Clinical Features	MRNA_CHIERARCHICAL		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
1p gain	9 (9%)	91	0.45522	0.643	0.066239	0.199	0.2386	0.437
1q gain	27 (27%)	73	0.02374	0.0968	9.9999e-06	0.00216	0.00069999	0.0126
2p gain	15 (15%)	85	0.84821	0.921	0.066869	0.199	0.28207	0.494
2q gain	14 (14%)	86	0.8039	0.885	0.067299	0.199	0.28156	0.494
3p gain	10 (10%)	90	0.22584	0.428	0.01865	0.0822	0.094289	0.26
3q gain	16 (16%)	84	0.24838	0.447	0.0052599	0.0437	0.0073899	0.0499
5p gain	5 (5%)	95	0.24063	0.437	0.81125	0.885	0.44546	0.634
6p gain	10 (10%)	90	0.18156	0.367	0.01214	0.0709	0.10498	0.273
6q gain	8 (8%)	92	0.38259	0.604	0.21142	0.408	0.72097	0.85
7p gain	13 (13%)	87	0.29296	0.502	0.58616	0.767	0.86138	0.927
7q gain	14 (14%)	86	0.14309	0.324	0.50714	0.693	0.79019	0.884
8p gain	19 (19%)	81	0.061329	0.189	0.7887	0.884	0.66999	0.822
8q gain	20 (20%)	80	0.054679	0.171	0.88252	0.937	0.59971	0.78
10p gain	25 (25%)	75	0.93322	0.953	0.7479	0.859	0.17195	0.357
10q gain	24 (24%)	76	0.73941	0.856	0.64793	0.817	0.10453	0.273
11p gain	3 (3%)	97	0.68354	0.829	0.10943	0.276	0.40402	0.61
11q gain	4 (4%)	96	0.38138	0.604	0.11144	0.276	0.40412	0.61
12p gain	10 (10%)	90	0.03534	0.124	0.49202	0.677	0.99214	0.992
12q gain	10 (10%)	90	0.03464	0.124	0.49221	0.677	0.99246	0.992
13q gain	6 (6%)	94	0.75289	0.86	0.00064999	0.0126	0.0077699	0.0509
14q gain	7 (7%)	93	0.45973	0.645	0.0039	0.0366	0.03398	0.124
16p gain	6 (6%)	94	0.1632	0.346	0.03999	0.135	0.32642	0.542
16q gain	5 (5%)	95	0.35854	0.587	0.14827	0.325	0.41687	0.625
17p gain	7 (7%)	93	0.092419	0.26	0.1365	0.314	0.17729	0.365
17q gain	6 (6%)	94	0.23434	0.433	0.20421	0.401	0.18112	0.367
18p gain	9 (9%)	91	0.1153	0.277	0.052359	0.166	0.070319	0.205
18q gain	7 (7%)	93	0.56627	0.755	0.14837	0.325	0.03863	0.132
19p gain	7 (7%)	93	0.91778	0.949	0.69501	0.835	0.30103	0.512
19q gain	8 (8%)	92	0.79517	0.885	0.33542	0.553	0.2925	0.502
20p gain	22 (22%)	78	0.03275	0.124	0.00049	0.0126	0.0482	0.155
20q gain	22 (22%)	78	0.11924	0.283	5e-05	0.0036	0.0059199	0.047
21q gain	6 (6%)	94	0.43399	0.634	0.00327	0.0336	0.21009	0.408
22q gain	8 (8%)	92	0.76608	0.866	0.00232	0.0299	0.16495	0.346
xp gain	8 (8%)	92	0.6109	0.79	0.87167	0.932	0.47735	0.665
xq gain	8 (8%)	92	0.3923	0.61	0.43904	0.634	0.52849	0.718
yp gain	14 (14%)	86	0.73642	0.856	0.38559	0.604	0.91598	0.949
yq gain	14 (14%)	86	0.74127	0.856	0.38418	0.604	0.91477	0.949
1p loss	4 (4%)	96	0.12154	0.285	0.0036	0.0353	0.0334	0.124
1q loss	3 (3%)	97	0.43838	0.634	0.0051599	0.0437	0.03519	0.124
3p loss	6 (6%)	94	0.43417	0.634	0.14876	0.325	0.03272	0.124
4p loss	12 (12%)	88	0.01538	0.0773	0.0091299	0.0563	0.01762	0.0793
4q loss	12 (12%)	88	0.01515	0.0773	0.0084999	0.054	0.01649	0.0774
5p loss	9 (9%)	91	0.31602	0.529	0.02149	0.0928	0.095069	0.26
5q loss	11 (11%)	89	0.18492	0.37	0.0060899	0.047	0.10129	0.27
7p loss	5 (5%)	95	0.72367	0.85	0.81057	0.885	0.4444	0.634
7q loss	5 (5%)	95	0.72173	0.85	0.81125	0.885	0.44586	0.634
8p loss	7 (7%)	93	0.15782	0.341	4e-05	0.0036	0.03009	0.12
8q loss	4 (4%)	96	0.66277	0.819	0.00068999	0.0126	0.19116	0.379
9p loss	14 (14%)	86	0.28332	0.494	0.01439	0.0758	0.00249	0.0299
9q loss	16 (16%)	84	0.12672	0.294	0.0073299	0.0499	0.01096	0.0658
10p loss	5 (5%)	95	0.89183	0.937	0.14389	0.324	0.093249	0.26
10q loss	4 (4%)	96	0.66197	0.819	0.084329	0.243	0.03568	0.124
11p loss	8 (8%)	92	0.76551	0.866	0.01283	0.0726	0.11137	0.276
11q loss	7 (7%)	93	0.42638	0.634	0.01311	0.0726	0.11264	0.276
12p loss	4 (4%)	96	0.93913	0.953	0.01593	0.0774	0.0065099	0.0485
12q loss	4 (4%)	96	0.93945	0.953	0.01635	0.0774	0.0067699	0.0487
13q loss	10 (10%)	90	0.21408	0.409	0.94792	0.957	0.6639	0.819
15q loss	13 (13%)	87	0.54674	0.738	0.00123	0.0204	9.9999e-05	0.0054
16p loss	6 (6%)	94	0.89315	0.937	0.00425	0.0382	0.04552	0.151
16q loss	7 (7%)	93	0.86278	0.927	0.00068999	0.0126	0.01438	0.0758
17p loss	13 (13%)	87	0.10092	0.27	0.00232	0.0299	0.00027	0.0108
17q loss	8 (8%)	92	0.40321	0.61	0.00238	0.0299	0.16041	0.343
18p loss	4 (4%)	96	0.93991	0.953	0.0223	0.0944	0.36916	0.6
18q loss	5 (5%)	95	0.72001	0.85	0.11423	0.277	0.67777	0.827
19p loss	6 (6%)	94	0.69605	0.835	0.00294	0.0318	0.31497	0.529
19q loss	6 (6%)	94	0.27819	0.494	0.02313	0.0961	0.5603	0.752
21q loss	5 (5%)	95	0.89095	0.937	0.11204	0.276	0.40046	0.61
22q loss	12 (12%)	88	0.38356	0.604	0.04687	0.153	0.01694	0.0779
xp loss	19 (19%)	81	0.65062	0.817	0.00046	0.0126	0.00249	0.0299
xq loss	19 (19%)	81	0.64809	0.817	3e-04	0.0108	0.00286	0.0318
yp loss	47 (47%)	53	0.64456	0.817	0.23199	0.433	0.57466	0.758
yq loss	47 (47%)	53	0.64561	0.817	0.23271	0.433	0.57518	0.758