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	17 (17%)	86	0.039874	1	0.90683	1	0.30753	1	0.39019	1	0.30358	1	0.30073	1	0.040248	1	0.30073	1
1q gain	32 (31%)	71	0.03132	1	0.14226	1	0.035196	1	0.027009	1	0.029177	1	0.010337	1	0.0074271	1	0.010337	1
2p gain	40 (39%)	63	0.00064163	0.404	0.3275	1	0.3599	1	0.60154	1	0.11592	1	0.68896	1	0.0092751	1	0.68896	1
2q gain	30 (29%)	73	0.067729	1	0.076247	1	0.63794	1	0.55082	1	0.42983	1	0.76451	1	0.023646	1	0.76451	1
3p gain	14 (14%)	89	0.13967	1	0.77946	1	0.42297	1	0.27166	1	0.10078	1	0.30627	1	0.053343	1	0.30627	1
3q gain	39 (38%)	64	2.6772e-05	0.0171	0.02482	1	0.059952	1	0.0057353	1	0.0021757	1	0.0013077	0.812	0.010223	1	0.0013077	0.812
4p gain	10 (10%)	93	0.91636	1	0.56483	1	0.84037	1	1	1	0.73479	1	1	1	1	1	1	1
4q gain	9 (9%)	94	0.56345	1	0.17771	1	0.23433	1	0.57594	1	0.18333	1	0.44266	1	0.53067	1	0.44266	1
5p gain	45 (44%)	58	0.028195	1	0.22247	1	0.4072	1	0.087444	1	0.29275	1	0.37527	1	0.35991	1	0.37527	1
5q gain	15 (15%)	88	0.65713	1	0.88492	1	0.74966	1	1	1	0.74936	1	0.57034	1	1	1	0.57034	1
6p gain	17 (17%)	86	0.52621	1	1	1	0.014574	1	0.62509	1	1	1	1	1	0.68117	1	1	1
6q gain	16 (16%)	87	0.19884	1	0.58358	1	0.0069159	1	0.69788	1	1	1	1	1	0.95637	1	1	1
7p gain	62 (60%)	41	0.024255	1	0.3998	1	0.0012644	0.786	0.24254	1	0.66672	1	0.41792	1	0.53492	1	0.41792	1
7q gain	49 (48%)	54	0.3578	1	0.074316	1	0.43675	1	0.78761	1	0.51405	1	0.39891	1	0.37101	1	0.39891	1
8p gain	39 (38%)	64	0.31069	1	0.43604	1	0.53665	1	1	1	0.79944	1	1	1	0.86686	1	1	1
8q gain	56 (54%)	47	0.1525	1	0.32494	1	0.93559	1	0.40331	1	0.79059	1	0.54571	1	0.76925	1	0.54571	1
9p gain	12 (12%)	91	1	1	0.66709	1	0.3461	1	0.3204	1	0.69663	1	0.52542	1	0.46345	1	0.52542	1
9q gain	23 (22%)	80	1	1	0.37989	1	0.39511	1	0.54659	1	0.41806	1	0.50018	1	0.59586	1	0.50018	1
10p gain	21 (20%)	82	0.64117	1	0.16099	1	0.50945	1	0.84071	1	0.090169	1	0.76442	1	0.21657	1	0.76442	1
10q gain	16 (16%)	87	0.19884	1	0.32375	1	1	1	0.16361	1	0.22079	1	1	1	0.33116	1	1	1
11p gain	20 (19%)	83	0.67296	1	0.77213	1	0.037192	1	0.59271	1	0.51301	1	0.47971	1	0.51775	1	0.47971	1
11q gain	19 (18%)	84	0.48689	1	0.18183	1	0.10582	1	0.092159	1	0.20591	1	0.19758	1	0.45088	1	0.19758	1
12p gain	36 (35%)	67	6.5594e-05	0.0418	0.068574	1	0.039898	1	0.0031582	1	0.012306	1	0.0047872	1	0.065558	1	0.0047872	1
12q gain	21 (20%)	82	0.0080721	1	0.25027	1	0.50483	1	0.03702	1	0.23896	1	0.33568	1	0.50957	1	0.33568	1
13q gain	24 (23%)	79	0.0003988	0.252	0.001126	0.704	0.005086	1	0.0034586	1	0.0013949	0.863	0.00059509	0.376	0.002043	1	0.00059509	0.376
14q gain	26 (25%)	77	0.1242	1	0.11273	1	0.23969	1	0.33932	1	0.46865	1	0.45687	1	0.23803	1	0.45687	1
15q gain	19 (18%)	84	0.70639	1	0.0487	1	0.4756	1	0.31666	1	0.1584	1	0.42626	1	0.68246	1	0.42626	1
16p gain	20 (19%)	83	0.027923	1	0.30503	1	0.022999	1	0.036522	1	0.09715	1	0.061241	1	0.068682	1	0.061241	1
16q gain	16 (16%)	87	0.023707	1	0.14395	1	0.0014349	0.887	0.056266	1	0.034453	1	0.059354	1	0.013273	1	0.059354	1
17p gain	19 (18%)	84	0.016948	1	0.07565	1	0.44957	1	0.85159	1	0.5859	1	0.67911	1	0.71363	1	0.67911	1
17q gain	24 (23%)	79	0.004411	1	0.30374	1	0.47203	1	0.41103	1	0.35158	1	0.45953	1	0.74937	1	0.45953	1
18p gain	28 (27%)	75	0.0077954	1	0.30131	1	0.43735	1	0.46723	1	0.44706	1	0.51733	1	0.40455	1	0.51733	1
18q gain	14 (14%)	89	0.5623	1	0.8134	1	0.82876	1	0.62509	1	0.81171	1	0.76535	1	0.95637	1	0.76535	1
19p gain	15 (15%)	88	0.024427	1	0.39901	1	0.96647	1	0.68031	1	0.76347	1	0.78169	1	0.35893	1	0.78169	1
19q gain	19 (18%)	84	0.0024118	1	0.09571	1	0.18825	1	0.083357	1	0.084848	1	0.062096	1	0.044567	1	0.062096	1
20p gain	53 (51%)	50	0.41238	1	0.18353	1	0.52024	1	0.30914	1	0.54027	1	0.44778	1	0.78224	1	0.44778	1
20q gain	60 (58%)	43	0.084618	1	0.02206	1	0.10561	1	0.07081	1	0.12035	1	0.051623	1	0.33498	1	0.051623	1
21q gain	8 (8%)	95	0.59117	1	0.70513	1	0.60177	1	0.092755	1	0.77515	1	0.72555	1	0.1081	1	0.72555	1
22q gain	19 (18%)	84	0.0025916	1	0.00010978	0.0698	0.001146	0.715	0.00066712	0.42	0.0020248	1	0.0010955	0.687	0.0096566	1	0.0010955	0.687
xq gain	21 (20%)	82	0.34171	1	0.23292	1	0.411	1	0.17614	1	0.44454	1	0.36971	1	0.62284	1	0.36971	1
1p loss	19 (18%)	84	0.059957	1	0.18183	1	0.19574	1	0.17052	1	0.20831	1	0.19758	1	0.59267	1	0.19758	1
1q loss	13 (13%)	90	0.0011466	0.715	0.063905	1	0.15834	1	0.1152	1	0.075956	1	0.10153	1	0.47621	1	0.10153	1
2p loss	5 (5%)	98	0.4381	1	0.13671	1	NA	NA	NA	NA	0.79577	1	1	1	0.86377	1	1	1
2q loss	11 (11%)	92	0.55865	1	0.0037716	1	0.016856	1	0.16972	1	0.13138	1	0.19354	1	0.21849	1	0.19354	1
3p loss	53 (51%)	50	0.10525	1	0.04124	1	0.51222	1	0.081116	1	0.1843	1	0.040024	1	0.18078	1	0.040024	1
3q loss	15 (15%)	88	0.1939	1	0.89476	1	0.12331	1	0.47388	1	0.53475	1	0.58714	1	0.94284	1	0.58714	1
4p loss	56 (54%)	47	0.0078298	1	0.48191	1	0.14276	1	0.45664	1	0.4462	1	0.16366	1	0.6982	1	0.16366	1
4q loss	49 (48%)	54	0.0052771	1	0.22917	1	0.056246	1	0.74672	1	0.58251	1	1	1	0.9176	1	1	1
5p loss	25 (24%)	78	0.24593	1	0.037622	1	0.072814	1	0.0021192	1	0.10647	1	0.11704	1	0.0090751	1	0.11704	1
5q loss	42 (41%)	61	0.52505	1	0.11047	1	0.33032	1	0.53944	1	0.66876	1	0.71863	1	0.29425	1	0.71863	1
6p loss	20 (19%)	83	0.23653	1	0.44591	1	0.17166	1	0.31342	1	0.61176	1	0.50018	1	0.60833	1	0.50018	1
6q loss	18 (17%)	85	0.68974	1	0.76005	1	0.2264	1	0.30987	1	0.50412	1	0.42109	1	0.80971	1	0.42109	1
7p loss	7 (7%)	96	0.79208	1	0.40013	1	0.30499	1	0.03587	1	0.83547	1	0.66659	1	0.0091933	1	0.66659	1
7q loss	12 (12%)	91	0.094344	1	0.016051	1	0.88805	1	0.62509	1	1	1	1	1	0.80139	1	1	1
8p loss	33 (32%)	70	0.79469	1	0.86327	1	0.61305	1	0.90076	1	0.85455	1	0.75624	1	0.81561	1	0.75624	1
8q loss	11 (11%)	92	0.78433	1	0.83884	1	0.64081	1	0.4922	1	0.81171	1	0.76535	1	0.28834	1	0.76535	1
9p loss	54 (52%)	49	0.44255	1	0.38636	1	0.61588	1	0.77384	1	0.62517	1	0.43309	1	0.80484	1	0.43309	1
9q loss	33 (32%)	70	0.32486	1	0.36769	1	0.85891	1	0.5583	1	0.44706	1	0.51733	1	0.16533	1	0.51733	1
10p loss	26 (25%)	77	0.1242	1	0.16659	1	0.70254	1	0.25328	1	0.61797	1	0.57472	1	0.84079	1	0.57472	1
10q loss	31 (30%)	72	0.0052049	1	0.010155	1	0.35163	1	0.032172	1	0.097649	1	0.043838	1	0.12362	1	0.043838	1
11p loss	29 (28%)	74	0.45404	1	0.70679	1	0.17511	1	0.47452	1	0.32189	1	0.29342	1	0.41839	1	0.29342	1
11q loss	32 (31%)	71	0.092779	1	0.7747	1	0.68644	1	0.10886	1	0.22163	1	0.22527	1	0.1979	1	0.22527	1
12p loss	18 (17%)	85	0.2887	1	0.14568	1	0.053991	1	0.0090028	1	0.0053797	1	0.0050423	1	0.076865	1	0.0050423	1
12q loss	17 (17%)	86	0.69582	1	0.2268	1	0.098016	1	0.048001	1	0.053595	1	0.030142	1	0.17095	1	0.030142	1
13q loss	41 (40%)	62	0.0055137	1	0.14485	1	0.12695	1	0.062138	1	0.073654	1	0.021307	1	0.010657	1	0.021307	1
14q loss	26 (25%)	77	0.10721	1	0.0051106	1	0.072814	1	0.10751	1	0.061888	1	0.11704	1	0.024884	1	0.11704	1
15q loss	25 (24%)	78	0.30157	1	0.22934	1	0.2306	1	0.2862	1	0.52913	1	0.45953	1	0.65458	1	0.45953	1
16p loss	27 (26%)	76	0.0010167	0.639	0.024916	1	0.17595	1	0.049495	1	0.12728	1	0.11704	1	0.13785	1	0.11704	1
16q loss	29 (28%)	74	0.00017619	0.112	0.030514	1	0.040014	1	0.027135	1	0.062074	1	0.053354	1	0.13267	1	0.053354	1
17p loss	37 (36%)	66	0.33358	1	0.00026152	0.166	0.074951	1	0.04037	1	0.05256	1	0.02386	1	0.033359	1	0.02386	1
17q loss	10 (10%)	93	0.91636	1	0.56483	1	0.43103	1	0.23792	1	0.26431	1	0.30702	1	0.13328	1	0.30702	1
18p loss	36 (35%)	67	0.13485	1	0.036507	1	0.38342	1	0.37255	1	0.071671	1	0.52647	1	0.089267	1	0.52647	1
18q loss	54 (52%)	49	0.84447	1	0.22108	1	0.49351	1	0.26763	1	0.13083	1	0.29953	1	0.21189	1	0.29953	1
19p loss	33 (32%)	70	0.02028	1	0.18684	1	0.71462	1	0.83488	1	0.055886	1	0.57656	1	0.078949	1	0.57656	1
19q loss	27 (26%)	76	0.010258	1	0.044999	1	0.73925	1	0.35557	1	0.05145	1	0.22493	1	0.31787	1	0.22493	1
20p loss	14 (14%)	89	1	1	0.77946	1	0.82272	1	0.82161	1	0.43714	1	0.73653	1	0.61126	1	0.73653	1
20q loss	5 (5%)	98	1	1	1	1	0.84244	1	0.63451	1	0.59859	1	0.57606	1	1	1	0.57606	1
21q loss	58 (56%)	45	0.61152	1	0.077103	1	0.014131	1	0.0069305	1	0.14995	1	0.052405	1	0.085737	1	0.052405	1
22q loss	37 (36%)	66	0.034144	1	0.006138	1	0.13404	1	0.21418	1	0.28692	1	0.2436	1	0.37546	1	0.2436	1
xq loss	24 (23%)	79	0.36989	1	0.072675	1	0.18441	1	0.22754	1	0.33411	1	0.38907	1	0.3978	1	0.38907	1