		Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_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
1p gain	21 (6%)	337	0.97137	1	0.65195	1	0.2131	1	0.21659	1	0.86661	1	0.23188	1	0.71876	1	0.14049	1	0.24425	1	0.61357	1
1q gain	74 (21%)	284	0.13272	1	0.10044	1	1.4978e-05	0.0112	0.011057	1	0.62705	1	0.52188	1	0.0032918	1	0.0017889	1	0.046228	1	0.085224	1
2p gain	85 (24%)	273	0.010309	1	0.016172	1	4.6924e-09	3.61e-06	1.9583e-05	0.0147	0.10485	1	0.36985	1	0.016498	1	0.00053126	0.38	0.98288	1	0.24943	1
2q gain	39 (11%)	319	0.21552	1	0.067931	1	0.00038047	0.276	0.0090505	1	0.44865	1	0.49672	1	0.0045574	1	0.0046095	1	0.85461	1	0.36056	1
3p gain	42 (12%)	316	0.53925	1	0.21493	1	0.0079748	1	0.00080209	0.569	0.74142	1	0.6165	1	0.13492	1	0.065087	1	0.88411	1	0.25139	1
3q gain	162 (45%)	196	0.071969	1	0.6531	1	0.023822	1	0.034291	1	0.49518	1	0.53657	1	0.44057	1	0.30541	1	0.72606	1	0.46491	1
4p gain	14 (4%)	344	0.1484	1	0.14985	1	0.02323	1	0.14883	1	0.19414	1	0.49317	1	0.012351	1	0.16277	1	1	1	0.92412	1
4q gain	7 (2%)	351	0.36322	1	1	1	0.45563	1	NA	NA	NA	NA	NA	NA	0.76682	1	0.3559	1	0.60951	1	0.74029	1
5p gain	163 (46%)	195	0.88631	1	0.84628	1	0.00018495	0.135	0.023824	1	0.28218	1	0.3023	1	0.15037	1	0.60176	1	0.4408	1	0.12464	1
5q gain	34 (9%)	324	0.091217	1	0.37059	1	0.036728	1	0.041372	1	0.66077	1	0.57816	1	0.15364	1	0.39191	1	0.68061	1	0.079143	1
6p gain	31 (9%)	327	0.0010169	0.716	0.0085349	1	0.00522	1	0.35112	1	0.57973	1	0.23705	1	0.044452	1	0.0014127	0.982	0.92334	1	1	1
6q gain	19 (5%)	339	0.0032122	1	0.017402	1	0.0052616	1	0.028344	1	0.72102	1	0.55515	1	0.18584	1	0.0011177	0.782	0.69595	1	0.42265	1
7p gain	94 (26%)	264	0.12859	1	0.17084	1	4.075e-05	0.0302	0.001063	0.746	0.8081	1	0.86728	1	0.25497	1	0.099375	1	0.92224	1	0.0099388	1
7q gain	88 (25%)	270	0.065972	1	0.097862	1	4.5017e-11	3.49e-08	3.6029e-06	0.00273	0.62196	1	0.70035	1	0.022673	1	0.026029	1	0.38394	1	0.0016374	1
8p gain	47 (13%)	311	0.12873	1	0.14267	1	0.19393	1	0.70558	1	0.78294	1	0.42749	1	0.070516	1	0.004551	1	0.25053	1	0.17832	1
8q gain	101 (28%)	257	0.036525	1	0.024581	1	0.014142	1	0.082371	1	0.75626	1	0.87702	1	0.011459	1	0.0012792	0.892	0.08233	1	0.15975	1
9p gain	19 (5%)	339	0.28964	1	0.13856	1	0.10235	1	0.92965	1	0.17317	1	0.0002552	0.186	0.0096746	1	0.017195	1	0.43646	1	0.05322	1
9q gain	28 (8%)	330	0.069877	1	0.029367	1	0.034214	1	0.084003	1	0.075259	1	0.0024803	1	0.0017707	1	0.0014985	1	0.25357	1	0.041263	1
10p gain	16 (4%)	342	0.2079	1	1	1	0.5923	1	0.22402	1	0.4632	1	0.10702	1	0.5246	1	1	1	0.86928	1	0.82033	1
10q gain	6 (2%)	352	NA	NA	NA	NA	0.52601	1	0.22273	1	0.10424	1	0.65065	1	0.57843	1	1	1	0.4934	1	1	1
11p gain	19 (5%)	339	0.90823	1	0.73368	1	0.87637	1	0.30594	1	0.79371	1	0.44486	1	0.8346	1	0.78914	1	0.43646	1	0.85224	1
11q gain	22 (6%)	336	0.041129	1	0.19349	1	0.20918	1	0.20665	1	0.94581	1	0.3808	1	0.43215	1	0.042257	1	0.85961	1	0.7551	1
12p gain	97 (27%)	261	0.014628	1	0.11889	1	1.7744e-05	0.0133	0.20845	1	0.18155	1	0.81732	1	0.15278	1	0.056541	1	0.77491	1	0.4886	1
12q gain	43 (12%)	315	0.029591	1	0.1428	1	2.3369e-05	0.0175	0.19635	1	0.14445	1	0.75934	1	0.53408	1	0.0086919	1	0.34848	1	0.28344	1
13q gain	8 (2%)	350	0.76867	1	1	1	0.60549	1	0.11755	1	0.28732	1	0.35113	1	0.13224	1	0.083452	1	0.7573	1	0.76466	1
14q gain	35 (10%)	323	0.086925	1	0.56842	1	0.94969	1	0.78048	1	0.86152	1	0.66415	1	0.34169	1	0.5218	1	0.080698	1	0.13884	1
15q gain	33 (9%)	325	0.2078	1	0.032532	1	0.010001	1	0.029594	1	0.21509	1	0.021403	1	0.0067201	1	0.057487	1	0.050167	1	0.0019332	1
16p gain	16 (4%)	342	0.58909	1	1	1	0.0009712	0.686	0.35504	1	0.72102	1	0.29146	1	0.52116	1	0.2662	1	0.86928	1	0.93367	1
16q gain	21 (6%)	337	0.23729	1	0.84377	1	8.244e-05	0.0608	0.62986	1	0.39681	1	0.12697	1	0.34511	1	0.73497	1	0.21787	1	0.59236	1
17p gain	9 (3%)	349	0.29798	1	0.08809	1	0.0037853	1	0.11755	1	0.068533	1	0.40643	1	0.35357	1	0.025972	1	0.28405	1	0.039515	1
17q gain	37 (10%)	321	0.012958	1	0.028176	1	1.0913e-07	8.32e-05	0.0033558	1	0.41942	1	0.75017	1	0.003283	1	0.0061884	1	0.52817	1	0.18562	1
18p gain	56 (16%)	302	0.0025961	1	9.5207e-06	0.00718	0.00024463	0.178	0.18518	1	0.13987	1	0.15047	1	0.039102	1	0.0097742	1	0.64855	1	0.10224	1
18q gain	39 (11%)	319	0.0024775	1	4.9465e-05	0.0367	0.0087195	1	0.65186	1	0.17522	1	0.060638	1	0.0087331	1	0.0040363	1	0.19332	1	0.055534	1
19p gain	35 (10%)	323	0.051591	1	0.16251	1	6.254e-05	0.0463	0.0046664	1	0.00049193	0.354	0.00194	1	0.069535	1	0.0086564	1	0.072342	1	0.3136	1
19q gain	50 (14%)	308	0.057664	1	0.7726	1	0.028504	1	0.69223	1	0.06802	1	0.021402	1	0.26977	1	0.077472	1	0.64232	1	0.95245	1
20p gain	97 (27%)	261	0.13174	1	0.037917	1	4.2859e-06	0.00324	0.05944	1	0.55805	1	0.28168	1	0.32182	1	0.32208	1	0.34252	1	0.014841	1
20q gain	88 (25%)	270	0.59314	1	0.46392	1	4.872e-06	0.00368	0.21554	1	0.76462	1	0.32782	1	0.10335	1	0.0031357	1	0.52293	1	0.018214	1
21q gain	18 (5%)	340	0.96811	1	0.42462	1	0.65475	1	0.03244	1	0.5776	1	0.96528	1	0.69725	1	0.35358	1	0.76091	1	0.1757	1
22q gain	84 (23%)	274	0.0036214	1	0.0085753	1	4.046e-05	0.0301	0.013083	1	0.25811	1	0.0075331	1	0.070527	1	0.056273	1	0.98288	1	0.012239	1
Xq gain	9 (3%)	349	0.76867	1	1	1	0.11583	1	0.62397	1	0.44953	1	0.58442	1	0.77288	1	0.15446	1	0.67831	1	0.21005	1
1p loss	52 (15%)	306	0.0024775	1	0.0004187	0.304	1.7728e-09	1.37e-06	1.1942e-06	0.000908	0.21129	1	0.12361	1	0.00076617	0.544	0.0070651	1	0.24255	1	0.021507	1
1q loss	9 (3%)	349	NA	NA	NA	NA	0.24973	1	0.35508	1	0.73727	1	0.75546	1	0.38529	1	0.2856	1	1	1	0.81074	1
2p loss	3 (1%)	355	NA	NA	NA	NA	0.30658	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
2q loss	11 (3%)	347	0.39507	1	1	1	0.0039379	1	0.012553	1	0.73758	1	0.58442	1	0.76877	1	0.78818	1	0.54024	1	0.74177	1
3p loss	148 (41%)	210	0.050134	1	0.44773	1	6.6408e-05	0.0491	3.0921e-05	0.023	0.66763	1	0.23475	1	0.64893	1	0.023334	1	0.76848	1	0.084304	1
3q loss	26 (7%)	332	0.26082	1	0.70138	1	0.032875	1	0.059066	1	0.77369	1	0.94141	1	0.38396	1	0.076884	1	0.74473	1	0.91318	1
4p loss	149 (42%)	209	0.17085	1	0.031897	1	2.2628e-08	1.74e-05	3.56e-08	2.72e-05	0.061908	1	0.45626	1	0.44112	1	0.033125	1	0.29969	1	0.23246	1
4q loss	128 (36%)	230	0.0079594	1	0.00097462	0.687	1.2995e-09	1e-06	3.743e-06	0.00283	0.017669	1	0.19428	1	0.013676	1	0.00387	1	0.070216	1	0.0068404	1
5p loss	24 (7%)	334	0.19793	1	0.51386	1	0.026942	1	0.24759	1	0.30886	1	0.43803	1	0.72729	1	0.39286	1	1	1	0.82951	1
5q loss	137 (38%)	221	0.18503	1	0.36302	1	7.552e-08	5.77e-05	1.6484e-09	1.27e-06	0.10332	1	0.1077	1	0.24583	1	0.38198	1	0.44545	1	0.28648	1
6p loss	34 (9%)	324	0.079844	1	0.016367	1	0.00037315	0.271	0.0018796	1	0.075465	1	0.031057	1	0.0037054	1	0.0092401	1	0.52045	1	0.21245	1
6q loss	40 (11%)	318	0.08274	1	0.011644	1	0.002303	1	0.016915	1	0.074785	1	0.14213	1	0.064435	1	0.1167	1	1	1	0.82558	1
7p loss	22 (6%)	336	0.40774	1	0.83372	1	0.0025297	1	0.019565	1	0.50184	1	0.10885	1	0.46247	1	0.18677	1	0.096789	1	0.10443	1
7q loss	11 (3%)	347	0.47205	1	0.8485	1	0.074627	1	0.50859	1	1	1	0.69466	1	0.082478	1	0.044966	1	0.38277	1	0.37702	1
8p loss	105 (29%)	253	0.27633	1	0.39643	1	3.4931e-06	0.00265	0.01541	1	0.21675	1	0.96612	1	0.3975	1	0.52535	1	0.78688	1	0.52413	1
8q loss	12 (3%)	346	0.2079	1	0.26173	1	0.0094108	1	0.30261	1	0.29598	1	0.62935	1	0.30341	1	0.067364	1	0.25044	1	0.85023	1
9p loss	149 (42%)	209	0.059096	1	0.49841	1	1.1684e-11	9.09e-09	2.8124e-08	2.15e-05	0.91629	1	0.32487	1	0.93589	1	0.59406	1	0.93637	1	0.70982	1
9q loss	94 (26%)	264	0.0026004	1	0.003846	1	5.6792e-11	4.4e-08	1.0237e-05	0.00771	0.93688	1	0.27375	1	0.0012543	0.876	9.5625e-05	0.0704	0.31352	1	0.011887	1
10p loss	81 (23%)	277	0.054263	1	0.13391	1	7.5739e-08	5.78e-05	8.397e-07	0.000639	1	1	0.063843	1	0.0033998	1	0.01083	1	0.076949	1	0.00020129	0.147
10q loss	82 (23%)	276	0.0091286	1	0.00015338	0.112	4.1372e-11	3.21e-08	2.7478e-05	0.0205	0.16927	1	0.0026251	1	0.00050315	0.361	0.00088588	0.626	0.055077	1	0.00043695	0.316
11p loss	57 (16%)	301	0.011825	1	0.31148	1	0.00069311	0.493	0.00058281	0.415	0.045323	1	0.013425	1	0.14037	1	0.094103	1	0.87233	1	0.37189	1
11q loss	37 (10%)	321	0.32228	1	0.56841	1	3.0968e-05	0.023	0.0005716	0.408	0.069466	1	0.24561	1	0.048409	1	0.054028	1	0.38413	1	0.27294	1
12p loss	6 (2%)	352	NA	NA	NA	NA	0.69034	1	0.17942	1	NA	NA	NA	NA	0.22465	1	0.43092	1	0.43222	1	0.57106	1
12q loss	5 (1%)	353	NA	NA	NA	NA	0.53198	1	0.17942	1	0.29619	1	0.43741	1	0.77511	1	0.091656	1	1	1	0.57106	1
13q loss	137 (38%)	221	0.20016	1	0.62629	1	1.2154e-08	9.33e-06	0.00047833	0.344	0.16163	1	0.35516	1	0.45238	1	0.58169	1	0.8083	1	0.041159	1
14q loss	67 (19%)	291	0.00058	0.414	0.021694	1	0.00049266	0.354	0.0011143	0.781	0.046073	1	0.016406	1	0.00010097	0.0742	6.4037e-09	4.92e-06	0.43363	1	0.061445	1
15q loss	40 (11%)	318	0.76434	1	0.11493	1	0.33612	1	0.0011491	0.803	0.0076185	1	0.00174	1	0.16922	1	0.011927	1	0.18777	1	0.35944	1
16p loss	55 (15%)	303	0.42164	1	0.42298	1	0.00016533	0.121	0.017551	1	0.41149	1	0.30133	1	0.33435	1	0.036748	1	0.30169	1	0.013348	1
16q loss	70 (20%)	288	0.065068	1	0.2372	1	0.0021031	1	0.011611	1	0.11136	1	0.17126	1	0.15364	1	0.0005197	0.372	0.90345	1	0.001294	0.901
17p loss	129 (36%)	229	0.10165	1	1	1	0.00012684	0.0931	7.3077e-05	0.0539	0.013307	1	0.112	1	0.49882	1	0.43679	1	0.19723	1	0.0021764	1
17q loss	22 (6%)	336	0.14736	1	0.19349	1	0.10382	1	0.012325	1	0.30306	1	0.94307	1	0.00084512	0.598	0.035177	1	0.8173	1	0.34969	1
18p loss	40 (11%)	318	0.83533	1	0.90723	1	0.013412	1	0.061173	1	0.27799	1	0.7177	1	0.021688	1	0.17933	1	0.66749	1	0.68581	1
18q loss	73 (20%)	285	0.58036	1	0.84409	1	0.0054811	1	0.1109	1	0.19345	1	0.56069	1	0.24372	1	0.91935	1	0.071808	1	0.98226	1
19p loss	60 (17%)	298	0.039371	1	0.045029	1	0.00047626	0.343	0.1852	1	0.70826	1	0.82708	1	0.0010458	0.735	2.3793e-05	0.0178	0.0021214	1	0.00044217	0.319
19q loss	40 (11%)	318	0.54085	1	0.2427	1	0.24893	1	0.022161	1	0.036643	1	0.11058	1	0.8114	1	0.13795	1	0.23457	1	0.34176	1
20p loss	17 (5%)	341	0.26792	1	0.023682	1	0.10135	1	0.20635	1	0.040797	1	0.57518	1	0.8022	1	0.59665	1	0.40102	1	0.3995	1
20q loss	20 (6%)	338	0.037591	1	0.020284	1	0.021311	1	0.14039	1	0.077419	1	0.46574	1	0.012559	1	0.010769	1	0.54089	1	0.16277	1
21q loss	111 (31%)	247	0.024673	1	0.016071	1	9.7269e-10	7.53e-07	1.3138e-05	0.00988	0.33796	1	0.22874	1	0.011505	1	0.015864	1	0.0096864	1	0.61048	1
22q loss	35 (10%)	323	0.05705	1	0.15715	1	0.50924	1	0.75426	1	0.60696	1	0.18797	1	0.45957	1	0.052444	1	0.10303	1	0.45872	1
Xq loss	14 (4%)	344	0.63366	1	1	1	0.4284	1	0.66447	1	0.28072	1	0.00042381	0.307	0.67435	1	0.85314	1	0.33458	1	0.31303	1
