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	23 (18%)	103	0.16448	1	0.30663	1	0.30619	1	0.6148	1	0.37651	1	0.61991	1	0.11042	1	0.87865	1
1q gain	40 (32%)	86	0.092459	1	0.34117	1	0.04347	1	0.01711	1	0.066649	1	0.092149	1	0.0094199	1	0.14122	1
2p gain	48 (38%)	78	3e-04	0.185	0.19584	1	0.37809	1	0.76423	1	0.01691	1	0.48442	1	0.0075399	1	0.15801	1
2q gain	35 (28%)	91	0.0408	1	0.13595	1	0.43177	1	0.25307	1	0.10364	1	0.64927	1	0.36571	1	0.73992	1
3p gain	19 (15%)	107	0.1516	1	0.2221	1	0.42322	1	0.32675	1	1	1	0.48404	1	0.72946	1	1	1
3q gain	53 (42%)	73	5.9999e-05	0.038	0.00362	1	0.059399	1	0.02168	1	0.12496	1	0.090829	1	0.15994	1	0.03535	1
4p gain	13 (10%)	113	0.80712	1	0.93169	1	0.93202	1	0.82276	1	1	1	0.60728	1	1	1	0.65634	1
4q gain	11 (9%)	115	0.34295	1	0.45391	1	0.41977	1	0.23147	1	0.62525	1	0.70267	1	0.82176	1	0.69893	1
5p gain	53 (42%)	73	0.02754	1	0.3787	1	0.50499	1	0.67214	1	0.31454	1	0.25404	1	0.21581	1	0.3181	1
5q gain	16 (13%)	110	0.74711	1	0.9383	1	0.82896	1	0.95716	1	0.30789	1	0.85032	1	0.41268	1	0.49478	1
6p gain	24 (19%)	102	0.52506	1	0.79836	1	0.01406	1	0.30897	1	0.68566	1	0.12829	1	0.59133	1	0.52482	1
6q gain	20 (16%)	106	0.28751	1	0.69468	1	0.0070299	1	0.27812	1	0.75226	1	0.58941	1	0.69691	1	0.745	1
7p gain	72 (57%)	54	0.04109	1	0.21042	1	0.00112	0.672	0.061809	1	0.02661	1	0.24257	1	0.10558	1	0.03884	1
7q gain	58 (46%)	68	0.2586	1	0.086079	1	0.20205	1	0.68854	1	0.34504	1	0.92741	1	0.39994	1	0.57142	1
8p gain	46 (37%)	80	0.081829	1	0.57808	1	0.65572	1	0.44139	1	0.60859	1	0.47413	1	0.5933	1	0.01772	1
8q gain	67 (53%)	59	0.02684	1	0.75102	1	1	1	0.56592	1	0.70379	1	0.53293	1	0.79784	1	0.36182	1
9p gain	11 (9%)	115	0.66762	1	0.77426	1	0.085819	1	0.090709	1	0.89099	1	0.6642	1	1	1	1	1
9q gain	25 (20%)	101	0.63356	1	0.61547	1	0.36377	1	0.42419	1	0.78198	1	0.29276	1	0.90002	1	0.19385	1
10p gain	24 (19%)	102	0.52694	1	0.01878	1	0.51665	1	0.88069	1	0.089999	1	0.51014	1	0.02353	1	0.2563	1
10q gain	17 (13%)	109	0.24164	1	0.11186	1	0.77995	1	0.34172	1	0.23604	1	0.54778	1	0.10955	1	0.29546	1
11p gain	27 (21%)	99	0.79024	1	0.84611	1	0.03369	1	0.10217	1	0.38397	1	0.32713	1	0.43194	1	0.39871	1
11q gain	24 (19%)	102	0.24917	1	0.14979	1	0.057659	1	0.077329	1	0.01475	1	0.10463	1	0.04068	1	0.03285	1
12p gain	45 (36%)	81	0.00017	0.106	0.01049	1	0.02402	1	0.0065799	1	0.02274	1	0.0065399	1	0.02311	1	0.01015	1
12q gain	26 (21%)	100	0.01947	1	0.04789	1	0.53005	1	0.070089	1	0.36866	1	0.33151	1	0.3135	1	0.43671	1
13q gain	27 (21%)	99	0.00453	1	0.00085999	0.52	0.01065	1	0.01915	1	6.9999e-05	0.0442	0.00078999	0.482	0.00023	0.143	0.00016	0.1
14q gain	31 (25%)	95	0.11785	1	0.17696	1	0.24888	1	0.064979	1	0.061049	1	0.059279	1	0.062249	1	0.11118	1
15q gain	24 (19%)	102	0.62676	1	0.03909	1	0.47573	1	0.65717	1	0.073249	1	0.2129	1	0.14679	1	0.04154	1
16p gain	29 (23%)	97	0.00425	1	0.03676	1	0.0206	1	0.12811	1	0.01908	1	0.02192	1	0.01209	1	0.0064399	1
16q gain	24 (19%)	102	0.00068999	0.422	0.01114	1	0.00127	0.759	0.01339	1	0.0098299	1	0.00219	1	0.00322	1	0.00135	0.806
17p gain	23 (18%)	103	0.01384	1	0.03452	1	0.46727	1	0.43762	1	0.66773	1	0.86157	1	0.38545	1	0.70603	1
17q gain	30 (24%)	96	0.00369	1	0.26557	1	0.49296	1	0.62286	1	0.61758	1	0.99033	1	0.6355	1	0.60342	1
18p gain	34 (27%)	92	0.0074499	1	0.69706	1	0.42841	1	0.51686	1	0.36589	1	0.941	1	0.66074	1	0.90559	1
18q gain	16 (13%)	110	0.01107	1	0.12357	1	0.77949	1	0.62235	1	0.34383	1	0.43578	1	0.48062	1	0.20126	1
19p gain	15 (12%)	111	0.47436	1	0.62458	1	0.92908	1	1	1	0.75269	1	0.91611	1	0.92541	1	0.9049	1
19q gain	20 (16%)	106	0.03523	1	0.21315	1	0.18091	1	0.14077	1	0.060509	1	0.16735	1	0.15943	1	0.059539	1
20p gain	64 (51%)	62	0.03434	1	0.15262	1	0.51602	1	0.28944	1	0.32063	1	0.72576	1	0.03923	1	0.1422	1
20q gain	69 (55%)	57	0.03139	1	0.01481	1	0.10422	1	0.078459	1	0.0077999	1	0.02529	1	0.00084999	0.516	0.00118	0.707
21q gain	11 (9%)	115	0.48192	1	0.29166	1	0.60131	1	0.5566	1	0.43526	1	0.45422	1	0.53025	1	0.23116	1
22q gain	23 (18%)	103	0.00026	0.161	7.9999e-05	0.0503	0.00080999	0.492	0.00047	0.29	0.00021	0.131	5.9999e-05	0.038	0.00015	0.0942	0.00034	0.21
xq gain	30 (24%)	96	0.059199	1	0.073709	1	0.43628	1	0.1982	1	0.03295	1	0.065969	1	0.04564	1	0.056879	1
1p loss	25 (20%)	101	0.087469	1	0.113	1	0.37136	1	0.3	1	0.31499	1	0.099629	1	0.12249	1	0.362	1
1q loss	17 (13%)	109	0.04147	1	0.11139	1	0.25832	1	0.26955	1	0.1025	1	0.25535	1	0.064929	1	0.13155	1
2p loss	6 (5%)	120	0.7603	1	0.14557	1	NA	NA	NA	NA	0.3315	1	0.17653	1	0.50115	1	0.79782	1
2q loss	14 (11%)	112	0.87665	1	0.2371	1	0.01616	1	0.04925	1	0.29387	1	0.15769	1	0.48248	1	0.31341	1
3p loss	67 (53%)	59	0.01017	1	0.0084099	1	0.52292	1	0.41251	1	0.00246	1	0.00228	1	0.00173	1	0.00148	0.882
3q loss	19 (15%)	107	0.1341	1	0.43406	1	0.11922	1	0.29192	1	0.58346	1	0.57278	1	0.33835	1	0.53852	1
4p loss	71 (56%)	55	0.0050799	1	0.25517	1	0.14055	1	0.39254	1	0.00229	1	0.26341	1	0.0082399	1	0.04778	1
4q loss	61 (48%)	65	0.04046	1	0.7347	1	0.091259	1	0.72816	1	0.33781	1	0.81853	1	0.26459	1	0.16443	1
5p loss	31 (25%)	95	0.094839	1	0.0055199	1	0.1376	1	0.12363	1	0.0077699	1	0.01129	1	0.00155	0.921	0.0127	1
5q loss	53 (42%)	73	0.36562	1	0.01599	1	0.4749	1	0.9165	1	0.054919	1	0.060159	1	0.04799	1	0.081399	1
6p loss	29 (23%)	97	0.03404	1	0.40051	1	0.17053	1	0.35912	1	0.25113	1	0.11646	1	0.43294	1	0.28616	1
6q loss	29 (23%)	97	0.26494	1	0.7013	1	0.24005	1	0.33271	1	0.3741	1	0.50253	1	0.72973	1	0.53969	1
7p loss	9 (7%)	117	0.61826	1	0.20571	1	0.32135	1	0.292	1	0.11583	1	0.070629	1	0.083149	1	0.066789	1
7q loss	12 (10%)	114	0.20869	1	0.19315	1	0.48033	1	0.59752	1	0.39965	1	0.5895	1	0.63422	1	0.49573	1
8p loss	40 (32%)	86	0.24281	1	0.23558	1	0.32179	1	0.17575	1	0.17444	1	0.65171	1	0.34857	1	0.52367	1
8q loss	13 (10%)	113	0.24149	1	0.59456	1	1	1	1	1	0.7405	1	0.30125	1	1	1	0.65734	1
9p loss	70 (56%)	56	0.48335	1	0.75029	1	0.3041	1	0.58837	1	0.059939	1	0.20782	1	0.29396	1	0.92229	1
9q loss	45 (36%)	81	0.081999	1	0.21521	1	0.82395	1	0.57113	1	0.27115	1	0.13276	1	0.20273	1	0.31826	1
10p loss	35 (28%)	91	0.03791	1	0.051269	1	0.56744	1	0.092739	1	0.15697	1	0.1432	1	0.03733	1	0.059039	1
10q loss	37 (29%)	89	0.01142	1	0.01091	1	0.37233	1	0.25438	1	0.04237	1	0.01549	1	0.0263	1	0.069069	1
11p loss	38 (30%)	88	0.24516	1	0.49294	1	0.18397	1	0.54142	1	1	1	0.36757	1	0.76822	1	0.86805	1
11q loss	43 (34%)	83	0.00172	1	0.38468	1	0.69751	1	0.22219	1	0.14828	1	0.25469	1	0.19768	1	0.15734	1
12p loss	19 (15%)	107	0.01735	1	0.00457	1	0.02324	1	0.01006	1	0.00272	1	0.01213	1	0.0096599	1	0.0022	1
12q loss	18 (14%)	108	0.32341	1	0.04155	1	0.02844	1	0.02251	1	0.02311	1	0.10073	1	0.061349	1	0.01321	1
13q loss	52 (41%)	74	0.02022	1	0.073609	1	0.12558	1	0.19629	1	0.01733	1	0.10991	1	0.075599	1	0.10782	1
14q loss	32 (25%)	94	0.0032	1	2e-04	0.125	0.072279	1	0.061909	1	0.00079999	0.487	5e-04	0.307	0.00023	0.143	0.00029	0.18
15q loss	33 (26%)	93	0.78688	1	0.34405	1	0.24382	1	0.46647	1	0.63889	1	0.33629	1	0.41872	1	0.055609	1
16p loss	32 (25%)	94	0.00156	0.925	0.00093999	0.566	0.17257	1	0.1916	1	0.00059999	0.368	0.00088999	0.538	0.00016	0.1	3e-05	0.0191
16q loss	34 (27%)	92	4e-05	0.0254	0.00093999	0.566	0.04006	1	0.25076	1	4e-05	0.0254	6.9999e-05	0.0442	2e-05	0.0127	9.9999e-06	0.00638
17p loss	47 (37%)	79	0.10147	1	0.00074999	0.458	0.073489	1	0.11117	1	0.00084999	0.516	0.00152	0.904	0.0086199	1	0.00088999	0.538
17q loss	17 (13%)	109	0.67256	1	0.62441	1	0.22132	1	0.13493	1	0.56533	1	0.87309	1	0.2509	1	0.91926	1
18p loss	44 (35%)	82	0.30093	1	0.01012	1	0.4026	1	0.43324	1	0.02693	1	0.061059	1	0.03352	1	0.02073	1
18q loss	66 (52%)	60	0.68983	1	0.22149	1	0.62845	1	0.78839	1	0.28636	1	0.16999	1	0.23262	1	0.16513	1
19p loss	43 (34%)	83	0.01392	1	0.095489	1	0.41313	1	0.69229	1	0.12003	1	0.090379	1	0.065739	1	0.03646	1
19q loss	35 (28%)	91	0.00059999	0.368	0.01641	1	0.63111	1	0.49918	1	0.060769	1	0.052449	1	0.062269	1	0.02134	1
20p loss	17 (13%)	109	0.32192	1	0.8876	1	0.82343	1	0.39002	1	0.92118	1	0.32196	1	1	1	0.26774	1
20q loss	7 (6%)	119	0.88796	1	0.77342	1	0.84088	1	0.85287	1	0.69231	1	0.3968	1	0.87414	1	0.17988	1
21q loss	73 (58%)	53	0.29994	1	0.01689	1	0.01427	1	0.02593	1	0.02019	1	0.04026	1	0.02063	1	0.02344	1
22q loss	45 (36%)	81	0.096599	1	0.00292	1	0.12935	1	0.41923	1	0.01172	1	0.1444	1	0.00476	1	0.0099999	1
xq loss	26 (21%)	100	0.02633	1	0.01028	1	0.1539	1	0.18223	1	0.082599	1	0.0114	1	0.083149	1	0.0168	1