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	10 (11%)	77	0.01481	1	0.78276	1	0.96134	1	0.60984	1	0.74007	1	0.39832	1	0.35464	1	0.75482	1
1q gain	21 (24%)	66	0.0089799	1	0.03005	1	0.051339	1	0.2254	1	0.71113	1	0.41211	1	0.69466	1	0.24781	1
2p gain	4 (5%)	83	0.10348	1	0.37611	1	0.61763	1	0.9015	1	0.052959	1	0.6138	1	0.25555	1	0.48074	1
2q gain	7 (8%)	80	0.51604	1	0.46102	1	0.31655	1	0.53715	1	0.26894	1	0.80591	1	0.01289	1	0.16833	1
3p gain	17 (20%)	70	0.00049	0.269	0.9314	1	0.70309	1	0.72746	1	1	1	1	1	0.5661	1	0.819	1
3q gain	19 (22%)	68	0.00019	0.105	0.76725	1	0.74633	1	0.52761	1	0.65122	1	0.93619	1	0.51861	1	0.76244	1
5p gain	24 (28%)	63	0.19527	1	0.32891	1	0.65878	1	0.58278	1	0.02209	1	0.093699	1	0.04486	1	0.38603	1
5q gain	15 (17%)	72	0.061249	1	0.35419	1	0.5277	1	0.95504	1	0.11954	1	0.12382	1	0.04768	1	0.63685	1
6p gain	7 (8%)	80	0.076199	1	0.095759	1	0.31607	1	0.33319	1	0.083599	1	0.35701	1	0.88015	1	0.93545	1
6q gain	4 (5%)	83	0.10205	1	0.636	1	0.8374	1	0.74497	1	0.56042	1	0.45005	1	0.5685	1	0.91174	1
7p gain	25 (29%)	62	0.01465	1	0.39155	1	0.24084	1	0.03994	1	0.03241	1	0.03542	1	0.18605	1	0.13549	1
7q gain	22 (25%)	65	0.02418	1	0.44667	1	0.44367	1	0.02031	1	0.066759	1	0.16957	1	0.40352	1	0.3805	1
8p gain	12 (14%)	75	0.04547	1	0.52207	1	0.75534	1	0.48776	1	0.17593	1	0.25351	1	0.21616	1	0.36801	1
8q gain	14 (16%)	73	0.04928	1	0.93321	1	0.73721	1	0.53164	1	0.29596	1	0.66283	1	0.39853	1	0.48466	1
9p gain	3 (3%)	84	0.70276	1	0.53351	1	0.32878	1	0.87231	1	0.18275	1	0.77381	1	0.33639	1	0.37294	1
9q gain	4 (5%)	83	0.5015	1	0.070879	1	0.44051	1	0.61538	1	0.060689	1	0.85353	1	1	1	0.71578	1
10p gain	3 (3%)	84	0.080039	1	0.7764	1	0.23946	1	0.7541	1	NA	NA	NA	NA	NA	NA	NA	NA
10q gain	3 (3%)	84	0.079499	1	0.7752	1	0.23725	1	0.75498	1	NA	NA	NA	NA	NA	NA	NA	NA
11p gain	11 (13%)	76	0.0081399	1	0.66246	1	0.51671	1	0.062069	1	0.1234	1	0.82734	1	0.59856	1	0.61809	1
11q gain	12 (14%)	75	0.0097999	1	0.38013	1	0.19886	1	0.03403	1	0.11356	1	0.4396	1	0.31541	1	0.30376	1
12p gain	18 (21%)	69	0.00038	0.209	0.81398	1	0.83475	1	0.94585	1	0.47871	1	0.92652	1	0.93521	1	0.8596	1
12q gain	18 (21%)	69	0.00028	0.155	0.81309	1	0.83222	1	0.9459	1	0.47985	1	0.9264	1	0.93619	1	0.85759	1
13q gain	5 (6%)	82	0.42342	1	0.096449	1	0.02395	1	0.096119	1	0.11494	1	0.89285	1	0.25896	1	0.71648	1
15q gain	11 (13%)	76	0.02528	1	0.00406	1	0.01408	1	0.12574	1	0.01112	1	0.17954	1	0.75268	1	0.6711	1
16p gain	17 (20%)	70	0.0069599	1	0.56808	1	0.03835	1	0.14773	1	0.03234	1	0.17161	1	0.57754	1	0.11289	1
16q gain	16 (18%)	71	0.00228	1	0.80328	1	0.04801	1	0.1165	1	0.16911	1	0.51285	1	0.74687	1	0.50985	1
17p gain	7 (8%)	80	0.21945	1	1	1	0.48168	1	0.77925	1	0.43401	1	0.04207	1	0.84992	1	0.069059	1
17q gain	17 (20%)	70	0.095069	1	0.31788	1	0.0099099	1	0.04936	1	0.088749	1	0.37495	1	0.74678	1	0.70462	1
18p gain	8 (9%)	79	0.067619	1	0.31652	1	0.11329	1	0.1845	1	0.04999	1	0.54152	1	0.13713	1	0.25478	1
18q gain	4 (5%)	83	0.088699	1	1	1	0.3659	1	0.6192	1	0.1813	1	0.84543	1	NA	NA	NA	NA
19p gain	14 (16%)	73	0.27308	1	0.03325	1	0.15302	1	0.28206	1	0.39725	1	0.92185	1	0.7885	1	0.25156	1
19q gain	10 (11%)	77	0.80521	1	0.1191	1	0.44874	1	0.60787	1	0.54971	1	1	1	0.71702	1	0.40182	1
20p gain	8 (9%)	79	0.69009	1	0.72719	1	0.24374	1	0.76963	1	0.60856	1	0.87593	1	0.88057	1	0.33202	1
20q gain	10 (11%)	77	0.204	1	0.90795	1	0.46423	1	0.8703	1	0.35639	1	0.79463	1	0.62407	1	0.1134	1
21q gain	6 (7%)	81	0.25237	1	0.61089	1	0.23104	1	0.23254	1	0.11364	1	0.80445	1	0.04016	1	0.086589	1
xq gain	6 (7%)	81	0.23193	1	0.49647	1	0.64842	1	0.87549	1	0.5638	1	0.91305	1	1	1	0.84729	1
1p loss	8 (9%)	79	0.02482	1	0.22455	1	0.40966	1	0.87114	1	0.11887	1	0.16314	1	0.1364	1	0.70643	1
2p loss	6 (7%)	81	0.68454	1	0.38569	1	0.10355	1	0.28499	1	0.11389	1	0.73512	1	0.25793	1	0.49623	1
2q loss	4 (5%)	83	0.63677	1	0.34322	1	0.69658	1	0.65828	1	0.67145	1	0.89878	1	0.78251	1	0.95188	1
3p loss	8 (9%)	79	0.36877	1	0.089979	1	0.15136	1	0.29553	1	0.72207	1	0.13106	1	0.19436	1	0.20643	1
3q loss	6 (7%)	81	0.71912	1	0.092329	1	0.23386	1	0.55458	1	0.8776	1	0.21673	1	0.3143	1	0.84635	1
4p loss	32 (37%)	55	3e-05	0.0167	0.32478	1	0.21953	1	0.00456	1	0.17475	1	0.71612	1	0.20726	1	0.66354	1
4q loss	33 (38%)	54	5.9999e-05	0.0333	0.10007	1	0.00388	1	5e-04	0.273	0.11805	1	0.1237	1	0.65571	1	0.22664	1
5p loss	4 (5%)	83	0.49995	1	0.69111	1	0.03132	1	0.61645	1	0.47869	1	0.31191	1	NA	NA	NA	NA
5q loss	9 (10%)	78	0.02498	1	0.83843	1	0.27988	1	0.22769	1	0.72331	1	0.27272	1	0.35082	1	0.54148	1
6p loss	9 (10%)	78	0.83417	1	0.32319	1	0.27546	1	0.39952	1	0.88667	1	0.50209	1	0.61004	1	0.03648	1
6q loss	29 (33%)	58	0.00327	1	0.21449	1	0.33164	1	0.518	1	1	1	0.83496	1	0.10324	1	0.36344	1
8p loss	13 (15%)	74	0.87022	1	0.69006	1	0.97522	1	0.90032	1	0.40164	1	0.35496	1	0.39865	1	0.85985	1
8q loss	4 (5%)	83	0.10382	1	0.3744	1	0.44179	1	0.61724	1	0.3568	1	0.84429	1	0.60999	1	0.63509	1
9p loss	28 (32%)	59	9.9999e-06	0.0056	0.01411	1	0.055699	1	0.0068699	1	0.8216	1	0.32195	1	0.62944	1	0.35913	1
9q loss	21 (24%)	66	0.00194	1	0.20663	1	0.17266	1	0.15215	1	1	1	0.2816	1	0.30178	1	0.13798	1
10p loss	24 (28%)	63	0.00428	1	0.00062999	0.343	0.12215	1	0.14068	1	0.81876	1	0.65847	1	0.65272	1	0.8896	1
10q loss	19 (22%)	68	0.02375	1	0.01629	1	0.5129	1	0.37775	1	0.19546	1	0.86632	1	0.64385	1	0.80487	1
11p loss	4 (5%)	83	0.68257	1	0.83079	1	0.36389	1	0.15119	1	0.61752	1	0.56468	1	1	1	0.95297	1
11q loss	5 (6%)	82	0.57863	1	0.61528	1	0.0072199	1	0.00304	1	0.44687	1	0.18256	1	1	1	0.33896	1
12p loss	4 (5%)	83	0.26136	1	0.070629	1	0.4416	1	0.24793	1	0.36022	1	0.24459	1	0.4642	1	0.90807	1
13q loss	33 (38%)	54	0.10334	1	0.73631	1	0.24593	1	0.44484	1	0.82993	1	1	1	0.0064599	1	0.30917	1
14q loss	35 (40%)	52	0.00035	0.192	0.35957	1	5e-05	0.0278	9.9999e-06	0.0056	0.00348	1	5e-04	0.273	0.00255	1	0.00028	0.155
15q loss	11 (13%)	76	0.11394	1	0.75936	1	0.32239	1	0.19822	1	0.25624	1	0.077469	1	0.78599	1	0.87562	1
16p loss	7 (8%)	80	0.0097199	1	0.19455	1	0.59783	1	0.12319	1	0.65075	1	0.59489	1	1	1	0.93949	1
16q loss	10 (11%)	77	0.04979	1	0.90539	1	0.25521	1	0.24899	1	0.66989	1	0.96595	1	0.59865	1	0.76849	1
17p loss	23 (26%)	64	0.34766	1	0.38285	1	0.76379	1	0.75948	1	0.0479	1	0.17134	1	0.23651	1	0.02956	1
17q loss	7 (8%)	80	0.55672	1	0.15492	1	0.67028	1	0.89607	1	0.31738	1	0.68785	1	0.3614	1	0.70573	1
18p loss	9 (10%)	78	0.13979	1	0.78244	1	0.92038	1	0.54617	1	0.3614	1	0.38691	1	0.43471	1	0.15547	1
18q loss	14 (16%)	73	0.40317	1	0.68577	1	0.76384	1	0.92802	1	0.051429	1	0.11107	1	0.47472	1	0.22175	1
19p loss	4 (5%)	83	0.68516	1	0.20198	1	0.61453	1	0.10703	1	1	1	0.47393	1	0.20396	1	0.27998	1
19q loss	7 (8%)	80	0.55904	1	0.04974	1	1	1	0.85253	1	1	1	0.5965	1	0.31472	1	0.93908	1
20p loss	14 (16%)	73	0.02594	1	0.11012	1	0.10827	1	0.64462	1	0.25108	1	0.086049	1	0.56296	1	0.062229	1
20q loss	3 (3%)	84	0.23898	1	0.3374	1	0.88957	1	0.41071	1	NA	NA	NA	NA	NA	NA	NA	NA
21q loss	11 (13%)	76	0.10952	1	0.01313	1	0.23949	1	0.075419	1	0.76	1	0.92905	1	0.099579	1	0.94923	1
22q loss	67 (77%)	20	0.0051099	1	5e-05	0.0278	0.03012	1	0.00368	1	1	1	0.80066	1	0.069159	1	0.096789	1
xq loss	28 (32%)	59	0.00195	1	0.00015	0.0831	0.01514	1	0.00304	1	0.3348	1	0.57566	1	0.01473	1	0.057499	1