		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	24 (5%)	503	0.82324	1	0.92455	1	9.9999e-06	0.00889	0.00059999	0.391	0.00048	0.317	0.0058999	1	0.0057099	1	0.00082999	0.527	0.00106	0.667	0.019	1	0.00382	1	0.10711	1
1q gain	51 (10%)	476	0.40801	1	0.89993	1	9.9999e-06	0.00889	0.01401	1	0.11969	1	0.088469	1	2e-05	0.0151	0.0087599	1	2e-05	0.0151	0.14644	1	0.00222	1	0.30426	1
2p gain	77 (15%)	450	0.70255	1	0.45968	1	9.9999e-06	0.00889	0.084469	1	0.0093299	1	0.32927	1	0.17743	1	0.03185	1	0.4018	1	0.02054	1	0.1309	1	0.36935	1
2q gain	79 (15%)	448	0.55991	1	0.26656	1	9.9999e-06	0.00889	0.17572	1	0.0094599	1	0.15051	1	0.15213	1	0.04211	1	0.54117	1	0.0058599	1	0.23396	1	0.25811	1
3p gain	19 (4%)	508	0.052139	1	0.4333	1	7.9999e-05	0.0562	0.54179	1	0.01714	1	0.00342	1	0.0084999	1	3e-05	0.022	6.9999e-05	0.0495	0.0059599	1	0.03614	1	0.0098699	1
3q gain	61 (12%)	466	0.0124	1	0.03045	1	9.9999e-06	0.00889	0.0037	1	0.0015	0.936	9.9999e-06	0.00889	3e-05	0.022	2e-05	0.0151	9.9999e-06	0.00889	3e-05	0.022	0.00061999	0.403	0.02094	1
4p gain	13 (2%)	514	NA	NA	NA	NA	0.35447	1	0.37504	1	0.31137	1	0.01789	1	0.00034	0.228	0.00101	0.636	9.9999e-05	0.0696	0.11634	1	0.36733	1	0.42028	1
4q gain	13 (2%)	514	NA	NA	NA	NA	0.35389	1	0.45841	1	0.31154	1	0.14668	1	0.00034	0.228	0.0095199	1	0.00018	0.123	0.23984	1	0.36323	1	0.42319	1
5p gain	193 (37%)	334	0.87933	1	0.92452	1	7.9999e-05	0.0562	0.2705	1	0.090539	1	0.83814	1	0.01313	1	0.070849	1	0.087549	1	0.73135	1	0.10725	1	0.79207	1
5q gain	207 (39%)	320	0.33578	1	0.62536	1	0.0086299	1	0.46207	1	0.39632	1	0.49459	1	0.071679	1	0.20983	1	0.53968	1	0.85391	1	0.22263	1	0.39383	1
6p gain	11 (2%)	516	NA	NA	NA	NA	0.074199	1	0.44508	1	0.04367	1	0.24431	1	0.79332	1	0.79836	1	0.86001	1	0.063799	1	0.7389	1	0.2798	1
6q gain	9 (2%)	518	NA	NA	NA	NA	0.15834	1	0.68312	1	0.0094999	1	0.34822	1	1	1	0.85103	1	1	1	0.15619	1	0.55382	1	0.53394	1
7p gain	171 (32%)	356	0.44993	1	0.85885	1	9.9999e-06	0.00889	0.00167	1	3e-05	0.022	0.01875	1	0.00013	0.0898	0.0088899	1	0.00324	1	0.25903	1	0.02337	1	0.55408	1
7q gain	172 (33%)	355	0.452	1	0.85991	1	9.9999e-06	0.00889	0.00479	1	3e-05	0.022	0.0071799	1	0.00011	0.0763	0.00418	1	0.00228	1	0.10059	1	0.067239	1	0.21313	1
8p gain	31 (6%)	496	NA	NA	NA	NA	9.9999e-06	0.00889	3e-04	0.202	0.01208	1	0.138	1	2e-05	0.0151	3e-05	0.022	9.9999e-06	0.00889	0.03393	1	0.00056999	0.373	0.0093799	1
8q gain	62 (12%)	465	0.22776	1	0.10366	1	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00012	0.0832	0.0099799	1	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	7.9999e-05	0.0562	9.9999e-06	0.00889	0.00039	0.26
9p gain	13 (2%)	514	NA	NA	NA	NA	0.30808	1	0.90315	1	0.82579	1	0.70962	1	0.25159	1	0.02243	1	0.93903	1	0.34998	1	0.37783	1	1	1
9q gain	12 (2%)	515	NA	NA	NA	NA	0.093129	1	0.91054	1	0.62603	1	0.4549	1	0.2416	1	0.03597	1	0.81585	1	0.25307	1	0.89777	1	0.61502	1
10p gain	17 (3%)	510	NA	NA	NA	NA	5e-05	0.0359	0.25436	1	0.35987	1	0.054979	1	0.00077999	0.497	0.00056999	0.373	0.059519	1	0.02629	1	0.5308	1	0.02257	1
10q gain	12 (2%)	515	NA	NA	NA	NA	0.00064999	0.421	0.11449	1	0.0484	1	0.13147	1	0.01192	1	0.0070599	1	0.065609	1	0.26903	1	0.57991	1	0.04079	1
11p gain	31 (6%)	496	0.2323	1	0.67155	1	6.9999e-05	0.0495	0.28647	1	0.11159	1	0.35513	1	0.28959	1	0.1305	1	0.21	1	0.34852	1	0.56808	1	0.04189	1
11q gain	29 (6%)	498	0.34141	1	0.90664	1	0.00018	0.123	0.5261	1	0.36425	1	0.88828	1	0.56594	1	0.35568	1	0.53931	1	0.55619	1	0.58193	1	0.28558	1
12p gain	121 (23%)	406	0.01336	1	0.0309	1	9.9999e-06	0.00889	3e-05	0.022	9.9999e-06	0.00889	5.9999e-05	0.0428	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00015	0.103	9.9999e-06	0.00889	0.00038	0.253
12q gain	122 (23%)	405	0.01336	1	0.03291	1	9.9999e-06	0.00889	5e-05	0.0359	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	4e-05	0.0289	9.9999e-06	0.00889	0.00027	0.183
13q gain	22 (4%)	505	NA	NA	NA	NA	0.39058	1	0.03895	1	0.72461	1	0.68602	1	0.073319	1	0.29614	1	0.34879	1	0.45237	1	0.64779	1	0.50554	1
14q gain	16 (3%)	511	0.76875	1	0.57314	1	0.04437	1	0.34768	1	0.02828	1	0.04562	1	0.0202	1	0.00058999	0.385	0.00229	1	0.0067899	1	0.76696	1	0.25828	1
15q gain	26 (5%)	501	1	1	0.11726	1	0.00499	1	0.72385	1	0.48871	1	0.6105	1	0.64502	1	0.15496	1	0.87062	1	0.18822	1	0.91805	1	1	1
16p gain	107 (20%)	420	0.27388	1	0.37948	1	0.00065999	0.426	0.16771	1	0.00194	1	0.17998	1	0.01428	1	0.00469	1	0.04673	1	0.03856	1	0.18351	1	0.083129	1
16q gain	99 (19%)	428	0.23371	1	0.34905	1	0.00052999	0.349	0.082259	1	0.00233	1	0.04194	1	0.01245	1	0.02053	1	0.01218	1	0.14737	1	0.068909	1	0.18918	1
17p gain	26 (5%)	501	0.01918	1	0.0052399	1	9.9999e-06	0.00889	0.77569	1	0.29493	1	0.081119	1	0.22907	1	0.050119	1	0.18371	1	0.42438	1	0.43212	1	0.03557	1
17q gain	33 (6%)	494	0.067809	1	0.02611	1	5.9999e-05	0.0428	0.2237	1	0.47623	1	0.074389	1	0.13858	1	0.02243	1	0.10767	1	0.23747	1	0.17409	1	0.01133	1
18p gain	25 (5%)	502	0.3138	1	0.075459	1	0.68418	1	0.47685	1	0.8488	1	0.02277	1	0.080609	1	0.58839	1	0.83241	1	0.6284	1	0.60125	1	0.065539	1
18q gain	25 (5%)	502	0.31296	1	0.074889	1	0.55406	1	0.55778	1	0.70253	1	0.087739	1	0.079639	1	0.58686	1	0.93113	1	0.62928	1	0.60297	1	0.065389	1
19p gain	51 (10%)	476	0.22681	1	0.48224	1	9.9999e-06	0.00889	6.9999e-05	0.0495	0.0085099	1	0.064199	1	0.00457	1	0.00042	0.279	9.9999e-05	0.0696	0.52259	1	0.11639	1	0.67518	1
19q gain	57 (11%)	470	0.10246	1	0.22448	1	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00061999	0.403	0.01044	1	0.00242	1	9.9999e-06	0.00889	2e-05	0.0151	0.28834	1	0.04606	1	0.37982	1
20p gain	112 (21%)	415	0.11739	1	0.1136	1	9.9999e-06	0.00889	2e-05	0.0151	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-05	0.0151	2e-05	0.0151	0.00015	0.103
20q gain	115 (22%)	412	0.04159	1	0.074239	1	9.9999e-06	0.00889	2e-05	0.0151	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-05	0.0151
21q gain	50 (9%)	477	0.26841	1	0.20759	1	9.9999e-06	0.00889	0.00143	0.894	0.00077999	0.497	0.30992	1	0.00069999	0.45	0.0080999	1	0.0098599	1	0.34021	1	0.064639	1	0.080719	1
22q gain	40 (8%)	487	0.32618	1	0.21752	1	0.00042	0.279	0.20783	1	0.36257	1	0.94863	1	0.10741	1	0.057389	1	0.0391	1	0.81704	1	0.44884	1	0.24969	1
xq gain	31 (6%)	496	0.39037	1	0.70295	1	0.03367	1	0.29206	1	0.0232	1	0.01861	1	0.18415	1	0.141	1	0.33951	1	0.62327	1	0.12919	1	0.067789	1
1p loss	57 (11%)	470	0.00083999	0.533	0.00283	1	9.9999e-06	0.00889	0.69811	1	0.00045	0.298	0.11718	1	0.13181	1	0.00016	0.11	0.0072499	1	0.00051999	0.343	0.195	1	0.070739	1
1q loss	36 (7%)	491	0.01093	1	0.01093	1	4e-05	0.0289	0.36854	1	0.01121	1	0.050069	1	0.0041	1	9.9999e-06	0.00889	0.01039	1	0.00073999	0.474	0.34471	1	0.10638	1
2p loss	14 (3%)	513	5.9999e-05	0.0428	0.00060999	0.397	0.00021	0.143	0.66208	1	5.9999e-05	0.0428	4e-05	0.0289	9.9999e-06	0.00889	9.9999e-06	0.00889	3e-05	0.022	9.9999e-06	0.00889	0.64229	1	0.01363	1
2q loss	14 (3%)	513	0.00021	0.143	0.00066999	0.431	0.0015	0.936	1	1	0.00012	0.0832	5e-05	0.0359	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.64377	1	0.01382	1
3p loss	380 (72%)	147	0.00319	1	0.01012	1	9.9999e-06	0.00889	0.00073999	0.474	0.02383	1	0.01697	1	9.9999e-06	0.00889	9.9999e-06	0.00889	0.085719	1	0.0068099	1	0.16547	1	0.01053	1
3q loss	99 (19%)	428	0.9231	1	0.51452	1	9.9999e-06	0.00889	0.43964	1	0.15318	1	0.28028	1	0.20182	1	0.02496	1	0.4961	1	0.75134	1	0.31592	1	0.97449	1
4p loss	72 (14%)	455	0.53129	1	0.81503	1	9.9999e-06	0.00889	0.00019	0.13	0.12346	1	0.67532	1	0.0015	0.936	0.00086999	0.551	0.83968	1	0.060779	1	0.11651	1	0.12953	1
4q loss	65 (12%)	462	0.38529	1	0.7825	1	9.9999e-06	0.00889	3e-05	0.022	0.090789	1	0.21459	1	0.00061999	0.403	9.9999e-06	0.00889	0.43751	1	0.02399	1	0.0484	1	0.11181	1
5p loss	7 (1%)	520	NA	NA	NA	NA	0.38603	1	0.28961	1	0.63656	1	0.063219	1	0.02668	1	0.01142	1	0.0316	1	0.01486	1	NA	NA	NA	NA
5q loss	6 (1%)	521	NA	NA	NA	NA	0.44754	1	0.54439	1	0.49787	1	0.15094	1	0.04496	1	0.01563	1	0.068819	1	0.02679	1	NA	NA	NA	NA
6p loss	100 (19%)	427	0.01092	1	0.01449	1	9.9999e-06	0.00889	5.9999e-05	0.0428	3e-05	0.022	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00034	0.228
6q loss	128 (24%)	399	0.04983	1	0.051119	1	9.9999e-06	0.00889	0.0058999	1	2e-05	0.0151	0.00128	0.803	6.9999e-05	0.0495	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00095999	0.606	2e-04	0.136	0.0069499	1
7p loss	3 (1%)	524	NA	NA	NA	NA	0.28022	1	NA	NA	NA	NA	NA	NA	0.058919	1	0.16541	1	0.054929	1	0.081719	1	0.062949	1	0.31847	1
7q loss	4 (1%)	523	NA	NA	NA	NA	0.10405	1	0.34218	1	0.075329	1	0.23225	1	0.04821	1	0.085919	1	0.29787	1	0.3366	1	0.062129	1	0.31286	1
8p loss	137 (26%)	390	0.37749	1	0.16699	1	2e-05	0.0151	0.27658	1	0.19718	1	0.24996	1	0.069029	1	0.00070999	0.456	0.03511	1	0.071119	1	0.20647	1	0.03081	1
8q loss	64 (12%)	463	0.64492	1	0.12687	1	0.44747	1	0.050089	1	0.28791	1	0.8832	1	0.5017	1	0.25241	1	0.41378	1	0.70399	1	0.1311	1	0.15758	1
9p loss	149 (28%)	378	0.00375	1	0.03669	1	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00016	0.11	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	7.9999e-05	0.0562
9q loss	150 (28%)	377	0.01026	1	0.058109	1	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-05	0.0151	0.00052999	0.349	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	7.9999e-05	0.0562
10p loss	67 (13%)	460	0.1734	1	0.4046	1	9.9999e-06	0.00889	0.081199	1	0.77404	1	0.03255	1	0.17495	1	0.00054999	0.361	0.02731	1	0.0098999	1	0.19338	1	0.17786	1
10q loss	89 (17%)	438	0.32909	1	0.39618	1	9.9999e-06	0.00889	0.00478	1	0.99052	1	0.01126	1	0.11056	1	0.00086999	0.551	0.051309	1	0.0073799	1	0.2948	1	0.04949	1
11p loss	18 (3%)	509	NA	NA	NA	NA	3e-05	0.022	0.0247	1	0.25654	1	0.02138	1	0.15475	1	0.02706	1	0.13667	1	0.01076	1	0.12602	1	0.0096399	1
11q loss	23 (4%)	504	0.18918	1	0.37456	1	9.9999e-06	0.00889	0.0052799	1	0.16223	1	0.02079	1	0.01393	1	0.00053999	0.355	0.01663	1	0.00122	0.766	0.051849	1	0.0057599	1
12p loss	4 (1%)	523	NA	NA	NA	NA	0.47585	1	NA	NA	NA	NA	NA	NA	0.43471	1	0.79043	1	0.4677	1	0.31193	1	NA	NA	NA	NA
12q loss	4 (1%)	523	NA	NA	NA	NA	1	1	NA	NA	0.36563	1	0.31932	1	1	1	1	1	0.23083	1	0.68591	1	NA	NA	NA	NA
13q loss	71 (13%)	456	0.00336	1	0.04659	1	9.9999e-06	0.00889	3e-04	0.202	2e-05	0.0151	0.00029	0.196	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.073309	1	3e-04	0.202
14q loss	216 (41%)	311	2e-05	0.0151	7.9999e-05	0.0562	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	0.0019	1
15q loss	36 (7%)	491	0.11753	1	0.33238	1	9.9999e-06	0.00889	0.00075999	0.485	0.02671	1	0.23019	1	9.9999e-06	0.00889	9.9999e-06	0.00889	0.00064999	0.421	0.0079899	1	0.0023	1	0.10533	1
16p loss	10 (2%)	517	NA	NA	NA	NA	0.077239	1	0.87648	1	0.02709	1	0.096329	1	0.29464	1	0.055809	1	0.072019	1	0.01671	1	0.57928	1	0.86727	1
16q loss	16 (3%)	511	NA	NA	NA	NA	0.01547	1	0.90886	1	0.03071	1	0.38136	1	0.21832	1	0.02992	1	0.0429	1	0.01001	1	0.26297	1	0.70337	1
17p loss	46 (9%)	481	0.00014	0.0966	0.00023	0.156	9.9999e-06	0.00889	0.087389	1	0.0090099	1	0.0079599	1	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-05	0.0151	0.24404	1	0.02192	1
17q loss	28 (5%)	499	0.00071999	0.462	0.00043	0.285	0.00034	0.228	0.53693	1	0.2203	1	0.02693	1	0.00029	0.196	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-04	0.136	0.49744	1	0.12354	1
18p loss	93 (18%)	434	0.056809	1	0.45745	1	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	5e-05	0.0359	9.9999e-06	0.00889
18q loss	95 (18%)	432	0.04532	1	0.21737	1	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	3e-05	0.022	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	9.9999e-06	0.00889	2e-05	0.0151	9.9999e-06	0.00889
19p loss	11 (2%)	516	NA	NA	NA	NA	5e-05	0.0359	0.03117	1	0.00317	1	0.00209	1	0.15645	1	0.0097799	1	0.2182	1	0.056559	1	0.12822	1	0.04685	1
19q loss	4 (1%)	523	NA	NA	NA	NA	0.0155	1	NA	NA	0.96601	1	0.078039	1	0.35132	1	0.51127	1	0.82678	1	0.54733	1	NA	NA	NA	NA
20p loss	8 (2%)	519	NA	NA	NA	NA	0.22772	1	1	1	0.02841	1	0.78779	1	0.091289	1	0.21727	1	0.01211	1	0.088439	1	NA	NA	NA	NA
20q loss	3 (1%)	524	NA	NA	NA	NA	0.27736	1	NA	NA	NA	NA	NA	NA	0.057849	1	0.13783	1	0.055099	1	0.081019	1	NA	NA	NA	NA
21q loss	55 (10%)	472	0.02587	1	0.089929	1	5.9999e-05	0.0428	0.01277	1	0.03027	1	0.0080899	1	0.0053299	1	6.9999e-05	0.0495	0.00351	1	0.00381	1	0.229	1	0.03443	1
22q loss	39 (7%)	488	0.01023	1	0.00142	0.889	9.9999e-06	0.00889	0.00348	1	0.00426	1	0.088139	1	9.9999e-06	0.00889	4e-05	0.0289	2e-05	0.0151	0.02226	1	0.0088199	1	0.22712	1
xq loss	47 (9%)	480	0.02397	1	0.064339	1	2e-05	0.0151	0.01683	1	0.17606	1	0.0088199	1	0.054579	1	0.00336	1	0.01003	1	0.00396	1	0.18647	1	0.02901	1
