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	28 (11%)	216	0.009294	1	0.26523	1	0.14788	1	0.51716	1	0.017804	1	0.13898	1	0.71084	1	0.22326	1
1q gain	77 (32%)	167	7.1457e-09	4.4e-06	0.008452	1	0.36626	1	0.17243	1	0.074499	1	0.62498	1	0.20529	1	0.016336	1
2p gain	30 (12%)	214	0.0032081	1	0.30673	1	0.069563	1	0.39109	1	0.011308	1	0.017253	1	0.083132	1	0.022617	1
2q gain	28 (11%)	216	0.0024594	1	0.47482	1	0.01976	1	0.3842	1	0.0035016	1	0.0046816	1	0.0082993	1	0.0016899	0.973
3p gain	23 (9%)	221	0.057977	1	0.067723	1	1	1	0.77075	1	0.17351	1	0.27067	1	0.57701	1	0.75753	1
3q gain	30 (12%)	214	0.15788	1	0.16407	1	0.56458	1	0.59406	1	0.36577	1	0.49681	1	0.84802	1	0.67015	1
4p gain	24 (10%)	220	0.001778	1	0.052276	1	0.97929	1	0.46856	1	0.7327	1	0.52567	1	0.69697	1	0.58571	1
4q gain	20 (8%)	224	0.0010149	0.588	0.035712	1	0.92289	1	0.9449	1	0.5136	1	0.53462	1	0.45753	1	0.61353	1
5p gain	28 (11%)	216	0.0096612	1	0.26523	1	0.75834	1	0.81906	1	0.84853	1	0.20099	1	0.24924	1	0.75396	1
5q gain	14 (6%)	230	0.021312	1	0.38881	1	0.62874	1	0.40445	1	0.45005	1	0.16674	1	0.35919	1	0.19277	1
6p gain	76 (31%)	168	2.2085e-10	1.37e-07	1.8746e-05	0.0113	0.089368	1	0.58862	1	0.1699	1	0.13348	1	0.01196	1	0.00052707	0.309
6q gain	18 (7%)	226	0.25042	1	0.056384	1	1	1	0.4979	1	0.74629	1	0.24514	1	0.45383	1	0.69844	1
7p gain	101 (41%)	143	3.047e-10	1.89e-07	0.10904	1	0.1947	1	0.29812	1	0.00022534	0.134	0.034301	1	0.82619	1	0.43145	1
7q gain	104 (43%)	140	6.5174e-12	4.05e-09	0.23604	1	0.13043	1	0.16729	1	0.00014027	0.0839	0.030804	1	0.31904	1	0.10848	1
8p gain	49 (20%)	195	1.1591e-09	7.16e-07	0.011834	1	0.056231	1	0.36356	1	0.015323	1	0.039816	1	0.73253	1	0.43822	1
8q gain	78 (32%)	166	1.6004e-09	9.87e-07	2.0133e-05	0.0121	0.60323	1	0.92449	1	0.0006092	0.356	0.0096755	1	0.42355	1	0.61966	1
9p gain	9 (4%)	235	0.76134	1	0.14419	1	0.11973	1	0.4352	1	0.39497	1	0.80535	1	0.7662	1	0.45921	1
9q gain	10 (4%)	234	0.098271	1	0.46761	1	0.23617	1	0.59993	1	0.78398	1	0.83607	1	0.7662	1	0.34079	1
11p gain	17 (7%)	227	0.0098626	1	0.90146	1	0.14706	1	0.47436	1	0.017171	1	0.48312	1	0.54106	1	0.076071	1
11q gain	15 (6%)	229	0.00031444	0.186	0.4127	1	0.30722	1	0.71982	1	0.021336	1	0.29787	1	0.77634	1	0.062498	1
12p gain	23 (9%)	221	4.4055e-07	0.000268	0.14692	1	0.88313	1	0.92836	1	0.0071064	1	0.084148	1	0.31662	1	0.44054	1
12q gain	11 (5%)	233	0.00069107	0.403	0.62881	1	0.84658	1	0.80659	1	0.046047	1	0.026098	1	0.42135	1	0.23135	1
13q gain	39 (16%)	205	7.0002e-06	0.00424	2.3002e-05	0.0138	0.39853	1	0.17425	1	0.019268	1	0.054461	1	0.39425	1	0.47737	1
14q gain	16 (7%)	228	0.034793	1	0.061424	1	0.043079	1	0.2567	1	1	1	0.79149	1	0.48378	1	0.80143	1
15q gain	35 (14%)	209	1.9991e-06	0.00122	0.41977	1	0.56665	1	0.91224	1	0.54602	1	0.24263	1	0.83316	1	0.095356	1
16p gain	16 (7%)	228	0.00055354	0.324	0.009132	1	0.45191	1	0.7244	1	0.037757	1	0.1249	1	0.674	1	0.51192	1
16q gain	15 (6%)	229	0.015371	1	0.046195	1	0.19217	1	0.52674	1	0.037335	1	0.23063	1	0.74306	1	0.22751	1
17p gain	16 (7%)	228	0.063618	1	0.20687	1	0.71856	1	0.79003	1	0.31701	1	0.46512	1	0.43153	1	0.47453	1
17q gain	28 (11%)	216	0.021379	1	0.044147	1	0.70178	1	0.29297	1	0.40816	1	0.19333	1	0.1533	1	0.54203	1
18p gain	27 (11%)	217	0.051139	1	0.16055	1	0.90985	1	0.80089	1	0.075409	1	0.071425	1	0.35645	1	0.29259	1
18q gain	16 (7%)	228	0.034793	1	0.21921	1	0.53556	1	0.30764	1	0.23601	1	0.044895	1	1	1	0.92652	1
19p gain	16 (7%)	228	0.0081165	1	0.028035	1	0.62295	1	0.20364	1	0.003821	1	0.0020668	1	0.2854	1	0.80143	1
19q gain	20 (8%)	224	0.0076074	1	0.039644	1	0.41539	1	0.6776	1	0.00029868	0.177	0.06836	1	0.72679	1	0.83371	1
20p gain	70 (29%)	174	6.076e-06	0.00369	0.0019492	1	0.34505	1	0.90363	1	0.00022481	0.134	0.0020441	1	0.05005	1	0.16741	1
20q gain	89 (36%)	155	1.6575e-08	1.02e-05	0.0019876	1	0.44788	1	0.80222	1	0.0025981	1	0.066369	1	0.38172	1	0.42035	1
21q gain	29 (12%)	215	0.038424	1	0.00026081	0.155	0.18161	1	0.40155	1	0.046068	1	0.0090832	1	0.46962	1	0.95571	1
22q gain	59 (24%)	185	0.0020942	1	0.19746	1	0.80323	1	0.93285	1	0.52749	1	0.86738	1	0.71707	1	0.58058	1
Xq gain	4 (2%)	240	0.82894	1	0.8353	1	1	1	0.50711	1	0.038031	1	0.11762	1	0.5664	1	0.42193	1
1p loss	15 (6%)	229	0.060475	1	0.025611	1	0.38276	1	0.41634	1	0.11572	1	0.35937	1	0.459	1	0.92652	1
1q loss	7 (3%)	237	0.063679	1	0.34458	1	0.5445	1	0.56303	1	0.17927	1	0.52496	1	0.69977	1	0.73375	1
2p loss	18 (7%)	226	0.0088328	1	0.1057	1	0.30574	1	0.038365	1	0.53256	1	0.2762	1	0.0012626	0.73	0.0016975	0.976
2q loss	19 (8%)	225	0.022495	1	0.01715	1	0.20779	1	0.14965	1	0.37648	1	0.23691	1	0.0022996	1	0.009869	1
3p loss	22 (9%)	222	0.058538	1	0.076118	1	0.38163	1	0.36403	1	0.0021041	1	0.026955	1	0.77819	1	0.47911	1
3q loss	19 (8%)	225	0.073473	1	0.060552	1	0.42121	1	0.20933	1	0.067474	1	0.34301	1	0.95413	1	0.31459	1
4p loss	30 (12%)	214	0.32186	1	0.1933	1	0.34168	1	0.13245	1	0.0047715	1	0.22141	1	0.40311	1	0.48171	1
4q loss	31 (13%)	213	0.14155	1	0.066384	1	0.30806	1	0.02057	1	0.006447	1	0.02852	1	0.2912	1	0.14277	1
5p loss	32 (13%)	212	0.70134	1	0.26232	1	0.27238	1	0.33303	1	0.36585	1	0.28314	1	0.091222	1	0.16556	1
5q loss	46 (19%)	198	0.51477	1	0.043646	1	0.068857	1	0.55318	1	0.47049	1	0.53581	1	0.57761	1	0.85982	1
6p loss	28 (11%)	216	0.0085675	1	0.21544	1	0.4665	1	0.34726	1	0.33179	1	0.25064	1	0.20925	1	0.10988	1
6q loss	90 (37%)	154	0.0001109	0.0664	0.00070463	0.41	0.35417	1	0.45416	1	0.0015765	0.91	0.06754	1	0.62244	1	0.27835	1
7p loss	7 (3%)	237	0.79857	1	0.034783	1	0.6645	1	0.47064	1	0.71565	1	0.78581	1	0.61809	1	1	1
7q loss	6 (2%)	238	0.676	1	0.091108	1	0.77926	1	0.70257	1	1	1	0.87549	1	1	1	1	1
8p loss	28 (11%)	216	0.067891	1	0.11105	1	0.05702	1	0.4862	1	0.059363	1	0.34934	1	0.20154	1	0.1332	1
8q loss	5 (2%)	239	1	1	0.07052	1	0.13857	1	0.51542	1	0.32679	1	0.2853	1	0.85315	1	1	1
9p loss	134 (55%)	110	3.3095e-08	2.03e-05	1.9293e-05	0.0117	0.18758	1	0.13065	1	0.00072084	0.419	0.00062669	0.366	0.73959	1	0.53196	1
9q loss	100 (41%)	144	0.0056598	1	0.00044053	0.259	0.44783	1	0.36355	1	0.34583	1	0.79413	1	0.7664	1	0.46435	1
10p loss	103 (42%)	141	2.1931e-07	0.000134	5.5327e-05	0.0333	0.4398	1	0.15768	1	3.9234e-07	0.000239	0.00044073	0.259	0.20226	1	0.32334	1
10q loss	112 (46%)	132	3.0176e-10	1.87e-07	9.7807e-05	0.0587	0.53898	1	0.19182	1	2.5192e-07	0.000154	0.00018684	0.112	0.51599	1	0.65869	1
11p loss	57 (23%)	187	0.0021874	1	0.0018017	1	0.48381	1	0.26981	1	0.079902	1	0.0091903	1	0.2234	1	0.41717	1
11q loss	64 (26%)	180	0.00038169	0.225	0.024619	1	0.91636	1	0.76364	1	0.096547	1	0.0074765	1	0.67974	1	0.64539	1
12p loss	15 (6%)	229	0.16712	1	0.0088094	1	0.50038	1	0.81364	1	0.27738	1	0.29787	1	0.77634	1	0.59941	1
12q loss	24 (10%)	220	0.0053754	1	0.0023858	1	0.83898	1	0.8748	1	0.5458	1	0.35591	1	0.88581	1	0.94712	1
13q loss	36 (15%)	208	0.32194	1	0.45389	1	0.17234	1	0.65644	1	0.38892	1	0.60893	1	0.12115	1	0.23557	1
14q loss	54 (22%)	190	6.9208e-08	4.24e-05	0.050793	1	0.41145	1	0.27586	1	0.0039697	1	0.32775	1	0.52198	1	0.43607	1
15q loss	15 (6%)	229	0.0002698	0.16	0.08491	1	0.6509	1	0.13763	1	0.6315	1	0.8843	1	0.20833	1	0.056783	1
16p loss	22 (9%)	222	0.02156	1	0.0056679	1	0.95625	1	0.2043	1	0.31325	1	0.39033	1	0.10884	1	0.32057	1
16q loss	46 (19%)	198	0.0058317	1	0.02925	1	0.57131	1	0.37339	1	0.021321	1	0.079051	1	0.13437	1	0.14584	1
17p loss	50 (20%)	194	0.61872	1	0.17506	1	0.4931	1	0.68797	1	0.051887	1	0.97769	1	0.74904	1	0.39836	1
17q loss	22 (9%)	222	0.080492	1	0.5136	1	0.38701	1	0.47028	1	0.055336	1	0.56177	1	0.66312	1	1	1
18p loss	48 (20%)	196	0.0038535	1	0.0043616	1	0.37245	1	0.41519	1	0.00088574	0.514	0.047288	1	0.97838	1	0.81545	1
18q loss	44 (18%)	200	0.012846	1	0.018225	1	0.050228	1	0.18768	1	0.093366	1	0.54979	1	0.93157	1	0.66577	1
19p loss	19 (8%)	225	0.21033	1	0.53995	1	0.0057819	1	0.53606	1	0.14857	1	0.13702	1	0.48462	1	0.64079	1
19q loss	19 (8%)	225	0.21997	1	0.36584	1	0.65383	1	0.3467	1	0.37648	1	0.54416	1	0.68458	1	0.64079	1
20p loss	12 (5%)	232	0.5281	1	0.42244	1	0.15262	1	0.74441	1	0.61524	1	0.28798	1	0.085783	1	0.45916	1
20q loss	3 (1%)	241	0.50252	1	0.18669	1	NA	NA	NA	NA	0.63565	1	0.30349	1	0.79261	1	1	1
21q loss	28 (11%)	216	0.26105	1	0.26523	1	0.823	1	0.63417	1	0.43599	1	0.75149	1	0.90331	1	0.55228	1
22q loss	19 (8%)	225	0.49801	1	0.20517	1	0.59089	1	0.42806	1	0.59804	1	0.5172	1	0.10254	1	0.58289	1
Xq loss	10 (4%)	234	0.27658	1	0.0032853	1	0.28298	1	0.18795	1	0.33545	1	0.061622	1	0.2433	1	0.50134	1