		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	5 (1%)	488	NA	NA	NA	NA	0.62741	1	NA	NA	0.43887	1	0.035855	1	0.84555	1	0.85029	1	0.51881	1	1	1
1q gain	32 (6%)	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	0.019589	1	0.85766	1
2p gain	48 (10%)	445	0.56067	1	0.47247	1	1.0848e-06	0.000671	0.65317	1	0.046154	1	0.78296	1	0.14408	1	0.078453	1	0.4915	1	0.34803	1
2q gain	49 (10%)	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	0.44216	1	0.34803	1
3p gain	7 (1%)	486	NA	NA	NA	NA	0.38574	1	1	1	0.10217	1	0.0032938	1	0.29418	1	0.16078	1	0.011147	1	0.13611	1
3q gain	27 (5%)	466	0.082325	1	0.085132	1	6.5793e-05	0.0375	0.080411	1	0.007183	1	0.00010715	0.0606	0.00039457	0.214	0.0093127	1	0.0010381	0.536	0.0029769	1
4p gain	8 (2%)	485	NA	NA	NA	NA	0.2057	1	0.60825	1	0.42832	1	0.080261	1	0.025659	1	0.37796	1	0.015548	1	0.2643	1
4q gain	8 (2%)	485	NA	NA	NA	NA	0.67035	1	0.79533	1	0.87831	1	0.33815	1	0.011216	1	0.5092	1	0.041127	1	0.2643	1
5p gain	141 (29%)	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	0.021627	1	0.054383	1
5q gain	156 (32%)	337	0.10537	1	0.12107	1	5.8712e-05	0.0336	0.37509	1	0.1584	1	0.17451	1	0.038112	1	0.0051214	1	0.045065	1	0.011492	1
6p gain	6 (1%)	487	NA	NA	NA	NA	0.77018	1	0.55518	1	0.8188	1	0.87678	1	0.21454	1	0.44902	1	0.44091	1	0.19183	1
6q gain	5 (1%)	488	NA	NA	NA	NA	0.53168	1	0.79533	1	0.57144	1	0.62591	1	0.44232	1	0.57135	1	0.8329	1	0.10409	1
7p gain	127 (26%)	366	0.87675	1	0.93891	1	5.0545e-06	0.00305	0.054291	1	0.00026802	0.147	0.0056517	1	0.067954	1	0.082377	1	0.0016959	0.855	0.64057	1
7q gain	129 (26%)	364	0.87675	1	0.93891	1	1.3614e-05	0.00809	0.041704	1	0.00011777	0.0663	0.00071795	0.378	0.058061	1	0.13146	1	0.00070459	0.372	0.88818	1
8p gain	14 (3%)	479	NA	NA	NA	NA	5.418e-05	0.0311	0.079578	1	0.086779	1	0.14595	1	0.00097842	0.509	0.00068297	0.361	0.010547	1	0.010667	1
8q gain	34 (7%)	459	0.053628	1	0.058091	1	2.747e-07	0.000173	0.0010457	0.536	0.010176	1	0.044916	1	1.1473e-07	7.26e-05	4.879e-05	0.0281	1.8826e-05	0.011	0.0040385	1
9p gain	8 (2%)	485	NA	NA	NA	NA	0.74129	1	0.24924	1	0.17017	1	0.17028	1	0.10317	1	0.05713	1	0.73368	1	0.042444	1
9q gain	8 (2%)	485	NA	NA	NA	NA	0.28254	1	1	1	0.10371	1	0.33815	1	0.52284	1	0.63567	1	0.6185	1	0.36177	1
10p gain	6 (1%)	487	NA	NA	NA	NA	0.39007	1	1	1	0.98053	1	1	1	0.267	1	0.31138	1	0.38654	1	0.57569	1
10q gain	4 (1%)	489	NA	NA	NA	NA	0.18428	1	1	1	0.71582	1	0.61472	1	0.68786	1	0.50758	1	0.32529	1	0.55868	1
11p gain	17 (3%)	476	0.76851	1	0.77815	1	0.00052935	0.284	0.77137	1	0.43744	1	0.3949	1	0.49103	1	0.26531	1	0.69928	1	0.47838	1
11q gain	15 (3%)	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	0.64658	1	0.47846	1
12p gain	78 (16%)	415	0.19401	1	0.16527	1	7.9908e-07	0.000496	0.0010394	0.536	5.6676e-07	0.000354	0.013931	1	1.1022e-05	0.00658	1.8938e-05	0.0111	3.7201e-07	0.000233	0.32421	1
12q gain	78 (16%)	415	0.19401	1	0.16527	1	7.9908e-07	0.000496	0.0010394	0.536	5.6676e-07	0.000354	0.014143	1	1.1022e-05	0.00658	1.8938e-05	0.0111	3.7201e-07	0.000233	0.32421	1
13q gain	14 (3%)	479	NA	NA	NA	NA	0.74221	1	0.076952	1	0.46728	1	0.77086	1	0.068473	1	0.63576	1	0.15674	1	0.49268	1
14q gain	5 (1%)	488	NA	NA	NA	NA	0.049557	1	0.60825	1	0.86889	1	0.059647	1	0.0035445	1	0.047744	1	0.12185	1	0.068463	1
15q gain	14 (3%)	479	NA	NA	NA	NA	0.094725	1	0.57818	1	0.64372	1	0.23718	1	0.11643	1	0.37881	1	0.8803	1	0.72568	1
16p gain	65 (13%)	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	0.31767	1	0.35671	1
16q gain	58 (12%)	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	0.43321	1	0.59421	1
17p gain	16 (3%)	477	0.0052247	1	0.0066496	1	0.00035713	0.195	0.4196	1	0.32105	1	0.033572	1	0.19135	1	0.032663	1	0.4043	1	0.046398	1
17q gain	22 (4%)	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	0.24864	1	0.0059539	1
18p gain	18 (4%)	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	0.28798	1	0.64109	1
18q gain	18 (4%)	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	0.28798	1	0.64109	1
19p gain	25 (5%)	468	0.18897	1	0.1968	1	3.3746e-05	0.0195	0.33956	1	0.044845	1	0.39709	1	0.042771	1	0.011532	1	0.025373	1	0.067951	1
19q gain	28 (6%)	465	0.053628	1	0.058091	1	3.0044e-06	0.00184	0.20068	1	0.055965	1	0.15391	1	0.018535	1	0.004142	1	0.0082806	1	0.028284	1
20p gain	66 (13%)	427	0.10193	1	0.10973	1	1.0457e-12	6.91e-10	0.00067423	0.358	0.00045333	0.244	0.00097912	0.509	3.5945e-06	0.0022	5.2899e-06	0.00318	4.4671e-06	0.00272	0.0080605	1
20q gain	68 (14%)	425	0.075297	1	0.092006	1	6.2337e-14	4.13e-11	0.00067423	0.358	3.5385e-05	0.0205	0.00085487	0.447	3.298e-07	0.000207	1.4673e-06	0.000907	2.0898e-07	0.000132	0.0055059	1
21q gain	33 (7%)	460	0.82033	1	0.81457	1	0.00011721	0.0661	0.09858	1	0.036798	1	0.83574	1	0.070901	1	0.080022	1	0.30691	1	1	1
22q gain	25 (5%)	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	0.82318	1	0.64945	1
Xq gain	11 (2%)	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	0.1526	1	0.16993	1
1p loss	32 (6%)	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	0.00281	0.0039972	1	1.361e-08	8.74e-06
1q loss	21 (4%)	472	0.021718	1	0.0028644	1	2.0871e-05	0.0122	0.90381	1	0.00016788	0.0938	0.0019091	0.958	6.6528e-05	0.0379	6.2684e-07	0.00039	0.019672	1	7.5387e-09	4.85e-06
2p loss	10 (2%)	483	0.00024867	0.137	0.00037409	0.204	1.5215e-05	0.00896	0.45635	1	1.3686e-05	0.00812	0.00018904	0.105	4.7244e-07	0.000295	1.8734e-08	1.2e-05	0.00057471	0.306	8.7237e-11	5.68e-08
2q loss	11 (2%)	482	0.00024867	0.137	0.00037409	0.204	4.754e-06	0.00288	1	1	0.00012943	0.0725	4.4152e-05	0.0255	8.96e-08	5.68e-05	7.9136e-08	5.03e-05	0.00023817	0.131	8.8269e-10	5.71e-07
3p loss	304 (62%)	189	0.012955	1	0.010206	1	6.3714e-24	4.24e-21	0.00052055	0.28	0.0001198	0.0673	1.7769e-05	0.0104	3.8542e-11	2.52e-08	7.0891e-10	4.59e-07	4.3958e-06	0.00268	6.9642e-08	4.44e-05
3q loss	73 (15%)	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	0.012182	1	0.33802	1
4p loss	35 (7%)	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	0.39336	1	0.70702	1
4q loss	28 (6%)	465	1	1	1	1	0.00022145	0.122	0.25535	1	0.25143	1	0.31278	1	0.063101	1	0.05733	1	0.78215	1	0.5118	1
6p loss	58 (12%)	435	0.013899	1	0.0028988	1	4.2674e-12	2.8e-09	0.0089899	1	0.00012166	0.0683	7.0349e-06	0.00422	0.00072213	0.38	0.0010519	0.538	6.3989e-09	4.13e-06	0.00019148	0.106
6q loss	82 (17%)	411	0.039296	1	0.012516	1	6.3378e-17	4.21e-14	0.12101	1	0.0013994	0.708	0.0010327	0.534	0.20388	1	0.47751	1	1.4309e-05	0.00847	0.00030994	0.17
8p loss	94 (19%)	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	0.21504	1	0.8631	1
8q loss	37 (8%)	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	0.28801	1	0.90796	1
9p loss	87 (18%)	406	0.37846	1	0.069376	1	9.2257e-25	6.15e-22	3.5676e-12	2.35e-09	0.0046325	1	0.0072553	1	1.3893e-11	9.1e-09	2.7121e-12	1.79e-09	7.473e-09	4.82e-06	0.1249	1
9q loss	92 (19%)	401	0.37846	1	0.069376	1	4.4289e-26	2.96e-23	4.2989e-13	2.85e-10	0.00099938	0.518	0.010359	1	1.315e-12	8.68e-10	3.9392e-14	2.62e-11	4.6723e-10	3.03e-07	0.11845	1
10p loss	32 (6%)	461	0.026008	1	0.02869	1	0.0002012	0.111	0.38225	1	0.19525	1	0.036955	1	0.012254	1	0.019724	1	0.56897	1	0.010113	1
10q loss	48 (10%)	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	0.35687	1	0.17052	1
11p loss	5 (1%)	488	NA	NA	NA	NA	0.12092	1	0.60825	1	0.15609	1	0.035855	1	0.35902	1	0.46204	1	0.60843	1	0.40395	1
11q loss	7 (1%)	486	NA	NA	NA	NA	0.05266	1	0.82585	1	0.053318	1	0.21517	1	0.37721	1	0.31138	1	0.33437	1	0.30093	1
13q loss	31 (6%)	462	0.025253	1	0.02806	1	6.3588e-05	0.0363	0.24729	1	0.001372	0.698	0.0013857	0.703	0.0024962	1	0.00045951	0.247	7.4275e-05	0.0422	0.001046	0.536
14q loss	158 (32%)	335	0.0017916	0.901	0.00095642	0.498	2.0238e-10	1.32e-07	3.0568e-05	0.0177	6.6084e-12	4.34e-09	2.0759e-07	0.000131	6.9702e-11	4.55e-08	2.8039e-07	0.000176	2.873e-06	0.00177	0.0027346	1
15q loss	12 (2%)	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	0.21091	1	0.22794	1
16q loss	5 (1%)	488	NA	NA	NA	NA	0.013543	1	NA	NA	0.16723	1	0.45624	1	1	1	0.29246	1	0.56905	1	0.42444	1
17p loss	25 (5%)	468	0.00011676	0.066	0.00017823	0.0995	4.3019e-06	0.00262	0.90782	1	2.9244e-05	0.017	5.1787e-06	0.00312	1.9025e-06	0.00117	1.5033e-08	9.64e-06	1.6275e-08	1.04e-05	8.3533e-09	5.37e-06
17q loss	12 (2%)	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	5.03e-05	7.6646e-05	0.0435	8.5008e-11	5.54e-08
18p loss	46 (9%)	447	0.19401	1	0.43305	1	3.017e-06	0.00185	0.01939	1	0.018255	1	0.0047251	1	6.0578e-06	0.00364	0.00019604	0.109	4.6294e-06	0.00281	0.0088683	1
18q loss	48 (10%)	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	1.514e-05	0.00893	0.0013782	0.7
19p loss	4 (1%)	489	NA	NA	NA	NA	0.18428	1	0.33163	1	0.2794	1	0.035855	1	0.34103	1	0.37884	1	0.88045	1	0.77451	1
20p loss	6 (1%)	487	NA	NA	NA	NA	0.047496	1	1	1	0.017173	1	0.87678	1	0.267	1	0.74728	1	0.092089	1	0.19183	1
21q loss	32 (6%)	461	0.014517	1	0.021914	1	0.00036659	0.2	0.47862	1	0.0050057	1	0.039896	1	0.0019241	0.964	1.7176e-05	0.0101	0.032198	1	0.00056956	0.305
22q loss	11 (2%)	482	NA	NA	NA	NA	0.0050112	1	0.16071	1	0.046179	1	0.39292	1	0.00088773	0.463	0.019143	1	0.3732	1	0.81646	1
Xq loss	7 (1%)	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	0.02786	1	0.0068545	1
