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	Chi-square test_P	Chi-square test_Q
1p gain	0 (0%)	133	1.6879e-05	0.0096	0.087753	1	0.4661	1	0.74432	1	0.024599	1	0.33203	1	0.23463	1	0.66404	1
1q gain	0 (0%)	117	0.017416	1	0.34798	1	0.94061	1	0.63731	1	0.091643	1	0.55933	1	0.51374	1	0.51516	1
2p gain	0 (0%)	120	2.9264e-05	0.0166	0.0001032	0.0582	0.21375	1	0.63731	1	0.038711	1	0.41503	1	0.085356	1	0.2564	1
2q gain	0 (0%)	139	0.014173	1	0.24148	1	0.6896	1	0.60471	1	0.016666	1	0.24937	1	0.18221	1	0.086309	1
3p gain	0 (0%)	122	0.00012779	0.0716	0.065218	1	0.028711	1	0.014554	1	0.051208	1	0.0012317	0.676	0.011574	1	0.024012	1
3q gain	0 (0%)	108	5.4374e-06	0.0031	0.22369	1	1	1	0.14212	1	0.22909	1	0.16132	1	0.16264	1	0.032695	1
4p gain	0 (0%)	142	0.89744	1	0.62452	1	1	1	1	1	1	1	1	1	0.51492	1	0.72413	1
4q gain	0 (0%)	147	0.79724	1	0.40509	1	NA	NA	NA	NA	1	1	0.60074	1	0.32074	1	0.31261	1
5p gain	0 (0%)	109	0.0023629	1	0.46897	1	0.028686	1	0.43569	1	0.35143	1	0.14797	1	0.11475	1	0.15197	1
5q gain	0 (0%)	133	0.060474	1	0.070677	1	0.22843	1	0.26132	1	0.93427	1	1	1	0.26605	1	0.61815	1
6p gain	0 (0%)	139	0.094283	1	0.14143	1	NA	NA	NA	NA	0.57125	1	1	1	0.21575	1	0.072375	1
6q gain	0 (0%)	144	0.061259	1	0.49449	1	NA	NA	NA	NA	0.11696	1	0.4274	1	0.02557	1	0.16967	1
7p gain	0 (0%)	105	0.0060823	1	0.0013473	0.737	0.83509	1	0.21142	1	0.095777	1	0.60513	1	0.013195	1	0.48635	1
7q gain	0 (0%)	109	0.0039052	1	0.076187	1	1	1	0.25837	1	0.17077	1	0.47773	1	0.39371	1	0.6603	1
8p gain	0 (0%)	135	0.017234	1	0.0033968	1	0.19229	1	0.25214	1	0.17828	1	0.25566	1	0.83144	1	0.39116	1
8q gain	0 (0%)	106	0.0028593	1	0.035581	1	0.62304	1	0.45906	1	0.12966	1	0.37187	1	0.84625	1	0.78851	1
9p gain	0 (0%)	135	0.04894	1	0.43663	1	0.18861	1	1	1	0.011394	1	0.010346	1	0.17516	1	0.51477	1
9q gain	0 (0%)	138	1	1	0.23206	1	0.2593	1	0.36582	1	0.038037	1	0.012233	1	1	1	0.86008	1
10p gain	0 (0%)	123	0.00064231	0.356	0.0012598	0.69	0.38191	1	0.016951	1	0.86924	1	0.23579	1	0.34837	1	0.09163	1
10q gain	0 (0%)	143	0.36296	1	0.18804	1	0.51237	1	0.29442	1	0.69452	1	0.2405	1	0.68577	1	0.72361	1
11p gain	0 (0%)	143	0.010574	1	0.86601	1	NA	NA	NA	NA	0.16314	1	0.32297	1	0.53605	1	0.48277	1
11q gain	0 (0%)	141	0.3274	1	0.35129	1	NA	NA	NA	NA	0.19838	1	0.21569	1	0.40489	1	0.74216	1
12p gain	0 (0%)	124	0.018395	1	0.65156	1	0.16295	1	0.47776	1	0.38074	1	0.04154	1	0.52829	1	0.25781	1
12q gain	0 (0%)	132	0.61695	1	0.24852	1	0.41907	1	0.55065	1	0.16721	1	0.06228	1	0.14413	1	0.19908	1
13q gain	0 (0%)	126	0.1057	1	0.81027	1	0.031759	1	0.084378	1	0.021529	1	0.38355	1	0.12396	1	0.43641	1
14q gain	0 (0%)	139	0.28113	1	0.8977	1	0.20595	1	0.57589	1	0.16152	1	0.057641	1	0.5213	1	0.1634	1
15q gain	0 (0%)	145	1	1	0.031388	1	0.29599	1	0.32754	1	0.11041	1	0.11499	1	1	1	0.85871	1
16p gain	0 (0%)	141	0.028814	1	0.84373	1	0.63787	1	1	1	0.44713	1	0.66809	1	0.61908	1	0.50373	1
16q gain	0 (0%)	137	0.0048985	1	0.26582	1	1	1	1	1	0.075509	1	0.22482	1	0.8142	1	0.81196	1
17p gain	0 (0%)	142	0.3656	1	0.66644	1	NA	NA	NA	NA	0.27117	1	0.32682	1	1	1	0.41906	1
17q gain	0 (0%)	126	0.00020516	0.114	0.018042	1	0.49688	1	0.16783	1	0.0078922	1	0.083308	1	0.15023	1	0.003071	1
18p gain	0 (0%)	126	5.4691e-05	0.0309	0.063266	1	0.65588	1	0.49748	1	0.0084655	1	0.15734	1	0.42862	1	0.076407	1
18q gain	0 (0%)	141	0.21826	1	0.59851	1	0.46507	1	0.083649	1	0.16493	1	0.11514	1	0.61908	1	0.92884	1
19p gain	0 (0%)	137	0.70664	1	0.039812	1	NA	NA	NA	NA	0.096571	1	0.1805	1	0.65054	1	0.58425	1
19q gain	0 (0%)	123	0.030469	1	0.2742	1	0.6325	1	1	1	0.10452	1	0.45401	1	0.7631	1	0.74158	1
20p gain	0 (0%)	96	0.022418	1	0.077142	1	0.41527	1	0.80463	1	0.4696	1	0.37972	1	0.46042	1	0.16337	1
20q gain	0 (0%)	90	0.026769	1	0.037134	1	0.43936	1	0.49442	1	0.078206	1	0.3921	1	0.023302	1	0.056342	1
21q gain	0 (0%)	123	0.015162	1	0.0011049	0.609	0.59828	1	0.5386	1	0.26405	1	0.10872	1	0.24429	1	0.37984	1
22q gain	0 (0%)	138	0.098335	1	0.16458	1	0.53575	1	0.57199	1	0.41406	1	0.4986	1	0.01661	1	0.23303	1
Xq gain	0 (0%)	144	0.023329	1	0.80129	1	NA	NA	NA	NA	0.11696	1	0.86569	1	0.76473	1	0.37122	1
1p loss	0 (0%)	146	0.19743	1	0.050893	1	NA	NA	NA	NA	0.29372	1	0.42089	1	0.35184	1	0.35868	1
2p loss	0 (0%)	142	0.41081	1	0.02291	1	NA	NA	NA	NA	0.095083	1	0.14916	1	1	1	0.65193	1
2q loss	0 (0%)	133	0.010774	1	0.47174	1	1	1	0.29442	1	0.19783	1	0.49823	1	1	1	0.81519	1
3p loss	0 (0%)	141	0.61544	1	0.77287	1	0.34475	1	0.4667	1	0.022429	1	0.078275	1	0.21976	1	0.62222	1
4p loss	0 (0%)	121	0.010047	1	0.29172	1	0.85302	1	0.76733	1	0.66707	1	0.68352	1	0.53426	1	0.37894	1
4q loss	0 (0%)	123	0.019665	1	0.81229	1	0.92169	1	1	1	0.5255	1	0.92234	1	0.53908	1	0.63187	1
5p loss	0 (0%)	136	0.0035333	1	0.41536	1	0.4242	1	1	1	0.47632	1	0.099227	1	0.16309	1	0.1627	1
5q loss	0 (0%)	115	0.00010329	0.0582	0.07164	1	0.64837	1	1	1	0.38828	1	0.57806	1	0.20987	1	0.021223	1
6p loss	0 (0%)	130	0.12389	1	0.1038	1	0.23336	1	0.45564	1	0.56123	1	0.81303	1	0.78191	1	0.13105	1
6q loss	0 (0%)	121	0.0003326	0.185	0.0088271	1	0.24675	1	0.80167	1	0.28571	1	0.13764	1	0.59623	1	0.49156	1
7q loss	0 (0%)	147	0.45256	1	0.2924	1	NA	NA	NA	NA	0.54651	1	0.31335	1	0.16027	1	0.8394	1
8p loss	0 (0%)	102	2.5397e-08	1.45e-05	1.9011e-05	0.0108	0.14267	1	0.28713	1	0.18898	1	0.61462	1	0.014725	1	0.14175	1
8q loss	0 (0%)	144	0.31679	1	0.062107	1	NA	NA	NA	NA	0.24162	1	0.14371	1	0.23189	1	0.035218	1
9p loss	0 (0%)	107	5.1541e-05	0.0292	0.0038243	1	0.0016696	0.912	0.12801	1	0.0063968	1	0.00014612	0.0817	0.89369	1	0.71904	1
9q loss	0 (0%)	109	0.037446	1	0.005446	1	0.001208	0.664	0.0083329	1	0.00021421	0.119	1.559e-06	0.00089	0.91685	1	0.73163	1
10p loss	0 (0%)	131	0.011577	1	0.8782	1	0.18861	1	0.52816	1	0.12828	1	0.1641	1	0.2576	1	0.26456	1
10q loss	0 (0%)	120	0.0002934	0.163	0.053763	1	0.92133	1	0.84318	1	0.63147	1	0.074525	1	0.029683	1	0.27799	1
11p loss	0 (0%)	103	0.0009515	0.525	0.00066129	0.366	0.25319	1	0.75596	1	0.032221	1	0.0057556	1	0.1147	1	0.95857	1
11q loss	0 (0%)	116	0.015056	1	0.020964	1	0.12012	1	0.42683	1	0.017898	1	0.17915	1	0.25001	1	0.43991	1
12p loss	0 (0%)	144	0.7655	1	0.16112	1	NA	NA	NA	NA	0.27082	1	0.2551	1	0.57664	1	0.44383	1
12q loss	0 (0%)	143	0.47659	1	0.86601	1	NA	NA	NA	NA	0.41231	1	0.41772	1	0.61061	1	0.025962	1
13q loss	0 (0%)	130	0.10209	1	0.31107	1	0.10353	1	0.14141	1	0.13723	1	0.2774	1	0.64389	1	0.18456	1
14q loss	0 (0%)	125	0.073171	1	0.027225	1	0.81766	1	0.31672	1	0.37044	1	0.47149	1	0.031189	1	0.22371	1
15q loss	0 (0%)	131	0.1749	1	0.094986	1	0.12078	1	0.41094	1	0.04948	1	0.19857	1	0.10304	1	0.017126	1
16p loss	0 (0%)	133	0.00011541	0.0649	0.27557	1	0.6034	1	1	1	0.021242	1	0.42055	1	0.10933	1	0.040208	1
16q loss	0 (0%)	133	0.00011541	0.0649	0.3993	1	0.74957	1	1	1	0.024599	1	0.63337	1	0.67406	1	0.12029	1
17p loss	0 (0%)	107	0.63705	1	0.13505	1	0.54073	1	0.80463	1	0.02159	1	0.33897	1	0.096105	1	0.37535	1
17q loss	0 (0%)	144	0.5652	1	0.039355	1	NA	NA	NA	NA	0.43718	1	0.30566	1	0.26688	1	0.53559	1
18p loss	0 (0%)	129	0.059289	1	0.034686	1	0.57262	1	0.45564	1	0.84511	1	0.10874	1	0.51349	1	0.18988	1
18q loss	0 (0%)	113	0.065375	1	0.71992	1	0.87641	1	0.094745	1	0.51925	1	0.051347	1	0.22414	1	0.15506	1
19p loss	0 (0%)	141	0.053053	1	0.93289	1	0.25229	1	0.14046	1	0.68675	1	0.54838	1	0.44098	1	0.049952	1
19q loss	0 (0%)	146	0.10643	1	0.70202	1	NA	NA	NA	NA	0.83286	1	0.83208	1	0.14661	1	0.12077	1
20p loss	0 (0%)	143	0.24064	1	0.055396	1	NA	NA	NA	NA	0.79118	1	0.1218	1	1	1	0.58919	1
21q loss	0 (0%)	134	0.66054	1	0.26201	1	0.4661	1	0.21582	1	0.38631	1	0.61624	1	0.94382	1	0.70399	1
22q loss	0 (0%)	121	0.0023775	1	0.66937	1	0.070593	1	0.12643	1	0.007647	1	0.57503	1	0.69302	1	0.020857	1
Xq loss	0 (0%)	147	0.15476	1	0.10172	1	NA	NA	NA	NA	0.47638	1	0.60074	1	0.45987	1	0.54763	1