		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%)	500	NA	NA	NA	NA	5.9999e-05	0.0427	0.00016	0.111	0.02421	1	1	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.0055799	1	2e-05	0.0147	0.01234	1	0.00014	0.0974
1q gain	23 (4%)	490	NA	NA	NA	NA	0.00023	0.157	0.00056999	0.377	0.43389	1	0.60664	1	5.9999e-05	0.0427	0.00045	0.3	0.12157	1	0.03157	1	0.03081	1	0.056819	1
2p gain	14 (3%)	499	NA	NA	NA	NA	0.01682	1	0.01496	1	0.30882	1	0.34476	1	0.01244	1	0.00103	0.664	0.60302	1	0.02116	1	0.88951	1	0.03994	1
2q gain	13 (3%)	500	NA	NA	NA	NA	0.03809	1	0.01033	1	0.30771	1	0.34271	1	0.03492	1	0.00068999	0.453	0.51244	1	0.01766	1	0.68407	1	0.04567	1
3p gain	11 (2%)	502	NA	NA	NA	NA	0.064709	1	0.32718	1	0.46286	1	0.20284	1	0.10813	1	0.10902	1	0.11864	1	0.2884	1	0.74331	1	0.19922	1
3q gain	8 (2%)	505	NA	NA	NA	NA	0.00191	1	0.10048	1	0.056389	1	0.36638	1	0.062769	1	0.00369	1	0.34173	1	0.13346	1	0.32962	1	0.14968	1
4p gain	13 (3%)	500	NA	NA	NA	NA	0.00060999	0.402	0.0070599	1	0.03239	1	0.89536	1	0.0084399	1	0.00177	1	0.19052	1	0.10552	1	0.33745	1	0.27494	1
4q gain	6 (1%)	507	NA	NA	NA	NA	0.03909	1	0.01762	1	0.11157	1	0.66997	1	0.01425	1	0.00355	1	0.26125	1	0.15005	1	0.38213	1	0.22196	1
5p gain	11 (2%)	502	NA	NA	NA	NA	0.0064399	1	0.00292	1	0.02136	1	0.60878	1	4e-05	0.029	9.9999e-05	0.07	0.02384	1	0.02683	1	0.14249	1	0.01591	1
5q gain	8 (2%)	505	NA	NA	NA	NA	0.00469	1	0.00025	0.17	NA	NA	NA	NA	0.00022	0.15	0.00018	0.124	0.01254	1	0.00097999	0.634	0.0085499	1	0.00058999	0.389
6p gain	7 (1%)	506	NA	NA	NA	NA	0.22467	1	0.0466	1	0.03775	1	0.51814	1	0.43403	1	0.097929	1	0.0234	1	0.063729	1	0.57233	1	0.03296	1
7p gain	121 (24%)	392	0.74486	1	0.7814	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00044	0.293	0.01164	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00263	1	9.9999e-06	0.00836	0.00039	0.262	9.9999e-06	0.00836
7q gain	151 (29%)	362	0.76166	1	0.51971	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00403	1	0.20049	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00328	1	9.9999e-06	0.00836	0.00078999	0.516	9.9999e-06	0.00836
8p gain	46 (9%)	467	NA	NA	NA	NA	8.9999e-05	0.0634	0.00133	0.849	0.063789	1	0.16028	1	0.02234	1	0.0056899	1	0.39073	1	0.41293	1	0.20671	1	0.071049	1
8q gain	56 (11%)	457	0.051479	1	0.40467	1	9.9999e-06	0.00836	5e-05	0.0359	0.0114	1	0.055839	1	0.00153	0.967	0.00049	0.325	0.1907	1	0.11953	1	0.067679	1	0.01541	1
9p gain	17 (3%)	496	NA	NA	NA	NA	0.01562	1	0.14865	1	0.29165	1	0.53063	1	0.064799	1	0.03655	1	0.83857	1	0.02608	1	0.86061	1	0.20397	1
9q gain	24 (5%)	489	NA	NA	NA	NA	0.01235	1	0.10478	1	0.25818	1	0.054329	1	0.03986	1	0.01364	1	0.42996	1	0.01045	1	0.58403	1	0.17303	1
10p gain	57 (11%)	456	1	1	0.04178	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.02112	1	0.553	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.054309	1	0.2951	1	0.47425	1	0.0056499	1
10q gain	12 (2%)	501	NA	NA	NA	NA	0.00132	0.843	0.02035	1	0.26709	1	0.51523	1	0.085429	1	0.03616	1	0.077919	1	0.03032	1	0.57968	1	0.20757	1
11p gain	31 (6%)	482	NA	NA	NA	NA	0.0326	1	0.00088999	0.578	0.02586	1	0.11009	1	0.0093299	1	0.00318	1	0.093679	1	0.02454	1	0.40686	1	0.0081999	1
11q gain	58 (11%)	455	0.61555	1	0.58176	1	0.1776	1	0.0106	1	0.081749	1	0.03072	1	0.062279	1	0.03661	1	0.54644	1	0.04638	1	0.64836	1	0.03188	1
12p gain	33 (6%)	480	0.7543	1	0.57968	1	0.00029	0.196	0.03292	1	0.25854	1	0.30888	1	0.04212	1	0.087529	1	0.087339	1	0.02153	1	0.19073	1	0.5585	1
12q gain	16 (3%)	497	NA	NA	NA	NA	0.0054599	1	0.10209	1	0.29373	1	0.53181	1	0.0054899	1	0.085139	1	0.16502	1	0.059179	1	0.11899	1	0.091009	1
13q gain	6 (1%)	507	NA	NA	NA	NA	0.38187	1	0.39671	1	0.79414	1	0.79482	1	0.23428	1	0.47369	1	0.35196	1	0.5877	1	0.4536	1	0.46914	1
14q gain	4 (1%)	509	NA	NA	NA	NA	0.82572	1	0.75815	1	NA	NA	NA	NA	0.71026	1	0.59043	1	0.21705	1	0.67972	1	0.27047	1	0.75853	1
15q gain	11 (2%)	502	NA	NA	NA	NA	0.00221	1	0.02028	1	0.04491	1	0.2172	1	0.04782	1	0.01337	1	0.17612	1	0.28771	1	0.47463	1	0.096369	1
16p gain	17 (3%)	496	NA	NA	NA	NA	0.48815	1	0.74478	1	0.5602	1	0.69794	1	0.074899	1	0.04791	1	0.11953	1	0.059169	1	0.11009	1	0.51535	1
16q gain	19 (4%)	494	NA	NA	NA	NA	0.26765	1	0.31541	1	0.47018	1	0.51302	1	0.15237	1	0.03404	1	0.054809	1	0.099919	1	0.13934	1	0.52998	1
17p gain	20 (4%)	493	NA	NA	NA	NA	0.48937	1	0.59567	1	0.34755	1	0.88806	1	0.18645	1	0.04546	1	0.18909	1	0.48536	1	0.68694	1	0.65418	1
17q gain	23 (4%)	490	NA	NA	NA	NA	0.68233	1	0.4486	1	0.34723	1	0.88474	1	0.34861	1	0.12073	1	0.10858	1	0.70001	1	0.42451	1	0.35813	1
18p gain	17 (3%)	496	NA	NA	NA	NA	0.00013	0.0906	0.00483	1	0.02325	1	0.44084	1	0.03091	1	0.01161	1	0.83856	1	0.092649	1	0.61181	1	0.03721	1
18q gain	13 (3%)	500	NA	NA	NA	NA	0.00097999	0.634	0.00355	1	0.081009	1	0.59907	1	0.00162	1	0.00023	0.157	0.50908	1	0.01722	1	0.18192	1	0.00453	1
19p gain	100 (19%)	413	0.22028	1	1	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.67689	1	0.42434	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00018	0.124	0.03853	1	0.23493	1	0.00254	1
19q gain	25 (5%)	488	NA	NA	NA	NA	9.9999e-06	0.00836	9.9999e-06	0.00836	0.056639	1	0.39947	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00243	1	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836
20p gain	43 (8%)	470	NA	NA	NA	NA	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00066999	0.441	0.17538	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.16025	1	9.9999e-06	0.00836	0.00094999	0.617	9.9999e-06	0.00836
20q gain	43 (8%)	470	NA	NA	NA	NA	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00072999	0.477	0.14376	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.04912	1	9.9999e-06	0.00836	4e-05	0.029	9.9999e-06	0.00836
21q gain	24 (5%)	489	NA	NA	NA	NA	0.0059599	1	0.0119	1	0.10956	1	0.39467	1	0.42805	1	0.21148	1	0.62313	1	0.098319	1	0.72809	1	0.079949	1
22q gain	23 (4%)	490	NA	NA	NA	NA	0.01198	1	4e-05	0.029	1	1	0.68601	1	0.00106	0.681	0.00038	0.255	0.11856	1	0.52654	1	0.04174	1	0.22368	1
xq gain	41 (8%)	472	NA	NA	NA	NA	9.9999e-06	0.00836	9.9999e-06	0.00836	0.2364	1	0.71365	1	9.9999e-05	0.07	9.9999e-06	0.00836	0.01769	1	0.55852	1	0.66957	1	0.01345	1
1p loss	184 (36%)	329	0.02947	1	0.00019	0.131	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00027	0.183	0.4584	1	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836
1q loss	25 (5%)	488	0.34443	1	0.15044	1	0.45527	1	0.063169	1	0.47528	1	0.46465	1	0.36098	1	0.2817	1	0.076099	1	0.41302	1	0.16303	1	0.13763	1
2p loss	21 (4%)	492	NA	NA	NA	NA	0.00024	0.163	0.04163	1	0.33314	1	1	1	0.16137	1	0.03031	1	0.072749	1	0.40467	1	0.72901	1	0.25901	1
2q loss	18 (4%)	495	NA	NA	NA	NA	0.00041	0.274	0.0057299	1	0.069449	1	0.60726	1	0.42334	1	0.12483	1	0.02605	1	0.81066	1	0.69093	1	0.38438	1
3p loss	30 (6%)	483	NA	NA	NA	NA	0.0048	1	0.058319	1	0.0063699	1	0.27172	1	0.03801	1	0.02111	1	0.00103	0.664	0.00047	0.312	0.19309	1	0.00293	1
3q loss	28 (5%)	485	0.17582	1	0.88167	1	0.0072299	1	0.13284	1	0.25164	1	0.76891	1	0.072299	1	0.062839	1	0.090319	1	0.01686	1	0.26902	1	0.03544	1
4p loss	71 (14%)	442	1	1	0.78304	1	0.0033	1	9.9999e-06	0.00836	0.35057	1	1	1	4e-05	0.029	9.9999e-06	0.00836	5e-05	0.0359	0.00034	0.229	4e-05	0.029	9.9999e-06	0.00836
4q loss	92 (18%)	421	1	1	0.40449	1	0.0065999	1	9.9999e-06	0.00836	0.25783	1	0.93066	1	0.00070999	0.465	9.9999e-06	0.00836	0.00021	0.144	0.00148	0.937	2e-05	0.0147	2e-05	0.0147
5p loss	34 (7%)	479	0.74502	1	0.066339	1	9.9999e-06	0.00836	9.9999e-05	0.07	0.91518	1	0.95357	1	0.17316	1	0.04353	1	0.10478	1	0.39202	1	0.73326	1	0.32521	1
5q loss	33 (6%)	480	0.44684	1	0.23912	1	9.9999e-06	0.00836	0.00017	0.118	0.0193	1	0.11906	1	0.02719	1	0.0064899	1	8.9999e-05	0.0634	0.16186	1	0.81056	1	0.61002	1
6p loss	30 (6%)	483	NA	NA	NA	NA	0.03329	1	0.058139	1	0.18718	1	0.68523	1	0.37109	1	0.46208	1	0.39974	1	0.40361	1	0.01227	1	0.00304	1
6q loss	63 (12%)	450	NA	NA	NA	NA	7.9999e-05	0.0566	0.00134	0.854	0.25081	1	0.56798	1	0.076459	1	0.01923	1	0.00122	0.781	0.17307	1	0.01369	1	4e-05	0.029
7p loss	3 (1%)	510	NA	NA	NA	NA	0.04989	1	0.24488	1	NA	NA	NA	NA	1	1	0.89528	1	1	1	1	1	NA	NA	NA	NA
7q loss	3 (1%)	510	NA	NA	NA	NA	0.04938	1	0.24292	1	NA	NA	NA	NA	0.37393	1	0.17645	1	1	1	1	1	NA	NA	NA	NA
8p loss	17 (3%)	496	0.61567	1	0.04262	1	2e-05	0.0147	5e-05	0.0359	0.01897	1	0.1524	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.11661	1	0.00145	0.919	0.81642	1	0.00027	0.183
8q loss	11 (2%)	502	NA	NA	NA	NA	2e-04	0.137	2e-05	0.0147	0.082299	1	0.36421	1	7.9999e-05	0.0566	6.9999e-05	0.0497	0.052419	1	0.00067999	0.447	0.37335	1	8.9999e-05	0.0634
9p loss	118 (23%)	395	0.38247	1	0.26639	1	9.9999e-06	0.00836	3e-04	0.203	0.03187	1	0.01977	1	0.094809	1	0.051009	1	0.89356	1	0.22081	1	0.28514	1	0.03461	1
9q loss	51 (10%)	462	NA	NA	NA	NA	0.15257	1	0.46131	1	0.62171	1	0.34272	1	0.46656	1	0.13221	1	0.39623	1	0.82437	1	0.593	1	0.03341	1
10p loss	83 (16%)	430	0.26893	1	0.88129	1	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00111	0.712	9.9999e-06	0.00836	9.9999e-06	0.00836	2e-05	0.0147	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836
10q loss	96 (19%)	417	0.27331	1	0.8828	1	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	0.00042	0.281	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836
11p loss	63 (12%)	450	1	1	0.03147	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.0122	1	0.7261	1	9.9999e-06	0.00836	9.9999e-06	0.00836	2e-05	0.0147	5e-05	0.0359	0.43427	1	0.01646	1
11q loss	21 (4%)	492	NA	NA	NA	NA	0.00017	0.118	6.9999e-05	0.0497	0.01752	1	0.65163	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.02484	1	6.9999e-05	0.0497	0.49173	1	4e-04	0.268
12p loss	26 (5%)	487	NA	NA	NA	NA	0.00381	1	0.063179	1	0.60593	1	1	1	0.40349	1	0.31959	1	0.079099	1	0.15234	1	0.55274	1	0.92998	1
12q loss	51 (10%)	462	1	1	0.57864	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.68115	1	0.11014	1	0.0070699	1	0.00288	1	0.0058299	1	0.33249	1	0.83443	1	0.80892	1
13q loss	116 (23%)	397	0.17933	1	8.9999e-05	0.0634	5e-05	0.0359	0.0058899	1	0.02625	1	0.62237	1	0.01593	1	0.0051599	1	0.03477	1	0.0132	1	0.29686	1	0.24009	1
14q loss	80 (16%)	433	0.46593	1	0.26641	1	0.00104	0.669	0.00016	0.111	0.04406	1	0.11494	1	2e-05	0.0147	3e-05	0.0218	0.01031	1	0.00082999	0.541	0.01139	1	0.00054999	0.364
15q loss	51 (10%)	462	1	1	0.70572	1	0.02829	1	0.00179	1	0.27113	1	0.04633	1	0.00094999	0.617	0.00139	0.883	0.23484	1	0.47261	1	0.057369	1	0.083879	1
16p loss	14 (3%)	499	NA	NA	NA	NA	0.00495	1	0.04302	1	0.86578	1	0.20067	1	0.02871	1	0.11963	1	0.82285	1	0.35653	1	0.70587	1	0.1357	1
16q loss	22 (4%)	491	NA	NA	NA	NA	0.0058199	1	0.00221	1	0.37586	1	0.068099	1	0.01684	1	0.091899	1	0.6639	1	0.00355	1	0.29538	1	0.0092599	1
17p loss	13 (3%)	500	NA	NA	NA	NA	0.094119	1	0.13245	1	1	1	0.78201	1	0.01386	1	0.062189	1	0.15816	1	0.0063399	1	0.71434	1	0.01141	1
17q loss	8 (2%)	505	NA	NA	NA	NA	0.11593	1	0.20007	1	0.83715	1	0.51038	1	0.27043	1	0.53136	1	0.16208	1	0.26486	1	1	1	0.02348	1
18p loss	68 (13%)	445	0.3206	1	0.02979	1	0.20276	1	0.00138	0.878	0.58152	1	0.10454	1	0.13403	1	0.02925	1	0.59723	1	0.91461	1	0.47059	1	0.51197	1
18q loss	62 (12%)	451	0.34344	1	0.15151	1	0.04626	1	0.00031	0.209	0.28817	1	0.097799	1	0.0309	1	0.00337	1	0.058109	1	0.71208	1	0.42286	1	0.52956	1
19p loss	25 (5%)	488	0.84734	1	0.43291	1	0.52599	1	0.87536	1	0.1027	1	0.80913	1	0.56247	1	0.45842	1	0.13147	1	0.1157	1	0.02592	1	0.055779	1
19q loss	209 (41%)	304	0.18614	1	0.01258	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.03842	1	0.33471	1	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836	9.9999e-06	0.00836
20p loss	7 (1%)	506	NA	NA	NA	NA	0.22479	1	0.15609	1	0.79333	1	1	1	0.2598	1	0.39453	1	0.4466	1	0.48198	1	0.71017	1	0.48113	1
20q loss	3 (1%)	510	NA	NA	NA	NA	0.25294	1	0.44614	1	NA	NA	NA	NA	0.02401	1	0.13775	1	0.23353	1	1	1	0.30122	1	0.88765	1
21q loss	36 (7%)	477	0.61234	1	0.04264	1	9.9999e-06	0.00836	0.00021	0.144	0.46439	1	0.65354	1	0.00087999	0.573	0.00046	0.306	0.24899	1	0.02644	1	0.50686	1	0.28816	1
22q loss	57 (11%)	456	0.81751	1	0.0068699	1	9.9999e-06	0.00836	9.9999e-06	0.00836	4e-05	0.029	0.0402	1	9.9999e-06	0.00836	9.9999e-06	0.00836	0.45333	1	0.00033	0.222	0.01159	1	0.00015	0.104
xq loss	69 (13%)	444	0.83731	1	0.26638	1	0.25402	1	0.0121	1	0.04484	1	0.02086	1	5e-05	0.0359	9.9999e-06	0.00836	7.9999e-05	0.0566	0.15048	1	0.0314	1	0.0082499	1
