		Molecular subtypes	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	Chi-square test_P	Chi-square test_Q
1p gain	0 (0%)	560	0.4079	1	0.37497	1	0.93194	1	0.56682	1	0.49717	1	0.12806	1	0.17804	1	0.33015	1	0.11131	1	0.91089	1	0.48452	1	0.0368	1
1q gain	0 (0%)	495	0.49725	1	0.96016	1	0.015823	1	0.82512	1	0.25495	1	0.15003	1	0.12824	1	0.075768	1	0.072884	1	0.97845	1	0.15877	1	0.0036042	1
2p gain	0 (0%)	515	0.060801	1	0.00032169	0.258	0.0081555	1	0.00050816	0.405	0.073493	1	0.35745	1	0.00022405	0.181	0.00013733	0.112	0.2161	1	0.020869	1	0.44539	1	0.0028167	1
2q gain	0 (0%)	516	0.017776	1	8.5204e-05	0.07	0.0010069	0.792	1.7053e-05	0.0142	0.20909	1	0.80609	1	0.00023412	0.189	0.00082411	0.65	0.25079	1	0.050357	1	0.91948	1	0.011592	1
3p gain	0 (0%)	539	0.13264	1	0.59276	1	0.00018128	0.147	0.1485	1	0.37425	1	0.76991	1	0.2599	1	0.88499	1	0.20792	1	0.36632	1	0.57147	1	0.060885	1
3q gain	0 (0%)	522	0.23493	1	0.089138	1	2.4908e-06	0.00209	0.015871	1	0.21465	1	0.65544	1	0.074996	1	0.58768	1	0.11128	1	0.54357	1	0.31191	1	0.13261	1
4p gain	0 (0%)	569	NA	NA	NA	NA	0.062196	1	0.22569	1	0.18379	1	0.33915	1	NA	NA	NA	NA	0.13662	1	0.052496	1	0.38522	1	0.2258	1
4q gain	0 (0%)	568	0.70693	1	0.71936	1	0.24967	1	0.78662	1	0.73233	1	0.64544	1	NA	NA	NA	NA	0.38271	1	0.80878	1	NA	NA	NA	NA
5p gain	0 (0%)	515	0.13784	1	0.66124	1	0.0015014	1	0.17379	1	0.79521	1	0.86337	1	0.40113	1	0.39993	1	0.7844	1	0.35435	1	0.85298	1	0.86274	1
5q gain	0 (0%)	542	0.52676	1	0.82563	1	0.0035603	1	0.095603	1	0.74224	1	0.557	1	0.72984	1	0.44647	1	0.81846	1	0.48285	1	0.48802	1	0.84876	1
6p gain	0 (0%)	498	0.18547	1	0.0029461	1	1.5453e-06	0.0013	0.27845	1	0.70357	1	0.12022	1	0.02271	1	0.22684	1	0.84813	1	0.39161	1	0.95161	1	0.21603	1
6q gain	0 (0%)	504	0.30905	1	0.04006	1	7.4722e-07	0.000633	0.11245	1	0.31702	1	0.041776	1	0.06068	1	0.57524	1	0.74931	1	0.25108	1	0.37195	1	0.060776	1
7p gain	0 (0%)	285	0.0015198	1	0.0019295	1	1.8943e-21	1.7e-18	8.5512e-08	7.35e-05	0.2196	1	0.031272	1	3.7185e-08	3.21e-05	9.5428e-05	0.0783	0.070344	1	0.030432	1	0.0086457	1	4.4071e-08	3.8e-05
7q gain	0 (0%)	320	0.001902	1	0.0088861	1	6.9527e-16	6.15e-13	5.9808e-06	0.005	0.77701	1	0.1801	1	8.7918e-07	0.000744	1.2379e-05	0.0103	0.24522	1	0.15535	1	0.046527	1	4.7276e-05	0.0391
8p gain	0 (0%)	467	0.96287	1	0.71705	1	1.0033e-08	8.68e-06	0.45355	1	0.28022	1	0.21454	1	0.18083	1	0.44035	1	0.49022	1	0.89065	1	0.1875	1	0.89754	1
8q gain	0 (0%)	340	0.14548	1	0.017245	1	1.0571e-33	9.52e-31	0.01351	1	0.15018	1	0.32957	1	0.0010965	0.862	0.026497	1	0.45899	1	0.63306	1	0.034458	1	0.14728	1
9p gain	0 (0%)	496	0.50322	1	1	1	0.17843	1	0.79069	1	0.91035	1	0.20389	1	0.53853	1	0.85475	1	0.78008	1	0.78126	1	0.81279	1	0.37918	1
9q gain	0 (0%)	511	0.38501	1	0.85376	1	0.214	1	0.58192	1	0.61199	1	0.033571	1	0.98879	1	0.69074	1	0.4082	1	0.73861	1	1	1	0.52457	1
10p gain	0 (0%)	547	0.19642	1	0.6282	1	0.009811	1	0.013528	1	0.67255	1	0.85739	1	0.61731	1	0.044579	1	0.6164	1	0.49637	1	0.0069747	1	0.45956	1
10q gain	0 (0%)	562	0.88738	1	0.2775	1	0.19283	1	0.05742	1	0.59674	1	0.2885	1	0.44811	1	0.076189	1	0.69363	1	0.90189	1	0.17412	1	0.69301	1
11p gain	0 (0%)	536	0.061484	1	0.2751	1	1.7136e-05	0.0142	0.00020421	0.165	0.8261	1	0.76414	1	0.049079	1	0.00015336	0.125	0.24559	1	0.88201	1	0.1422	1	0.0071319	1
11q gain	0 (0%)	536	0.095636	1	0.029856	1	1.3278e-06	0.00112	0.00072544	0.575	0.4972	1	0.65066	1	0.035611	1	0.0052563	1	0.55893	1	0.40622	1	0.0037827	1	0.058245	1
12p gain	0 (0%)	482	0.38323	1	0.63092	1	0.25584	1	0.020495	1	0.62854	1	0.20534	1	0.023201	1	0.013443	1	0.21996	1	0.11247	1	0.0013235	1	0.01144	1
12q gain	0 (0%)	497	0.32848	1	0.76337	1	0.098608	1	0.0023722	1	0.91035	1	0.33852	1	0.035315	1	0.01536	1	0.22169	1	0.16642	1	0.0013589	1	0.0067303	1
13q gain	0 (0%)	261	4.3773e-07	0.000373	0.00010867	0.089	1.6222e-37	1.46e-34	2.8624e-08	2.47e-05	0.012869	1	0.068273	1	8.5412e-09	7.4e-06	6.3955e-07	0.000542	0.010037	1	0.44955	1	2.855e-07	0.000244	1.211e-10	1.05e-07
14q gain	0 (0%)	556	0.51891	1	0.25062	1	0.030087	1	0.70869	1	0.72426	1	0.39691	1	0.060477	1	0.047976	1	1	1	0.37109	1	0.11031	1	0.076	1
15q gain	0 (0%)	568	NA	NA	NA	NA	0.51457	1	0.88205	1	0.13298	1	0.13101	1	1	1	0.24372	1	0.86981	1	0.37371	1	0.10456	1	0.86592	1
16p gain	0 (0%)	479	0.088167	1	0.16461	1	1.2625e-16	1.12e-13	0.0011867	0.932	0.94091	1	0.029508	1	0.022796	1	0.13645	1	0.57733	1	0.34666	1	0.6308	1	0.0067844	1
16q gain	0 (0%)	479	0.09877	1	0.17393	1	3.0211e-18	2.69e-15	0.00041269	0.33	0.99134	1	0.018203	1	0.019816	1	0.060159	1	0.46459	1	0.27723	1	0.21359	1	0.0016631	1
17p gain	0 (0%)	562	0.77999	1	0.0070285	1	1	1	0.9225	1	0.55159	1	0.72078	1	0.015683	1	0.0089989	1	0.69363	1	0.90189	1	0.36112	1	0.64538	1
17q gain	0 (0%)	508	0.050357	1	0.034999	1	0.00026856	0.216	0.0027104	1	0.64927	1	0.074817	1	1.4683e-05	0.0122	0.0019486	1	0.078543	1	0.35388	1	0.47398	1	0.25682	1
18p gain	0 (0%)	554	0.20744	1	0.059231	1	0.00061013	0.484	0.01034	1	0.51436	1	0.89691	1	0.13285	1	0.39087	1	0.56836	1	0.39747	1	0.55046	1	0.34569	1
18q gain	0 (0%)	563	NA	NA	NA	NA	0.17246	1	0.0073909	1	0.6479	1	0.4677	1	0.12238	1	0.85815	1	0.10546	1	0.13438	1	0.61067	1	0.34931	1
19p gain	0 (0%)	523	0.1938	1	0.14574	1	5.843e-05	0.0482	0.018809	1	0.59774	1	0.028523	1	0.42326	1	0.47411	1	0.71797	1	0.74542	1	0.96463	1	0.074721	1
19q gain	0 (0%)	514	0.01571	1	0.041236	1	0.012239	1	0.077723	1	0.23252	1	0.038311	1	0.50709	1	0.51206	1	0.83213	1	0.49525	1	0.41961	1	0.16303	1
20p gain	0 (0%)	287	0.00014513	0.118	1.6458e-07	0.000141	4.248e-22	3.81e-19	0.00010565	0.0866	0.0072474	1	0.022228	1	3.1963e-07	0.000273	3.2029e-07	0.000273	0.62537	1	0.47156	1	0.00074249	0.587	6.8141e-08	5.87e-05
20q gain	0 (0%)	172	4.3778e-17	3.89e-14	4.3814e-16	3.88e-13	2.2246e-46	2.01e-43	1.6821e-12	1.48e-09	0.00031096	0.25	0.00013315	0.109	9.0343e-18	8.04e-15	1.1305e-13	9.97e-11	0.46311	1	0.10066	1	2.6529e-09	2.3e-06	1.3945e-21	1.25e-18
21q gain	0 (0%)	556	0.45625	1	0.71465	1	0.0026802	1	0.70869	1	0.47988	1	0.089505	1	0.61942	1	0.83363	1	0.68566	1	0.14321	1	0.92611	1	0.61735	1
22q gain	0 (0%)	568	0.69094	1	0.0070285	1	0.23406	1	0.57323	1	0.68516	1	0.4704	1	0.68907	1	0.49881	1	0.45861	1	0.59561	1	NA	NA	NA	NA
Xq gain	0 (0%)	558	0.17835	1	0.4456	1	0.016685	1	0.33957	1	0.24406	1	0.31333	1	0.84629	1	1	1	0.48172	1	0.70461	1	0.52102	1	0.88108	1
1p loss	0 (0%)	507	0.24462	1	0.0044288	1	7.5476e-06	0.0063	0.00018947	0.153	0.98399	1	0.82093	1	0.076382	1	0.0082272	1	0.19261	1	0.62049	1	0.97299	1	0.036654	1
1q loss	0 (0%)	550	0.55906	1	0.0258	1	0.082264	1	0.1552	1	0.82472	1	0.94863	1	0.1581	1	0.32381	1	0.42483	1	0.72532	1	1	1	0.2022	1
2p loss	0 (0%)	565	1	1	0.73888	1	0.073513	1	NA	NA	0.016828	1	0.65784	1	NA	NA	NA	NA	0.015125	1	0.013286	1	NA	NA	NA	NA
2q loss	0 (0%)	567	0.73955	1	0.61416	1	0.54823	1	NA	NA	0.15705	1	0.29927	1	NA	NA	NA	NA	0.058427	1	0.045527	1	NA	NA	NA	NA
3p loss	0 (0%)	540	1	1	0.29167	1	0.83112	1	0.83444	1	0.70251	1	0.53595	1	0.44134	1	0.15697	1	0.10485	1	0.72944	1	0.58823	1	0.30175	1
3q loss	0 (0%)	558	0.44953	1	0.01378	1	0.75688	1	0.019803	1	0.090255	1	0.39819	1	0.3845	1	0.18399	1	0.73957	1	0.7721	1	0.90295	1	0.41055	1
4p loss	0 (0%)	453	0.22709	1	0.2084	1	5.4975e-11	4.79e-08	0.0027558	1	0.69281	1	0.88949	1	0.0061971	1	0.057158	1	0.045027	1	0.76936	1	0.080228	1	0.027335	1
4q loss	0 (0%)	462	0.21346	1	0.13368	1	3.1754e-12	2.79e-09	0.0088832	1	0.60616	1	0.81014	1	0.0021315	1	0.053451	1	0.012191	1	0.56362	1	0.034572	1	0.047982	1
5p loss	0 (0%)	541	0.26897	1	0.44993	1	0.00054432	0.433	0.09278	1	0.55563	1	0.44868	1	0.23394	1	0.035241	1	0.96862	1	0.82879	1	0.72655	1	0.088353	1
5q loss	0 (0%)	515	0.014448	1	0.01062	1	5.5316e-07	0.00047	0.1697	1	0.18571	1	0.81164	1	0.021113	1	0.09854	1	0.96346	1	0.57856	1	0.5183	1	0.039907	1
6p loss	0 (0%)	557	0.13176	1	0.18635	1	0.026043	1	0.27803	1	0.6111	1	0.64127	1	0.88965	1	0.60116	1	0.60161	1	0.92285	1	1	1	0.64645	1
6q loss	0 (0%)	542	0.78382	1	0.62104	1	0.09827	1	0.93869	1	0.13243	1	0.14518	1	0.73685	1	0.67654	1	0.26225	1	0.29769	1	0.6785	1	0.79925	1
7q loss	0 (0%)	572	NA	NA	NA	NA	0.21176	1	NA	NA	0.8342	1	1	1	NA	NA	NA	NA	0.76387	1	1	1	NA	NA	NA	NA
8p loss	0 (0%)	430	0.0040565	1	0.0018576	1	1.1426e-18	1.02e-15	0.00010881	0.089	0.28049	1	0.039313	1	0.11036	1	0.15185	1	0.51503	1	0.73021	1	0.0023182	1	0.0076679	1
8q loss	0 (0%)	563	0.66875	1	0.66654	1	0.082808	1	0.58	1	0.02371	1	0.53258	1	1	1	0.8276	1	0.15853	1	0.27077	1	1	1	0.69156	1
9p loss	0 (0%)	536	0.9107	1	0.28571	1	2.8967e-05	0.024	0.0049885	1	0.24717	1	0.14697	1	0.10225	1	0.022105	1	0.12745	1	1	1	0.28396	1	0.051546	1
9q loss	0 (0%)	538	0.24114	1	0.0096951	1	1.9547e-06	0.00164	0.00046787	0.373	0.69204	1	0.20908	1	0.021351	1	0.016716	1	0.049149	1	0.81952	1	0.12211	1	0.022846	1
10p loss	0 (0%)	535	0.71966	1	0.48999	1	0.00086224	0.679	0.43399	1	0.05304	1	0.68205	1	0.40869	1	0.53216	1	0.13213	1	0.59051	1	1	1	0.97304	1
10q loss	0 (0%)	529	0.33458	1	0.41893	1	1.4367e-06	0.00121	0.14795	1	0.020449	1	0.7719	1	0.10225	1	0.2311	1	0.71404	1	0.81051	1	0.39843	1	0.91576	1
11p loss	0 (0%)	535	0.72982	1	0.33609	1	0.0097676	1	0.70517	1	0.32176	1	0.20106	1	0.071558	1	0.083775	1	0.11333	1	0.35936	1	0.080344	1	0.062947	1
11q loss	0 (0%)	524	0.82653	1	0.46367	1	0.0016581	1	0.32175	1	0.73107	1	0.29206	1	0.099677	1	0.50904	1	0.12883	1	0.83548	1	0.074249	1	0.0058251	1
12p loss	0 (0%)	542	0.093826	1	0.22765	1	5.424e-07	0.000461	0.27062	1	0.69409	1	0.37272	1	0.20105	1	0.46045	1	0.54148	1	0.22186	1	0.076449	1	0.63306	1
12q loss	0 (0%)	547	0.35195	1	0.083441	1	1.1071e-06	0.000936	0.52115	1	0.8849	1	0.61896	1	0.14256	1	0.18877	1	0.6164	1	0.6809	1	0.13179	1	0.73635	1
13q loss	0 (0%)	563	0.29716	1	0.28202	1	0.049459	1	0.1813	1	0.071568	1	0.10777	1	0.23575	1	0.66836	1	0.7263	1	0.40273	1	0.43782	1	0.44469	1
14q loss	0 (0%)	432	6.5175e-05	0.0537	2.8353e-07	0.000243	1.1184e-31	1.01e-28	1.633e-07	0.00014	0.00036383	0.291	0.011993	1	1.7256e-07	0.000148	0.00070476	0.559	0.11445	1	0.70906	1	1.5063e-06	0.00127	0.00014546	0.118
15q loss	0 (0%)	419	0.0050013	1	0.003108	1	2.0874e-24	1.88e-21	0.013087	1	0.3029	1	0.83197	1	1.1894e-05	0.00992	0.00057188	0.455	0.3675	1	0.24605	1	0.008727	1	0.00015827	0.129
16p loss	0 (0%)	560	0.26576	1	0.18385	1	0.09948	1	0.1813	1	0.56058	1	0.64644	1	0.58888	1	0.60116	1	1	1	0.91089	1	0.60237	1	0.60535	1
16q loss	0 (0%)	558	0.028437	1	0.24292	1	0.0022089	1	0.49305	1	0.45925	1	0.74782	1	0.091107	1	0.12148	1	0.13425	1	0.25684	1	0.38576	1	0.33986	1
17p loss	0 (0%)	323	0.00027732	0.223	0.0017644	1	5.4882e-22	4.92e-19	1.432e-06	0.00121	0.3171	1	0.48564	1	3.2518e-06	0.00272	0.00079532	0.628	0.027	1	0.49718	1	6.5374e-05	0.0538	0.00031275	0.251
17q loss	0 (0%)	530	0.84393	1	0.48675	1	0.0023038	1	0.92563	1	0.57629	1	0.58734	1	0.10108	1	0.10474	1	0.11572	1	0.63456	1	0.19847	1	0.30434	1
18p loss	0 (0%)	251	1.2405e-13	1.09e-10	3.4045e-12	2.99e-09	4.2634e-47	3.85e-44	1.3507e-18	1.2e-15	0.012006	1	0.015022	1	5.387e-16	4.77e-13	2.735e-11	2.39e-08	0.065035	1	0.7872	1	1.0751e-10	9.36e-08	7.8323e-12	6.85e-09
18q loss	0 (0%)	223	1.3553e-12	1.19e-09	4.3076e-12	3.77e-09	6.8004e-51	6.15e-48	1.9883e-19	1.78e-16	0.024108	1	0.094846	1	3.958e-16	3.51e-13	3.6833e-09	3.19e-06	0.0093757	1	0.37782	1	1.0659e-09	9.26e-07	5.1599e-12	4.51e-09
19p loss	0 (0%)	555	0.73955	1	0.4311	1	1.4622e-05	0.0122	0.047613	1	0.57892	1	0.70494	1	0.0015479	1	0.0028882	1	0.23499	1	0.37109	1	0.051435	1	0.55767	1
19q loss	0 (0%)	557	0.73955	1	0.4311	1	0.00023546	0.19	0.12783	1	0.62489	1	0.91243	1	0.0015479	1	0.0028882	1	0.42424	1	0.097617	1	0.054211	1	0.4083	1
20p loss	0 (0%)	528	0.041217	1	0.18413	1	4.5625e-07	0.000388	0.1166	1	0.7701	1	0.36523	1	0.57735	1	0.39072	1	0.55412	1	0.48621	1	0.80462	1	0.68574	1
21q loss	0 (0%)	461	0.3047	1	0.4869	1	3.6397e-05	0.0301	0.078168	1	0.3278	1	0.3099	1	0.23518	1	0.3916	1	0.11838	1	0.3424	1	0.38349	1	0.16561	1
22q loss	0 (0%)	453	0.014768	1	0.0060575	1	7.7977e-14	6.89e-11	0.27793	1	0.41859	1	0.26407	1	0.067555	1	0.064607	1	0.066218	1	0.10019	1	0.0022603	1	0.095419	1
Xq loss	0 (0%)	564	0.76483	1	1	1	0.33904	1	0.50745	1	0.10782	1	0.49495	1	0.01571	1	0.067381	1	0.51495	1	0.65187	1	0.24724	1	0.176	1
