Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Chi-square test_P	Chi-square 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	4 (4%)	86	0.085344	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
1q gain	8 (9%)	82	0.15689	1	0.50758	1	0.046121	1	0.16732	1	0.064502	1	0.85474	1	0.29901	1	0.85148	1
2p gain	13 (14%)	77	0.00022389	0.125	0.0012731	0.686	0.011904	1	0.00028129	0.156	0.37256	1	0.12101	1	0.080335	1	0.059779	1
2q gain	12 (13%)	78	0.003761	1	0.0015639	0.834	0.018256	1	0.0041461	1	0.055266	1	0.031042	1	0.019	1	0.027974	1
3p gain	13 (14%)	77	0.060624	1	0.11155	1	0.33051	1	0.27436	1	0.40665	1	0.13882	1	0.31138	1	0.22679	1
3q gain	15 (17%)	75	0.053912	1	0.086243	1	0.05279	1	0.6225	1	0.65309	1	0.54511	1	0.55837	1	0.56004	1
4p gain	37 (41%)	53	7.7987e-05	0.0444	0.043191	1	4.7857e-05	0.0276	0.00034964	0.193	0.27153	1	0.39402	1	0.6353	1	0.57178	1
4q gain	33 (37%)	57	0.00023648	0.132	0.042	1	1.7637e-05	0.0103	7.2608e-05	0.0415	0.52839	1	0.65747	1	0.56603	1	0.77095	1
5p gain	57 (63%)	33	3.2492e-06	0.00193	0.031047	1	0.0006028	0.329	5.5904e-05	0.0321	0.23683	1	0.37604	1	0.065328	1	0.38451	1
5q gain	53 (59%)	37	2.9027e-05	0.0168	0.0094334	1	0.00068726	0.374	1.3422e-05	0.00787	0.32837	1	0.20179	1	0.34634	1	0.20977	1
6p gain	18 (20%)	72	0.058298	1	0.65273	1	0.068611	1	0.93678	1	0.14872	1	0.1022	1	0.19688	1	0.25749	1
6q gain	16 (18%)	74	0.0018935	1	0.45328	1	0.19238	1	0.52723	1	0.28894	1	0.22506	1	0.25904	1	0.50138	1
7p gain	48 (53%)	42	0.00054367	0.297	0.11306	1	0.00014413	0.0813	0.0023096	1	0.86517	1	0.68505	1	0.8594	1	0.45735	1
7q gain	48 (53%)	42	6.7174e-05	0.0385	0.11306	1	3.5408e-06	0.0021	0.00019188	0.108	0.86517	1	0.47375	1	1	1	0.31023	1
8p gain	32 (36%)	58	0.0022625	1	0.13669	1	0.1654	1	0.2462	1	0.11651	1	0.30737	1	0.02668	1	0.51539	1
8q gain	38 (42%)	52	0.019092	1	0.28604	1	0.40084	1	0.5018	1	0.47081	1	0.55237	1	0.085709	1	0.77845	1
9p gain	20 (22%)	70	2.3787e-05	0.0138	0.004017	1	0.01018	1	0.0016107	0.857	0.37455	1	0.42665	1	0.23328	1	0.33591	1
9q gain	29 (32%)	61	0.00018626	0.105	0.0040662	1	0.026643	1	0.00026365	0.147	0.033146	1	0.27868	1	0.018809	1	0.18276	1
10p gain	25 (28%)	65	0.00046729	0.257	0.063237	1	4.6877e-05	0.027	0.00048313	0.265	0.033146	1	0.64348	1	0.10357	1	0.53166	1
10q gain	26 (29%)	64	0.00035183	0.194	0.076283	1	3.3942e-05	0.0196	0.0011104	0.6	0.019521	1	0.91868	1	0.07035	1	0.88002	1
11p gain	5 (6%)	85	0.04782	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
11q gain	6 (7%)	84	0.12576	1	0.12556	1	0.044579	1	0.17178	1	0.1869	1	1	1	0.44517	1	0.80807	1
12p gain	64 (71%)	26	1.6644e-05	0.00972	0.19871	1	0.00021393	0.12	0.0047633	1	0.23534	1	0.47119	1	0.07035	1	0.53166	1
12q gain	64 (71%)	26	1.5763e-06	0.000939	0.29766	1	0.00071306	0.387	0.012882	1	0.22554	1	0.80193	1	0.03894	1	0.91762	1
13q gain	6 (7%)	84	0.91912	1	0.47779	1	0.039219	1	0.36258	1	0.14101	1	0.85474	1	0.29901	1	0.85148	1
14q gain	21 (23%)	69	0.0071771	1	0.056239	1	0.00050812	0.278	0.0001126	0.0638	9.9033e-06	0.00583	1.308e-05	0.00768	9.6381e-06	0.00569	3.5675e-06	0.00211
15q gain	11 (12%)	79	0.22089	1	0.056336	1	0.010629	1	0.011615	1	0.36186	1	0.16321	1	0.2478	1	0.11354	1
16p gain	49 (54%)	41	9.8611e-08	5.9e-05	0.012436	1	8.7435e-06	0.00517	1.0115e-05	0.00595	0.046824	1	0.25039	1	0.01106	1	0.53105	1
16q gain	47 (52%)	43	2.9804e-07	0.000178	0.0092972	1	0.00011476	0.065	3.0527e-05	0.0177	0.024016	1	0.25039	1	0.01106	1	0.53105	1
17p gain	5 (6%)	85	0.11328	1	0.50916	1	0.68684	1	0.11307	1	0.20769	1	0.37541	1	0.14012	1	0.13981	1
17q gain	7 (8%)	83	0.0098057	1	0.50916	1	0.68684	1	0.11307	1	0.20769	1	0.37541	1	0.14012	1	0.13981	1
18p gain	6 (7%)	84	0.42194	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
18q gain	5 (6%)	85	0.59769	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
19p gain	56 (62%)	34	0.011798	1	0.049649	1	0.0012861	0.691	0.0012773	0.687	0.43765	1	0.72907	1	0.36576	1	0.39319	1
19q gain	52 (58%)	38	0.0020234	1	0.052408	1	0.00037816	0.208	0.0023555	1	0.14144	1	0.43098	1	0.095648	1	0.18538	1
20p gain	46 (51%)	44	1.9467e-06	0.00116	0.22589	1	0.00011965	0.0676	0.0073803	1	0.0049016	1	0.0026447	1	0.00014654	0.0825	0.012828	1
20q gain	49 (54%)	41	1.9936e-05	0.0116	0.062664	1	7.0205e-05	0.0402	0.0030127	1	0.018626	1	0.016215	1	0.00082422	0.447	0.022528	1
21q gain	31 (34%)	59	0.033058	1	0.0084163	1	0.020312	1	0.0013697	0.733	0.012183	1	0.055731	1	0.026361	1	0.032665	1
22q gain	3 (3%)	87	0.49579	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
xq gain	40 (44%)	50	1.5058e-05	0.00881	0.1671	1	0.0016441	0.873	0.014766	1	0.78352	1	0.35419	1	0.61711	1	0.23663	1
1p loss	29 (32%)	61	0.2146	1	0.16782	1	0.41431	1	0.090404	1	0.47082	1	0.50068	1	0.71727	1	0.67661	1
1q loss	20 (22%)	70	0.54558	1	0.098898	1	0.94384	1	0.798	1	0.36412	1	0.27134	1	0.5796	1	0.36298	1
2p loss	17 (19%)	73	0.00050816	0.278	0.025496	1	0.58767	1	0.46768	1	0.03567	1	0.27513	1	0.12657	1	0.33552	1
2q loss	15 (17%)	75	7.7514e-05	0.0442	0.002401	1	0.11463	1	0.087502	1	0.028342	1	0.17041	1	0.11463	1	0.27511	1
3p loss	20 (22%)	70	0.036305	1	0.10929	1	0.11467	1	0.21449	1	0.4843	1	0.35969	1	0.2037	1	0.22853	1
3q loss	20 (22%)	70	0.011727	1	0.12746	1	0.024141	1	0.065495	1	0.1973	1	0.11783	1	0.040005	1	0.072361	1
4p loss	10 (11%)	80	0.034518	1	0.18134	1	0.023203	1	0.053728	1	0.30833	1	0.54687	1	0.4233	1	0.55562	1
4q loss	11 (12%)	79	0.091557	1	0.061233	1	0.0072832	1	0.018694	1	0.24969	1	0.64176	1	0.37952	1	0.46608	1
5p loss	8 (9%)	82	0.16809	1	0.059657	1	0.22915	1	0.00181	0.959	0.77163	1	1	1	0.45397	1	1	1
5q loss	7 (8%)	83	0.62092	1	0.50758	1	0.2759	1	0.16732	1	0.65776	1	0.59691	1	0.86224	1	0.61408	1
6p loss	19 (21%)	71	0.043802	1	0.83305	1	0.59423	1	0.38961	1	0.60727	1	0.73692	1	0.8159	1	0.58598	1
6q loss	22 (24%)	68	0.011581	1	0.88062	1	0.60718	1	0.6153	1	0.71969	1	0.85196	1	0.72369	1	0.68178	1
7p loss	5 (6%)	85	0.394	1	0.51728	1	0.90985	1	0.81454	1	0.81627	1	0.071991	1	0.68142	1	0.08645	1
7q loss	6 (7%)	84	0.2873	1	0.25411	1	0.62016	1	0.4417	1	1	1	0.053847	1	0.59294	1	0.064679	1
8p loss	16 (18%)	74	0.0096271	1	0.20632	1	0.1805	1	0.070165	1	0.19179	1	0.056108	1	0.017495	1	0.030885	1
8q loss	12 (13%)	78	0.0020606	1	0.082868	1	0.032982	1	0.028304	1	0.077738	1	0.06796	1	0.033998	1	0.034426	1
9p loss	20 (22%)	70	0.00092866	0.502	0.03801	1	9.3893e-05	0.0533	0.0023111	1	0.0087246	1	0.53155	1	0.059367	1	0.5124	1
9q loss	11 (12%)	79	0.13467	1	0.93198	1	0.08068	1	0.43198	1	0.55796	1	1	1	0.83028	1	0.89905	1
10p loss	12 (13%)	78	0.81981	1	0.41817	1	0.26505	1	0.82196	1	0.68272	1	0.64176	1	0.61614	1	0.46608	1
10q loss	10 (11%)	80	0.48408	1	0.56738	1	0.5355	1	0.90012	1	1	1	0.51773	1	0.89096	1	0.52756	1
11p loss	24 (27%)	66	0.0012901	0.692	0.014911	1	0.22345	1	0.54797	1	0.27743	1	0.56744	1	0.4194	1	0.58541	1
11q loss	23 (26%)	67	4.8057e-05	0.0276	0.0026582	1	0.14291	1	0.35194	1	0.097487	1	0.39154	1	0.20809	1	0.44657	1
12p loss	5 (6%)	85	0.18885	1	0.26199	1	0.62016	1	1	1	0.1028	1	1	1	0.010697	1	1	1
12q loss	4 (4%)	86	0.10792	1	0.098182	1	0.44106	1	0.55729	1	0.33126	1	0.79075	1	0.042677	1	1	1
13q loss	39 (43%)	51	0.010371	1	0.083798	1	0.60034	1	0.76762	1	0.76081	1	0.89979	1	0.91496	1	0.76559	1
14q loss	18 (20%)	72	0.023199	1	0.44676	1	0.018424	1	0.0040556	1	0.37711	1	0.33202	1	0.27653	1	0.17421	1
15q loss	21 (23%)	69	0.029921	1	0.3602	1	0.11016	1	0.17231	1	0.57149	1	0.84341	1	0.33089	1	0.91197	1
16p loss	6 (7%)	84	0.12576	1	0.057501	1	0.0021497	1	0.080099	1	0.012846	1	0.25805	1	0.031522	1	0.22578	1
16q loss	5 (6%)	85	0.27239	1	0.035556	1	0.057462	1	0.021411	1	0.16888	1	1	1	0.36003	1	1	1
17p loss	32 (36%)	58	0.0014108	0.753	0.00030532	0.169	0.011907	1	0.01996	1	0.073493	1	0.092165	1	0.05141	1	0.043731	1
17q loss	24 (27%)	66	0.00019854	0.111	0.0044717	1	0.11892	1	0.03718	1	0.066665	1	0.11758	1	0.077693	1	0.06312	1
18p loss	37 (41%)	53	0.026398	1	0.24179	1	0.77061	1	0.75634	1	0.68413	1	0.49181	1	0.84984	1	0.59274	1
18q loss	35 (39%)	55	0.044405	1	0.39873	1	0.81128	1	0.92681	1	0.47081	1	0.47187	1	0.73169	1	0.62983	1
19p loss	5 (6%)	85	0.04782	1	0.35565	1	0.1575	1	0.77865	1	0.13933	1	0.70574	1	0.21454	1	0.72317	1
19q loss	4 (4%)	86	0.10792	1	0.67302	1	0.77362	1	0.47352	1	0.78469	1	1	1	0.21454	1	1	1
20p loss	9 (10%)	81	0.0077361	1	0.28199	1	0.2134	1	0.028038	1	0.067752	1	0.63917	1	0.16924	1	0.64493	1
20q loss	3 (3%)	87	0.55135	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
21q loss	15 (17%)	75	0.014738	1	0.36582	1	0.25616	1	0.23375	1	0.22366	1	0.24478	1	0.2327	1	0.10741	1
22q loss	48 (53%)	42	0.078114	1	0.075317	1	0.60375	1	0.5837	1	0.8593	1	0.72514	1	0.7944	1	0.68016	1
xq loss	17 (19%)	73	0.002159	1	0.25501	1	0.033456	1	0.020698	1	0.70653	1	0.85134	1	0.13794	1	0.67199	1