		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	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
1q gain	8 (7%)	109	0.4375	1	NA	NA	0.20656	1	0.00017187	0.0658	0.0023236	0.836	0.0082681	1	0.43276	1	0.14501	1
2p gain	11 (9%)	106	0.55	1	0.75	1	0.0030227	1	0.14936	1	0.58457	1	0.33789	1	0.86852	1	0.066903	1
2q gain	13 (11%)	104	0.55	1	0.75	1	0.0017846	0.65	0.28607	1	0.32901	1	0.20533	1	0.85617	1	0.17405	1
3p gain	28 (24%)	89	0.30245	1	0.055944	1	2.1043e-14	8.44e-12	0.029744	1	0.00026832	0.101	3.6444e-07	0.000144	0.037482	1	1.2176e-05	0.00477
3q gain	32 (27%)	85	0.30245	1	0.055944	1	3.7871e-10	1.5e-07	0.024544	1	3.6453e-05	0.0141	6.94e-06	0.00273	0.0091092	1	0.00024562	0.0928
4p gain	4 (3%)	113	0.175	1	NA	NA	0.43783	1	NA	NA	0.45704	1	1	1	0.68274	1	0.88102	1
4q gain	3 (3%)	114	0.4375	1	NA	NA	0.77719	1	NA	NA	0.64474	1	0.60211	1	0.76737	1	0.61752	1
5p gain	11 (9%)	106	0.175	1	NA	NA	0.22956	1	0.18006	1	0.15575	1	0.80008	1	0.69689	1	0.73064	1
5q gain	11 (9%)	106	0.175	1	NA	NA	0.22956	1	0.18006	1	0.57862	1	0.80008	1	0.91915	1	0.30126	1
6p gain	4 (3%)	113	0.4375	1	NA	NA	0.43783	1	0.45581	1	0.11386	1	0.6766	1	0.16515	1	0.37418	1
6q gain	3 (3%)	114	0.4375	1	NA	NA	0.11302	1	NA	NA	0.40969	1	1	1	0.2315	1	0.39696	1
7p gain	64 (55%)	53	0.63287	1	0.43182	1	3.4663e-10	1.38e-07	0.00033398	0.125	5.6531e-05	0.0217	2.0139e-05	0.00785	0.011017	1	0.0089565	1
7q gain	65 (56%)	52	0.63287	1	0.43182	1	7.1753e-11	2.86e-08	0.0010958	0.405	0.00018097	0.0691	3.7395e-05	0.0144	0.0041915	1	0.011319	1
8p gain	7 (6%)	110	1	1	NA	NA	0.71951	1	0.077605	1	0.73212	1	0.2325	1	0.61673	1	0.85363	1
8q gain	9 (8%)	108	1	1	NA	NA	0.37061	1	0.0234	1	0.24306	1	0.06828	1	0.18729	1	0.76683	1
10p gain	4 (3%)	113	1	1	NA	NA	0.17348	1	NA	NA	0.64474	1	0.60211	1	0.18898	1	0.88102	1
10q gain	3 (3%)	114	1	1	NA	NA	0.30988	1	NA	NA	NA	NA	NA	NA	0.45351	1	0.34091	1
12p gain	36 (31%)	81	1	1	0.090909	1	0.034478	1	0.27606	1	0.16103	1	0.064767	1	0.14633	1	0.096765	1
12q gain	36 (31%)	81	1	1	0.090909	1	0.034478	1	0.27606	1	0.16103	1	0.064767	1	0.14633	1	0.096765	1
13q gain	14 (12%)	103	1	1	NA	NA	0.045427	1	0.45457	1	0.32428	1	0.044459	1	0.74724	1	0.085169	1
16p gain	54 (46%)	63	0.12622	1	0.06993	1	0.00020466	0.0778	0.35203	1	0.0087431	1	0.00018232	0.0695	0.0026753	0.96	0.00070573	0.264
16q gain	51 (44%)	66	0.30245	1	0.055944	1	2.2506e-05	0.00875	0.1172	1	0.0041868	1	1.4611e-05	0.00571	0.001788	0.65	0.00022323	0.0846
17p gain	61 (52%)	56	0.63287	1	0.43182	1	1.0154e-14	4.08e-12	5.3322e-05	0.0205	3.4862e-05	0.0135	2.2101e-06	0.000871	0.12863	1	0.0019703	0.713
17q gain	71 (61%)	46	0.30769	1	0.80769	1	1.3202e-09	5.23e-07	0.014299	1	0.014371	1	0.0009262	0.344	0.36247	1	0.15623	1
18p gain	6 (5%)	111	0.55	1	0.14107	1	0.04888	1	0.32667	1	0.86321	1	1	1	0.84473	1	0.87666	1
18q gain	4 (3%)	113	0.4375	1	NA	NA	0.0020868	0.753	0.32667	1	0.76956	1	0.43158	1	0.91039	1	0.33092	1
20p gain	37 (32%)	80	0.12622	1	0.16171	1	0.0029396	1	0.10581	1	0.00072212	0.269	0.015179	1	0.30486	1	0.1252	1
20q gain	38 (32%)	79	0.31469	1	0.11888	1	0.005945	1	0.29307	1	0.00081338	0.303	0.038136	1	0.1792	1	0.37105	1
21q gain	4 (3%)	113	0.4375	1	NA	NA	0.3168	1	NA	NA	NA	NA	NA	NA	0.10965	1	0.049206	1
Xq gain	4 (3%)	113	1	1	NA	NA	0.11265	1	0.45581	1	0.45704	1	1	1	0.56989	1	0.88102	1
1p loss	12 (10%)	105	1	1	NA	NA	0.11857	1	1	1	0.61111	1	0.58893	1	0.011426	1	0.087304	1
1q loss	7 (6%)	110	1	1	NA	NA	0.099817	1	0.19809	1	0.10312	1	0.43158	1	0.035924	1	0.012377	1
3p loss	7 (6%)	110	0.4375	1	NA	NA	0.0033471	1	0.0027356	0.979	0.05796	1	0.014854	1	0.059111	1	0.22061	1
3q loss	3 (3%)	114	NA	NA	NA	NA	0.024757	1	0.040143	1	0.028791	1	0.07623	1	0.52056	1	0.72027	1
4p loss	10 (9%)	107	1	1	NA	NA	0.082567	1	0.0014106	0.518	0.0039859	1	0.086648	1	0.85332	1	0.90019	1
4q loss	10 (9%)	107	1	1	NA	NA	0.011224	1	0.0014106	0.518	0.099931	1	0.06828	1	0.85332	1	0.69791	1
5p loss	5 (4%)	112	NA	NA	NA	NA	0.28648	1	0.43362	1	0.11386	1	0.062599	1	0.23631	1	0.91577	1
5q loss	5 (4%)	112	NA	NA	NA	NA	0.41106	1	0.43362	1	0.40969	1	0.21053	1	0.23631	1	0.91577	1
6p loss	9 (8%)	108	1	1	NA	NA	0.10685	1	0.56808	1	0.4679	1	1	1	0.33091	1	0.53877	1
6q loss	11 (9%)	106	1	1	NA	NA	0.082178	1	0.20504	1	0.37371	1	0.5581	1	0.7825	1	0.69318	1
8p loss	3 (3%)	114	1	1	NA	NA	0.14273	1	NA	NA	NA	NA	NA	NA	1	1	0.61752	1
9p loss	14 (12%)	103	1	1	0.75	1	0.012323	1	0.0013458	0.495	0.0078208	1	0.067805	1	0.23186	1	0.58728	1
9q loss	14 (12%)	103	1	1	NA	NA	0.053111	1	0.001255	0.463	0.025579	1	0.13122	1	0.36974	1	0.2539	1
10p loss	6 (5%)	111	1	1	NA	NA	0.00029486	0.111	0.19892	1	0.26949	1	0.17956	1	0.26483	1	0.67481	1
10q loss	7 (6%)	110	0.4375	1	NA	NA	0.0033471	1	0.086764	1	0.26949	1	0.087115	1	0.61673	1	0.22061	1
11p loss	8 (7%)	109	1	1	NA	NA	0.066393	1	0.043416	1	0.26949	1	0.14512	1	1	1	0.44693	1
11q loss	10 (9%)	107	NA	NA	NA	NA	0.036152	1	0.0065237	1	0.29584	1	0.056335	1	0.96768	1	0.90019	1
13q loss	10 (9%)	107	1	1	NA	NA	0.17832	1	0.0014106	0.518	0.09099	1	0.40301	1	0.35517	1	0.23386	1
14q loss	20 (17%)	97	1	1	0.38462	1	2.8337e-11	1.13e-08	0.38963	1	0.13535	1	0.097727	1	0.45719	1	0.96763	1
15q loss	10 (9%)	107	1	1	NA	NA	0.036152	1	0.32017	1	0.57862	1	0.48748	1	0.57334	1	0.81565	1
16q loss	3 (3%)	114	NA	NA	NA	NA	0.14273	1	0.040143	1	NA	NA	NA	NA	0.86195	1	0.2861	1
17p loss	5 (4%)	112	0.4375	1	NA	NA	0.41106	1	0.010573	1	0.028791	1	0.07623	1	0.21863	1	0.25082	1
18p loss	17 (15%)	100	1	1	NA	NA	0.90465	1	0.067464	1	0.077193	1	0.011421	1	0.15845	1	0.44549	1
18q loss	18 (15%)	99	1	1	NA	NA	0.91038	1	0.03176	1	0.039207	1	0.0036251	1	0.32182	1	0.3728	1
19p loss	4 (3%)	113	NA	NA	NA	NA	0.09543	1	1	1	NA	NA	NA	NA	0.7457	1	0.33092	1
19q loss	3 (3%)	114	NA	NA	NA	NA	0.14273	1	0.60262	1	NA	NA	NA	NA	0.27872	1	0.61752	1
21q loss	12 (10%)	105	0.55	1	0.4125	1	0.50033	1	0.35469	1	0.24646	1	0.72792	1	0.21884	1	0.28387	1
22q loss	21 (18%)	96	1	1	NA	NA	0.0091565	1	0.097063	1	0.67259	1	0.047716	1	0.18587	1	0.43329	1
Xq loss	3 (3%)	114	1	1	NA	NA	0.30988	1	NA	NA	NA	NA	NA	NA	0.76737	1	0.10025	1
