Molecular subtypes	CN_CNMF		METHLYATION_CNMF		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
3p gain	5 (8%)	61	0.72059	1	0.69826	1	1	1	0.94236	1	0.35572	1	0.13368	1
3q gain	5 (8%)	61	0.72059	1	0.69826	1	1	1	0.94236	1	0.35572	1	0.13368	1
4p gain	18 (27%)	48	0.38274	1	0.81276	1	4.5618e-05	0.0142	0.00016144	0.0486	0.45547	1	0.10005	1
4q gain	17 (26%)	49	0.36204	1	0.70104	1	0.00017284	0.0519	0.00078384	0.228	0.26188	1	0.097737	1
5p gain	5 (8%)	61	0.54894	1	0.69826	1	1	1	0.83932	1	1	1	0.13368	1
5q gain	5 (8%)	61	0.54894	1	0.69826	1	1	1	0.83932	1	1	1	0.13368	1
7p gain	18 (27%)	48	0.38274	1	0.38415	1	0.0090598	1	0.019103	1	0.64579	1	1	1
7q gain	18 (27%)	48	0.38274	1	0.38415	1	0.0090598	1	0.019103	1	0.64579	1	1	1
8p gain	13 (20%)	53	0.27392	1	0.086484	1	0.027588	1	0.084812	1	0.38997	1	1	1
8q gain	14 (21%)	52	0.15727	1	0.10479	1	0.0099404	1	0.031654	1	0.64869	1	1	1
9p gain	8 (12%)	58	1	1	0.60857	1	0.91094	1	0.8411	1	0.71385	1	0.29802	1
9q gain	8 (12%)	58	1	1	0.60857	1	0.91094	1	0.8411	1	0.71385	1	0.29802	1
11p gain	13 (20%)	53	0.51686	1	0.27062	1	0.00028747	0.0851	0.00015643	0.0472	1	1	0.18649	1
11q gain	14 (21%)	52	0.6059	1	0.27306	1	8.3317e-05	0.0257	2.7835e-05	0.00874	1	1	0.18625	1
12p gain	14 (21%)	52	0.68779	1	0.43722	1	0.012927	1	0.054195	1	0.41417	1	1	1
12q gain	13 (20%)	53	0.76351	1	0.70859	1	0.013508	1	0.019127	1	0.38997	1	0.67517	1
14q gain	16 (24%)	50	0.34021	1	0.55403	1	0.00070572	0.206	0.0033198	0.903	0.44529	1	0.43576	1
15q gain	14 (21%)	52	0.22401	1	0.24905	1	0.0011285	0.324	0.0064571	1	0.80341	1	0.67109	1
16p gain	15 (23%)	51	0.55562	1	0.79974	1	9.2138e-05	0.0282	0.00093591	0.271	0.11187	1	0.10551	1
16q gain	15 (23%)	51	0.55562	1	0.79974	1	9.2138e-05	0.0282	0.00093591	0.271	0.11187	1	0.10551	1
18p gain	14 (21%)	52	0.47487	1	0.29369	1	0.0061976	1	0.019056	1	1	1	0.38645	1
18q gain	13 (20%)	53	0.67133	1	0.58063	1	0.0040916	1	0.01832	1	0.79327	1	1	1
19p gain	11 (17%)	55	0.86679	1	0.83007	1	0.002063	0.571	0.0021875	0.601	0.34683	1	0.33662	1
19q gain	9 (14%)	57	0.71339	1	0.71963	1	0.0026896	0.734	0.0037186	1	0.12557	1	0.34107	1
20p gain	14 (21%)	52	0.22401	1	0.67219	1	0.0046788	1	0.0037669	1	0.41417	1	0.67109	1
20q gain	15 (23%)	51	0.28224	1	0.39728	1	0.0071321	1	0.007431	1	0.61061	1	1	1
21q gain	3 (5%)	63	0.64565	1	NA	NA	0.32734	1	0.3326	1	0.76731	1	0.36058	1
22q gain	15 (23%)	51	0.88188	1	0.11643	1	0.074818	1	0.1964	1	0.93195	1	1	1
Xq gain	9 (14%)	57	1	1	0.50262	1	8.8354e-05	0.0271	0.0041691	1	0.2702	1	0.34107	1
1p loss	48 (73%)	18	0.34162	1	5.8851e-06	0.00189	8.2551e-06	0.00264	1.794e-05	0.0057	0.079829	1	0.0010279	0.296
1q loss	47 (71%)	19	0.3196	1	1.0573e-05	0.00337	3.1061e-05	0.00972	6.5948e-05	0.0205	0.031569	1	0.0015701	0.443
2p loss	43 (65%)	23	0.082806	1	4.5713e-06	0.00148	8.3099e-09	2.82e-06	2.255e-07	7.58e-05	0.013246	1	0.00059168	0.174
2q loss	43 (65%)	23	0.082806	1	4.5713e-06	0.00148	8.3099e-09	2.82e-06	2.255e-07	7.58e-05	0.013246	1	0.00059168	0.174
3p loss	7 (11%)	59	0.082637	1	1	1	0.25175	1	0.0055363	1	0.48246	1	0.58064	1
3q loss	6 (9%)	60	0.03256	1	0.5323	1	0.13499	1	0.0012588	0.358	0.34751	1	0.58525	1
5p loss	7 (11%)	59	0.30229	1	0.17498	1	0.03288	1	0.0047778	1	0.19606	1	0.58064	1
5q loss	7 (11%)	59	0.30229	1	0.17498	1	0.03288	1	0.0047778	1	0.19606	1	0.58064	1
6p loss	47 (71%)	19	0.3196	1	0.00013204	0.0401	1.2588e-06	0.000417	2.6697e-05	0.00844	0.031569	1	0.0015701	0.443
6q loss	47 (71%)	19	0.3196	1	0.00013204	0.0401	1.2588e-06	0.000417	2.6697e-05	0.00844	0.031569	1	0.0015701	0.443
8p loss	9 (14%)	57	8.1131e-08	2.73e-05	0.057575	1	0.053142	1	0.0035954	0.974	0.12557	1	0.34107	1
8q loss	8 (12%)	58	5.8622e-07	0.000195	0.038075	1	0.13361	1	0.0043369	1	0.25107	1	0.58572	1
9p loss	8 (12%)	58	1	1	1	1	0.17123	1	0.57907	1	0.71385	1	0.29802	1
9q loss	8 (12%)	58	1	1	1	1	0.17123	1	0.57907	1	0.71385	1	0.29802	1
10p loss	44 (67%)	22	0.26056	1	0.001983	0.553	2.5078e-06	0.00082	3.0256e-06	0.000983	0.19008	1	0.050602	1
10q loss	44 (67%)	22	0.26056	1	0.001983	0.553	2.5078e-06	0.00082	3.0256e-06	0.000983	0.19008	1	0.050602	1
11p loss	5 (8%)	61	1	1	0.59319	1	0.1289	1	0.40773	1	0.60592	1	1	1
11q loss	5 (8%)	61	1	1	0.59319	1	0.1289	1	0.40773	1	0.60592	1	1	1
13q loss	37 (56%)	29	0.11621	1	0.0092328	1	0.0012333	0.351	0.00050604	0.149	0.54777	1	0.036005	1
16p loss	3 (5%)	63	1	1	0.4166	1	0.012566	1	0.0014772	0.418	1	1	1	1
16q loss	4 (6%)	62	0.68502	1	0.65254	1	0.0021853	0.601	8.579e-05	0.0264	1	1	0.45192	1
17p loss	45 (68%)	21	0.15807	1	1.3075e-06	0.00043	2.6135e-09	8.91e-07	3.0024e-07	1e-04	0.0037178	1	0.00025533	0.0761
17q loss	45 (68%)	21	0.15807	1	1.3075e-06	0.00043	2.6135e-09	8.91e-07	3.0024e-07	1e-04	0.0037178	1	0.00025533	0.0761
18p loss	5 (8%)	61	0.25683	1	0.11837	1	0.013408	1	0.0012	0.343	0.60592	1	1	1
18q loss	7 (11%)	59	0.22153	1	0.17498	1	0.048087	1	0.017848	1	0.48246	1	1	1
21q loss	28 (42%)	38	1	1	0.018296	1	0.22985	1	0.037913	1	0.74188	1	0.72234	1
22q loss	5 (8%)	61	0.72059	1	0.11837	1	0.74533	1	0.37957	1	0.35572	1	1	1
Xq loss	33 (50%)	33	0.71256	1	2.4497e-05	0.00777	7.9561e-05	0.0247	0.00021664	0.0648	0.046646	1	0.0020839	0.575