Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Chi-square test_P	Chi-square 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
1p gain	11 (3%)	341	0.3792	1	0.69428	1	0.95498	1	0.63963	1	0.17908	1	0.33985	1	0.86085	1	1	1
1q gain	42 (12%)	310	0.00012214	0.0711	0.001875	1	0.48962	1	0.50408	1	0.012861	1	0.0049911	1	0.032925	1	0.24817	1
2p gain	31 (9%)	321	9.1862e-05	0.0538	0.00010253	0.06	0.36829	1	0.8024	1	0.014559	1	0.023634	1	0.69683	1	0.20434	1
2q gain	21 (6%)	331	0.0052746	1	0.0018745	1	0.50888	1	0.92793	1	0.078134	1	0.12668	1	0.8785	1	0.13604	1
3p gain	29 (8%)	323	0.48881	1	8.2588e-05	0.0486	0.046811	1	0.58313	1	0.0032341	1	0.0032582	1	0.00043283	0.245	0.11113	1
3q gain	112 (32%)	240	0.00082464	0.464	4.2678e-05	0.0254	0.22801	1	0.51965	1	0.017811	1	0.0038388	1	0.00021471	0.123	0.27038	1
4p gain	13 (4%)	339	0.015345	1	0.064019	1	0.23083	1	1	1	0.16623	1	0.22798	1	0.041682	1	0.23707	1
4q gain	9 (3%)	343	0.066086	1	0.10256	1	0.67858	1	1	1	0.57619	1	0.63001	1	0.91737	1	0.79462	1
5p gain	88 (25%)	264	5.6393e-09	3.49e-06	0.032589	1	0.66604	1	0.42984	1	0.57882	1	0.4094	1	1	1	0.66972	1
5q gain	28 (8%)	324	0.043249	1	0.69268	1	1	1	1	1	0.81884	1	0.46147	1	1	1	0.4568	1
6p gain	26 (7%)	326	0.017244	1	0.046554	1	0.21472	1	0.54651	1	0.90196	1	0.87117	1	0.90098	1	0.22056	1
6q gain	19 (5%)	333	0.41193	1	0.082072	1	0.67736	1	0.7637	1	0.72713	1	0.37765	1	1	1	0.45263	1
7p gain	78 (22%)	274	2.9546e-05	0.0176	0.00040615	0.232	0.62271	1	0.64007	1	0.81655	1	0.93919	1	0.73815	1	0.46523	1
7q gain	48 (14%)	304	7.083e-10	4.43e-07	1.0098e-06	0.000612	0.48832	1	0.92025	1	0.27532	1	0.11215	1	0.141	1	0.90365	1
8p gain	53 (15%)	299	0.0079594	1	0.002003	1	0.72763	1	0.11397	1	0.38091	1	0.31331	1	0.12341	1	0.34905	1
8q gain	145 (41%)	207	4.9719e-09	3.08e-06	0.00034122	0.195	0.51953	1	0.21946	1	0.52011	1	0.51899	1	0.48353	1	0.049351	1
9p gain	43 (12%)	309	0.00011001	0.0642	0.05949	1	0.42109	1	0.3031	1	0.28772	1	0.64347	1	0.39849	1	0.4913	1
9q gain	58 (16%)	294	0.00068632	0.387	0.0312	1	0.23934	1	0.10927	1	0.21546	1	0.1307	1	0.34483	1	0.42644	1
10p gain	12 (3%)	340	0.53907	1	0.0027806	1	0.79843	1	0.75176	1	0.054985	1	0.068933	1	0.11986	1	0.26208	1
10q gain	6 (2%)	346	0.19361	1	0.33841	1	0.57047	1	0.25633	1	1	1	1	1	0.6765	1	1	1
11p gain	17 (5%)	335	0.00020192	0.116	0.67008	1	0.83275	1	0.39868	1	0.75433	1	0.8449	1	0.86015	1	0.27278	1
11q gain	17 (5%)	335	0.029746	1	0.49414	1	0.36248	1	1	1	0.19491	1	0.28408	1	0.9516	1	0.38073	1
12p gain	65 (18%)	287	1.6377e-07	1e-04	1.8913e-05	0.0113	0.66266	1	0.72499	1	0.0039875	1	0.00061189	0.346	7.6425e-05	0.0452	0.010552	1
12q gain	26 (7%)	326	0.19383	1	0.0041952	1	0.17331	1	0.69526	1	0.064466	1	0.0017438	0.971	0.015965	1	0.082827	1
13q gain	18 (5%)	334	0.10114	1	0.035201	1	0.35004	1	0.64494	1	0.60305	1	0.90447	1	0.70548	1	0.75238	1
14q gain	58 (16%)	294	0.00013129	0.076	0.015916	1	0.44543	1	0.066651	1	0.027051	1	0.027049	1	0.030873	1	0.056627	1
15q gain	12 (3%)	340	0.48945	1	0.27242	1	0.54243	1	0.44416	1	0.87182	1	0.25473	1	0.81327	1	0.21087	1
16p gain	22 (6%)	330	0.0078536	1	8.4477e-05	0.0497	0.025886	1	0.36183	1	0.24107	1	0.9576	1	0.78091	1	0.45017	1
16q gain	30 (9%)	322	0.0018033	1	0.0042262	1	0.78258	1	0.6587	1	0.02658	1	0.43686	1	0.88455	1	0.073361	1
17p gain	20 (6%)	332	0.00036744	0.21	0.082378	1	0.54375	1	0.46842	1	0.17981	1	0.56103	1	0.17995	1	0.4182	1
17q gain	25 (7%)	327	0.00062467	0.353	0.096343	1	0.089322	1	0.51356	1	0.18967	1	0.051935	1	0.22289	1	0.41748	1
18p gain	55 (16%)	297	0.0001222	0.0711	0.058147	1	0.31798	1	0.38549	1	0.1137	1	0.0048968	1	0.40201	1	0.76625	1
18q gain	20 (6%)	332	0.0059015	1	0.00017731	0.102	0.53084	1	0.39868	1	0.019169	1	0.017071	1	0.0016361	0.915	1	1
19p gain	12 (3%)	340	0.33241	1	0.0049465	1	0.094528	1	0.08425	1	0.38904	1	0.023114	1	0.17956	1	0.26208	1
19q gain	21 (6%)	331	0.18659	1	0.058112	1	0.78795	1	0.40195	1	0.15755	1	0.31863	1	0.10447	1	0.80104	1
20p gain	68 (19%)	284	7.504e-06	0.00451	7.9034e-05	0.0467	0.062017	1	0.17483	1	0.61705	1	0.36452	1	0.21558	1	0.3509	1
20q gain	72 (20%)	280	8.4634e-07	0.000515	0.00011228	0.0655	0.92412	1	0.88442	1	0.49461	1	0.72582	1	0.54854	1	0.228	1
21q gain	9 (3%)	343	0.18187	1	0.77263	1	1	1	1	1	0.019285	1	0.055196	1	0.032136	1	1	1
22q gain	42 (12%)	310	0.00015986	0.0924	8.2145e-05	0.0485	0.64105	1	0.40527	1	0.07753	1	0.018974	1	0.43642	1	0.94682	1
Xq gain	23 (7%)	329	0.0014515	0.813	0.088752	1	0.23668	1	0.17691	1	0.5031	1	0.91288	1	0.79708	1	0.90592	1
1p loss	16 (5%)	336	4.3488e-10	2.72e-07	9.7016e-07	0.000589	0.11385	1	0.12346	1	0.012862	1	0.015561	1	0.016282	1	0.54281	1
2p loss	6 (2%)	346	0.96934	1	0.044052	1	0.68434	1	1	1	0.11466	1	0.074255	1	0.026214	1	0.17069	1
2q loss	10 (3%)	342	0.39425	1	0.093899	1	0.22852	1	0.44867	1	0.014727	1	0.013987	1	0.083147	1	0.029738	1
3p loss	133 (38%)	219	8.2427e-13	5.18e-10	3.1562e-07	0.000193	0.30389	1	0.76626	1	0.36547	1	0.17578	1	0.12604	1	0.82077	1
3q loss	22 (6%)	330	0.016821	1	0.11526	1	0.33083	1	0.42769	1	0.8813	1	0.95942	1	0.27548	1	0.80699	1
4p loss	82 (23%)	270	5.832e-12	3.66e-09	2.9767e-08	1.83e-05	0.13533	1	0.0374	1	0.0022697	1	0.00012281	0.0712	0.00017245	0.0995	0.051081	1
4q loss	55 (16%)	297	5.7324e-09	3.54e-06	3.382e-06	0.00204	0.29267	1	0.14673	1	0.014799	1	0.002775	1	0.0010747	0.604	0.091293	1
5p loss	8 (2%)	344	0.03138	1	0.0059774	1	0.61148	1	0.82051	1	0.076327	1	0.088792	1	0.057513	1	0.76979	1
5q loss	63 (18%)	289	2.1547e-14	1.36e-11	7.2711e-10	4.54e-07	0.43417	1	0.52807	1	0.0057458	1	4.5279e-05	0.0269	0.059377	1	1	1
6p loss	19 (5%)	333	0.096958	1	0.012689	1	0.0042131	1	0.16918	1	0.031706	1	0.1111	1	0.0076589	1	0.23482	1
6q loss	21 (6%)	331	0.19904	1	0.070076	1	0.010568	1	0.072535	1	0.37927	1	0.39162	1	0.054688	1	0.3083	1
7p loss	5 (1%)	347	0.9824	1	0.38838	1	NA	NA	NA	NA	0.3907	1	0.45231	1	0.23041	1	1	1
7q loss	8 (2%)	344	0.15467	1	0.3712	1	0.75237	1	0.75688	1	0.31521	1	0.906	1	0.16379	1	0.31664	1
8p loss	78 (22%)	274	1.7957e-06	0.00109	6.6589e-06	0.00401	0.89106	1	1	1	0.61931	1	0.4853	1	0.10569	1	0.46993	1
8q loss	7 (2%)	345	0.32213	1	0.060447	1	0.8451	1	0.65804	1	1	1	0.49561	1	0.27264	1	0.75856	1
9p loss	93 (26%)	259	1.6584e-09	1.03e-06	2.2482e-08	1.38e-05	0.48439	1	0.84682	1	0.31139	1	0.069576	1	0.013896	1	0.26726	1
9q loss	31 (9%)	321	0.003446	1	0.067865	1	0.89979	1	0.477	1	0.82908	1	0.85521	1	0.97109	1	0.067768	1
10p loss	52 (15%)	300	8.9333e-05	0.0524	0.065611	1	0.26984	1	0.59353	1	0.93707	1	0.80499	1	0.5392	1	0.42979	1
10q loss	29 (8%)	323	8.1238e-08	4.98e-05	0.0066735	1	0.48032	1	0.74201	1	0.033397	1	0.0012307	0.69	0.00041896	0.238	0.56766	1
11p loss	48 (14%)	304	0.00025684	0.147	0.04444	1	0.11004	1	0.69922	1	0.0017333	0.967	0.0059758	1	0.063089	1	0.81651	1
11q loss	69 (20%)	283	2.1905e-13	1.38e-10	7.2849e-05	0.0432	0.86409	1	0.59353	1	0.011524	1	0.050969	1	0.05813	1	0.83366	1
12p loss	13 (4%)	339	0.041409	1	0.13896	1	0.16933	1	0.20953	1	0.46806	1	0.45915	1	0.5974	1	0.19766	1
12q loss	8 (2%)	344	0.31533	1	0.073031	1	0.76577	1	0.67098	1	0.20101	1	0.30816	1	0.60511	1	0.079745	1
13q loss	72 (20%)	280	2.38e-07	0.000145	9.4774e-10	5.9e-07	0.31542	1	0.43888	1	0.028593	1	2.3757e-05	0.0142	0.0061641	1	0.33861	1
14q loss	18 (5%)	334	0.40863	1	0.041537	1	0.14112	1	0.63963	1	0.010806	1	0.015397	1	0.0085821	1	0.29893	1
15q loss	27 (8%)	325	0.0038668	1	0.17291	1	0.39892	1	0.31817	1	0.4575	1	0.24642	1	0.27174	1	0.18916	1
16p loss	12 (3%)	340	0.070625	1	0.029407	1	0.10935	1	0.29441	1	0.041388	1	0.013987	1	0.09213	1	0.10837	1
16q loss	29 (8%)	323	0.0070367	1	4.1892e-05	0.025	0.034717	1	0.0054587	1	4.7208e-07	0.000287	1.3363e-08	8.24e-06	0.00041896	0.238	0.0095489	1
17p loss	49 (14%)	303	0.021079	1	1.2742e-05	0.00765	0.74831	1	0.56729	1	0.63743	1	0.021813	1	0.17801	1	0.78221	1
17q loss	6 (2%)	346	0.044614	1	0.023184	1	0.43841	1	0.40247	1	0.45621	1	0.86093	1	0.51744	1	1	1
18p loss	30 (9%)	322	0.031346	1	0.024259	1	0.8461	1	0.34382	1	0.57825	1	0.74676	1	0.45736	1	0.63168	1
18q loss	93 (26%)	259	1.918e-09	1.19e-06	6.7269e-08	4.13e-05	0.38631	1	0.19722	1	0.019171	1	0.5121	1	0.0072573	1	0.32074	1
19p loss	27 (8%)	325	0.012987	1	0.11275	1	0.73735	1	0.94066	1	0.11829	1	0.41646	1	0.87737	1	0.11286	1
19q loss	21 (6%)	331	0.0035027	1	0.18043	1	0.13134	1	0.29347	1	0.69431	1	0.83272	1	0.23882	1	1	1
20p loss	22 (6%)	330	0.028261	1	0.31927	1	0.30236	1	0.81443	1	0.22385	1	0.090392	1	0.55047	1	0.25435	1
20q loss	10 (3%)	342	0.022158	1	0.21225	1	0.65112	1	0.77935	1	0.035931	1	0.046799	1	0.78837	1	0.80483	1
21q loss	63 (18%)	289	2.1597e-06	0.0013	0.010851	1	0.94232	1	0.20446	1	0.8923	1	0.51213	1	0.64871	1	0.47255	1
22q loss	26 (7%)	326	0.0033051	1	0.030467	1	1	1	0.77877	1	0.39131	1	0.77198	1	0.0075763	1	0.7672	1
Xq loss	8 (2%)	344	0.06711	1	0.076335	1	0.9034	1	0.13033	1	0.80412	1	0.80209	1	1	1	0.76979	1