		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	Chi-square test_P	Chi-square 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	Chi-square test_P	Chi-square test_Q
1p gain	23 (4%)	491	1	1	1	1	1.2977e-07	0.000104	0.001635	1	0.0013723	0.878	0.0061724	1	0.011148	1	0.0019676	1	0.00057185	0.385	0.26083	1	0.024995	1	0.024438	1
1q gain	51 (10%)	463	0.41028	1	0.41105	1	1.739e-15	1.51e-12	0.036895	1	0.087509	1	0.031246	1	1.8455e-05	0.0137	0.0003644	0.251	2.1621e-05	0.016	0.95431	1	0.030816	1	0.012968	1
2p gain	76 (15%)	438	0.56067	1	0.40029	1	2.5277e-09	2.08e-06	0.20097	1	0.011792	1	0.87127	1	0.16516	1	0.035061	1	0.64367	1	0.092769	1	0.068226	1	0.092169	1
2q gain	77 (15%)	437	0.56067	1	0.40029	1	2.1372e-07	0.00017	0.29955	1	0.011511	1	0.93353	1	0.15625	1	0.035353	1	0.71198	1	0.092769	1	0.14957	1	0.06886	1
3p gain	20 (4%)	494	0.053628	1	0.062305	1	0.00038028	0.262	0.58508	1	0.044393	1	0.00059042	0.396	0.0050634	1	0.0021316	1	6.1301e-05	0.0443	0.00020037	0.141	0.0020248	1	0.062799	1
3q gain	60 (12%)	454	0.012193	1	0.018801	1	2.992e-11	2.52e-08	0.011088	1	0.0005637	0.38	5.9745e-07	0.000468	1.3025e-05	0.00979	1.8656e-06	0.00144	1.4503e-08	1.18e-05	4.11e-06	0.00313	0.00018116	0.128	0.11098	1
4p gain	13 (3%)	501	NA	NA	NA	NA	0.066822	1	0.377	1	0.25321	1	0.0017483	1	0.00041753	0.285	0.069184	1	0.00020836	0.146	0.022606	1	0.04843	1	6.8806e-05	0.0495
4q gain	13 (3%)	501	NA	NA	NA	NA	0.27281	1	0.4491	1	0.25321	1	0.020053	1	0.00041753	0.285	0.14424	1	0.00020836	0.146	0.022606	1	0.04843	1	6.8806e-05	0.0495
5p gain	190 (37%)	324	0.83527	1	0.77796	1	0.00010055	0.0719	0.17234	1	0.084287	1	0.11267	1	0.01276	1	0.00077043	0.509	0.10875	1	0.80736	1	0.12817	1	0.54011	1
5q gain	204 (40%)	310	0.29223	1	0.21196	1	0.0072302	1	0.38892	1	0.39791	1	0.10276	1	0.073103	1	0.004592	1	0.56599	1	0.36722	1	0.22025	1	0.41665	1
6p gain	11 (2%)	503	NA	NA	NA	NA	0.20224	1	0.34049	1	0.067197	1	0.58657	1	0.79359	1	0.84603	1	0.79606	1	1	1	0.84479	1	0.25694	1
6q gain	9 (2%)	505	NA	NA	NA	NA	0.092594	1	0.56926	1	0.01678	1	0.76641	1	1	1	1	1	1	1	0.77855	1	1	1	0.44652	1
7p gain	168 (33%)	346	0.41594	1	0.57703	1	9.5326e-14	8.24e-11	0.006273	1	1.608e-05	0.012	0.001785	1	0.00012737	0.0908	0.0018137	1	0.0063545	1	0.64774	1	0.03771	1	0.26091	1
7q gain	169 (33%)	345	0.41594	1	0.57703	1	1.2362e-13	1.06e-10	0.015616	1	2.7813e-05	0.0205	0.00069173	0.461	0.00014448	0.102	0.0015943	1	0.0079715	1	0.42935	1	0.052025	1	0.037532	1
8p gain	31 (6%)	483	NA	NA	NA	NA	6.2901e-09	5.13e-06	0.00096443	0.627	0.0095995	1	0.20166	1	1.9133e-05	0.0142	0.00032891	0.227	6.9829e-06	0.00529	0.005817	1	0.005203	1	0.048524	1
8q gain	59 (11%)	455	0.22618	1	0.32459	1	9.2983e-19	8.15e-16	6.5387e-06	0.00496	5.2134e-05	0.0379	0.021314	1	8.3582e-12	7.08e-09	1.1988e-09	9.88e-07	6.4942e-11	5.44e-08	0.0024	1	6.5068e-07	0.000508	0.0025459	1
9p gain	13 (3%)	501	NA	NA	NA	NA	0.010615	1	0.90154	1	0.80592	1	0.71552	1	0.23751	1	0.40884	1	0.93798	1	0.016571	1	0.72708	1	0.52894	1
9q gain	12 (2%)	502	NA	NA	NA	NA	0.00080601	0.53	0.8353	1	0.56846	1	0.29075	1	0.25124	1	0.55519	1	0.80609	1	0.028855	1	1	1	0.73698	1
10p gain	17 (3%)	497	NA	NA	NA	NA	0.00092871	0.606	0.11259	1	0.27557	1	0.47235	1	0.00083984	0.551	0.00017957	0.127	0.074982	1	0.43347	1	0.46558	1	0.1385	1
10q gain	12 (2%)	502	NA	NA	NA	NA	0.0011718	0.756	0.082229	1	0.067334	1	0.54603	1	0.014208	1	0.0075141	1	0.07645	1	0.34781	1	0.37319	1	0.27049	1
11p gain	31 (6%)	483	0.23165	1	0.25217	1	1.4164e-05	0.0106	0.30823	1	0.19528	1	0.24639	1	0.29046	1	0.18161	1	0.31251	1	0.02754	1	0.2054	1	0.33024	1
11q gain	29 (6%)	485	0.34099	1	0.53903	1	0.00027581	0.191	0.18751	1	0.4232	1	0.51319	1	0.54853	1	0.483	1	0.59303	1	0.021835	1	0.52254	1	0.24327	1
12p gain	120 (23%)	394	0.012874	1	0.014228	1	9.5341e-14	8.24e-11	0.00017395	0.123	1.3367e-12	1.14e-09	0.0010333	0.67	1.9085e-11	1.61e-08	2.3652e-12	2.01e-09	1.0992e-10	9.16e-08	0.023612	1	7.3513e-08	5.91e-05	0.0059756	1
12q gain	120 (23%)	394	0.012874	1	0.014228	1	1.7388e-13	1.49e-10	0.00011834	0.0845	1.8657e-13	1.6e-10	0.00043125	0.293	6.3994e-11	5.36e-08	2.3652e-12	2.01e-09	3.2044e-11	2.69e-08	0.051759	1	7.3513e-08	5.91e-05	0.0059756	1
13q gain	22 (4%)	492	NA	NA	NA	NA	0.24913	1	0.010383	1	0.64797	1	0.56881	1	0.074695	1	0.51241	1	0.43162	1	0.71238	1	0.93097	1	0.17829	1
14q gain	16 (3%)	498	0.76851	1	0.78254	1	0.0012732	0.82	0.32823	1	0.012121	1	0.0069981	1	0.019591	1	0.04921	1	0.0098736	1	0.0052486	1	0.37319	1	0.013885	1
15q gain	26 (5%)	488	1	1	1	1	0.0010562	0.683	0.59897	1	0.45203	1	0.15002	1	0.63015	1	0.85627	1	0.67295	1	0.28434	1	0.48932	1	0.36945	1
16p gain	107 (21%)	407	0.28203	1	0.33712	1	0.00082708	0.543	0.39878	1	0.0014674	0.936	0.04981	1	0.013888	1	0.0052391	1	0.06864	1	0.68745	1	0.12292	1	0.27505	1
16q gain	99 (19%)	415	0.23296	1	0.21777	1	0.00043863	0.297	0.22724	1	0.0023038	1	0.063492	1	0.012236	1	0.024196	1	0.024285	1	0.5168	1	0.0301	1	0.31629	1
17p gain	25 (5%)	489	0.018559	1	0.034912	1	2.8378e-05	0.0209	0.72735	1	0.32918	1	0.073361	1	0.23738	1	0.058921	1	0.29576	1	0.055509	1	0.29142	1	0.13384	1
17q gain	31 (6%)	483	0.069157	1	0.098773	1	8.0483e-05	0.0578	0.39423	1	0.49259	1	0.076145	1	0.13418	1	0.017119	1	0.18229	1	0.031931	1	0.11168	1	0.066682	1
18p gain	25 (5%)	489	0.31209	1	0.25229	1	0.081021	1	0.40519	1	0.83155	1	0.19135	1	0.076104	1	0.93608	1	0.68709	1	0.64179	1	0.69148	1	0.17698	1
18q gain	25 (5%)	489	0.31209	1	0.25229	1	0.11692	1	0.41315	1	0.73299	1	0.51027	1	0.076104	1	0.93608	1	0.85862	1	0.64179	1	0.69148	1	0.17698	1
19p gain	51 (10%)	463	0.22618	1	0.32459	1	1.9806e-09	1.63e-06	0.0025242	1	0.009356	1	0.052125	1	0.0046699	1	0.0027681	1	0.00019168	0.135	0.0088533	1	0.026056	1	0.94211	1
19q gain	57 (11%)	457	0.10193	1	0.14864	1	2.3573e-11	1.99e-08	0.00028698	0.199	0.0010206	0.662	0.0061868	1	0.0019696	1	0.0007751	0.512	2.9682e-05	0.0218	0.0033262	1	0.008053	1	0.82835	1
20p gain	111 (22%)	403	0.11564	1	0.16346	1	7.5684e-22	6.67e-19	5.6154e-05	0.0408	1.0713e-07	8.58e-05	0.0017354	1	1.1463e-12	9.78e-10	2.1646e-12	1.84e-09	3.3246e-10	2.76e-07	0.00024148	0.169	6.1763e-07	0.000484	0.031619	1
20q gain	114 (22%)	400	0.045714	1	0.06749	1	2.8202e-23	2.49e-20	5.6154e-05	0.0408	6.7616e-09	5.51e-06	0.00089632	0.586	2.6207e-14	2.27e-11	1.8956e-13	1.62e-10	3.5466e-11	2.98e-08	0.00015388	0.109	2.7048e-07	0.000214	0.019653	1
21q gain	50 (10%)	464	0.26897	1	0.27964	1	3.4252e-06	0.00262	0.0086674	1	0.0011012	0.711	0.50897	1	0.00070514	0.469	0.0018901	1	0.0090762	1	1	1	0.057446	1	0.14145	1
22q gain	40 (8%)	474	0.32729	1	0.028901	1	5.7764e-05	0.0418	0.67931	1	0.37794	1	0.5812	1	0.11002	1	0.14795	1	0.073698	1	0.22791	1	0.015619	1	0.16821	1
xq gain	30 (6%)	484	0.38945	1	0.32803	1	0.20356	1	0.70536	1	0.021708	1	0.01187	1	0.17941	1	0.31743	1	0.43719	1	0.90891	1	0.2941	1	0.19072	1
1p loss	56 (11%)	458	0.001279	0.822	0.0003887	0.267	1.0959e-09	9.04e-07	0.46941	1	0.00049161	0.333	0.17796	1	0.13739	1	0.0026206	1	0.034557	1	1.9705e-08	1.6e-05	0.39409	1	0.0002484	0.173
1q loss	36 (7%)	478	0.010729	1	0.013331	1	5.0319e-10	4.16e-07	0.28899	1	0.010192	1	0.069504	1	0.0041572	1	0.0006778	0.452	0.042093	1	2.54e-08	2.05e-05	0.48807	1	1.4115e-05	0.0106
2p loss	14 (3%)	500	3.5787e-05	0.0261	6.2984e-05	0.0454	1.3759e-06	0.00107	0.66785	1	4.5828e-05	0.0334	2.3548e-06	0.00181	2.389e-07	0.00019	4.7333e-09	3.88e-06	8.4032e-05	0.0602	4.5032e-12	3.82e-09	0.074089	1	1.6425e-13	1.41e-10
2q loss	14 (3%)	500	0.00024867	0.173	0.00038936	0.267	1.3759e-06	0.00107	1	1	0.00031624	0.219	2.3548e-06	0.00181	2.389e-07	0.00019	6.3947e-08	5.15e-05	2.3246e-05	0.0172	2.5255e-10	2.1e-07	0.074089	1	1.6425e-13	1.41e-10
3p loss	370 (72%)	144	0.0034866	1	0.00066344	0.443	4.7214e-24	4.18e-21	0.020668	1	0.019708	1	0.0048183	1	1.7167e-08	1.39e-05	3.3584e-10	2.78e-07	0.016449	1	2.8143e-05	0.0207	0.12799	1	5.2707e-06	0.004
3q loss	102 (20%)	412	0.71975	1	0.71847	1	0.00040706	0.278	0.35862	1	0.17274	1	0.084517	1	0.18705	1	0.28968	1	0.90605	1	0.16651	1	0.18545	1	0.34207	1
4p loss	71 (14%)	443	0.53135	1	0.38886	1	3.038e-09	2.49e-06	0.0013598	0.872	0.084529	1	0.33647	1	0.0018307	1	0.001661	1	0.84687	1	0.31241	1	0.074322	1	0.3747	1
4q loss	65 (13%)	449	0.38705	1	0.34568	1	1.0368e-11	8.77e-09	0.00052903	0.358	0.051013	1	0.19873	1	0.0007696	0.509	9.7825e-06	0.00739	0.38181	1	0.1413	1	0.040575	1	0.29318	1
5p loss	7 (1%)	507	NA	NA	NA	NA	0.022751	1	0.29091	1	0.65716	1	0.2869	1	0.026634	1	0.020876	1	0.028471	1	0.035394	1	NA	NA	NA	NA
5q loss	6 (1%)	508	NA	NA	NA	NA	0.048911	1	0.53395	1	0.47139	1	0.62591	1	0.045315	1	0.047501	1	0.060248	1	0.0053338	1	NA	NA	NA	NA
6p loss	99 (19%)	415	0.011254	1	0.0028151	1	8.4777e-16	7.38e-13	0.00072253	0.48	3.739e-06	0.00285	0.00025843	0.18	3.0524e-08	2.47e-05	5.756e-07	0.000452	7.9898e-11	6.68e-08	0.00027829	0.193	4.38e-07	0.000345	0.0096066	1
6q loss	126 (25%)	388	0.047526	1	0.021165	1	6.5753e-15	5.69e-12	0.043405	1	2.5682e-05	0.019	0.0032678	1	0.00013393	0.0952	0.0049725	1	3.8577e-07	0.000304	0.023316	1	0.00013175	0.0938	0.080071	1
7p loss	3 (1%)	511	NA	NA	NA	NA	0.18065	1	NA	NA	NA	NA	NA	NA	0.058084	1	0.12839	1	0.055624	1	0.28915	1	0.058067	1	0.64978	1
7q loss	4 (1%)	510	NA	NA	NA	NA	0.091473	1	0.36257	1	0.097958	1	1	1	0.049093	1	0.061549	1	0.033514	1	0.51949	1	0.058067	1	0.64978	1
8p loss	136 (26%)	378	0.35372	1	0.42649	1	8.214e-05	0.0589	0.21585	1	0.18521	1	0.29062	1	0.06917	1	0.066076	1	0.083482	1	0.054194	1	0.1504	1	0.32392	1
8q loss	67 (13%)	447	0.64737	1	0.74664	1	0.13285	1	0.10561	1	0.2891	1	0.48572	1	0.70745	1	0.59358	1	0.58861	1	0.33427	1	0.2373	1	0.51485	1
9p loss	146 (28%)	368	0.004171	1	0.00053301	0.36	2.0616e-47	1.83e-44	1.7559e-19	1.54e-16	4.8897e-06	0.00372	0.00093462	0.608	2.1213e-22	1.87e-19	1.1769e-25	1.04e-22	2.9656e-15	2.57e-12	3.4902e-05	0.0255	1.0379e-10	8.66e-08	0.0024222	1
9q loss	147 (29%)	367	0.010069	1	0.0014349	0.917	3.0559e-46	2.71e-43	1.8014e-18	1.58e-15	1.0599e-06	0.000824	0.0015911	1	6.7853e-23	5.99e-20	3.2585e-25	2.89e-22	1.2924e-16	1.13e-13	0.00015857	0.112	4.5506e-10	3.76e-07	0.00043017	0.293
10p loss	66 (13%)	448	0.17348	1	0.23862	1	4.9617e-09	4.06e-06	0.055321	1	0.74237	1	0.26738	1	0.17548	1	0.31593	1	0.066988	1	0.026962	1	0.090587	1	0.083959	1
10q loss	87 (17%)	427	0.31524	1	0.36049	1	2.1212e-08	1.72e-05	0.0071475	1	0.99022	1	0.14926	1	0.10962	1	0.18593	1	0.10864	1	0.12792	1	0.13816	1	0.02138	1
11p loss	18 (4%)	496	NA	NA	NA	NA	3.3998e-05	0.0249	0.047325	1	0.13967	1	0.55314	1	0.15013	1	0.066196	1	0.18099	1	0.047559	1	0.064433	1	0.1135	1
11q loss	23 (4%)	491	0.18897	1	0.20731	1	5.9057e-07	0.000464	0.014251	1	0.10125	1	0.41768	1	0.012636	1	0.0039088	1	0.028216	1	0.11292	1	0.028451	1	0.22716	1
12p loss	3 (1%)	511	NA	NA	NA	NA	0.34351	1	NA	NA	NA	NA	NA	NA	0.43658	1	1	1	0.44733	1	0.44785	1	NA	NA	NA	NA
12q loss	4 (1%)	510	NA	NA	NA	NA	0.57723	1	NA	NA	0.52479	1	0.18488	1	1	1	1	1	0.21252	1	0.75642	1	NA	NA	NA	NA
13q loss	69 (13%)	445	0.0030403	1	0.0045545	1	9.3251e-11	7.79e-08	0.00073734	0.489	7.6632e-06	0.00579	0.0030671	1	4.0978e-06	0.00312	3.542e-07	0.00028	3.2289e-06	0.00247	0.0019374	1	0.050021	1	0.0084363	1
14q loss	214 (42%)	300	3.1171e-05	0.0228	4.3065e-05	0.0314	6.373e-18	5.58e-15	6.2116e-08	5.01e-05	1.0117e-13	8.72e-11	1.2787e-07	0.000102	1.9674e-21	1.73e-18	7.8869e-16	6.88e-13	2.4086e-11	2.03e-08	0.16478	1	8.2463e-07	0.000642	2.8956e-05	0.0213
15q loss	35 (7%)	479	0.11774	1	0.12687	1	2.5903e-10	2.15e-07	0.0078729	1	0.041965	1	0.4139	1	3.1992e-06	0.00245	8.1493e-07	0.000636	0.0023116	1	0.077961	1	0.0023059	1	0.42142	1
16p loss	10 (2%)	504	NA	NA	NA	NA	0.27549	1	0.63136	1	0.036005	1	0.83662	1	0.29266	1	0.045009	1	0.26908	1	0.12509	1	0.37319	1	0.54552	1
16q loss	15 (3%)	499	NA	NA	NA	NA	0.060168	1	0.34392	1	0.05764	1	0.59467	1	0.199	1	0.0059297	1	0.1029	1	0.034093	1	0.70976	1	0.71489	1
17p loss	45 (9%)	469	0.00013537	0.0961	0.00027063	0.188	5.3523e-09	4.38e-06	0.13987	1	0.0051073	1	0.0016327	1	1.6084e-06	0.00124	1.4045e-07	0.000112	9.5891e-08	7.69e-05	1.6947e-06	0.00131	0.033483	1	0.019891	1
17q loss	28 (5%)	486	0.00061803	0.414	0.00091193	0.595	2.4215e-06	0.00186	0.58508	1	0.15674	1	0.023748	1	0.00038636	0.265	5.8652e-05	0.0424	1.1448e-05	0.00863	9.1408e-07	0.000711	0.16006	1	1.8147e-05	0.0135
18p loss	91 (18%)	423	0.057359	1	0.13502	1	1.3644e-13	1.17e-10	2.6816e-07	0.000212	3.0725e-08	2.48e-05	0.0018299	1	7.0848e-19	6.22e-16	1.8899e-15	1.64e-12	3.6147e-11	3.03e-08	1.702e-05	0.0127	4.4229e-07	0.000348	0.0086229	1
18q loss	93 (18%)	421	0.046805	1	0.064915	1	2.2901e-13	1.96e-10	1.9663e-06	0.00152	1.9858e-07	0.000158	0.0067011	1	6.4189e-18	5.61e-15	4.0978e-15	3.55e-12	1.1052e-10	9.2e-08	1.3993e-05	0.0105	1.6751e-07	0.000134	0.0023338	1
19p loss	11 (2%)	503	NA	NA	NA	NA	0.00042566	0.29	0.060367	1	0.00058958	0.396	0.00078757	0.519	0.16512	1	0.017552	1	0.26904	1	0.17825	1	0.11468	1	0.0082664	1
19q loss	4 (1%)	510	NA	NA	NA	NA	0.013448	1	NA	NA	0.88973	1	0.16833	1	0.35162	1	0.38764	1	0.83014	1	1	1	NA	NA	NA	NA
20p loss	8 (2%)	506	NA	NA	NA	NA	0.22297	1	1	1	0.058197	1	1	1	0.090709	1	0.44503	1	0.015546	1	0.081109	1	NA	NA	NA	NA
20q loss	3 (1%)	511	NA	NA	NA	NA	0.18065	1	NA	NA	NA	NA	NA	NA	0.058084	1	0.76285	1	0.055624	1	0.00883	1	NA	NA	NA	NA
21q loss	55 (11%)	459	0.026008	1	0.030636	1	9.2451e-09	7.53e-06	0.024137	1	0.027744	1	0.0078775	1	0.0057273	1	0.0013451	0.864	0.0099019	1	0.00084949	0.556	0.213	1	0.016975	1
22q loss	39 (8%)	475	0.010053	1	0.015526	1	5.8477e-09	4.78e-06	0.0069517	1	0.0042271	1	0.035821	1	6.2408e-07	0.000488	2.8401e-06	0.00218	1.1754e-05	0.00885	0.12697	1	0.00065593	0.439	0.49849	1
xq loss	46 (9%)	468	0.02379	1	0.0091659	1	1.9654e-05	0.0146	0.022161	1	0.14324	1	0.0038202	1	0.055348	1	0.0041925	1	0.015832	1	1.4272e-05	0.0107	0.027045	1	0.016682	1
