		Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		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	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	13 (3%)	499	NA	NA	NA	NA	0.00017	0.116	0.00012	0.0832	0.02456	1	1	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.0079999	1	9.9999e-06	0.0084	9.9999e-05	0.0698	9.9999e-06	0.0084
1q gain	23 (4%)	489	NA	NA	NA	NA	0.00073999	0.48	0.00031	0.209	0.43297	1	0.60496	1	3e-05	0.0216	0.00046	0.306	0.35621	1	0.00339	1	0.00145	0.911	0.0051299	1
2p gain	14 (3%)	498	NA	NA	NA	NA	0.060249	1	0.02841	1	0.31065	1	0.34481	1	0.01316	1	0.00084999	0.546	0.42576	1	0.13568	1	0.10998	1	0.17009	1
2q gain	13 (3%)	499	NA	NA	NA	NA	0.13799	1	0.02302	1	0.31102	1	0.34615	1	0.03497	1	0.00056999	0.376	0.37507	1	0.03427	1	0.091189	1	0.10544	1
3p gain	11 (2%)	501	NA	NA	NA	NA	0.35407	1	0.18063	1	0.46369	1	0.20173	1	0.10754	1	0.11045	1	0.15111	1	0.096269	1	0.19999	1	0.18427	1
3q gain	8 (2%)	504	NA	NA	NA	NA	0.21555	1	0.067999	1	0.055239	1	0.36701	1	0.062819	1	0.0037	1	0.34562	1	0.083629	1	0.12861	1	0.14229	1
4p gain	13 (3%)	499	NA	NA	NA	NA	0.01152	1	0.0195	1	0.0332	1	0.89511	1	0.0082499	1	0.0016	0.998	0.195	1	0.27239	1	0.087599	1	0.068069	1
4q gain	6 (1%)	506	NA	NA	NA	NA	0.0367	1	0.04325	1	0.11314	1	0.6686	1	0.0157	1	0.00357	1	0.26269	1	0.2161	1	0.04999	1	0.15764	1
5p gain	11 (2%)	501	NA	NA	NA	NA	0.01184	1	0.00212	1	0.02178	1	0.6067	1	7.9999e-05	0.0562	9.9999e-05	0.0698	0.02362	1	0.03076	1	0.00017	0.116	0.0081999	1
5q gain	8 (2%)	504	NA	NA	NA	NA	0.00318	1	0.00015	0.103	NA	NA	NA	NA	0.00016	0.11	0.00016	0.11	0.01298	1	0.00071999	0.469	0.00016	0.11	0.00079999	0.516
6p gain	7 (1%)	505	NA	NA	NA	NA	0.00072999	0.474	0.04663	1	0.03754	1	0.51717	1	0.44126	1	0.097689	1	0.02645	1	0.04218	1	0.01998	1	0.02438	1
7p gain	120 (23%)	392	0.74314	1	0.78138	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00037	0.248	0.01143	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00385	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
7q gain	150 (29%)	362	0.76605	1	0.51964	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00412	1	0.19959	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.01068	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
8p gain	45 (9%)	467	NA	NA	NA	NA	9.9999e-06	0.0084	0.00288	1	0.063359	1	0.16069	1	0.01889	1	0.0053499	1	0.56502	1	0.25547	1	0.058079	1	0.03675	1
8q gain	55 (11%)	457	0.052679	1	0.40773	1	9.9999e-06	0.0084	0.00016	0.11	0.01118	1	0.058079	1	0.00125	0.792	0.00044	0.293	0.21539	1	0.0264	1	0.0028	1	0.00219	1
9p gain	17 (3%)	495	NA	NA	NA	NA	0.01129	1	0.14321	1	0.29689	1	0.53099	1	0.066179	1	0.03618	1	0.8583	1	0.074729	1	0.28258	1	0.0492	1
9q gain	23 (4%)	489	NA	NA	NA	NA	0.01993	1	0.13243	1	0.25654	1	0.054579	1	0.03022	1	0.01296	1	0.55976	1	0.065559	1	0.03779	1	0.04748	1
10p gain	56 (11%)	456	1	1	0.04191	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.02094	1	0.55351	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.063949	1	0.092459	1	0.00395	1	0.00089999	0.574
10q gain	12 (2%)	500	NA	NA	NA	NA	5.9999e-05	0.0426	0.03895	1	0.26581	1	0.51666	1	0.085329	1	0.03699	1	0.12293	1	0.55409	1	0.077469	1	0.47279	1
11p gain	31 (6%)	481	NA	NA	NA	NA	0.079419	1	0.00055999	0.37	0.02596	1	0.1084	1	0.01005	1	0.0033	1	0.10129	1	0.02035	1	0.18407	1	0.00153	0.958
11q gain	58 (11%)	454	0.61409	1	0.58015	1	0.33495	1	0.01557	1	0.081369	1	0.03162	1	0.061379	1	0.03815	1	0.37045	1	0.0277	1	0.40359	1	0.00377	1
12p gain	32 (6%)	480	0.75416	1	0.58269	1	7.9999e-05	0.0562	0.04792	1	0.25975	1	0.31013	1	0.01947	1	0.056929	1	0.03578	1	0.01804	1	0.00413	1	0.02311	1
12q gain	16 (3%)	496	NA	NA	NA	NA	0.00061999	0.407	0.04586	1	0.29378	1	0.53268	1	0.0061099	1	0.086459	1	0.025	1	0.060739	1	0.00126	0.798	0.0235	1
13q gain	6 (1%)	506	NA	NA	NA	NA	0.37416	1	0.43552	1	0.79421	1	0.79357	1	0.23459	1	0.47408	1	0.43413	1	0.26547	1	0.87568	1	0.49157	1
14q gain	4 (1%)	508	NA	NA	NA	NA	1	1	0.89199	1	NA	NA	NA	NA	0.70979	1	0.59574	1	0.49674	1	0.62438	1	0.13969	1	0.32406	1
15q gain	11 (2%)	501	NA	NA	NA	NA	0.00206	1	0.02083	1	0.04498	1	0.21643	1	0.04951	1	0.01317	1	0.11042	1	0.14232	1	0.03286	1	0.108	1
16p gain	16 (3%)	496	NA	NA	NA	NA	0.51873	1	0.53498	1	0.56162	1	0.6976	1	0.15132	1	0.091919	1	0.1777	1	0.34103	1	0.40386	1	0.14017	1
16q gain	19 (4%)	493	NA	NA	NA	NA	0.0448	1	0.23315	1	0.47277	1	0.51604	1	0.15452	1	0.03383	1	0.057709	1	0.97682	1	0.24937	1	0.49076	1
17p gain	20 (4%)	492	NA	NA	NA	NA	0.29842	1	0.30157	1	0.3453	1	0.88583	1	0.18822	1	0.04646	1	0.15013	1	0.34829	1	0.085529	1	0.19332	1
17q gain	23 (4%)	489	NA	NA	NA	NA	0.60251	1	0.1817	1	0.34649	1	0.88528	1	0.34839	1	0.12095	1	0.074279	1	0.30905	1	0.31221	1	0.12703	1
18p gain	16 (3%)	496	NA	NA	NA	NA	6.9999e-05	0.0493	0.0080499	1	0.02248	1	0.44237	1	0.0264	1	0.0095599	1	0.64308	1	0.33442	1	0.31291	1	0.20452	1
18q gain	13 (3%)	499	NA	NA	NA	NA	0.00076999	0.498	0.01034	1	0.082009	1	0.59752	1	0.00149	0.934	3e-04	0.202	0.63388	1	0.059659	1	0.083569	1	0.01547	1
19p gain	101 (20%)	411	0.22041	1	1	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.67475	1	0.42366	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.01136	1	0.00164	1	9.9999e-06	0.0084	2e-05	0.0145
19q gain	25 (5%)	487	NA	NA	NA	NA	9.9999e-06	0.0084	9.9999e-06	0.0084	0.058689	1	0.39594	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00291	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
20p gain	43 (8%)	469	NA	NA	NA	NA	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00071999	0.469	0.17471	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.11177	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
20q gain	43 (8%)	469	NA	NA	NA	NA	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00062999	0.412	0.14531	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.04294	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
21q gain	24 (5%)	488	NA	NA	NA	NA	0.0105	1	0.00275	1	0.10846	1	0.39204	1	0.42476	1	0.21141	1	0.7229	1	0.10308	1	0.32887	1	0.20814	1
22q gain	23 (4%)	489	NA	NA	NA	NA	0.01315	1	9.9999e-06	0.0084	1	1	0.68649	1	0.0014	0.882	0.00031	0.209	0.30483	1	0.04092	1	0.03375	1	0.00013	0.0898
xq gain	40 (8%)	472	NA	NA	NA	NA	9.9999e-06	0.0084	9.9999e-06	0.0084	0.23432	1	0.71619	1	5.9999e-05	0.0426	2e-05	0.0145	0.071149	1	0.0224	1	0.0225	1	0.0064299	1
1p loss	183 (36%)	329	0.02834	1	0.00028	0.189	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00018	0.123	0.37314	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
1q loss	23 (4%)	489	0.3451	1	0.15196	1	0.73528	1	0.03665	1	0.67621	1	0.54413	1	0.39139	1	0.20117	1	0.16538	1	0.26001	1	0.29277	1	0.29638	1
2p loss	21 (4%)	491	NA	NA	NA	NA	4e-05	0.0286	0.056829	1	0.33135	1	1	1	0.16494	1	0.03073	1	0.15106	1	0.25914	1	0.37948	1	0.15136	1
2q loss	18 (4%)	494	NA	NA	NA	NA	0.00011	0.0763	0.0087099	1	0.068509	1	0.60629	1	0.42569	1	0.12542	1	0.02836	1	0.40019	1	0.43817	1	0.24157	1
3p loss	30 (6%)	482	NA	NA	NA	NA	0.00039	0.261	0.16428	1	0.0063399	1	0.2685	1	0.03931	1	0.02185	1	0.0084899	1	0.01478	1	0.01388	1	0.01234	1
3q loss	28 (5%)	484	0.17278	1	0.88192	1	0.00138	0.871	0.15097	1	0.25675	1	0.76784	1	0.073489	1	0.063129	1	0.15733	1	0.16992	1	0.1429	1	0.02069	1
4p loss	71 (14%)	441	1	1	0.78176	1	0.051039	1	9.9999e-06	0.0084	0.35243	1	1	1	5e-05	0.0356	9.9999e-06	0.0084	2e-05	0.0145	2e-05	0.0145	0.02053	1	9.9999e-06	0.0084
4q loss	91 (18%)	421	1	1	0.40303	1	0.01561	1	9.9999e-06	0.0084	0.25765	1	0.93168	1	0.00082999	0.534	3e-05	0.0216	9.9999e-06	0.0084	9.9999e-06	0.0084	0.065049	1	9.9999e-06	0.0084
5p loss	34 (7%)	478	0.74239	1	0.066899	1	9.9999e-06	0.0084	0.00047	0.312	0.91655	1	0.95314	1	0.17241	1	0.04394	1	0.070909	1	0.36598	1	0.36586	1	0.1316	1
5q loss	33 (6%)	479	0.44563	1	0.23576	1	9.9999e-06	0.0084	0.00018	0.123	0.01978	1	0.11649	1	0.02653	1	0.0065899	1	3e-05	0.0216	0.092869	1	0.061789	1	0.00159	0.994
6p loss	30 (6%)	482	NA	NA	NA	NA	0.00135	0.853	0.12271	1	0.18666	1	0.68774	1	0.37943	1	0.45963	1	0.67495	1	0.17749	1	0.67405	1	0.0075199	1
6q loss	63 (12%)	449	NA	NA	NA	NA	9.9999e-06	0.0084	0.00178	1	0.2532	1	0.56525	1	0.078709	1	0.01946	1	0.00499	1	0.01155	1	0.01628	1	0.0068099	1
7p loss	3 (1%)	509	NA	NA	NA	NA	0.60528	1	0.32556	1	NA	NA	NA	NA	1	1	0.89605	1	1	1	0.70867	1	1	1	0.63466	1
7q loss	3 (1%)	509	NA	NA	NA	NA	0.04766	1	0.3249	1	NA	NA	NA	NA	0.37286	1	0.17612	1	1	1	0.88935	1	0.59875	1	0.63384	1
8p loss	17 (3%)	495	0.61414	1	0.04368	1	9.9999e-06	0.0084	5e-05	0.0356	0.01846	1	0.15345	1	9.9999e-06	0.0084	2e-05	0.0145	0.078119	1	0.00087999	0.564	5.9999e-05	0.0426	0.00196	1
8q loss	11 (2%)	501	NA	NA	NA	NA	9.9999e-05	0.0698	3e-05	0.0216	0.080349	1	0.366	1	8.9999e-05	0.063	8.9999e-05	0.063	0.11898	1	0.00266	1	0.00059999	0.394	0.00289	1
9p loss	118 (23%)	394	0.38337	1	0.26617	1	9.9999e-06	0.0084	5.9999e-05	0.0426	0.03099	1	0.02035	1	0.092829	1	0.050149	1	0.85584	1	0.16807	1	0.38931	1	0.04953	1
9q loss	51 (10%)	461	NA	NA	NA	NA	0.053509	1	0.24079	1	0.6212	1	0.34076	1	0.47381	1	0.13887	1	0.36013	1	0.92429	1	0.87338	1	0.33756	1
10p loss	83 (16%)	429	0.27088	1	0.88309	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00087999	0.564	9.9999e-06	0.0084	9.9999e-06	0.0084	6.9999e-05	0.0493	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
10q loss	96 (19%)	416	0.2709	1	0.88163	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00051999	0.344	9.9999e-06	0.0084	9.9999e-06	0.0084	2e-05	0.0145	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
11p loss	63 (12%)	449	1	1	0.03116	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.01199	1	0.72635	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.00067999	0.443	0.00024	0.163	0.00095999	0.611	0.00025	0.169
11q loss	21 (4%)	491	NA	NA	NA	NA	0.00012	0.0832	9.9999e-05	0.0698	0.01771	1	0.65026	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.062659	1	0.00061999	0.407	0.0014	0.882	0.00015	0.103
12p loss	26 (5%)	486	NA	NA	NA	NA	0.0097399	1	0.011	1	0.60522	1	1	1	0.40126	1	0.32646	1	0.055519	1	0.46922	1	0.34925	1	0.38123	1
12q loss	51 (10%)	461	1	1	0.58209	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.68536	1	0.11195	1	0.0068599	1	0.00265	1	0.00369	1	0.30158	1	0.1584	1	0.16011	1
13q loss	115 (22%)	397	0.18144	1	4e-05	0.0286	9.9999e-06	0.0084	0.04179	1	0.02435	1	0.62731	1	0.01393	1	0.00394	1	0.10673	1	0.14941	1	0.02105	1	0.084899	1
14q loss	80 (16%)	432	0.4649	1	0.26768	1	0.00025	0.169	0.00057999	0.382	0.04557	1	0.11603	1	2e-05	0.0145	2e-05	0.0145	0.01056	1	0.00081999	0.528	0.00039	0.261	0.00046	0.306
15q loss	51 (10%)	461	1	1	0.70709	1	0.23978	1	0.00047	0.312	0.27223	1	0.04619	1	0.00122	0.775	0.00166	1	0.39479	1	0.3413	1	0.076159	1	0.04486	1
16p loss	14 (3%)	498	NA	NA	NA	NA	0.00337	1	0.12572	1	0.86586	1	0.20211	1	0.02839	1	0.11847	1	0.59221	1	0.75227	1	0.5285	1	0.77686	1
16q loss	22 (4%)	490	NA	NA	NA	NA	0.00359	1	0.0064399	1	0.37458	1	0.065719	1	0.01743	1	0.092379	1	0.64736	1	0.16927	1	0.54813	1	0.055149	1
17p loss	13 (3%)	499	NA	NA	NA	NA	0.01477	1	0.21386	1	1	1	0.7829	1	0.0137	1	0.063929	1	0.26911	1	0.0069399	1	0.071789	1	0.02438	1
17q loss	8 (2%)	504	NA	NA	NA	NA	0.11238	1	0.25788	1	0.83541	1	0.50904	1	0.27712	1	0.53186	1	0.15905	1	0.14828	1	0.17178	1	0.15201	1
18p loss	68 (13%)	444	0.32039	1	0.03091	1	0.55999	1	0.02601	1	0.58037	1	0.10594	1	0.13761	1	0.03111	1	0.48393	1	0.5575	1	0.21432	1	0.71058	1
18q loss	62 (12%)	450	0.34132	1	0.15211	1	0.17617	1	0.00035	0.235	0.28442	1	0.097339	1	0.03188	1	0.00347	1	0.050469	1	0.34635	1	0.12213	1	0.43642	1
19p loss	23 (4%)	489	0.84637	1	0.43142	1	0.53908	1	0.82197	1	0.10134	1	0.80977	1	0.73541	1	0.65014	1	0.43876	1	0.15548	1	0.53092	1	0.17218	1
19q loss	209 (41%)	303	0.18259	1	0.01341	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.03819	1	0.33026	1	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084	9.9999e-06	0.0084
20p loss	7 (1%)	505	NA	NA	NA	NA	0.22107	1	0.22737	1	0.79287	1	1	1	0.26651	1	0.3921	1	1	1	0.31998	1	0.31687	1	0.17819	1
20q loss	3 (1%)	509	NA	NA	NA	NA	0.24072	1	0.49134	1	NA	NA	NA	NA	0.02322	1	0.13805	1	0.21631	1	0.70491	1	0.56871	1	0.63368	1
21q loss	36 (7%)	476	0.61559	1	0.04242	1	9.9999e-06	0.0084	0.00047	0.312	0.46253	1	0.65398	1	0.00090999	0.58	0.00063999	0.418	0.37843	1	0.11442	1	0.01856	1	0.00465	1
22q loss	57 (11%)	455	0.81537	1	0.0065499	1	9.9999e-06	0.0084	9.9999e-06	0.0084	5.9999e-05	0.0426	0.03982	1	9.9999e-06	0.0084	9.9999e-06	0.0084	0.50135	1	0.00441	1	0.00288	1	0.00019	0.129
xq loss	69 (13%)	443	0.83896	1	0.26623	1	0.70518	1	0.00496	1	0.04364	1	0.01988	1	5e-05	0.0356	9.9999e-06	0.0084	0.00077999	0.504	0.00088999	0.569	0.00028	0.189	5.9999e-05	0.0426
