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	12 (7%)	153	0.0083699	0.167	0.60935	0.889	0.40909	0.801	0.23171	0.664	0.25138	0.683	0.26377	0.687	0.39124	0.782	0.59418	0.883	1	1	0.46101	0.829	0.57633	0.881	0.58649	0.881
1q gain	33 (20%)	132	0.17796	0.658	0.27174	0.687	0.01197	0.195	0.28392	0.693	0.23002	0.664	0.17946	0.658	0.077429	0.494	0.95346	1	0.91872	1	0.8414	1	1	1	0.34982	0.757
2p gain	40 (24%)	125	0.75758	0.961	0.0073599	0.157	0.00021	0.0134	0.094639	0.52	0.54746	0.877	0.67567	0.928	0.02268	0.276	0.0132	0.204	0.17802	0.658	0.051489	0.395	0.66709	0.925	0.61239	0.891
2q gain	41 (25%)	124	0.36507	0.768	0.03203	0.344	0.00162	0.0555	0.0287	0.32	0.79268	0.977	0.58236	0.881	0.04238	0.373	0.00197	0.0591	0.2689	0.687	0.2347	0.669	0.13376	0.62	0.19202	0.658
3p gain	27 (16%)	138	0.457	0.829	0.88973	1	0.24468	0.678	0.23319	0.666	0.23847	0.671	0.44845	0.823	0.17684	0.658	0.92915	1	0.29925	0.7	0.35901	0.768	0.65493	0.915	0.71027	0.943
3q gain	33 (20%)	132	0.7302	0.949	0.55034	0.877	0.02158	0.269	0.27599	0.687	0.3918	0.782	0.17884	0.658	0.12443	0.6	0.73173	0.949	0.30722	0.709	0.25323	0.683	0.62693	0.9	0.95961	1
4p gain	9 (5%)	156	0.423	0.814	0.94117	1	0.69713	0.932	0.91838	1	0.069429	0.46	0.03228	0.344	0.5128	0.855	0.62984	0.9	0.18382	0.658	0.37361	0.77	0.72562	0.947	0.91265	1
4q gain	5 (3%)	160	0.27711	0.687	0.78322	0.971	0.68577	0.931	NA	NA	0.04532	0.384	0.16078	0.648	0.62056	0.897	1	1	0.84481	1	1	1	NA	NA	NA	NA
5p gain	35 (21%)	130	0.8044	0.978	0.11903	0.592	0.01952	0.251	0.084129	0.5	0.51829	0.855	0.72564	0.947	0.11044	0.564	0.00042	0.0202	0.47939	0.842	1	1	0.75721	0.961	0.60164	0.884
5q gain	24 (15%)	141	0.2687	0.687	0.036	0.36	0.21126	0.658	0.34752	0.757	0.42901	0.816	0.60357	0.886	0.4796	0.842	0.090279	0.512	1	1	0.52299	0.855	1	1	0.48088	0.842
6p gain	40 (24%)	125	0.15332	0.64	0.59436	0.883	0.00011	0.00812	0.35102	0.757	0.51793	0.855	0.32873	0.737	0.90102	1	0.50134	0.855	0.16011	0.648	0.49389	0.855	0.46116	0.829	0.96156	1
6q gain	35 (21%)	130	0.44747	0.823	0.19293	0.658	3e-05	0.00262	0.2605	0.687	0.63062	0.9	0.45285	0.826	0.50085	0.855	0.52961	0.86	0.052939	0.397	0.422	0.813	0.2065	0.658	0.55769	0.877
7p gain	102 (62%)	63	0.03619	0.36	0.0050399	0.131	9.9999e-06	0.00107	0.13716	0.62	0.84125	1	0.01755	0.241	0.00078999	0.033	9.9999e-06	0.00107	0.03867	0.364	0.096969	0.523	0.59653	0.884	0.3709	0.768
7q gain	87 (53%)	78	0.078709	0.494	0.01136	0.189	2e-05	0.00192	0.20991	0.658	0.95383	1	0.02337	0.28	0.0050299	0.131	0.00101	0.0388	0.24776	0.68	0.48572	0.846	1	1	0.55321	0.877
8p gain	40 (24%)	125	0.44772	0.823	0.25206	0.683	0.0068999	0.155	0.03792	0.364	0.20657	0.658	0.0062499	0.15	0.57912	0.881	0.29884	0.7	0.96557	1	0.082319	0.497	0.82679	0.997	0.052899	0.397
8q gain	90 (55%)	75	0.088429	0.511	0.19535	0.658	9.9999e-06	0.00107	0.0213	0.269	0.55591	0.877	0.20966	0.658	0.37208	0.768	0.2052	0.658	0.57296	0.88	0.080619	0.496	0.0114	0.189	0.49939	0.855
9p gain	43 (26%)	122	0.18934	0.658	0.38689	0.78	0.04782	0.39	0.03258	0.344	0.44059	0.821	0.191	0.658	0.056519	0.414	0.29701	0.7	0.1907	0.658	0.21737	0.658	0.95891	1	0.74507	0.96
9q gain	35 (21%)	130	0.46863	0.832	0.52641	0.858	0.20956	0.658	0.091799	0.512	0.1897	0.658	0.098839	0.528	0.33502	0.744	0.30246	0.703	0.59922	0.884	0.58872	0.881	0.86426	1	0.84076	1
10p gain	12 (7%)	153	0.71561	0.946	0.15887	0.648	0.42756	0.816	0.27001	0.687	0.36827	0.768	0.89437	1	0.14157	0.63	0.20349	0.658	0.83038	0.999	1	1	0.84245	1	0.69386	0.932
10q gain	7 (4%)	158	0.27601	0.687	0.16576	0.658	0.25493	0.686	0.79399	0.977	0.45246	0.826	0.71212	0.944	0.83197	1	0.50121	0.855	0.63888	0.906	0.86102	1	NA	NA	NA	NA
11p gain	32 (19%)	133	0.094799	0.52	0.43023	0.816	0.11163	0.567	0.41606	0.812	0.98885	1	0.75081	0.961	0.18683	0.658	0.14556	0.632	0.084959	0.5	0.20766	0.658	0.26347	0.687	0.71822	0.946
11q gain	27 (16%)	138	0.14234	0.63	0.43168	0.817	0.01889	0.251	0.12102	0.596	0.99125	1	0.26209	0.687	0.00495	0.131	0.0018	0.0576	0.16793	0.658	0.44261	0.821	0.17805	0.658	0.27419	0.687
12p gain	33 (20%)	132	0.20997	0.658	0.13594	0.62	0.18828	0.658	0.24595	0.678	0.161	0.648	0.69165	0.932	0.04375	0.378	0.20076	0.658	0.76526	0.961	0.54925	0.877	0.31249	0.715	0.67014	0.926
12q gain	21 (13%)	144	0.20535	0.658	0.26507	0.687	0.95955	1	0.6599	0.921	0.27442	0.687	0.54812	0.877	0.028	0.316	0.38662	0.78	0.34693	0.757	0.80224	0.978	0.1557	0.644	1	1
13q gain	114 (69%)	51	0.31429	0.715	0.2986	0.7	9.9999e-06	0.00107	0.058249	0.419	0.56236	0.877	0.10612	0.551	0.0060899	0.15	0.00029	0.0155	0.04196	0.373	0.03937	0.367	1	1	0.82752	0.997
14q gain	8 (5%)	157	0.60075	0.884	0.68681	0.931	0.096939	0.523	0.25305	0.683	0.72163	0.947	0.86149	1	0.4728	0.837	0.91186	1	0.63983	0.906	0.86089	1	NA	NA	NA	NA
15q gain	4 (2%)	161	NA	NA	NA	NA	0.29257	0.7	0.10242	0.54	0.50589	0.855	1	1	0.53881	0.871	0.59898	0.884	0.39245	0.782	0.76139	0.961	NA	NA	NA	NA
16p gain	41 (25%)	124	0.45347	0.826	0.77667	0.967	0.00023	0.0138	0.01611	0.227	0.88708	1	0.3468	0.757	0.12702	0.601	0.36767	0.768	0.35123	0.757	0.67797	0.928	0.63844	0.906	0.94391	1
16q gain	41 (25%)	124	0.18828	0.658	0.50929	0.855	9.9999e-06	0.00107	0.0064999	0.152	0.69785	0.932	0.04992	0.39	0.0093899	0.173	0.1049	0.548	0.0087899	0.169	0.24475	0.678	0.59007	0.881	0.76018	0.961
17p gain	10 (6%)	155	0.02517	0.298	0.081579	0.496	0.58613	0.881	0.18202	0.658	0.92547	1	0.46784	0.832	0.42696	0.816	0.42157	0.813	0.2748	0.687	0.33199	0.739	NA	NA	NA	NA
17q gain	31 (19%)	134	0.75437	0.961	0.69737	0.932	0.01945	0.251	0.2559	0.686	0.79836	0.978	0.27972	0.687	0.78308	0.971	0.22148	0.659	0.79976	0.978	0.27745	0.687	0.38943	0.781	0.37019	0.768
18p gain	8 (5%)	157	0.50338	0.855	0.73108	0.949	0.2606	0.687	0.0127	0.203	0.93618	1	0.90705	1	0.87763	1	0.38445	0.78	0.6319	0.9	0.55821	0.877	1	1	1	1
18q gain	6 (4%)	159	NA	NA	NA	NA	0.46407	0.829	0.03247	0.344	0.86315	1	0.58705	0.881	0.64804	0.914	0.22925	0.664	0.5545	0.877	0.62686	0.9	1	1	1	1
19p gain	33 (20%)	132	0.25997	0.687	0.45475	0.827	0.00212	0.0617	0.82787	0.997	0.98406	1	0.19588	0.658	0.85648	1	0.062199	0.433	0.88248	1	0.91845	1	0.51605	0.855	0.2775	0.687
19q gain	33 (20%)	132	0.57198	0.88	0.65274	0.915	0.01449	0.214	0.28918	0.699	0.88169	1	0.66387	0.924	0.80284	0.978	0.14888	0.633	0.52286	0.855	0.49613	0.855	0.51774	0.855	0.27896	0.687
20p gain	105 (64%)	60	0.3546	0.762	0.28515	0.693	0.054799	0.408	0.58783	0.881	0.00242	0.0683	0.44145	0.821	0.21642	0.658	0.8233	0.997	0.17466	0.658	0.14831	0.633	0.18676	0.658	0.5242	0.856
20q gain	146 (88%)	19	0.12598	0.6	0.16469	0.656	5e-05	0.004	0.079189	0.494	0.03743	0.364	0.24426	0.678	0.60872	0.889	0.00071999	0.0314	0.33183	0.739	0.39786	0.789	0.50087	0.855	0.69489	0.932
21q gain	10 (6%)	155	0.04797	0.39	0.99178	1	0.11629	0.581	0.5653	0.879	0.078489	0.494	0.30351	0.704	0.45099	0.826	0.92129	1	1	1	0.72631	0.947	NA	NA	NA	NA
22q gain	9 (5%)	156	0.22775	0.664	0.04907	0.39	0.067429	0.459	0.5457	0.877	0.090469	0.512	0.93576	1	0.36611	0.768	0.19726	0.658	0.87295	1	1	1	NA	NA	NA	NA
xp gain	31 (19%)	134	0.04097	0.373	0.13747	0.62	0.1328	0.62	0.52011	0.855	0.5141	0.855	0.94182	1	0.30042	0.7	0.57321	0.88	0.64312	0.908	0.76283	0.961	0.34424	0.757	0.40531	0.798
xq gain	32 (19%)	133	0.2928	0.7	0.50891	0.855	0.19751	0.658	0.5197	0.855	0.13438	0.62	0.6804	0.928	0.057219	0.416	0.64242	0.908	0.59584	0.884	0.80503	0.978	0.23656	0.671	0.30025	0.7
1p loss	46 (28%)	119	0.3839	0.78	0.069449	0.46	0.00134	0.0495	0.2129	0.658	0.39505	0.785	0.17288	0.658	0.2522	0.683	0.17	0.658	0.32854	0.737	0.61041	0.889	0.92552	1	0.44301	0.821
1q loss	28 (17%)	137	0.65077	0.915	0.19447	0.658	0.00041	0.0202	0.2224	0.659	0.76193	0.961	0.15117	0.634	0.03361	0.351	0.38226	0.779	0.38933	0.781	0.37162	0.768	0.91405	1	0.12193	0.597
2p loss	11 (7%)	154	0.18042	0.658	0.51574	0.855	0.12037	0.596	0.75749	0.961	0.59159	0.882	0.40162	0.795	0.47796	0.842	0.059339	0.422	0.42146	0.813	0.60491	0.887	NA	NA	NA	NA
2q loss	7 (4%)	158	0.36191	0.768	0.15682	0.646	0.20381	0.658	NA	NA	0.27838	0.687	0.52126	0.855	0.46813	0.832	0.050139	0.39	0.064529	0.442	0.26575	0.687	NA	NA	NA	NA
3p loss	15 (9%)	150	0.88947	1	0.79747	0.978	0.062709	0.433	0.1262	0.6	0.24251	0.678	0.21801	0.658	0.24544	0.678	0.55644	0.877	0.47828	0.842	0.13486	0.62	0.062669	0.433	0.11283	0.567
3q loss	10 (6%)	155	0.5037	0.855	0.85623	1	0.10501	0.548	0.15419	0.641	0.2314	0.664	0.51512	0.855	0.20982	0.658	0.22003	0.659	0.46487	0.829	0.01015	0.184	0.29333	0.7	0.61482	0.893
4p loss	60 (36%)	105	0.21773	0.658	0.50049	0.855	0.00027	0.0152	0.55883	0.877	0.42938	0.816	0.23124	0.664	0.68468	0.931	0.56022	0.877	0.67849	0.928	0.10027	0.532	0.259	0.687	0.37196	0.768
4q loss	67 (41%)	98	0.46331	0.829	0.36783	0.768	9.9999e-06	0.00107	0.1805	0.658	0.42494	0.814	0.04118	0.373	0.76427	0.961	0.43812	0.821	0.65458	0.915	0.21687	0.658	0.60883	0.889	0.85172	1
5p loss	27 (16%)	138	0.073809	0.482	0.92368	1	0.052019	0.396	0.58145	0.881	0.40553	0.798	0.82335	0.997	0.8704	1	0.2475	0.68	0.30051	0.7	0.6793	0.928	0.34725	0.757	0.0384	0.364
5q loss	40 (24%)	125	0.04269	0.373	0.02653	0.311	0.0017	0.0563	0.70428	0.938	0.73072	0.949	0.87801	1	0.91798	1	0.22123	0.659	0.84643	1	0.21007	0.658	0.27171	0.687	0.11244	0.567
6p loss	14 (8%)	151	0.38069	0.779	0.41753	0.813	0.3703	0.768	0.14871	0.633	0.38521	0.78	0.69396	0.932	0.62428	0.9	0.16746	0.658	0.85892	1	0.57777	0.881	NA	NA	NA	NA
6q loss	23 (14%)	142	0.050289	0.39	0.73728	0.954	0.01572	0.225	0.13731	0.62	0.20595	0.658	0.89769	1	0.077819	0.494	0.14481	0.632	0.1422	0.63	0.29809	0.7	0.01101	0.189	0.48301	0.845
7q loss	3 (2%)	162	NA	NA	NA	NA	0.11014	0.564	NA	NA	0.7179	0.946	0.43942	0.821	0.04555	0.384	0.75992	0.961	0.7725	0.967	1	1	NA	NA	NA	NA
8p loss	75 (45%)	90	0.095979	0.523	0.42443	0.814	0.00158	0.0555	0.47933	0.842	0.16999	0.658	0.27777	0.687	0.01737	0.241	0.18163	0.658	1	1	0.85225	1	0.66138	0.922	0.050329	0.39
8q loss	10 (6%)	155	1	1	0.44604	0.823	0.4155	0.812	0.1607	0.648	0.76081	0.961	0.14509	0.632	0.58528	0.881	0.33895	0.751	0.90324	1	0.42112	0.813	0.091339	0.512	0.36692	0.768
9p loss	23 (14%)	142	0.03428	0.354	0.93298	1	0.49537	0.855	0.31623	0.717	0.70706	0.94	0.81047	0.984	0.4582	0.829	0.5134	0.855	0.90523	1	0.0474	0.39	0.91012	1	0.14948	0.633
9q loss	23 (14%)	142	0.0134	0.204	0.80456	0.978	0.28617	0.694	0.22296	0.659	0.75519	0.961	0.94829	1	0.53381	0.866	0.19729	0.658	0.66748	0.925	0.00191	0.0591	0.76002	0.961	0.068029	0.46
10p loss	34 (21%)	131	0.14915	0.633	0.068719	0.46	0.03816	0.364	0.0499	0.39	0.090639	0.512	0.04425	0.379	0.30611	0.708	0.57371	0.88	0.78871	0.976	0.13723	0.62	0.84525	1	0.88296	1
10q loss	38 (23%)	127	0.01333	0.204	0.12556	0.6	0.01959	0.251	0.087019	0.506	0.092399	0.513	0.01557	0.225	0.40626	0.798	0.073109	0.481	0.93002	1	0.086819	0.506	0.88974	1	0.73707	0.954
11p loss	24 (15%)	141	0.02746	0.314	0.48524	0.846	0.00065999	0.0302	0.19587	0.658	0.58855	0.881	0.56762	0.879	0.01059	0.185	0.20358	0.658	0.91261	1	0.71278	0.944	0.21778	0.658	0.2286	0.664
11q loss	30 (18%)	135	0.0078699	0.162	0.31383	0.715	0.00090999	0.0364	0.27485	0.687	0.94438	1	0.43619	0.821	0.0071699	0.156	0.0079499	0.162	0.22239	0.659	0.37667	0.774	0.27661	0.687	0.21965	0.659
12p loss	23 (14%)	142	0.55373	0.877	0.62601	0.9	0.17951	0.658	0.27988	0.687	0.91837	1	0.56706	0.879	0.69461	0.932	0.34041	0.751	0.48628	0.846	0.77636	0.967	0.1448	0.632	0.61666	0.893
12q loss	24 (15%)	141	0.58472	0.881	0.6309	0.9	0.0403	0.372	0.37984	0.779	0.33997	0.751	0.83677	1	0.78626	0.974	0.27987	0.687	0.26884	0.687	0.26933	0.687	0.77411	0.967	1	1
13q loss	6 (4%)	159	NA	NA	NA	NA	0.04189	0.373	0.22843	0.664	0.28465	0.693	0.75361	0.961	1	1	0.34823	0.757	0.73999	0.956	0.86127	1	NA	NA	NA	NA
14q loss	67 (41%)	98	0.4872	0.846	0.18681	0.658	9.9999e-06	0.00107	0.12261	0.597	0.95663	1	0.89743	1	0.36406	0.768	0.076999	0.494	0.31389	0.715	0.19948	0.658	0.60146	0.884	0.95191	1
15q loss	72 (44%)	93	0.04662	0.389	0.15038	0.633	0.00014	0.0096	0.86354	1	0.098919	0.528	0.62855	0.9	0.4484	0.823	0.40368	0.797	0.79187	0.977	0.56289	0.877	0.84506	1	0.75515	0.961
16p loss	9 (5%)	156	0.21508	0.658	0.89317	1	0.22905	0.664	0.28382	0.693	0.35645	0.764	0.51748	0.855	0.17548	0.658	0.91165	1	0.56143	0.877	1	1	0.65263	0.915	0.53532	0.867
16q loss	14 (8%)	151	0.091269	0.512	0.85194	1	0.0054599	0.138	0.93683	1	0.38946	0.781	0.66848	0.925	0.25055	0.683	0.95514	1	0.24557	0.678	0.85789	1	0.72597	0.947	0.56932	0.88
17p loss	105 (64%)	60	0.56164	0.877	0.13745	0.62	0.0085599	0.168	0.44008	0.821	0.57313	0.88	0.59022	0.881	0.43534	0.821	0.56586	0.879	0.97234	1	0.26841	0.687	0.51878	0.855	0.86635	1
17q loss	28 (17%)	137	0.67377	0.927	0.66511	0.924	0.055879	0.413	0.46193	0.829	0.67193	0.926	0.23762	0.671	0.35184	0.757	0.36197	0.768	0.52885	0.86	0.54657	0.877	0.3298	0.738	1	1
18p loss	128 (78%)	37	0.14981	0.633	0.67216	0.926	9.9999e-06	0.00107	0.03571	0.36	0.55149	0.877	0.31646	0.717	0.080949	0.496	0.01413	0.212	0.084479	0.5	0.16388	0.656	0.79957	0.978	0.8332	1
18q loss	138 (84%)	27	0.03635	0.36	0.20041	0.658	9.9999e-06	0.00107	0.081429	0.496	0.78015	0.97	0.13847	0.621	0.03209	0.344	0.01943	0.251	0.22546	0.664	0.02737	0.314	0.55789	0.877	0.82423	0.997
19p loss	24 (15%)	141	0.51031	0.855	0.83537	1	0.058479	0.419	0.95677	1	0.71831	0.946	0.85368	1	0.32536	0.733	0.29577	0.7	0.29344	0.7	0.02232	0.275	0.56215	0.877	0.68859	0.932
19q loss	22 (13%)	143	0.21353	0.658	0.57717	0.881	0.30901	0.711	0.89309	1	0.63958	0.906	0.67967	0.928	0.35183	0.757	0.51444	0.855	0.061689	0.433	0.0092299	0.173	0.76256	0.961	0.76569	0.961
20p loss	24 (15%)	141	0.61611	0.893	0.70197	0.936	0.0069599	0.155	0.49477	0.855	0.16135	0.648	0.8886	1	0.19129	0.658	0.68532	0.931	0.77442	0.967	0.18309	0.658	0.72294	0.947	0.17945	0.658
21q loss	68 (41%)	97	0.17447	0.658	0.36698	0.768	0.42008	0.813	0.96374	1	0.3817	0.779	0.74396	0.96	0.93115	1	0.69132	0.932	0.58878	0.881	0.18239	0.658	0.20815	0.658	0.079279	0.494
22q loss	58 (35%)	107	0.43941	0.821	0.23751	0.671	0.10963	0.564	0.87243	1	0.64967	0.914	0.29737	0.7	0.46289	0.829	0.16751	0.658	0.32181	0.727	0.18105	0.658	0.12422	0.6	0.01039	0.185
xp loss	28 (17%)	137	0.91619	1	0.75016	0.961	0.084529	0.5	0.21646	0.658	0.43625	0.821	0.2973	0.7	0.79107	0.977	0.69344	0.932	0.80395	0.978	0.45887	0.829	0.94178	1	0.77379	0.967
xq loss	26 (16%)	139	0.98267	1	0.52309	0.855	0.19136	0.658	0.214	0.658	0.88376	1	0.62996	0.9	0.72256	0.947	0.88391	1	0.86979	1	0.31011	0.712	0.86279	1	0.85932	1