Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Chi-square test_P	Chi-square 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	12 (4%)	310	0.7136	1	0.48566	1	0.22894	1	0.76034	1	0.099958	1	0.22091	1	0.81195	1	0.57293	1
1q gain	41 (13%)	281	0.0068617	1	0.00075519	0.43	0.96627	1	0.23397	1	0.0074847	1	0.0027915	1	0.0069213	1	0.12091	1
2p gain	30 (9%)	292	0.00018769	0.108	0.00021263	0.122	0.7555	1	0.9459	1	0.021879	1	0.036074	1	0.41494	1	0.65356	1
2q gain	20 (6%)	302	0.015243	1	0.0034679	1	0.89844	1	1	1	0.10872	1	0.15713	1	0.83289	1	0.58152	1
3p gain	27 (8%)	295	3.6983e-05	0.0219	3.6601e-05	0.0217	0.67174	1	0.18218	1	0.0015812	0.89	0.001817	1	0.0041422	1	0.08143	1
3q gain	104 (32%)	218	0.00035154	0.201	4.0313e-05	0.0238	0.20102	1	0.13095	1	0.012022	1	0.0017957	1	0.00068051	0.388	0.14852	1
4p gain	13 (4%)	309	0.0039091	1	0.064019	1	0.29199	1	1	1	0.16623	1	0.22798	1	0.34974	1	0.26777	1
4q gain	9 (3%)	313	0.23256	1	0.10256	1	0.29459	1	1	1	0.57619	1	0.63001	1	0.91726	1	0.62426	1
5p gain	82 (25%)	240	2.5361e-08	1.56e-05	0.043708	1	0.62242	1	0.56208	1	0.39944	1	0.4094	1	0.70957	1	0.51257	1
5q gain	28 (9%)	294	0.10617	1	0.69268	1	0.82538	1	0.82835	1	0.81884	1	0.46147	1	0.96811	1	0.26062	1
6p gain	26 (8%)	296	0.065231	1	0.046554	1	0.76206	1	0.49582	1	0.90196	1	0.87117	1	0.9004	1	1	1
6q gain	19 (6%)	303	0.01984	1	0.082072	1	0.45971	1	0.82835	1	0.72713	1	0.37765	1	0.82685	1	0.79045	1
7p gain	72 (22%)	250	1.1217e-06	0.000679	0.00015522	0.0902	0.88988	1	0.87504	1	0.86777	1	0.8952	1	0.48492	1	0.47178	1
7q gain	45 (14%)	277	6.967e-06	0.00417	1.0098e-06	0.000612	0.81	1	0.80532	1	0.27532	1	0.11215	1	0.14301	1	0.18628	1
8p gain	49 (15%)	273	7.8503e-06	0.00469	0.002003	1	0.66963	1	0.18019	1	0.38091	1	0.31331	1	0.28741	1	0.166	1
8q gain	129 (40%)	193	2.2487e-07	0.000137	0.00028003	0.16	0.79781	1	0.43119	1	0.56757	1	0.65111	1	0.56996	1	0.090486	1
9p gain	38 (12%)	284	0.00020261	0.117	0.05949	1	0.3435	1	0.4383	1	0.28772	1	0.64347	1	0.4414	1	0.94625	1
9q gain	47 (15%)	275	4.3282e-06	0.00261	0.010276	1	0.35521	1	0.30102	1	0.38289	1	0.19076	1	0.21962	1	0.52426	1
10p gain	12 (4%)	310	0.50958	1	0.0027806	1	0.18854	1	0.52142	1	0.054985	1	0.068933	1	0.25606	1	0.16159	1
10q gain	6 (2%)	316	0.44526	1	0.33841	1	0.73665	1	0.76833	1	1	1	1	1	0.67341	1	0.74983	1
11p gain	16 (5%)	306	0.0075758	1	0.67008	1	1	1	0.32315	1	0.75433	1	0.8449	1	0.85296	1	0.76469	1
11q gain	16 (5%)	306	0.10323	1	0.40726	1	0.624	1	1	1	0.15852	1	0.2952	1	0.65285	1	1	1
12p gain	61 (19%)	261	1.9712e-07	0.00012	1.8913e-05	0.0113	0.94907	1	0.68811	1	0.0039875	1	0.00061189	0.349	0.00012481	0.0726	0.068729	1
12q gain	25 (8%)	297	0.010694	1	0.002095	1	1	1	0.39646	1	0.039783	1	0.00086857	0.493	0.0038736	1	0.051026	1
13q gain	17 (5%)	305	0.0011721	0.661	0.035201	1	0.17206	1	0.80473	1	0.60305	1	0.90447	1	0.49784	1	0.28939	1
14q gain	52 (16%)	270	9.9599e-08	6.11e-05	0.015916	1	0.19035	1	0.11573	1	0.027051	1	0.027049	1	0.021894	1	0.11312	1
15q gain	13 (4%)	309	0.37003	1	0.27528	1	1	1	0.43313	1	0.72671	1	0.12361	1	0.48943	1	0.38081	1
16p gain	21 (7%)	301	0.0010872	0.614	8.4477e-05	0.0493	0.028593	1	0.12288	1	0.24107	1	0.9576	1	0.70572	1	0.66198	1
16q gain	28 (9%)	294	0.0083137	1	0.0042262	1	0.39093	1	1	1	0.02658	1	0.43686	1	0.60719	1	0.088373	1
17p gain	19 (6%)	303	0.0039607	1	0.082378	1	0.88787	1	0.40819	1	0.17981	1	0.56103	1	0.29451	1	0.38367	1
17q gain	23 (7%)	299	0.15094	1	0.096343	1	0.27522	1	0.49975	1	0.18967	1	0.051935	1	0.25585	1	0.58087	1
18p gain	52 (16%)	270	4.8489e-06	0.00291	0.058147	1	0.90728	1	0.2516	1	0.1137	1	0.0048968	1	0.50388	1	0.4135	1
18q gain	20 (6%)	302	0.00024082	0.138	0.00017731	0.103	0.15748	1	0.32315	1	0.019169	1	0.017071	1	0.009118	1	1	1
19p gain	12 (4%)	310	0.0030572	1	0.0049465	1	0.18435	1	0.096207	1	0.38904	1	0.023114	1	0.19375	1	0.16159	1
19q gain	21 (7%)	301	0.0059141	1	0.058112	1	0.87864	1	0.38127	1	0.15755	1	0.31863	1	0.22679	1	0.38917	1
20p gain	65 (20%)	257	3.1823e-07	0.000194	7.9034e-05	0.0463	0.29599	1	0.14871	1	0.61705	1	0.36452	1	0.53498	1	0.72593	1
20q gain	70 (22%)	252	3.2562e-09	2.03e-06	6.0967e-05	0.0358	0.87566	1	0.75327	1	0.48295	1	0.78852	1	0.98477	1	0.44732	1
21q gain	9 (3%)	313	0.089029	1	0.77263	1	0.68196	1	1	1	0.019285	1	0.055196	1	0.26869	1	0.8047	1
22q gain	39 (12%)	283	0.0066518	1	8.2145e-05	0.0481	0.56935	1	0.41661	1	0.07753	1	0.018974	1	0.25717	1	0.52657	1
Xq gain	21 (7%)	301	0.008975	1	0.10941	1	0.18663	1	0.16223	1	0.33321	1	0.76977	1	1	1	0.82345	1
1p loss	16 (5%)	306	5.1262e-08	3.15e-05	9.7016e-07	0.000589	0.17298	1	0.066231	1	0.012862	1	0.015561	1	0.063529	1	0.33802	1
2p loss	5 (2%)	317	0.692	1	0.011758	1	0.11988	1	1	1	0.054007	1	0.036052	1	0.070817	1	0.21324	1
2q loss	9 (3%)	313	0.57314	1	0.06623	1	0.064353	1	0.42388	1	0.031299	1	0.025751	1	0.10686	1	0.010511	1
3p loss	125 (39%)	197	1.8649e-12	1.17e-09	1.5268e-07	9.34e-05	0.68182	1	0.86096	1	0.35344	1	0.1488	1	0.051785	1	0.47212	1
3q loss	21 (7%)	301	0.066539	1	0.11526	1	0.64243	1	0.45282	1	0.8813	1	0.95942	1	0.17364	1	0.54891	1
4p loss	78 (24%)	244	1.761e-11	1.11e-08	4.5635e-08	2.81e-05	0.32993	1	0.16987	1	0.0045716	1	0.00027455	0.158	0.00016982	0.0985	0.097737	1
4q loss	51 (16%)	271	4.0769e-09	2.54e-06	5.9352e-06	0.00356	0.37799	1	0.24313	1	0.028144	1	0.0052221	1	0.0021317	1	0.03604	1
5p loss	10 (3%)	312	0.0027442	1	0.0036713	1	0.72685	1	1	1	0.28669	1	0.39935	1	0.037119	1	1	1
5q loss	62 (19%)	260	1.6724e-10	1.05e-07	2.3072e-10	1.44e-07	0.048537	1	0.32724	1	0.011121	1	5.518e-05	0.0325	0.0050595	1	0.5499	1
6p loss	19 (6%)	303	0.13454	1	0.012689	1	0.10045	1	0.11617	1	0.031706	1	0.1111	1	0.028568	1	0.10638	1
6q loss	21 (7%)	301	0.23742	1	0.070076	1	0.04742	1	0.052852	1	0.37927	1	0.39162	1	0.10747	1	0.087538	1
7p loss	5 (2%)	317	0.12112	1	0.38838	1	NA	NA	NA	NA	0.3907	1	0.45231	1	0.014001	1	1	1
7q loss	9 (3%)	313	0.045428	1	0.16118	1	1	1	0.74002	1	0.36294	1	0.69365	1	0.087761	1	0.069221	1
8p loss	70 (22%)	252	9.2502e-05	0.0539	1.393e-05	0.0083	0.97581	1	1	1	0.72595	1	0.59037	1	0.1312	1	0.27461	1
8q loss	6 (2%)	316	0.15312	1	0.10459	1	0.63753	1	0.76833	1	1	1	0.51457	1	0.88077	1	1	1
9p loss	89 (28%)	233	9.9474e-09	6.17e-06	1.2443e-08	7.7e-06	0.38419	1	0.94475	1	0.25175	1	0.052937	1	0.0024265	1	0.077005	1
9q loss	31 (10%)	291	0.0084554	1	0.067865	1	0.78518	1	0.49572	1	0.82908	1	0.85521	1	0.70368	1	0.0023315	1
10p loss	47 (15%)	275	0.010709	1	0.071899	1	0.60483	1	0.44611	1	0.85777	1	0.7506	1	0.27001	1	0.3933	1
10q loss	26 (8%)	296	0.011275	1	0.0029624	1	0.89331	1	0.47524	1	0.03058	1	0.0010733	0.607	0.007128	1	0.25762	1
11p loss	41 (13%)	281	0.00089271	0.506	0.04444	1	0.68811	1	0.8071	1	0.0017333	0.974	0.0059758	1	0.039162	1	0.40578	1
11q loss	62 (19%)	260	7.4881e-09	4.65e-06	7.5501e-05	0.0443	0.94514	1	0.58948	1	0.011212	1	0.062164	1	0.3016	1	0.89652	1
12p loss	12 (4%)	310	0.041808	1	0.13896	1	0.33788	1	0.19873	1	0.46806	1	0.45915	1	0.34231	1	0.41046	1
12q loss	8 (2%)	314	0.19719	1	0.073031	1	0.61425	1	0.66597	1	0.20101	1	0.30816	1	0.60454	1	0.010733	1
13q loss	65 (20%)	257	8.9973e-10	5.62e-07	9.4774e-10	5.91e-07	0.85732	1	0.69192	1	0.028593	1	2.3757e-05	0.0141	0.028907	1	0.061314	1
14q loss	16 (5%)	306	0.12069	1	0.041537	1	0.36982	1	0.72626	1	0.010806	1	0.015397	1	0.1439	1	0.33802	1
15q loss	23 (7%)	299	0.10021	1	0.13597	1	0.41995	1	0.15026	1	0.70773	1	0.35953	1	0.32456	1	0.52237	1
16p loss	12 (4%)	310	0.59662	1	0.029407	1	0.07802	1	0.27374	1	0.041388	1	0.013987	1	0.10008	1	0.10571	1
16q loss	26 (8%)	296	0.037094	1	4.1892e-05	0.0247	0.055794	1	0.0053247	1	4.7208e-07	0.000287	1.3363e-08	8.26e-06	0.0034038	1	0.011615	1
17p loss	45 (14%)	277	0.2494	1	1.2742e-05	0.00761	0.57723	1	0.67707	1	0.63743	1	0.021813	1	0.49224	1	0.44006	1
17q loss	5 (2%)	317	0.20955	1	0.0040175	1	0.11943	1	0.66597	1	0.14826	1	0.38635	1	0.52446	1	0.108	1
18p loss	29 (9%)	293	0.0069972	1	0.024259	1	0.76358	1	0.49232	1	0.57825	1	0.74676	1	0.22539	1	0.65356	1
18q loss	91 (28%)	231	2.1353e-11	1.34e-08	3.1613e-08	1.95e-05	0.28955	1	0.10713	1	0.013355	1	0.44236	1	0.10555	1	0.75007	1
19p loss	27 (8%)	295	0.019841	1	0.11275	1	0.59771	1	0.87457	1	0.11829	1	0.41646	1	0.54928	1	0.48799	1
19q loss	20 (6%)	302	0.031426	1	0.18043	1	0.53134	1	0.51911	1	0.69431	1	0.83272	1	0.2771	1	0.81352	1
20p loss	21 (7%)	301	0.054379	1	0.31927	1	0.51783	1	0.81478	1	0.22385	1	0.090392	1	0.33251	1	0.20391	1
20q loss	10 (3%)	312	0.038898	1	0.21225	1	0.63753	1	0.60102	1	0.035931	1	0.046799	1	0.51193	1	0.65864	1
21q loss	57 (18%)	265	3.9073e-06	0.00236	0.010851	1	0.91955	1	0.31787	1	0.8923	1	0.51213	1	0.18079	1	0.21263	1
22q loss	25 (8%)	297	3.092e-06	0.00187	0.030467	1	0.39622	1	1	1	0.39131	1	0.77198	1	0.0021294	1	0.8566	1
Xq loss	8 (2%)	314	0.3278	1	0.12184	1	0.19365	1	0.34117	1	0.49882	1	1	1	0.49707	1	0.22103	1