		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	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
1p gain	0 (0%)	488	NA	NA	NA	NA	0.62741	1	NA	NA	0.43887	1	0.035855	1	0.84555	1	0.85029	1	0.4573	1	1	1
1q gain	0 (0%)	461	0.61119	1	1	1	1.0459e-05	0.00625	0.45189	1	0.43377	1	0.19022	1	0.0097169	1	0.15038	1	0.013372	1	0.18921	1
2p gain	0 (0%)	445	0.56067	1	0.47247	1	1.0848e-06	0.000674	0.65317	1	0.046154	1	0.78296	1	0.14408	1	0.078453	1	0.2281	1	0.16042	1
2q gain	0 (0%)	444	0.56067	1	0.47247	1	4.9027e-05	0.0282	0.82441	1	0.052756	1	0.86158	1	0.051935	1	0.049818	1	0.14587	1	0.16042	1
3p gain	0 (0%)	486	NA	NA	NA	NA	0.38574	1	1	1	0.10217	1	0.0032938	1	0.29418	1	0.16078	1	0.011355	1	0.052832	1
3q gain	0 (0%)	466	0.082325	1	0.085132	1	6.5793e-05	0.0376	0.080411	1	0.007183	1	0.00010715	0.0609	0.00039457	0.214	0.0093127	1	0.0003395	0.186	0.0076133	1
4p gain	0 (0%)	485	NA	NA	NA	NA	0.2057	1	0.60825	1	0.42832	1	0.080261	1	0.025659	1	0.37796	1	0.00050042	0.268	0.040706	1
4q gain	0 (0%)	485	NA	NA	NA	NA	0.67035	1	0.79533	1	0.87831	1	0.33815	1	0.011216	1	0.5092	1	0.0039355	1	0.14678	1
5p gain	0 (0%)	352	0.59284	1	0.59153	1	1.2527e-05	0.00745	0.44108	1	0.081729	1	0.054605	1	0.045779	1	0.0084423	1	0.036235	1	0.0059502	1
5q gain	0 (0%)	337	0.10537	1	0.12107	1	5.8712e-05	0.0337	0.37509	1	0.1584	1	0.17451	1	0.038112	1	0.0051214	1	0.11594	1	0.0014103	0.714
6p gain	0 (0%)	487	NA	NA	NA	NA	0.77018	1	0.55518	1	0.8188	1	0.87678	1	0.21454	1	0.44902	1	0.34197	1	0.38929	1
6q gain	0 (0%)	488	NA	NA	NA	NA	0.53168	1	0.79533	1	0.57144	1	0.62591	1	0.44232	1	0.57135	1	0.73725	1	0.43074	1
7p gain	0 (0%)	366	0.87675	1	0.93891	1	5.0545e-06	0.00307	0.054291	1	0.00026802	0.148	0.0056517	1	0.067954	1	0.082377	1	0.025081	1	0.70261	1
7q gain	0 (0%)	364	0.87675	1	0.93891	1	1.3614e-05	0.00809	0.041704	1	0.00011777	0.0665	0.00071795	0.378	0.058061	1	0.13146	1	0.012911	1	0.48104	1
8p gain	0 (0%)	479	NA	NA	NA	NA	5.418e-05	0.0312	0.079578	1	0.086779	1	0.14595	1	0.00097842	0.507	0.00068297	0.361	0.0030191	1	0.11654	1
8q gain	0 (0%)	459	0.053628	1	0.058091	1	2.747e-07	0.000173	0.0010457	0.535	0.010176	1	0.044916	1	1.1473e-07	7.27e-05	4.879e-05	0.0282	6.766e-06	0.00409	0.018229	1
9p gain	0 (0%)	485	NA	NA	NA	NA	0.74129	1	0.24924	1	0.17017	1	0.17028	1	0.10317	1	0.05713	1	0.90224	1	0.030618	1
9q gain	0 (0%)	485	NA	NA	NA	NA	0.28254	1	1	1	0.10371	1	0.33815	1	0.52284	1	0.63567	1	0.60179	1	0.17809	1
10p gain	0 (0%)	487	NA	NA	NA	NA	0.39007	1	1	1	0.98053	1	1	1	0.267	1	0.31138	1	0.76999	1	0.38929	1
10q gain	0 (0%)	489	NA	NA	NA	NA	0.18428	1	1	1	0.71582	1	0.61472	1	0.68786	1	0.50758	1	0.83162	1	0.36659	1
11p gain	0 (0%)	476	0.76851	1	0.77815	1	0.00052935	0.283	0.77137	1	0.43744	1	0.3949	1	0.49103	1	0.26531	1	0.94985	1	0.40973	1
11q gain	0 (0%)	478	0.76851	1	0.77815	1	0.0011789	0.601	0.69815	1	0.54134	1	0.48032	1	0.58591	1	0.50493	1	0.94611	1	0.35537	1
12p gain	0 (0%)	415	0.19401	1	0.16527	1	7.9908e-07	0.000498	0.0010394	0.534	5.6676e-07	0.000355	0.013931	1	1.1022e-05	0.00658	1.8938e-05	0.0111	6.9492e-06	0.00419	0.71233	1
12q gain	0 (0%)	415	0.19401	1	0.16527	1	7.9908e-07	0.000498	0.0010394	0.534	5.6676e-07	0.000355	0.014143	1	1.1022e-05	0.00658	1.8938e-05	0.0111	6.9492e-06	0.00419	0.61721	1
13q gain	0 (0%)	479	NA	NA	NA	NA	0.74221	1	0.076952	1	0.46728	1	0.77086	1	0.068473	1	0.63576	1	0.61422	1	0.91356	1
14q gain	0 (0%)	488	NA	NA	NA	NA	0.049557	1	0.60825	1	0.86889	1	0.059647	1	0.0035445	1	0.047744	1	0.065944	1	0.0053427	1
15q gain	0 (0%)	479	NA	NA	NA	NA	0.094725	1	0.57818	1	0.64372	1	0.23718	1	0.11643	1	0.37881	1	0.83526	1	0.50332	1
16p gain	0 (0%)	428	0.10023	1	0.21177	1	0.15276	1	0.68944	1	0.01148	1	0.066314	1	0.63473	1	0.11281	1	0.15601	1	0.5981	1
16q gain	0 (0%)	435	0.07055	1	0.17117	1	0.17461	1	0.90922	1	0.044287	1	0.12194	1	0.69647	1	0.33614	1	0.22959	1	0.90341	1
17p gain	0 (0%)	477	0.0052247	1	0.0066496	1	0.00035713	0.196	0.4196	1	0.32105	1	0.033572	1	0.19135	1	0.032663	1	0.72594	1	0.048765	1
17q gain	0 (0%)	471	0.0082659	1	0.010223	1	0.0048052	1	0.11876	1	0.55304	1	0.054698	1	0.25322	1	0.0094887	1	0.41669	1	0.022547	1
18p gain	0 (0%)	475	0.076398	1	0.039003	1	0.23818	1	0.15286	1	0.31926	1	0.14269	1	0.097694	1	0.40967	1	0.90877	1	0.74438	1
18q gain	0 (0%)	475	0.076398	1	0.039003	1	0.23818	1	0.15286	1	0.31926	1	0.14269	1	0.097694	1	0.40967	1	0.90877	1	0.74438	1
19p gain	0 (0%)	468	0.18897	1	0.1968	1	3.3746e-05	0.0196	0.33956	1	0.044845	1	0.39709	1	0.042771	1	0.011532	1	0.042287	1	0.065961	1
19q gain	0 (0%)	465	0.053628	1	0.058091	1	3.0044e-06	0.00185	0.20068	1	0.055965	1	0.15391	1	0.018535	1	0.004142	1	0.013987	1	0.06605	1
20p gain	0 (0%)	427	0.10193	1	0.10973	1	1.0457e-12	6.9e-10	0.00067423	0.357	0.00045333	0.244	0.00097912	0.507	3.5945e-06	0.00221	5.2899e-06	0.00321	2.5415e-06	0.00157	0.034351	1
20q gain	0 (0%)	425	0.075297	1	0.092006	1	6.2337e-14	4.13e-11	0.00067423	0.357	3.5385e-05	0.0205	0.00085487	0.446	3.298e-07	0.000207	1.4673e-06	0.00091	1.8346e-07	0.000116	0.034979	1
21q gain	0 (0%)	460	0.82033	1	0.81457	1	0.00011721	0.0663	0.09858	1	0.036798	1	0.83574	1	0.070901	1	0.080022	1	0.29502	1	0.81064	1
22q gain	0 (0%)	468	0.58042	1	0.039003	1	0.00039943	0.216	0.075575	1	0.45167	1	0.21702	1	0.82643	1	0.84565	1	0.9646	1	0.84436	1
Xq gain	0 (0%)	482	0.41403	1	0.43151	1	0.63929	1	0.57818	1	0.39249	1	0.48252	1	0.19785	1	0.2766	1	0.36314	1	0.30563	1
1p loss	0 (0%)	461	0.00083595	0.438	6.1992e-05	0.0355	0.0039487	1	0.19754	1	5.0549e-08	3.23e-05	0.00043538	0.235	0.012254	1	4.6432e-06	0.00283	0.018745	1	1.007e-10	6.52e-08
1q loss	0 (0%)	472	0.021718	1	0.0028644	1	2.0871e-05	0.0122	0.90381	1	0.00016788	0.0942	0.0019091	0.96	6.6528e-05	0.0379	6.2684e-07	0.000391	0.049287	1	2.8841e-11	1.88e-08
2p loss	0 (0%)	483	0.00024867	0.138	0.00037409	0.204	1.5215e-05	0.00898	0.45635	1	1.3686e-05	0.00812	0.00018904	0.106	4.7244e-07	0.000297	1.8734e-08	1.2e-05	0.00059758	0.318	1.2533e-12	8.26e-10
2q loss	0 (0%)	482	0.00024867	0.138	0.00037409	0.204	4.754e-06	0.0029	1	1	0.00012943	0.0727	4.4152e-05	0.0255	8.96e-08	5.69e-05	7.9136e-08	5.04e-05	0.00019855	0.111	4.8112e-12	3.15e-09
3p loss	0 (0%)	189	0.012955	1	0.010206	1	6.3714e-24	4.24e-21	0.00052055	0.278	0.0001198	0.0676	1.7769e-05	0.0104	3.8542e-11	2.51e-08	7.0891e-10	4.57e-07	4.2268e-05	0.0245	5.0825e-14	3.37e-11
3q loss	0 (0%)	420	0.70139	1	0.69959	1	0.0014361	0.725	0.19173	1	0.18206	1	0.0066057	1	0.51828	1	0.80379	1	0.82187	1	0.0098553	1
4p loss	0 (0%)	458	0.28864	1	0.29647	1	0.065781	1	0.27395	1	0.81614	1	0.94781	1	0.088816	1	0.36552	1	0.5131	1	0.74876	1
4q loss	0 (0%)	465	1	1	1	1	0.00022145	0.123	0.25535	1	0.25143	1	0.31278	1	0.063101	1	0.05733	1	0.96875	1	0.37116	1
6p loss	0 (0%)	435	0.013899	1	0.0028988	1	4.2674e-12	2.8e-09	0.0089899	1	0.00012166	0.0685	7.0349e-06	0.00423	0.00072213	0.38	0.0010519	0.538	2.8747e-09	1.85e-06	0.00039442	0.214
6q loss	0 (0%)	411	0.039296	1	0.012516	1	6.3378e-17	4.21e-14	0.12101	1	0.0013994	0.71	0.0010327	0.532	0.20388	1	0.47751	1	1.4245e-05	0.00843	0.0022635	1
8p loss	0 (0%)	399	0.77713	1	0.78081	1	0.047016	1	0.70561	1	0.72351	1	0.49983	1	0.18497	1	0.63325	1	0.17331	1	0.45046	1
8q loss	0 (0%)	456	0.49011	1	0.58627	1	0.74744	1	0.25514	1	0.53952	1	0.7855	1	0.11152	1	0.026589	1	0.70861	1	0.40997	1
9p loss	0 (0%)	406	0.37846	1	0.069376	1	9.2257e-25	6.15e-22	3.5676e-12	2.34e-09	0.0046325	1	0.0072553	1	1.3893e-11	9.06e-09	2.7121e-12	1.78e-09	8.7344e-09	5.6e-06	0.20099	1
9q loss	0 (0%)	401	0.37846	1	0.069376	1	4.4289e-26	2.96e-23	4.2989e-13	2.84e-10	0.00099938	0.516	0.010359	1	1.315e-12	8.65e-10	3.9392e-14	2.62e-11	3.8216e-10	2.46e-07	0.17316	1
10p loss	0 (0%)	461	0.026008	1	0.02869	1	0.0002012	0.112	0.38225	1	0.19525	1	0.036955	1	0.012254	1	0.019724	1	0.15453	1	0.00046991	0.252
10q loss	0 (0%)	445	0.097195	1	0.11948	1	0.0026344	1	0.040882	1	0.22014	1	0.012532	1	0.094952	1	0.12585	1	0.31235	1	0.014631	1
11p loss	0 (0%)	488	NA	NA	NA	NA	0.12092	1	0.60825	1	0.15609	1	0.035855	1	0.35902	1	0.46204	1	0.54528	1	0.087946	1
11q loss	0 (0%)	486	NA	NA	NA	NA	0.05266	1	0.82585	1	0.053318	1	0.21517	1	0.37721	1	0.31138	1	0.3494	1	0.029845	1
13q loss	0 (0%)	462	0.025253	1	0.02806	1	6.3588e-05	0.0364	0.24729	1	0.001372	0.698	0.0013857	0.704	0.0024962	1	0.00045951	0.247	0.00083783	0.438	0.00028462	0.157
14q loss	0 (0%)	335	0.0017916	0.903	0.00095642	0.496	2.0238e-10	1.31e-07	3.0568e-05	0.0178	6.6084e-12	4.32e-09	2.0759e-07	0.000131	6.9702e-11	4.52e-08	2.8039e-07	0.000177	4.3263e-06	0.00264	0.50712	1
15q loss	0 (0%)	481	0.58042	1	0.58403	1	0.021316	1	0.37272	1	0.45072	1	0.70387	1	0.073285	1	0.13618	1	0.23177	1	1	1
16q loss	0 (0%)	488	NA	NA	NA	NA	0.013543	1	NA	NA	0.16723	1	0.45624	1	1	1	0.29246	1	0.83162	1	0.26215	1
17p loss	0 (0%)	468	0.00011676	0.0662	0.00017823	0.0998	4.3019e-06	0.00263	0.90782	1	2.9244e-05	0.017	5.1787e-06	0.00314	1.9025e-06	0.00118	1.5033e-08	9.62e-06	4.9039e-07	0.000307	8.5376e-09	5.48e-06
17q loss	0 (0%)	481	0.00066805	0.355	0.00077017	0.404	0.00022423	0.124	0.45635	1	1.4598e-05	0.00863	1.0235e-05	0.00613	1.9121e-06	0.00118	7.9136e-08	5.04e-05	8.9765e-05	0.0511	4.0474e-11	2.63e-08
18p loss	0 (0%)	447	0.19401	1	0.43305	1	3.017e-06	0.00186	0.01939	1	0.018255	1	0.0047251	1	6.0578e-06	0.00366	0.00019604	0.109	0.00036016	0.197	0.0026242	1
18q loss	0 (0%)	445	0.2588	1	0.23793	1	3.6093e-06	0.00221	0.032401	1	0.055096	1	0.012751	1	2.8663e-05	0.0167	0.00057363	0.306	0.00094833	0.493	0.0054578	1
19p loss	0 (0%)	489	NA	NA	NA	NA	0.18428	1	0.33163	1	0.2794	1	0.035855	1	0.34103	1	0.37884	1	0.83162	1	0.26215	1
20p loss	0 (0%)	487	NA	NA	NA	NA	0.047496	1	1	1	0.017173	1	0.87678	1	0.267	1	0.74728	1	0.072132	1	0.23201	1
21q loss	0 (0%)	461	0.014517	1	0.021914	1	0.00036659	0.2	0.47862	1	0.0050057	1	0.039896	1	0.0019241	0.966	1.7176e-05	0.0101	0.2401	1	9.5148e-06	0.00571
22q loss	0 (0%)	482	NA	NA	NA	NA	0.0050112	1	0.16071	1	0.046179	1	0.39292	1	0.00088773	0.463	0.019143	1	0.36314	1	0.53066	1
Xq loss	0 (0%)	486	0.039423	1	0.077238	1	0.30836	1	0.82585	1	0.38057	1	0.56426	1	0.067592	1	0.0076322	1	0.026872	1	0.0084587	1
