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
1p gain	4 (11%)	31	0.6026	1	0.61898	1	1	1	NA	NA	0.28409	1	0.21536	1	1	1	0.8278	1
1q gain	12 (34%)	23	0.011643	1	0.033973	1	0.64241	1	0.57018	1	0.24922	1	0.50043	1	0.15181	1	0.048881	1
2p gain	3 (9%)	32	1	1	1	1	0.47895	1	NA	NA	0.28409	1	0.51008	1	0.23797	1	0.51471	1
3p gain	3 (9%)	32	0.22857	1	0.2437	1	0.47895	1	NA	NA	0.52273	1	NA	NA	1	1	0.75735	1
3q gain	4 (11%)	31	0.6026	1	0.61898	1	1	1	0.75439	1	0.28409	1	0.21536	1	1	1	1	1
4p gain	8 (23%)	27	0.040752	1	0.1009	1	0.15712	1	0.029102	1	1	1	0.22574	1	0.05288	1	0.084453	1
4q gain	4 (11%)	31	0.1039	1	0.1186	1	0.21842	1	0.0087719	1	1	1	0.575	1	0.11301	1	0.29293	1
5p gain	4 (11%)	31	0.1039	1	0.1186	1	0.47895	1	NA	NA	1	1	1	1	0.23797	1	0.091912	1
5q gain	4 (11%)	31	0.1039	1	0.1186	1	0.47895	1	NA	NA	1	1	1	1	0.23797	1	0.091912	1
6p gain	14 (40%)	21	0.01526	1	0.0005561	0.229	0.19681	1	0.25705	1	0.032786	1	0.13	1	0.078991	1	0.016742	1
6q gain	3 (9%)	32	0.6026	1	0.2437	1	1	1	0.088596	1	1	1	1	1	0.23797	1	0.091912	1
7p gain	10 (29%)	25	0.71119	1	0.45819	1	1	1	0.8483	1	0.70981	1	0.0081636	1	0.24012	1	0.88581	1
7q gain	9 (26%)	26	1	1	0.70027	1	1	1	0.8483	1	1	1	0.0047525	1	0.25693	1	0.68111	1
8p gain	8 (23%)	27	0.22848	1	0.1009	1	1	1	0.50299	1	0.031946	1	0.061811	1	0.10002	1	0.68111	1
8q gain	11 (31%)	24	0.027491	1	0.0094713	1	0.64241	1	0.33359	1	0.0049843	1	0.015283	1	0.71756	1	0.2072	1
12p gain	4 (11%)	31	1	1	0.61898	1	1	1	0.50299	1	0.27126	1	0.31371	1	1	1	0.51471	1
12q gain	3 (9%)	32	0.6026	1	1	1	0.56579	1	1	1	0.28409	1	0.21536	1	0.57136	1	0.51471	1
13q gain	3 (9%)	32	0.6026	1	0.2437	1	0.18947	1	NA	NA	1	1	1	1	1	1	0.75735	1
15q gain	4 (11%)	31	0.6026	1	0.1186	1	0.47895	1	NA	NA	1	1	1	1	0.23797	1	0.51471	1
17q gain	5 (14%)	30	0.045455	1	0.057009	1	0.21842	1	0.22018	1	0.63014	1	0.8109	1	0.11301	1	0.024905	1
18p gain	8 (23%)	27	0.22848	1	0.41928	1	0.15712	1	0.33359	1	0.029865	1	0.036286	1	1	1	0.46668	1
18q gain	4 (11%)	31	0.6026	1	0.61898	1	1	1	0.15	1	0.27126	1	0.057551	1	1	1	0.29293	1
19q gain	3 (9%)	32	1	1	1	1	0.47895	1	NA	NA	0.52273	1	NA	NA	1	1	0.51471	1
20p gain	10 (29%)	25	0.26423	1	0.13396	1	0.40586	1	0.02185	1	0.054471	1	0.0048908	1	0.24012	1	0.71452	1
20q gain	12 (34%)	23	0.28899	1	0.16292	1	0.65342	1	0.083949	1	0.021971	1	0.00034578	0.142	0.27138	1	1	1
21q gain	5 (14%)	30	0.33766	1	0.057009	1	1	1	0.0087719	1	0.63014	1	0.8109	1	1	1	0.58254	1
22q gain	7 (20%)	28	0.087683	1	0.19868	1	0.31889	1	0.21981	1	0.064845	1	0.057611	1	1	1	0.44444	1
1p loss	4 (11%)	31	0.6026	1	0.1186	1	1	1	NA	NA	0.27126	1	0.31371	1	0.29942	1	1	1
2p loss	4 (11%)	31	0.6026	1	1	1	0.47895	1	NA	NA	0.60997	1	0.41048	1	0.11301	1	0.51471	1
2q loss	5 (14%)	30	0.33766	1	1	1	0.47895	1	NA	NA	1	1	0.65962	1	0.052581	1	0.24336	1
4p loss	4 (11%)	31	0.6026	1	0.1186	1	1	1	NA	NA	0.27126	1	0.23394	1	0.61284	1	0.29293	1
4q loss	3 (9%)	32	0.22857	1	0.2437	1	NA	NA	NA	NA	0.28409	1	0.51008	1	0.18717	1	NA	NA
6p loss	4 (11%)	31	0.6026	1	1	1	1	1	NA	NA	1	1	0.575	1	0.61284	1	0.8278	1
6q loss	9 (26%)	26	0.12121	1	0.70027	1	0.64241	1	1	1	0.10739	1	0.13881	1	0.25693	1	0.59864	1
8p loss	3 (9%)	32	0.22857	1	0.2437	1	0.47895	1	NA	NA	0.28409	1	0.51008	1	0.49198	1	NA	NA
9p loss	14 (40%)	21	0.73322	1	0.72824	1	0.66992	1	0.84441	1	0.48606	1	0.32265	1	0.078991	1	0.22781	1
9q loss	10 (29%)	25	0.71119	1	1	1	0.64241	1	1	1	0.70981	1	0.104	1	0.24012	1	0.16737	1
10p loss	15 (43%)	20	0.17558	1	0.4916	1	1	1	0.16855	1	0.16036	1	0.094734	1	0.4953	1	0.048883	1
10q loss	13 (37%)	22	0.48868	1	0.7372	1	1	1	0.054219	1	0.27752	1	0.12038	1	0.47641	1	0.36517	1
11p loss	9 (26%)	26	0.44302	1	0.70027	1	0.64241	1	0.33359	1	0.10739	1	0.17512	1	0.69739	1	0.055752	1
11q loss	11 (31%)	24	0.14635	1	0.069323	1	0.19681	1	0.007986	1	0.0020684	0.848	0.0094649	1	0.45127	1	0.41305	1
12p loss	3 (9%)	32	0.22857	1	0.2437	1	0.47895	1	NA	NA	0.28409	1	0.21536	1	0.49198	1	NA	NA
12q loss	4 (11%)	31	0.6026	1	0.61898	1	0.21842	1	0.43509	1	0.27126	1	0.31371	1	0.61284	1	0.29293	1
13q loss	6 (17%)	29	0.65815	1	0.68044	1	0.59133	1	0.50299	1	1	1	0.21794	1	0.19601	1	0.65362	1
14q loss	5 (14%)	30	1	1	0.36497	1	0.59133	1	1	1	0.63014	1	0.8109	1	1	1	0.58254	1
15q loss	3 (9%)	32	1	1	1	1	0.47895	1	NA	NA	0.28409	1	0.51008	1	1	1	0.51471	1
16p loss	5 (14%)	30	0.33766	1	1	1	1	1	NA	NA	0.63014	1	0.8109	1	0.61284	1	0.8278	1
16q loss	8 (23%)	27	0.69057	1	0.41928	1	1	1	1	1	0.67756	1	0.85454	1	0.10389	1	0.65362	1
17p loss	3 (9%)	32	1	1	1	1	1	1	1	1	1	1	0.21536	1	0.23797	1	0.51471	1
17q loss	3 (9%)	32	0.6026	1	1	1	0.56579	1	1	1	1	1	0.21536	1	1	1	1	1
18p loss	3 (9%)	32	0.6026	1	0.56455	1	0.18947	1	NA	NA	1	1	0.032625	1	1	1	0.29412	1
18q loss	4 (11%)	31	1	1	1	1	0.56579	1	0.58246	1	1	1	0.057551	1	0.61284	1	0.8278	1
19q loss	3 (9%)	32	1	1	1	1	1	1	NA	NA	0.28409	1	0.032625	1	0.57136	1	1	1
21q loss	5 (14%)	30	1	1	0.63127	1	1	1	0.79773	1	1	1	0.16798	1	0.35473	1	0.48688	1
22q loss	3 (9%)	32	1	1	0.2437	1	0.47895	1	NA	NA	1	1	1	1	0.49198	1	NA	NA