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	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
1p gain	8 (13%)	54	0.4291	1	0.80366	1	0.66142	1	0.47884	1	0.17037	1	0.71164	1	0.86702	1	0.72849	1
1q gain	29 (47%)	33	0.0082759	1	0.35196	1	1	1	0.40276	1	0.10975	1	0.20377	1	0.96788	1	0.9283	1
2p gain	10 (16%)	52	0.36084	1	0.57041	1	1	1	0.079687	1	0.11179	1	0.30706	1	0.96424	1	0.8668	1
2q gain	10 (16%)	52	0.36084	1	0.57041	1	1	1	0.079687	1	0.11179	1	0.30706	1	0.96424	1	0.8668	1
3p gain	6 (10%)	56	0.017618	1	0.49165	1	0.10603	1	0.72126	1	0.08099	1	0.099146	1	0.53087	1	0.40753	1
3q gain	7 (11%)	55	0.11376	1	0.53719	1	0.10603	1	0.72126	1	0.13381	1	0.45329	1	0.30067	1	0.11097	1
4p gain	5 (8%)	57	0.072988	1	0.093027	1	1	1	0.53169	1	1	1	0.62501	1	0.18857	1	0.46955	1
4q gain	5 (8%)	57	0.072988	1	0.093027	1	1	1	0.53169	1	1	1	0.62501	1	0.18857	1	0.46955	1
5p gain	3 (5%)	59	0.2146	1	0.50193	1	NA	NA	NA	NA	0.18464	1	1	1	1	1	0.15658	1
6p gain	28 (45%)	34	0.0013072	0.664	0.00027917	0.143	1	1	0.39519	1	0.088669	1	0.20096	1	0.056571	1	0.047787	1
6q gain	3 (5%)	59	0.11148	1	0.28157	1	0.48718	1	NA	NA	0.62538	1	0.78678	1	0.76388	1	1	1
7p gain	11 (18%)	51	0.0060101	1	0.015228	1	0.34165	1	0.28055	1	0.12105	1	1	1	0.065322	1	0.22417	1
7q gain	9 (15%)	53	0.0013109	0.665	0.25468	1	0.60499	1	0.26749	1	0.029418	1	0.53689	1	0.54872	1	0.85881	1
8p gain	13 (21%)	49	0.31288	1	0.025293	1	1	1	0.26739	1	9.8815e-05	0.0508	0.060602	1	0.25175	1	1	1
8q gain	21 (34%)	41	0.034252	1	0.003265	1	0.30084	1	0.2437	1	5.8166e-05	0.03	0.028587	1	0.62573	1	0.91954	1
9q gain	4 (6%)	58	0.22989	1	0.445	1	1	1	0.099526	1	0.24532	1	0.16126	1	0.9094	1	0.40688	1
11p gain	5 (8%)	57	0.80477	1	0.72659	1	1	1	NA	NA	0.72948	1	1	1	0.42204	1	1	1
11q gain	5 (8%)	57	0.80477	1	0.72659	1	1	1	NA	NA	0.72948	1	1	1	0.42204	1	1	1
12p gain	4 (6%)	58	0.10254	1	1	1	0.48718	1	NA	NA	0.24532	1	0.66752	1	0.13699	1	0.092531	1
13q gain	18 (29%)	44	0.028166	1	0.00022323	0.115	0.71643	1	0.39783	1	0.00048389	0.246	0.017961	1	0.079691	1	0.10178	1
14q gain	5 (8%)	57	0.17145	1	0.85221	1	1	1	NA	NA	0.51546	1	0.83519	1	0.12473	1	1	1
15q gain	7 (11%)	55	0.71156	1	1	1	1	1	NA	NA	0.53333	1	0.14147	1	0.84878	1	0.712	1
16p gain	7 (11%)	55	0.032951	1	0.023056	1	1	1	NA	NA	0.00038632	0.197	0.013963	1	0.677	1	0.85067	1
16q gain	6 (10%)	56	0.093751	1	0.066925	1	1	1	NA	NA	0.001415	0.716	0.043718	1	0.79166	1	0.66789	1
17p gain	3 (5%)	59	0.2146	1	1	1	1	1	NA	NA	0.058699	1	0.11666	1	0.08395	1	0.26282	1
17q gain	9 (15%)	53	0.37866	1	0.2831	1	0.40748	1	0.55596	1	0.20448	1	0.083024	1	0.54872	1	1	1
18p gain	4 (6%)	58	0.32081	1	0.25135	1	1	1	NA	NA	0.83038	1	1	1	0.28863	1	1	1
18q gain	4 (6%)	58	0.32081	1	0.25135	1	1	1	NA	NA	0.83038	1	1	1	0.28863	1	1	1
19p gain	6 (10%)	56	0.093751	1	0.14502	1	0.60499	1	0.74881	1	0.08099	1	0.42235	1	0.42596	1	0.32219	1
19q gain	7 (11%)	55	0.57859	1	0.26863	1	0.60499	1	0.22039	1	0.03583	1	0.19955	1	0.57341	1	0.19811	1
20p gain	13 (21%)	49	0.091703	1	0.087777	1	1	1	0.054553	1	0.0026083	1	0.0069722	1	0.8993	1	0.89256	1
20q gain	18 (29%)	44	0.10788	1	0.11896	1	1	1	0.35366	1	0.10393	1	0.28137	1	0.67623	1	0.91021	1
21q gain	9 (15%)	53	0.30376	1	0.60079	1	1	1	0.099526	1	0.029418	1	0.010845	1	0.74064	1	0.64936	1
22q gain	11 (18%)	51	0.0066044	1	0.53563	1	0.66142	1	0.13411	1	0.12105	1	0.58443	1	0.41671	1	0.54697	1
2q loss	3 (5%)	59	0.40592	1	0.28157	1	0.48718	1	NA	NA	0.62538	1	0.11666	1	0.22562	1	1	1
3p loss	4 (6%)	58	0.35351	1	0.82857	1	1	1	0.47274	1	1	1	1	1	0.26002	1	0.40688	1
3q loss	4 (6%)	58	0.90363	1	0.37561	1	1	1	0.47274	1	1	1	1	1	0.67575	1	0.40688	1
4p loss	9 (15%)	53	0.049713	1	0.73649	1	0.091476	1	0.26194	1	0.0095758	1	0.029287	1	0.020422	1	0.055235	1
4q loss	10 (16%)	52	0.01153	1	1	1	0.043596	1	0.12097	1	0.0031083	1	0.016306	1	0.0047531	1	0.020165	1
5p loss	14 (23%)	48	0.37387	1	0.073299	1	1	1	0.29746	1	0.47761	1	0.45528	1	0.24722	1	0.65157	1
5q loss	15 (24%)	47	0.30577	1	0.007558	1	1	1	0.31588	1	0.061466	1	0.04829	1	0.97461	1	0.65783	1
6p loss	7 (11%)	55	0.4441	1	0.076944	1	1	1	NA	NA	0.051853	1	0.27145	1	0.32935	1	0.85067	1
6q loss	28 (45%)	34	0.0030637	1	0.73123	1	0.11097	1	0.58917	1	0.11094	1	0.31864	1	0.2361	1	0.79624	1
7p loss	3 (5%)	59	0.78001	1	0.28157	1	1	1	NA	NA	0.62538	1	0.11666	1	0.76388	1	1	1
8p loss	11 (18%)	51	0.6003	1	0.37893	1	0.019656	1	0.9709	1	0.7143	1	0.58443	1	0.0015658	0.791	0.22417	1
8q loss	3 (5%)	59	0.88154	1	0.10357	1	0.23077	1	0.65808	1	0.37118	1	0.43649	1	0.08395	1	1	1
9p loss	38 (61%)	24	0.25691	1	0.11798	1	0.20493	1	0.35291	1	0.31235	1	0.75185	1	0.7139	1	0.53248	1
9q loss	30 (48%)	32	0.4097	1	0.36727	1	0.74753	1	0.81395	1	0.65578	1	0.57887	1	0.51259	1	0.86312	1
10p loss	25 (40%)	37	6.876e-06	0.00355	0.0094903	1	1	1	0.044964	1	0.013264	1	0.12872	1	0.33377	1	0.58086	1
10q loss	27 (44%)	35	0.0003019	0.154	0.053338	1	1	1	0.044964	1	0.016786	1	0.2249	1	0.66916	1	0.42517	1
11p loss	19 (31%)	43	0.63216	1	0.017961	1	0.30084	1	0.27307	1	0.37159	1	0.68644	1	0.97935	1	1	1
11q loss	22 (35%)	40	0.9213	1	0.44707	1	0.74105	1	0.29195	1	0.75425	1	0.79059	1	0.94855	1	0.65766	1
12p loss	8 (13%)	54	0.81117	1	0.25319	1	1	1	0.23599	1	0.8903	1	0.88974	1	0.74345	1	1	1
12q loss	11 (18%)	51	0.48412	1	0.14836	1	0.66142	1	0.17986	1	1	1	1	1	0.90922	1	1	1
13q loss	6 (10%)	56	0.93769	1	0.22394	1	1	1	0.60177	1	0.64983	1	1	1	0.27441	1	0.82933	1
14q loss	13 (21%)	49	0.0015724	0.793	0.20236	1	1	1	0.6526	1	0.67565	1	0.67021	1	0.72174	1	0.10335	1
15q loss	6 (10%)	56	0.047149	1	0.066925	1	1	1	NA	NA	0.87071	1	1	1	0.62121	1	0.32219	1
16p loss	3 (5%)	59	0.2146	1	0.50193	1	NA	NA	NA	NA	0.26735	1	1	1	0.58302	1	0.69646	1
16q loss	12 (19%)	50	0.65457	1	0.56712	1	1	1	0.25952	1	0.22548	1	1	1	0.42331	1	0.12279	1
17p loss	20 (32%)	42	0.26885	1	0.34072	1	0.30084	1	0.32608	1	0.66082	1	0.73208	1	0.7051	1	0.60416	1
17q loss	4 (6%)	58	0.075431	1	1	1	0.48718	1	NA	NA	0.24532	1	0.16126	1	0.26002	1	0.40688	1
18p loss	12 (19%)	50	0.1251	1	0.78078	1	1	1	0.60077	1	0.51805	1	0.17218	1	0.60917	1	0.48794	1
18q loss	11 (18%)	51	0.14012	1	0.84307	1	1	1	0.53965	1	0.7143	1	0.32338	1	0.79957	1	0.54697	1
19p loss	8 (13%)	54	0.063503	1	1	1	1	1	0.86625	1	0.8903	1	1	1	0.1702	1	0.72849	1
19q loss	6 (10%)	56	0.23687	1	0.86777	1	1	1	0.43511	1	0.033118	1	0.42235	1	0.79166	1	1	1
21q loss	6 (10%)	56	1	1	0.66035	1	0.60499	1	0.17497	1	0.15679	1	0.6328	1	0.58915	1	0.18593	1
22q loss	8 (13%)	54	0.16773	1	0.45065	1	0.66142	1	0.71668	1	0.286	1	0.090922	1	0.80406	1	0.85881	1