Molecular subtypes	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
1q gain	16 (4%)	414	7.8478e-05	0.02	0.0375	1	0.015485	1	0.091137	1	0.032849	1	0.023488	1	0.15246	1	0.054718	1
4p gain	4 (1%)	426	3.7275e-05	0.00992	0.016667	1	NA	NA	NA	NA	0.037328	1	0.034754	1	0.10794	1	0.098615	1
4q gain	4 (1%)	426	3.7275e-05	0.00992	0.016667	1	NA	NA	NA	NA	0.037328	1	0.034754	1	0.10794	1	0.098615	1
5p gain	16 (4%)	414	2.6145e-17	8.03e-15	0.0073334	1	1	1	0.091137	1	0.009181	1	0.010143	1	0.00068641	0.153	0.00053012	0.121
5q gain	13 (3%)	417	6.4258e-16	1.97e-13	0.00027568	0.0659	0.90182	1	0.022387	1	0.0007819	0.174	0.00096209	0.212	0.00018831	0.0461	8.5677e-05	0.0216
7p gain	17 (4%)	413	3.7851e-21	1.17e-18	0.0011351	0.246	1	1	0.0054084	1	0.00067709	0.152	0.00055404	0.126	0.00026757	0.0642	9.9761e-05	0.025
7q gain	19 (4%)	411	6.8069e-24	2.1e-21	0.00016582	0.0411	0.50205	1	0.0012608	0.269	0.00026248	0.0635	0.00017753	0.0437	3.7862e-05	0.00992	9.444e-06	0.00261
11p gain	5 (1%)	425	0.0019465	0.403	0.0059773	1	NA	NA	NA	NA	0.017465	1	0.0093618	1	0.0020365	0.42	0.0012429	0.266
11q gain	4 (1%)	426	0.00034013	0.0803	0.016667	1	NA	NA	NA	NA	0.037328	1	0.034754	1	0.0071188	1	0.0048044	0.942
12p gain	12 (3%)	418	7.6621e-12	2.32e-09	1.6779e-06	0.000487	0.90182	1	0.022387	1	7.2608e-06	0.00203	4.9537e-06	0.0014	1.437e-05	0.00394	3.7073e-06	0.00106
12q gain	12 (3%)	418	7.6621e-12	2.32e-09	1.6779e-06	0.000487	0.90182	1	0.022387	1	7.2608e-06	0.00203	4.9537e-06	0.0014	1.437e-05	0.00394	3.7073e-06	0.00106
14q gain	7 (2%)	423	2.1856e-07	6.36e-05	0.0010326	0.226	1	1	0.22796	1	0.0021724	0.441	0.0012213	0.264	0.0043229	0.852	0.0020381	0.42
16p gain	12 (3%)	418	3.9122e-13	1.19e-10	0.00035114	0.0818	0.5038	1	0.024519	1	0.00024548	0.0597	0.00016938	0.0418	0.0001045	0.0261	4.8906e-05	0.0125
16q gain	10 (2%)	420	3.4252e-12	1.04e-09	0.0025462	0.509	0.85771	1	0.11381	1	0.0017879	0.374	0.0014714	0.309	0.0013732	0.29	0.00063429	0.143
17p gain	11 (3%)	419	1.492e-07	4.37e-05	6.6063e-06	0.00185	0.77339	1	0.0079877	1	1.8887e-05	0.00512	1.9539e-05	0.00528	4.5917e-05	0.0118	1.3472e-05	0.0037
17q gain	12 (3%)	418	1.2096e-07	3.56e-05	1.6779e-06	0.000487	0.79522	1	0.0092359	1	7.2608e-06	0.00203	4.9537e-06	0.0014	1.437e-05	0.00394	3.7073e-06	0.00106
19p gain	3 (1%)	427	0.00049738	0.115	0.074786	1	NA	NA	NA	NA	0.10131	1	0.082165	1	0.024732	1	0.01844	1
19q gain	4 (1%)	426	3.7275e-05	0.00992	0.016667	1	0.638	1	0.040019	1	0.037328	1	0.034754	1	0.0071188	1	0.0048044	0.942
20p gain	8 (2%)	422	8.6686e-10	2.59e-07	0.016574	1	1	1	0.038534	1	0.013499	1	0.011473	1	0.012156	1	0.0055486	1
20q gain	8 (2%)	422	8.6686e-10	2.59e-07	0.016574	1	1	1	0.038534	1	0.013499	1	0.011473	1	0.012156	1	0.0055486	1
21q gain	3 (1%)	427	0.0034365	0.68	0.074786	1	NA	NA	NA	NA	0.10131	1	0.082165	1	0.024732	1	0.01844	1
1p loss	3 (1%)	427	0.00049738	0.115	0.53286	1	NA	NA	NA	NA	0.48875	1	0.19532	1	0.29385	1	0.35744	1
2p loss	8 (2%)	422	1.6966e-08	5e-06	0.00021068	0.0514	1	1	0.038534	1	0.00065513	0.147	0.00033468	0.0793	4.5909e-05	0.0118	2.0607e-05	0.00554
2q loss	7 (2%)	423	1.3096e-08	3.88e-06	0.0010326	0.226	0.83749	1	0.039843	1	0.0021724	0.441	0.0012213	0.264	0.00016355	0.0407	8.141e-05	0.0207
3q loss	3 (1%)	427	0.00049738	0.115	0.074786	1	NA	NA	NA	NA	0.10131	1	0.082165	1	0.024732	1	0.01844	1
6q loss	3 (1%)	427	0.02721	1	0.074786	1	NA	NA	NA	NA	0.10131	1	0.082165	1	0.024732	1	0.01844	1
8p loss	4 (1%)	426	3.7275e-05	0.00992	0.041929	1	NA	NA	NA	NA	0.037328	1	0.034754	1	0.0071188	1	0.0048044	0.942
8q loss	4 (1%)	426	3.7275e-05	0.00992	0.041929	1	NA	NA	NA	NA	0.037328	1	0.034754	1	0.0071188	1	0.0048044	0.942
9p loss	10 (2%)	420	5.238e-10	1.57e-07	0.89745	1	0.55717	1	0.07399	1	0.24986	1	0.52702	1	0.18196	1	0.15822	1
9q loss	14 (3%)	416	1.4616e-10	4.4e-08	0.79619	1	0.21263	1	0.0022799	0.458	0.44224	1	0.82309	1	0.19327	1	0.25582	1
10p loss	4 (1%)	426	3.7275e-05	0.00992	0.26001	1	NA	NA	NA	NA	0.24371	1	0.089531	1	0.10794	1	0.098615	1
10q loss	4 (1%)	426	3.7275e-05	0.00992	0.26001	1	NA	NA	NA	NA	0.24371	1	0.089531	1	0.10794	1	0.098615	1
11p loss	5 (1%)	425	2.7125e-06	0.000778	0.056959	1	0.50445	1	1	1	0.04977	1	0.13239	1	0.037989	1	0.022119	1
11q loss	6 (1%)	424	2.5061e-05	0.00672	0.033247	1	0.39122	1	0.77586	1	0.018762	1	0.067366	1	0.012965	1	0.0068102	1
13q loss	11 (3%)	419	0.0021102	0.43	0.023465	1	0.078387	1	0.85614	1	0.098123	1	0.11664	1	0.012031	1	0.0028917	0.575
15q loss	6 (1%)	424	0.00094255	0.208	0.0073549	1	0.45915	1	0.22796	1	0.017465	1	0.0093618	1	0.00057895	0.131	0.00031925	0.076
17p loss	7 (2%)	423	0.0017966	0.374	1	1	1	1	1	1	0.82619	1	0.88586	1	0.11176	1	0.49254	1
18p loss	4 (1%)	426	0.00034013	0.0803	0.17501	1	1	1	0.1817	1	0.24371	1	0.089531	1	0.072595	1	0.038284	1
18q loss	4 (1%)	426	0.00034013	0.0803	0.17501	1	1	1	0.1817	1	0.24371	1	0.089531	1	0.072595	1	0.038284	1
19p loss	4 (1%)	426	0.23207	1	0.016667	1	0.28556	1	0.34786	1	0.037328	1	0.034754	1	0.0071188	1	0.0048044	0.942
21q loss	5 (1%)	425	3.115e-05	0.00832	0.017034	1	0.38943	1	0.040019	1	0.04977	1	0.13239	1	0.037989	1	0.022119	1
22q loss	54 (13%)	376	3.2788e-45	1.02e-42	0.0012921	0.274	0.12216	1	0.10363	1	3.6434e-09	1.08e-06	2.171e-07	6.34e-05	0.00026651	0.0642	8.2785e-05	0.0209