67	7.9999e-05	0.0454	0.00271	1	0.13319	1	0.12758	1	0.10418	1	0.82443	1	0.21707	1	0.89872	1
12p loss	5 (6%)	85	0.22941	1	0.25523	1	0.61991	1	0.03858	1	0.104	1	0.51715	1	0.01083	1	0.01712	1
12q loss	4 (4%)	86	0.24791	1	0.04946	1	0.44076	1	0.0096999	1	0.33017	1	0.23712	1	0.04222	1	0.00337	1
13q loss	39 (43%)	51	0.01001	1	0.079459	1	0.6249	1	0.88443	1	0.75261	1	0.30198	1	0.91015	1	0.28528	1
14q loss	18 (20%)	72	0.0275	1	0.444	1	0.01815	1	0.04699	1	0.4127	1	0.52979	1	0.27243	1	0.90042	1
15q loss	21 (23%)	69	0.01819	1	0.41415	1	0.10975	1	0.23109	1	0.60661	1	0.04041	1	0.37255	1	0.16244	1
16p loss	6 (7%)	84	0.17302	1	0.050589	1	0.00209	1	0.00412	1	0.01332	1	0.44287	1	0.03107	1	0.53666	1
16q loss	5 (6%)	85	0.31811	1	0.077099	1	0.058219	1	0.085599	1	0.16659	1	0.30259	1	0.36121	1	0.89399	1
17p loss	32 (36%)	58	0.00109	0.579	0.00019	0.106	0.01175	1	0.01347	1	0.081199	1	0.00286	1	0.050839	1	0.01413	1
17q loss	24 (27%)	66	0.00028	0.154	0.0054099	1	0.11983	1	0.03339	1	0.066599	1	0.01987	1	0.075899	1	0.18226	1
18p loss	37 (41%)	53	0.02613	1	0.25935	1	0.77635	1	0.64579	1	0.69198	1	0.69273	1	0.87512	1	0.28389	1
18q loss	35 (39%)	55	0.04558	1	0.42564	1	0.8235	1	0.93517	1	0.49586	1	0.91392	1	0.75995	1	0.099309	1
19p loss	5 (6%)	85	0.11203	1	0.44341	1	0.15674	1	0.01316	1	0.13875	1	0.71522	1	0.21439	1	0.03209	1
19q loss	4 (4%)	86	0.24679	1	0.7052	1	0.77344	1	0.11933	1	0.78298	1	0.20535	1	0.21582	1	0.03211	1
20p loss	9 (10%)	81	0.01026	1	0.30312	1	0.2152	1	0.1269	1	0.068129	1	0.44337	1	0.16973	1	0.76389	1
20q loss	3 (3%)	87	0.45628	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
21q loss	15 (17%)	75	0.0087099	1	0.3374	1	0.25608	1	0.252	1	0.22289	1	0.50982	1	0.23347	1	0.81491	1
22q loss	48 (53%)	42	0.077689	1	0.080959	1	0.62019	1	0.2818	1	0.87441	1	0.82793	1	0.80044	1	0.72932	1
xq loss	17 (19%)	73	0.00153	0.799	0.24581	1	0.03375	1	0.04476	1	0.65156	1	0.1717	1	0.13931	1	0.45023	1