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	37 (18%)	171	0.16271	1	0.63058	1	0.31771	1	0.2018	1	0.38979	1	0.02378	1	0.64233	1	0.096859	1
1q gain	118 (57%)	90	9.9999e-06	0.0064	0.00018	0.111	5e-05	0.0314	0.0064099	1	0.63209	1	0.03913	1	0.57241	1	0.00311	1
2p gain	29 (14%)	179	0.27518	1	0.53054	1	0.36766	1	0.16668	1	0.96663	1	0.72665	1	0.43386	1	0.74346	1
2q gain	26 (12%)	182	0.26395	1	0.66891	1	0.14366	1	0.083059	1	0.71148	1	0.85943	1	0.30342	1	0.50379	1
3p gain	22 (11%)	186	0.0258	1	0.71824	1	0.47579	1	0.63987	1	0.91723	1	0.45724	1	0.36089	1	0.91871	1
3q gain	24 (12%)	184	0.02025	1	0.68075	1	0.69061	1	0.45452	1	0.75189	1	0.34539	1	0.24224	1	0.53705	1
4p gain	18 (9%)	190	0.02821	1	0.18478	1	0.3251	1	0.23388	1	0.18838	1	0.69323	1	0.52269	1	0.93544	1
4q gain	6 (3%)	202	0.44307	1	0.38467	1	0.52529	1	0.43387	1	0.57879	1	0.68879	1	0.01232	1	0.89115	1
5p gain	78 (38%)	130	0.00036	0.218	0.01522	1	0.88418	1	0.61502	1	0.5584	1	0.91997	1	0.77894	1	0.33002	1
5q gain	56 (27%)	152	4e-05	0.0252	0.10798	1	0.91245	1	0.85454	1	0.86108	1	0.99483	1	0.9845	1	0.99913	1
6p gain	66 (32%)	142	2e-05	0.0127	0.00063999	0.385	0.00233	1	0.10478	1	0.34784	1	0.00076999	0.461	0.085279	1	0.01612	1
6q gain	40 (19%)	168	0.00402	1	0.054889	1	0.052259	1	0.24452	1	0.51827	1	0.03546	1	0.078049	1	0.32501	1
7p gain	63 (30%)	145	0.81078	1	0.35076	1	0.66267	1	0.34759	1	0.060029	1	0.4415	1	0.1033	1	0.32784	1
7q gain	65 (31%)	143	0.81207	1	0.01588	1	0.89764	1	0.81724	1	0.052999	1	0.22534	1	0.03308	1	0.75044	1
8p gain	41 (20%)	167	0.0054199	1	0.073549	1	0.2545	1	0.12216	1	0.14894	1	0.6033	1	0.087099	1	0.25536	1
8q gain	101 (49%)	107	9.9999e-06	0.0064	0.27067	1	0.0247	1	0.04645	1	0.17445	1	0.15376	1	0.48361	1	0.076139	1
9p gain	12 (6%)	196	0.28384	1	0.49085	1	0.04426	1	0.43157	1	0.80492	1	0.73267	1	0.554	1	0.69751	1
9q gain	13 (6%)	195	0.12563	1	0.86276	1	0.04359	1	0.26483	1	0.30831	1	0.74587	1	0.53212	1	0.93554	1
10p gain	33 (16%)	175	0.10877	1	0.00334	1	0.02361	1	0.00023	0.141	0.14455	1	0.38933	1	0.00103	0.611	0.04396	1
10q gain	20 (10%)	188	0.0092599	1	0.00263	1	0.00017	0.106	0.02206	1	0.055809	1	0.097219	1	0.01204	1	0.15757	1
11p gain	15 (7%)	193	0.94388	1	0.35271	1	0.28687	1	0.31654	1	0.26364	1	0.14445	1	0.00326	1	0.69024	1
11q gain	14 (7%)	194	1	1	1	1	0.74167	1	0.75112	1	0.38362	1	0.85604	1	0.19508	1	1	1
12p gain	26 (12%)	182	0.47889	1	0.072809	1	0.00417	1	3e-04	0.183	0.44245	1	0.16173	1	4e-04	0.242	0.12057	1
12q gain	30 (14%)	178	0.42781	1	0.40167	1	0.0085899	1	0.00171	1	0.53741	1	0.20467	1	0.00368	1	0.31914	1
13q gain	14 (7%)	194	0.10007	1	0.20598	1	0.03303	1	0.62805	1	0.49329	1	0.01475	1	0.04089	1	0.53331	1
14q gain	12 (6%)	196	0.26128	1	0.64912	1	0.29693	1	0.17775	1	0.93142	1	0.62103	1	0.74172	1	0.61821	1
15q gain	18 (9%)	190	1	1	0.41466	1	0.9067	1	0.62079	1	0.20883	1	0.42356	1	0.81669	1	0.59735	1
16p gain	19 (9%)	189	0.31559	1	0.75393	1	0.69205	1	0.54305	1	1	1	0.48769	1	0.33053	1	0.076439	1
16q gain	10 (5%)	198	0.84555	1	0.73056	1	0.065859	1	0.33498	1	0.2595	1	0.8619	1	0.055359	1	0.12103	1
17p gain	17 (8%)	191	0.90036	1	0.03415	1	0.43492	1	0.10593	1	1	1	0.41559	1	0.81961	1	0.65432	1
17q gain	52 (25%)	156	0.01254	1	0.060649	1	0.29683	1	0.03385	1	1	1	0.40083	1	0.45662	1	0.66999	1
18p gain	17 (8%)	191	0.19189	1	0.072369	1	0.00254	1	0.0012	0.708	0.17432	1	0.03435	1	0.01798	1	0.057769	1
18q gain	15 (7%)	193	0.48942	1	0.061959	1	0.00087999	0.525	0.00087999	0.525	0.40161	1	0.067069	1	0.03134	1	0.11435	1
19p gain	39 (19%)	169	0.081059	1	0.00012	0.0746	3e-05	0.019	0.00047	0.283	0.01274	1	0.00275	1	0.00227	1	0.00195	1
19q gain	46 (22%)	162	0.03236	1	0.00033	0.2	0.00022	0.136	0.00105	0.622	0.03766	1	0.0094699	1	0.00313	1	0.00072999	0.438
20p gain	63 (30%)	145	7.9999e-05	0.05	0.03639	1	0.00435	1	0.01721	1	0.43812	1	0.04949	1	0.00183	1	0.092449	1
20q gain	65 (31%)	143	5e-05	0.0314	0.02157	1	0.0066199	1	0.01348	1	0.38409	1	0.064719	1	0.0074199	1	0.083029	1
21q gain	17 (8%)	191	0.143	1	0.72377	1	0.59228	1	0.32165	1	0.94842	1	0.33022	1	0.24726	1	0.52387	1
22q gain	28 (13%)	180	0.055509	1	0.02551	1	0.00436	1	0.0065799	1	0.10341	1	0.35564	1	0.097909	1	0.40642	1
xq gain	36 (17%)	172	0.0036	1	0.02672	1	0.70279	1	0.37314	1	0.10309	1	0.28436	1	0.20703	1	0.1299	1
1p loss	46 (22%)	162	0.00102	0.606	3e-05	0.019	3e-05	0.019	0.095489	1	0.01626	1	0.0352	1	0.04935	1	0.02749	1
1q loss	14 (7%)	194	0.53364	1	0.29896	1	0.21054	1	0.38368	1	0.35893	1	0.32473	1	0.33543	1	0.84144	1
2p loss	20 (10%)	188	0.062019	1	0.91228	1	0.2936	1	0.55893	1	0.10086	1	0.38012	1	0.20143	1	0.74552	1
2q loss	22 (11%)	186	0.01818	1	0.77261	1	0.30422	1	0.50831	1	0.0266	1	0.70037	1	0.70555	1	0.72326	1
3p loss	30 (14%)	178	0.21359	1	0.16102	1	0.01918	1	0.0064099	1	0.26387	1	0.19348	1	0.02607	1	0.00323	1
3q loss	19 (9%)	189	1	1	0.90143	1	0.28552	1	0.19618	1	0.13913	1	0.41942	1	0.070609	1	0.14301	1
4p loss	55 (26%)	153	0.00027	0.166	0.068099	1	0.00419	1	0.15415	1	0.72861	1	0.01337	1	0.11052	1	0.099309	1
4q loss	77 (37%)	131	9.9999e-06	0.0064	0.00328	1	0.00039	0.236	0.43408	1	0.9308	1	0.04747	1	0.1165	1	0.085349	1
5p loss	15 (7%)	193	0.55441	1	0.93962	1	0.47252	1	0.88471	1	0.66066	1	0.4708	1	0.0195	1	0.66266	1
5q loss	23 (11%)	185	0.21451	1	0.54136	1	0.25446	1	0.11784	1	0.42262	1	0.12583	1	0.20259	1	0.4453	1
6p loss	21 (10%)	187	0.91711	1	0.83833	1	0.2155	1	1	1	0.03014	1	0.89767	1	0.41644	1	0.28215	1
6q loss	56 (27%)	152	0.79704	1	0.61602	1	0.56463	1	0.78508	1	0.16981	1	0.22822	1	0.91012	1	0.32557	1
7p loss	12 (6%)	196	0.51873	1	0.32562	1	0.00395	1	0.63145	1	0.866	1	0.79925	1	0.75497	1	0.35529	1
7q loss	16 (8%)	192	0.7169	1	0.20602	1	0.01002	1	0.51555	1	0.63581	1	0.32555	1	0.79907	1	0.21051	1
8p loss	101 (49%)	107	0.0085199	1	0.04627	1	0.19293	1	0.88345	1	0.22857	1	0.43135	1	0.055449	1	0.13201	1
8q loss	24 (12%)	184	0.00017	0.106	0.83772	1	0.094619	1	0.12745	1	0.96147	1	0.90175	1	0.41563	1	0.19721	1
9p loss	66 (32%)	142	0.00266	1	0.15443	1	0.62432	1	0.80379	1	0.57925	1	0.54078	1	0.8875	1	0.63226	1
9q loss	64 (31%)	144	0.03427	1	0.04276	1	0.38521	1	0.31657	1	0.7742	1	0.3139	1	0.81451	1	0.51339	1
10p loss	29 (14%)	179	0.79223	1	0.45694	1	0.092609	1	0.34213	1	0.1646	1	0.02878	1	0.38621	1	0.081809	1
10q loss	49 (24%)	159	0.62036	1	0.79034	1	4e-05	0.0252	0.24196	1	0.22184	1	0.00116	0.686	0.40239	1	0.01324	1
11p loss	40 (19%)	168	0.21729	1	0.46116	1	0.23208	1	0.16877	1	0.54199	1	0.19447	1	0.24284	1	0.16615	1
11q loss	43 (21%)	165	0.20882	1	0.1507	1	0.46292	1	0.30861	1	0.33501	1	0.38692	1	0.37012	1	0.44416	1
12p loss	40 (19%)	168	0.04316	1	0.072929	1	0.095519	1	0.62473	1	0.22638	1	0.21858	1	0.24187	1	0.17551	1
12q loss	22 (11%)	186	0.18672	1	0.53245	1	0.60071	1	0.76489	1	0.48612	1	0.88018	1	0.42395	1	0.87017	1
13q loss	73 (35%)	135	2e-04	0.123	0.28321	1	0.24832	1	0.02168	1	0.59073	1	0.13782	1	0.23127	1	0.14273	1
14q loss	64 (31%)	144	0.0012	0.708	0.36726	1	0.02617	1	0.00354	1	0.27634	1	0.23246	1	0.10043	1	0.14165	1
15q loss	45 (22%)	163	0.01755	1	0.13971	1	0.053689	1	0.03336	1	0.82413	1	0.01994	1	0.00363	1	0.082479	1
16p loss	63 (30%)	145	0.0049	1	0.074029	1	2e-05	0.0127	0.00027	0.166	0.43757	1	0.00027	0.166	0.00063999	0.385	0.00017	0.106
16q loss	78 (38%)	130	2e-05	0.0127	5.9999e-05	0.0376	2e-05	0.0127	3e-04	0.183	0.20484	1	0.0079199	1	0.0094899	1	0.00011	0.0685
17p loss	110 (53%)	98	0.00031	0.188	0.086579	1	0.23989	1	0.23052	1	0.04149	1	0.003	1	0.01678	1	0.0053099	1
17q loss	32 (15%)	176	0.10397	1	0.60167	1	0.40864	1	0.84687	1	0.67989	1	0.8347	1	0.54938	1	0.5411	1
18p loss	43 (21%)	165	0.02941	1	0.00295	1	0.69959	1	0.32962	1	0.72419	1	0.35122	1	0.49294	1	0.1939	1
18q loss	46 (22%)	162	0.00077999	0.466	0.00378	1	0.73315	1	0.27239	1	0.42294	1	0.17729	1	0.073539	1	0.03729	1
19p loss	29 (14%)	179	0.00027	0.166	0.02822	1	0.17284	1	0.52515	1	0.30822	1	0.0076899	1	0.9891	1	0.097199	1
19q loss	23 (11%)	185	9.9999e-05	0.0624	0.39696	1	0.30421	1	0.12177	1	0.81131	1	0.00088999	0.53	0.3705	1	0.16173	1
20p loss	13 (6%)	195	0.41211	1	0.57007	1	0.6498	1	0.051899	1	0.57889	1	0.73173	1	0.18098	1	0.16674	1
20q loss	9 (4%)	199	0.69164	1	0.62072	1	0.56527	1	0.065889	1	0.57604	1	0.94892	1	0.28381	1	0.3818	1
21q loss	59 (28%)	149	0.02073	1	0.88146	1	0.01805	1	0.33353	1	0.3301	1	0.00142	0.835	0.02168	1	0.081489	1
22q loss	51 (25%)	157	0.6899	1	0.64003	1	0.53326	1	0.34203	1	0.39873	1	0.21771	1	0.51386	1	0.10678	1
xq loss	36 (17%)	172	0.00169	0.992	0.050889	1	0.8398	1	0.81005	1	0.67324	1	0.93403	1	0.42374	1	0.92887	1