Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		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	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
1q gain	0 (0%)	118	0.4375	1	NA	NA	0.0055266	1	0.00035264	0.13	0.0023236	0.813	0.0082681	1	0.43276	1	0.14501	1
2p gain	0 (0%)	114	0.55	1	0.75	1	0.060745	1	0.13248	1	0.58457	1	0.33789	1	0.86852	1	0.066903	1
2q gain	0 (0%)	112	0.55	1	0.75	1	0.030896	1	0.35395	1	0.32901	1	0.20533	1	0.85617	1	0.17405	1
3p gain	0 (0%)	98	0.30245	1	0.055944	1	7.9897e-15	3.22e-12	0.01319	1	0.00026832	0.0993	3.6444e-07	0.000144	0.037482	1	1.2176e-05	0.0047
3q gain	0 (0%)	94	0.30245	1	0.055944	1	1.9475e-12	7.83e-10	0.0073928	1	3.6453e-05	0.0139	6.94e-06	0.0027	0.0091092	1	0.00024562	0.0914
4p gain	0 (0%)	123	0.175	1	NA	NA	0.38217	1	NA	NA	0.45704	1	1	1	0.68274	1	0.88102	1
4q gain	0 (0%)	124	0.4375	1	NA	NA	0.57205	1	NA	NA	0.64474	1	0.60211	1	0.76737	1	0.61752	1
5p gain	0 (0%)	113	0.175	1	NA	NA	1.956e-08	7.8e-06	0.052112	1	0.15575	1	0.80008	1	0.69689	1	0.73064	1
5q gain	0 (0%)	113	0.175	1	NA	NA	2.1846e-10	8.74e-08	0.052112	1	0.57862	1	0.80008	1	0.91915	1	0.30126	1
6p gain	0 (0%)	123	0.4375	1	NA	NA	0.50268	1	0.43969	1	0.11386	1	0.6766	1	0.16515	1	0.37418	1
6q gain	0 (0%)	124	0.4375	1	NA	NA	0.2129	1	NA	NA	0.40969	1	1	1	0.2315	1	0.39696	1
7p gain	0 (0%)	60	0.63287	1	0.43182	1	2.6924e-07	0.000107	2.6171e-06	0.00103	5.6531e-05	0.0214	2.0139e-05	0.00771	0.011017	1	0.0089565	1
7q gain	0 (0%)	59	0.63287	1	0.43182	1	5.7917e-08	2.31e-05	9.3727e-06	0.00363	0.00018097	0.068	3.7395e-05	0.0142	0.0041915	1	0.011319	1
8p gain	0 (0%)	118	1	1	NA	NA	0.3183	1	0.08702	1	0.73212	1	0.2325	1	0.61673	1	0.85363	1
8q gain	0 (0%)	116	1	1	NA	NA	0.0044568	1	0.013112	1	0.24306	1	0.06828	1	0.18729	1	0.76683	1
10p gain	0 (0%)	123	1	1	NA	NA	0.18407	1	NA	NA	0.64474	1	0.60211	1	0.18898	1	0.88102	1
10q gain	0 (0%)	124	1	1	NA	NA	0.39289	1	NA	NA	NA	NA	NA	NA	0.45351	1	0.34091	1
12p gain	0 (0%)	87	1	1	0.090909	1	0.0005503	0.201	0.83267	1	0.16103	1	0.064767	1	0.14633	1	0.096765	1
12q gain	0 (0%)	87	1	1	0.090909	1	0.0005503	0.201	0.83267	1	0.16103	1	0.064767	1	0.14633	1	0.096765	1
13q gain	0 (0%)	113	1	1	NA	NA	0.0066167	1	0.17939	1	0.32428	1	0.044459	1	0.74724	1	0.085169	1
16p gain	0 (0%)	67	0.12622	1	0.06993	1	4.1871e-06	0.00164	0.22101	1	0.0087431	1	0.00018232	0.0684	0.0026753	0.934	0.00070573	0.256
16q gain	0 (0%)	69	0.30245	1	0.055944	1	9.1728e-06	0.00356	0.052066	1	0.0041868	1	1.4611e-05	0.00563	0.001788	0.629	0.00022323	0.0835
17p gain	0 (0%)	61	0.63287	1	0.43182	1	9.5237e-08	3.78e-05	1.303e-06	0.000513	3.4862e-05	0.0133	2.2101e-06	0.000869	0.12863	1	0.0019703	0.692
17q gain	0 (0%)	50	0.30769	1	0.80769	1	5.3976e-06	0.00211	0.0010394	0.372	0.014371	1	0.0009262	0.333	0.36247	1	0.15623	1
18p gain	0 (0%)	121	0.55	1	0.14107	1	0.16019	1	0.32858	1	0.86321	1	1	1	0.84473	1	0.87666	1
18q gain	0 (0%)	123	0.4375	1	NA	NA	0.022734	1	0.32858	1	0.76956	1	0.43158	1	0.91039	1	0.33092	1
20p gain	0 (0%)	88	0.12622	1	0.16171	1	0.018488	1	0.074275	1	0.00072212	0.261	0.015179	1	0.30486	1	0.1252	1
20q gain	0 (0%)	87	0.31469	1	0.11888	1	0.010669	1	0.14225	1	0.00081338	0.294	0.038136	1	0.1792	1	0.37105	1
21q gain	0 (0%)	122	0.4375	1	NA	NA	0.63705	1	0.46806	1	NA	NA	NA	NA	0.10965	1	0.049206	1
Xq gain	0 (0%)	122	1	1	NA	NA	0.12068	1	0.13651	1	0.45704	1	1	1	0.56989	1	0.88102	1
1p loss	0 (0%)	113	1	1	NA	NA	0.025597	1	0.32846	1	0.61111	1	0.58893	1	0.011426	1	0.087304	1
1q loss	0 (0%)	120	1	1	NA	NA	0.017063	1	0.19265	1	0.10312	1	0.43158	1	0.035924	1	0.012377	1
3p loss	0 (0%)	119	0.4375	1	NA	NA	0.0013844	0.493	0.001421	0.504	0.05796	1	0.014854	1	0.059111	1	0.22061	1
3q loss	0 (0%)	124	NA	NA	NA	NA	0.24826	1	0.033451	1	0.028791	1	0.07623	1	0.52056	1	0.72027	1
4p loss	0 (0%)	116	1	1	NA	NA	0.0002471	0.0917	0.0044897	1	0.01289	1	0.17956	1	0.53459	1	1	1
4q loss	0 (0%)	115	1	1	NA	NA	0.0010367	0.372	0.0015337	0.543	0.099931	1	0.06828	1	0.85332	1	0.69791	1
5p loss	0 (0%)	122	NA	NA	NA	NA	0.009317	1	0.24587	1	0.11386	1	0.062599	1	0.23631	1	0.91577	1
5q loss	0 (0%)	121	NA	NA	NA	NA	1.9632e-05	0.00754	0.22958	1	0.40969	1	0.21053	1	0.23631	1	0.91577	1
6p loss	0 (0%)	118	1	1	NA	NA	0.00043016	0.158	0.44293	1	0.4679	1	1	1	0.33091	1	0.53877	1
6q loss	0 (0%)	115	1	1	NA	NA	0.0010706	0.382	0.066048	1	0.37371	1	0.5581	1	0.7825	1	0.69318	1
8p loss	0 (0%)	124	1	1	NA	NA	0.84646	1	NA	NA	NA	NA	NA	NA	1	1	0.61752	1
9p loss	0 (0%)	112	1	1	0.75	1	0.00016946	0.0639	0.00031813	0.117	0.0078208	1	0.067805	1	0.23186	1	0.58728	1
9q loss	0 (0%)	110	1	1	NA	NA	0.00044463	0.163	3.1693e-05	0.0121	0.025579	1	0.13122	1	0.36974	1	0.2539	1
10p loss	0 (0%)	120	1	1	NA	NA	0.017063	1	0.056021	1	0.26949	1	0.17956	1	0.26483	1	0.67481	1
10q loss	0 (0%)	119	0.4375	1	NA	NA	0.0069639	1	0.036236	1	0.26949	1	0.087115	1	0.61673	1	0.22061	1
11p loss	0 (0%)	118	1	1	NA	NA	0.16736	1	0.11298	1	0.26949	1	0.14512	1	1	1	0.44693	1
11q loss	0 (0%)	116	NA	NA	NA	NA	0.0051233	1	0.003541	1	0.29584	1	0.056335	1	0.96768	1	0.90019	1
13q loss	0 (0%)	115	1	1	NA	NA	0.019023	1	0.0015337	0.543	0.09099	1	0.40301	1	0.35517	1	0.23386	1
14q loss	0 (0%)	104	1	1	0.38462	1	1.5409e-11	6.18e-09	0.26683	1	0.13535	1	0.097727	1	0.45719	1	0.96763	1
15q loss	0 (0%)	116	1	1	NA	NA	0.0040672	1	0.11903	1	0.57862	1	0.48748	1	0.57334	1	0.81565	1
16q loss	0 (0%)	124	NA	NA	NA	NA	0.63224	1	0.13911	1	NA	NA	NA	NA	0.86195	1	0.2861	1
17p loss	0 (0%)	122	0.4375	1	NA	NA	0.75642	1	0.043589	1	0.028791	1	0.07623	1	0.21863	1	0.25082	1
18p loss	0 (0%)	108	1	1	NA	NA	0.086322	1	0.030625	1	0.077193	1	0.011421	1	0.15845	1	0.44549	1
18q loss	0 (0%)	107	1	1	NA	NA	0.20869	1	0.015507	1	0.039207	1	0.0036251	1	0.32182	1	0.3728	1
19p loss	0 (0%)	123	NA	NA	NA	NA	0.051328	1	1	1	NA	NA	NA	NA	0.7457	1	0.33092	1
19q loss	0 (0%)	123	NA	NA	NA	NA	0.051328	1	1	1	NA	NA	NA	NA	0.27872	1	0.61752	1
21q loss	0 (0%)	112	0.55	1	0.4125	1	0.5038	1	0.23138	1	0.24646	1	0.72792	1	0.21884	1	0.28387	1
22q loss	0 (0%)	103	1	1	NA	NA	0.00023314	0.087	0.0027113	0.944	0.67259	1	0.047716	1	0.18587	1	0.43329	1
Xq loss	0 (0%)	124	1	1	NA	NA	0.63224	1	NA	NA	NA	NA	NA	NA	0.76737	1	0.10025	1