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	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	Fisher's exact test_P	Fisher's exact test_Q
1p gain	5 (11%)	41	0.85242	1	0.77146	1	0.4	1	0.4	1	0.63536	1	0.75421	1	0.65211	1	1	1
1q gain	12 (26%)	34	0.06232	1	0.46954	1	1	1	1	1	0.49423	1	0.46145	1	1	1	0.75496	1
3p gain	3 (7%)	43	1	1	0.47368	1	0.57368	1	0.57368	1	0.28239	1	0.63131	1	1	1	0.097252	1
3q gain	3 (7%)	43	1	1	0.47368	1	0.57368	1	0.57368	1	0.28239	1	0.63131	1	1	1	0.097252	1
4p gain	3 (7%)	43	0.61449	1	0.42135	1	NA	NA	NA	NA	0.28239	1	0.63131	1	1	1	1	1
5p gain	7 (15%)	39	0.44723	1	0.3897	1	0.29624	1	0.29624	1	1	1	0.81424	1	1	1	0.86794	1
5q gain	3 (7%)	43	0.61449	1	0.86568	1	NA	NA	NA	NA	1	1	1	1	1	1	0.40634	1
6p gain	14 (30%)	32	0.027553	1	0.0094412	1	1	1	1	1	0.73658	1	0.30545	1	0.097714	1	0.18444	1
6q gain	3 (7%)	43	0.35415	1	0.86568	1	NA	NA	NA	NA	0.13289	1	NA	NA	0.21212	1	NA	NA
7p gain	19 (41%)	27	0.92968	1	0.14729	1	0.27697	1	0.27697	1	1	1	0.88638	1	0.54344	1	0.58162	1
7q gain	18 (39%)	28	0.74286	1	0.11694	1	0.53044	1	0.53044	1	1	1	0.88638	1	0.7588	1	0.92288	1
8p gain	7 (15%)	39	0.25668	1	0.52499	1	0.30175	1	0.30175	1	0.69501	1	0.33058	1	1	1	0.12443	1
8q gain	15 (33%)	31	0.00024505	0.0831	0.88238	1	0.81424	1	0.81424	1	1	1	0.60783	1	0.54629	1	0.91606	1
13q gain	4 (9%)	42	0.20698	1	0.10364	1	NA	NA	NA	NA	0.62078	1	0.34426	1	0.32572	1	1	1
18p gain	7 (15%)	39	0.52631	1	0.88018	1	0.78947	1	0.78947	1	0.034623	1	0.090328	1	1	1	0.86794	1
18q gain	8 (17%)	38	0.55396	1	0.62818	1	0.29624	1	0.29624	1	0.22918	1	0.51871	1	0.70496	1	0.88879	1
20p gain	9 (20%)	37	0.51617	1	0.44662	1	0.47368	1	0.47368	1	0.4455	1	0.080694	1	0.46893	1	0.70203	1
20q gain	11 (24%)	35	0.28122	1	0.82125	1	0.47368	1	0.47368	1	0.49423	1	0.15679	1	0.50295	1	0.55574	1
21q gain	3 (7%)	43	0.61449	1	0.47368	1	NA	NA	NA	NA	1	1	0.14043	1	0.23636	1	0.7945	1
22q gain	5 (11%)	41	1	1	0.58079	1	0.14962	1	0.14962	1	0.62078	1	0.34426	1	1	1	0.82756	1
2p loss	5 (11%)	41	0.027678	1	0.58079	1	0.05447	1	0.05447	1	1	1	0.41388	1	0.65211	1	0.61116	1
2q loss	4 (9%)	42	0.087802	1	0.51523	1	0.14962	1	0.14962	1	0.62078	1	0.34426	1	0.32572	1	0.66729	1
4p loss	7 (15%)	39	0.78079	1	0.16146	1	NA	NA	NA	NA	0.69501	1	1	1	0.68857	1	1	1
4q loss	9 (20%)	37	0.17787	1	0.1337	1	0.76316	1	0.76316	1	1	1	1	1	0.26692	1	0.79712	1
5q loss	6 (13%)	40	0.40027	1	0.24606	1	NA	NA	NA	NA	1	1	1	1	0.6695	1	0.53888	1
6q loss	15 (33%)	31	0.032242	1	0.59812	1	0.28896	1	0.28896	1	0.73488	1	0.15775	1	0.75202	1	0.65989	1
8p loss	11 (24%)	35	0.15848	1	0.82125	1	0.63158	1	0.63158	1	0.45965	1	0.6238	1	1	1	0.23856	1
8q loss	5 (11%)	41	0.027678	1	0.28531	1	NA	NA	NA	NA	1	1	1	1	0.65211	1	0.82756	1
9p loss	25 (54%)	21	0.0057425	1	0.0012053	0.406	0.3047	1	0.3047	1	1	1	0.70034	1	0.015674	1	0.0093281	1
9q loss	15 (33%)	31	0.37708	1	0.06333	1	1	1	1	1	0.75232	1	0.67801	1	0.22634	1	0.053801	1
10p loss	19 (41%)	27	0.00031388	0.106	0.50802	1	0.086687	1	0.086687	1	1	1	1	1	0.075243	1	1	1
10q loss	22 (48%)	24	3.0135e-05	0.0102	0.041687	1	0.086687	1	0.086687	1	0.75462	1	0.8037	1	0.037682	1	0.40593	1
11p loss	8 (17%)	38	0.25097	1	0.42073	1	0.43158	1	0.43158	1	0.68823	1	0.35078	1	0.4427	1	0.5239	1
11q loss	10 (22%)	36	0.14529	1	0.11154	1	1	1	1	1	0.27573	1	0.19998	1	0.47637	1	0.89434	1
12p loss	6 (13%)	40	1	1	0.14494	1	0.14962	1	0.14962	1	0.38587	1	0.10179	1	0.39554	1	0.40904	1
12q loss	8 (17%)	38	1	1	0.40933	1	0.4	1	0.4	1	1	1	0.6904	1	0.4427	1	0.5239	1
13q loss	7 (15%)	39	0.78079	1	0.7051	1	NA	NA	NA	NA	0.22918	1	0.51871	1	0.68857	1	0.28671	1
14q loss	6 (13%)	40	0.02172	1	0.0044162	1	NA	NA	NA	NA	1	1	0.35412	1	0.39554	1	0.050637	1
16p loss	3 (7%)	43	0.25652	1	0.13365	1	NA	NA	NA	NA	0.54493	1	0.22891	1	0.59154	1	0.40634	1
16q loss	13 (28%)	33	0.54749	1	0.022756	1	1	1	1	1	0.48369	1	0.14515	1	0.50116	1	0.31868	1
17p loss	8 (17%)	38	1	1	0.86435	1	NA	NA	NA	NA	0.68823	1	0.83488	1	0.70496	1	0.20882	1
17q loss	5 (11%)	41	0.091163	1	0.66756	1	NA	NA	NA	NA	0.63536	1	0.75421	1	0.65211	1	0.82756	1
18p loss	5 (11%)	41	0.58754	1	0.39044	1	NA	NA	NA	NA	0.63536	1	0.75421	1	0.65211	1	0.82756	1
18q loss	4 (9%)	42	0.80928	1	0.20572	1	NA	NA	NA	NA	1	1	1	1	1	1	1	1
19q loss	3 (7%)	43	0.7722	1	0.47368	1	NA	NA	NA	NA	0.54493	1	0.42063	1	0.23636	1	0.40634	1
21q loss	6 (13%)	40	0.34268	1	0.7444	1	0.63158	1	0.63158	1	0.34365	1	0.30043	1	1	1	0.72409	1
22q loss	5 (11%)	41	0.7162	1	0.39044	1	NA	NA	NA	NA	1	1	1	1	1	1	0.15433	1