		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	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	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
1p gain	0 (0%)	414	1	1	1	1	3.6007e-08	2.57e-05	0.00056497	0.351	0.081519	1	0.024133	1	0.024329	1	0.30953	1	0.63509	1	0.76296	1
1q gain	0 (0%)	295	0.46488	1	0.88479	1	0.035246	1	1.8806e-05	0.0127	0.13068	1	0.14618	1	0.00065946	0.407	0.70272	1	0.53406	1	0.59776	1
2p gain	0 (0%)	422	0.03123	1	0.015087	1	6.9979e-08	4.99e-05	3.8879e-06	0.00268	0.078071	1	0.030149	1	0.00025572	0.163	0.0012367	0.746	0.00021023	0.135	0.0051153	1
2q gain	0 (0%)	427	0.0302	1	0.025306	1	1.6942e-06	0.00118	7.9235e-07	0.000555	0.25214	1	0.27599	1	0.00018355	0.119	0.01826	1	0.00016153	0.105	0.0020987	1
3p gain	0 (0%)	459	NA	NA	NA	NA	0.032214	1	0.046198	1	0.13709	1	0.27068	1	0.0070266	1	0.0018011	1	0.87616	1	0.66359	1
3q gain	0 (0%)	443	NA	NA	NA	NA	0.002502	1	0.0023517	1	0.078299	1	0.022215	1	0.0045641	1	0.10727	1	0.042959	1	0.35803	1
4p gain	0 (0%)	442	0.55363	1	0.41815	1	0.0035245	1	0.010189	1	0.072717	1	0.034995	1	0.75953	1	0.31103	1	0.49098	1	0.36811	1
4q gain	0 (0%)	461	NA	NA	NA	NA	0.037947	1	0.83822	1	0.2221	1	0.27068	1	0.77525	1	0.23221	1	0.1036	1	0.12614	1
5p gain	0 (0%)	294	0.48692	1	0.4185	1	9.1029e-15	6.65e-12	0.15626	1	0.23307	1	0.63629	1	0.018798	1	0.031342	1	0.18992	1	0.09707	1
5q gain	0 (0%)	416	0.017738	1	0.64431	1	0.045138	1	0.00074201	0.456	0.54134	1	0.18722	1	0.016558	1	0.041062	1	0.35649	1	0.1043	1
6p gain	0 (0%)	401	0.29183	1	0.05069	1	0.01985	1	3.7746e-06	0.0026	0.0093568	1	0.26104	1	0.00282	1	0.26136	1	0.070268	1	0.34207	1
6q gain	0 (0%)	452	NA	NA	NA	NA	0.40991	1	0.0096519	1	0.10777	1	0.064469	1	0.05183	1	0.46338	1	0.060574	1	0.023244	1
7p gain	0 (0%)	318	0.75419	1	0.5228	1	3.0761e-18	2.25e-15	1.9669e-06	0.00137	8.9258e-05	0.0586	0.0094814	1	3.8872e-06	0.00268	7.4731e-07	0.000524	0.00055258	0.344	0.0052468	1
7q gain	0 (0%)	361	0.38828	1	0.70175	1	5.8646e-09	4.21e-06	0.0004719	0.295	0.078881	1	0.29831	1	1.6806e-05	0.0113	1.2179e-05	0.00827	0.14224	1	0.23816	1
8p gain	0 (0%)	413	NA	NA	NA	NA	3.7361e-10	2.7e-07	0.0032345	1	0.59752	1	0.84164	1	4.3248e-05	0.0288	0.0056838	1	0.42377	1	0.17641	1
8q gain	0 (0%)	328	0.064056	1	0.19076	1	1.9041e-21	1.4e-18	3.3188e-07	0.000235	0.035664	1	0.0042398	1	0.0009253	0.564	0.0011681	0.707	3.0562e-07	0.000216	3.9735e-07	0.000281
9p gain	0 (0%)	458	NA	NA	NA	NA	0.01734	1	0.011241	1	1	1	0.84262	1	0.34728	1	0.23704	1	0.47093	1	0.22682	1
9q gain	0 (0%)	465	NA	NA	NA	NA	0.27415	1	0.5904	1	0.39223	1	0.26858	1	0.47005	1	1	1	0.25536	1	0.23916	1
10p gain	0 (0%)	423	NA	NA	NA	NA	0.041705	1	0.00011027	0.0721	0.16869	1	0.16046	1	0.0038482	1	0.1072	1	0.095504	1	0.27651	1
10q gain	0 (0%)	444	NA	NA	NA	NA	0.10669	1	0.023719	1	0.55524	1	0.18774	1	1.6662e-05	0.0113	0.25291	1	0.6092	1	0.29237	1
11p gain	0 (0%)	437	NA	NA	NA	NA	0.052748	1	0.041882	1	0.1006	1	0.47594	1	0.052974	1	0.27356	1	0.031261	1	0.12947	1
11q gain	0 (0%)	421	0.11976	1	0.15726	1	0.00091473	0.559	0.013133	1	0.00082362	0.505	0.019571	1	0.0049001	1	0.0020662	1	0.0033314	1	0.019345	1
12p gain	0 (0%)	415	0.56496	1	0.13192	1	3.0173e-14	2.2e-11	8.574e-05	0.0564	0.17972	1	0.1154	1	0.00096369	0.586	0.00037483	0.237	0.00025698	0.164	0.0035673	1
12q gain	0 (0%)	426	0.56496	1	0.13192	1	2.8963e-12	2.11e-09	0.00018438	0.119	0.15757	1	0.089273	1	0.0001892	0.122	0.0012316	0.744	0.0074355	1	0.075678	1
13q gain	0 (0%)	457	NA	NA	NA	NA	0.22626	1	0.027219	1	0.43272	1	0.29381	1	0.1062	1	0.16349	1	0.83309	1	0.26942	1
14q gain	0 (0%)	416	NA	NA	NA	NA	4.9039e-06	0.00336	2.9768e-06	0.00206	0.12705	1	0.51774	1	0.00056561	0.351	0.018435	1	0.0071956	1	0.00035498	0.225
15q gain	0 (0%)	458	NA	NA	NA	NA	0.26273	1	0.54151	1	0.81901	1	0.5781	1	0.20013	1	0.21241	1	0.54771	1	0.41528	1
16p gain	0 (0%)	405	0.35825	1	0.32152	1	0.32844	1	0.00034914	0.221	0.087838	1	0.44803	1	0.00017912	0.116	0.015049	1	0.15498	1	0.098429	1
16q gain	0 (0%)	430	0.19234	1	0.051411	1	0.42796	1	0.0097721	1	0.025313	1	0.025242	1	0.010324	1	0.2222	1	0.16319	1	0.060455	1
17p gain	0 (0%)	444	NA	NA	NA	NA	8.7254e-06	0.00595	0.00042658	0.268	0.66456	1	0.53278	1	0.60899	1	0.33428	1	0.063377	1	0.14613	1
17q gain	0 (0%)	394	0.044722	1	0.70175	1	4.6891e-08	3.35e-05	1.3902e-06	0.00097	0.42297	1	0.19877	1	0.0057512	1	0.059537	1	0.021788	1	0.029841	1
18p gain	0 (0%)	430	NA	NA	NA	NA	2.1329e-06	0.00148	0.0011183	0.678	0.071061	1	0.20947	1	0.25595	1	0.053992	1	0.016315	1	0.016446	1
18q gain	0 (0%)	446	NA	NA	NA	NA	2.196e-05	0.0148	0.00060846	0.377	0.089952	1	0.037314	1	0.034272	1	0.001393	0.834	0.10155	1	0.033611	1
19p gain	0 (0%)	466	NA	NA	NA	NA	0.77335	1	0.37216	1	0.7761	1	1	1	0.48209	1	1	1	0.5117	1	0.86194	1
19q gain	0 (0%)	450	NA	NA	NA	NA	0.00046067	0.288	0.17589	1	0.40228	1	0.014388	1	0.0034072	1	0.043147	1	0.096592	1	0.068345	1
20p gain	0 (0%)	411	0.023526	1	0.012653	1	3.0574e-06	0.00211	2.7756e-05	0.0186	0.024914	1	0.68732	1	5.7439e-05	0.0381	0.00013508	0.0881	0.018901	1	0.0077237	1
20q gain	0 (0%)	396	0.0023737	1	0.0021899	1	4.7968e-07	0.000337	5.0053e-09	3.6e-06	0.0013155	0.789	0.091419	1	5.5892e-06	0.00382	6.1501e-05	0.0407	0.0021202	1	0.0022979	1
21q gain	0 (0%)	431	0.19234	1	0.15726	1	4.9992e-05	0.0332	3.4241e-05	0.0229	0.09138	1	0.052338	1	0.23005	1	0.16999	1	0.059583	1	0.3802	1
22q gain	0 (0%)	452	NA	NA	NA	NA	0.060988	1	0.12997	1	0.78173	1	0.17219	1	0.17515	1	0.39831	1	0.092872	1	0.056439	1
Xq gain	0 (0%)	453	0.7496	1	0.59113	1	0.00023724	0.152	0.042457	1	0.43272	1	0.5983	1	0.29945	1	0.37763	1	0.62499	1	0.64074	1
1p loss	0 (0%)	444	NA	NA	NA	NA	0.0044453	1	0.00021355	0.137	0.11126	1	0.19883	1	0.1126	1	0.18866	1	0.78901	1	0.14613	1
1q loss	0 (0%)	461	NA	NA	NA	NA	0.061871	1	0.081099	1	0.2221	1	0.015141	1	0.54429	1	0.34281	1	0.41776	1	0.096849	1
2p loss	0 (0%)	466	NA	NA	NA	NA	0.93066	1	0.46619	1	1	1	0.61732	1	0.54815	1	1	1	0.7577	1	0.86194	1
2q loss	0 (0%)	468	NA	NA	NA	NA	0.1486	1	0.22703	1	NA	NA	NA	NA	0.8702	1	1	1	0.54389	1	0.79746	1
3p loss	0 (0%)	379	0.2081	1	0.17643	1	0.00045648	0.286	1.5326e-05	0.0104	0.15622	1	0.4015	1	0.5391	1	0.035977	1	0.031344	1	0.021083	1
3q loss	0 (0%)	416	0.55363	1	0.41815	1	0.010691	1	0.0033496	1	0.34086	1	0.93304	1	0.13975	1	0.4478	1	0.42921	1	0.024215	1
4p loss	0 (0%)	434	NA	NA	NA	NA	1.2563e-05	0.00852	6.4378e-05	0.0425	0.19181	1	0.24819	1	0.00066842	0.412	4.1306e-05	0.0276	0.00010188	0.0667	0.0080962	1
4q loss	0 (0%)	427	0.0060484	1	0.0070565	1	2.2044e-10	1.6e-07	4.2432e-07	0.000299	0.46872	1	0.5783	1	9.0995e-05	0.0597	9.3857e-08	6.66e-05	0.00038576	0.243	0.00057878	0.359
5p loss	0 (0%)	457	NA	NA	NA	NA	0.006451	1	0.0080031	1	0.30598	1	0.77738	1	0.64004	1	0.034773	1	0.16976	1	0.22682	1
5q loss	0 (0%)	414	0.023526	1	0.012653	1	3.4011e-05	0.0228	1.0066e-05	0.00685	0.038819	1	0.098574	1	0.00012422	0.0811	0.043005	1	0.0094389	1	0.0055304	1
6p loss	0 (0%)	434	0.33468	1	0.30806	1	0.025173	1	0.037418	1	0.20205	1	0.53707	1	0.16187	1	0.97294	1	0.23891	1	0.74495	1
6q loss	0 (0%)	367	0.80335	1	0.72164	1	0.070422	1	4.3992e-06	0.00302	0.1041	1	0.033507	1	0.015677	1	0.15354	1	0.3975	1	0.86816	1
7p loss	0 (0%)	458	0.55363	1	0.41815	1	0.0072296	1	0.31247	1	0.52239	1	0.93754	1	0.024383	1	0.066953	1	0.10006	1	0.80139	1
7q loss	0 (0%)	455	0.52998	1	0.18587	1	0.030531	1	0.41084	1	0.68724	1	0.82053	1	0.3147	1	0.27243	1	1	1	0.73423	1
8p loss	0 (0%)	354	0.10434	1	0.17288	1	4.7485e-14	3.46e-11	1.9961e-06	0.00139	0.1732	1	0.028147	1	0.040251	1	0.0024567	1	0.02715	1	0.0097918	1
8q loss	0 (0%)	455	NA	NA	NA	NA	0.00094334	0.574	0.090013	1	0.001241	0.747	0.0052641	1	0.3281	1	0.0477	1	0.95096	1	0.68982	1
9p loss	0 (0%)	333	0.15472	1	0.20593	1	2.7013e-08	1.93e-05	2.5852e-05	0.0174	0.34531	1	0.049049	1	0.0089313	1	0.027491	1	0.79679	1	0.70065	1
9q loss	0 (0%)	355	0.46164	1	0.47514	1	8.1724e-08	5.81e-05	1.0698e-08	7.67e-06	0.3234	1	0.144	1	0.019314	1	0.013123	1	0.10131	1	0.21023	1
10p loss	0 (0%)	437	0.90089	1	0.8178	1	0.00070668	0.435	0.00088884	0.544	0.052545	1	0.099122	1	0.083242	1	0.51045	1	0.045349	1	0.012846	1
10q loss	0 (0%)	427	0.7496	1	0.59113	1	0.0012414	0.747	0.0045419	1	0.015725	1	0.058513	1	0.025841	1	0.6089	1	0.31149	1	0.026391	1
11p loss	0 (0%)	440	0.33468	1	0.10222	1	0.0005298	0.331	0.84564	1	0.0045403	1	0.026834	1	0.041971	1	0.053973	1	0.15863	1	0.097656	1
11q loss	0 (0%)	443	0.47379	1	0.15726	1	0.0027079	1	0.49977	1	0.010249	1	0.025131	1	0.452	1	0.21063	1	0.38362	1	0.82731	1
12p loss	0 (0%)	435	0.7282	1	0.8178	1	0.22911	1	0.00065309	0.404	0.81934	1	0.53401	1	0.071998	1	0.59252	1	0.26859	1	0.7113	1
12q loss	0 (0%)	449	NA	NA	NA	NA	0.078702	1	0.13092	1	0.88633	1	0.30468	1	0.40413	1	0.92078	1	0.38626	1	0.82205	1
13q loss	0 (0%)	363	0.084587	1	0.041059	1	3.554e-21	2.61e-18	6.4648e-07	0.000454	0.28492	1	0.0093561	1	0.0009661	0.586	0.066814	1	0.0030566	1	0.032817	1
14q loss	0 (0%)	426	0.40121	1	0.41815	1	0.0631	1	0.02449	1	0.030579	1	0.004879	1	0.097075	1	0.66507	1	0.075483	1	0.16714	1
15q loss	0 (0%)	377	0.40454	1	0.21903	1	5.2574e-12	3.82e-09	1.4103e-09	1.02e-06	0.48115	1	0.018752	1	6.09e-05	0.0403	0.00041818	0.263	0.00026922	0.171	0.00023871	0.153
16p loss	0 (0%)	435	NA	NA	NA	NA	0.0003069	0.195	0.001816	1	0.044709	1	0.28061	1	0.13474	1	0.11394	1	0.096874	1	0.08083	1
16q loss	0 (0%)	416	0.015881	1	1	1	4.6443e-06	0.00319	0.0014839	0.887	0.0059521	1	0.0085501	1	0.0080295	1	0.22754	1	0.014852	1	0.21784	1
17p loss	0 (0%)	363	0.12966	1	0.30099	1	5.858e-06	0.004	0.0035343	1	0.057179	1	0.20966	1	0.44973	1	0.44425	1	0.59165	1	0.60028	1
17q loss	0 (0%)	455	NA	NA	NA	NA	0.1551	1	0.02222	1	0.066137	1	0.89735	1	0.47569	1	0.1977	1	0.85377	1	0.027051	1
18p loss	0 (0%)	397	0.41986	1	0.41218	1	1.1432e-05	0.00777	0.019843	1	0.88021	1	0.22337	1	0.033477	1	0.28945	1	0.68816	1	0.858	1
18q loss	0 (0%)	364	0.41986	1	0.41218	1	1.6812e-09	1.21e-06	0.00016049	0.104	0.30099	1	0.12927	1	0.0002544	0.163	0.024221	1	0.1353	1	0.95043	1
19p loss	0 (0%)	360	0.64867	1	0.68791	1	1.5576e-09	1.12e-06	7.1483e-08	5.09e-05	0.86711	1	0.68957	1	7.5294e-05	0.0496	0.1159	1	0.0060342	1	0.014327	1
19q loss	0 (0%)	405	0.71049	1	0.72164	1	0.00019019	0.123	0.028818	1	0.77814	1	0.43291	1	0.0081357	1	0.4376	1	0.018108	1	0.070492	1
20p loss	0 (0%)	411	0.19188	1	0.41218	1	0.00019416	0.125	0.053462	1	0.0063065	1	0.025187	1	0.1137	1	0.18236	1	0.725	1	0.1084	1
20q loss	0 (0%)	448	NA	NA	NA	NA	0.26161	1	0.13942	1	0.32479	1	0.3064	1	0.41852	1	0.33318	1	0.63504	1	0.55499	1
21q loss	0 (0%)	406	NA	NA	NA	NA	3.0301e-12	2.2e-09	9.9995e-08	7.09e-05	0.10286	1	0.017555	1	1.4239e-06	0.000992	4.4379e-07	0.000312	3.1081e-05	0.0208	8.05e-07	0.000563
22q loss	0 (0%)	382	0.30751	1	0.32108	1	5.7463e-10	4.15e-07	4.5583e-05	0.0303	0.0090911	1	0.010973	1	0.020166	1	0.0074711	1	0.00039775	0.251	0.00182	1
Xq loss	0 (0%)	461	NA	NA	NA	NA	0.25276	1	0.28051	1	0.7403	1	0.57183	1	0.055361	1	0.36283	1	0.79361	1	0.34957	1
