		Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		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	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	0 (0%)	373	0.8156	1	0.64165	1	0.48564	1	0.60704	1	0.86727	1	0.24709	1	0.36001	1	0.17895	1	0.59568	1	0.91794	1
1q gain	0 (0%)	314	0.13272	1	0.10044	1	4.6141e-05	0.0338	0.014355	1	0.62657	1	0.47196	1	0.0072602	1	0.0080141	1	0.0071909	1	0.0060049	1
2p gain	0 (0%)	300	0.0069813	1	0.010523	1	1.0079e-11	7.83e-09	6.9144e-05	0.0505	0.065662	1	0.21632	1	0.00013075	0.0949	7.0367e-06	0.00524	0.86518	1	0.019518	1
2q gain	0 (0%)	354	0.12585	1	0.018064	1	5.4084e-06	0.00403	0.0039887	1	0.1881	1	0.30626	1	0.00059262	0.418	0.00076314	0.536	0.48684	1	0.30136	1
3p gain	0 (0%)	350	0.53925	1	0.21493	1	0.012253	1	0.00037495	0.268	0.74148	1	0.48568	1	0.17738	1	0.16522	1	0.86798	1	0.11024	1
3q gain	0 (0%)	217	0.071969	1	0.6531	1	0.011381	1	0.037327	1	0.30122	1	0.40231	1	0.038889	1	0.19253	1	0.94207	1	0.53314	1
4p gain	0 (0%)	383	0.1484	1	0.14985	1	0.0062022	1	0.15643	1	0.13225	1	0.46423	1	0.0063224	1	0.010181	1	0.50027	1	0.54652	1
4q gain	0 (0%)	390	1	1	0.7151	1	0.063381	1	NA	NA	NA	NA	NA	NA	0.77106	1	0.012835	1	0.8628	1	1	1
5p gain	0 (0%)	212	0.85011	1	0.95357	1	1.8679e-06	0.0014	0.011327	1	0.21576	1	0.25047	1	0.091044	1	0.22788	1	0.54575	1	0.55656	1
5q gain	0 (0%)	354	0.075361	1	0.27863	1	0.098474	1	0.14781	1	0.68738	1	0.65592	1	0.077393	1	0.12426	1	0.50669	1	0.1504	1
6p gain	0 (0%)	361	0.0021312	1	0.010633	1	0.00057352	0.406	0.5445	1	0.64273	1	0.27902	1	0.26134	1	0.0077402	1	0.97139	1	0.91622	1
6q gain	0 (0%)	373	0.0028901	1	0.073023	1	0.0002334	0.168	0.0013192	0.914	0.72331	1	0.59445	1	0.083587	1	0.019587	1	0.65693	1	0.39931	1
7p gain	0 (0%)	288	0.17281	1	0.24789	1	2.7782e-06	0.00208	0.0012111	0.84	0.73142	1	0.9882	1	0.063911	1	0.0020504	1	0.45103	1	0.037235	1
7q gain	0 (0%)	296	0.065972	1	0.097862	1	1.7193e-13	1.34e-10	5.6477e-07	0.000429	0.82541	1	0.84978	1	0.001387	0.958	1.0313e-05	0.00764	0.15132	1	0.0066638	1
8p gain	0 (0%)	349	0.12873	1	0.14267	1	0.03157	1	0.087495	1	0.75552	1	0.44108	1	0.066771	1	0.001632	1	0.21738	1	0.092605	1
8q gain	0 (0%)	283	0.032641	1	0.03107	1	0.013483	1	0.0043869	1	0.70845	1	0.61797	1	0.0024587	1	0.0020676	1	0.013585	1	0.099365	1
9p gain	0 (0%)	378	0.28964	1	0.13856	1	0.14518	1	0.871	1	0.17173	1	0.00021605	0.156	0.089935	1	0.010966	1	0.44555	1	0.10892	1
9q gain	0 (0%)	365	0.18569	1	0.074962	1	0.0043232	1	0.046996	1	0.074636	1	0.0021231	1	0.015746	1	0.012754	1	0.034975	1	0.1213	1
10p gain	0 (0%)	375	0.2079	1	1	1	0.4224	1	0.37172	1	0.5302	1	0.3894	1	0.58121	1	0.73368	1	0.33237	1	0.5095	1
10q gain	0 (0%)	389	NA	NA	NA	NA	0.32748	1	1	1	0.16228	1	0.68423	1	0.27483	1	0.6661	1	1	1	0.63434	1
11p gain	0 (0%)	374	1	1	0.92855	1	0.1362	1	0.12012	1	0.39773	1	0.27166	1	0.39214	1	0.11569	1	0.71843	1	0.66111	1
11q gain	0 (0%)	371	0.095959	1	0.49131	1	0.017092	1	0.034195	1	0.7732	1	0.37894	1	0.69106	1	0.10835	1	0.92655	1	0.60754	1
12p gain	0 (0%)	286	0.014628	1	0.11889	1	1.0288e-06	0.000778	0.078419	1	0.19698	1	0.59275	1	0.027944	1	0.065559	1	0.90678	1	0.3835	1
12q gain	0 (0%)	348	0.04883	1	0.25761	1	1.15e-06	0.000868	0.033894	1	0.21615	1	0.77484	1	0.41696	1	0.016147	1	0.56454	1	0.52623	1
13q gain	0 (0%)	387	0.76867	1	1	1	0.0030647	1	0.58205	1	0.28874	1	0.34943	1	0.6564	1	0.90301	1	0.40547	1	0.91173	1
14q gain	0 (0%)	356	0.10256	1	0.81952	1	0.54851	1	0.29611	1	1	1	0.67612	1	0.10982	1	0.41204	1	0.083059	1	0.034844	1
15q gain	0 (0%)	358	0.20566	1	0.033363	1	0.0017337	1	0.017602	1	0.19324	1	0.11233	1	0.0014833	1	0.073294	1	0.0022795	1	0.0095207	1
16p gain	0 (0%)	380	0.58909	1	1	1	0.00099342	0.691	0.3643	1	0.72331	1	0.34116	1	0.65169	1	0.14683	1	0.70757	1	0.66203	1
16q gain	0 (0%)	374	0.23729	1	0.84377	1	3.9893e-05	0.0293	0.42857	1	0.4554	1	0.15359	1	0.44119	1	0.95348	1	0.58244	1	0.30225	1
17p gain	0 (0%)	386	0.29798	1	0.08809	1	0.00089051	0.622	0.1235	1	0.06691	1	0.34268	1	0.20355	1	0.050399	1	0.0062208	1	0.011913	1
17q gain	0 (0%)	353	0.012958	1	0.028176	1	2.3598e-07	0.00018	0.0022885	1	0.41989	1	0.4197	1	0.0013779	0.954	0.0037042	1	0.16427	1	0.044251	1
18p gain	0 (0%)	330	0.0023568	1	9.4497e-06	0.00701	1.6587e-07	0.000126	0.022592	1	0.17522	1	0.091672	1	0.0028689	1	0.00030038	0.215	0.34803	1	0.022462	1
18q gain	0 (0%)	353	0.0078267	1	0.0004187	0.299	0.0028538	1	0.16515	1	0.13598	1	0.02853	1	0.0019382	1	0.0062125	1	0.087334	1	0.00074079	0.521
19p gain	0 (0%)	357	0.051591	1	0.16251	1	1.8649e-06	0.0014	0.0041479	1	0.00046844	0.333	0.0016581	1	0.0087636	1	0.0027812	1	0.04496	1	0.093325	1
19q gain	0 (0%)	339	0.057664	1	0.7726	1	0.00036831	0.263	0.38073	1	0.059527	1	0.019025	1	0.02182	1	0.0045326	1	0.77772	1	0.70539	1
20p gain	0 (0%)	288	0.13174	1	0.037917	1	5.0493e-08	3.87e-05	0.015861	1	0.68384	1	0.19449	1	0.096893	1	0.20996	1	0.27254	1	0.0077883	1
20q gain	0 (0%)	302	0.67207	1	0.59929	1	1.6017e-08	1.23e-05	0.18368	1	0.88479	1	0.33121	1	0.074609	1	0.047459	1	0.88213	1	0.16492	1
21q gain	0 (0%)	378	0.96811	1	0.42462	1	0.83924	1	0.0018712	1	0.52434	1	0.93666	1	0.68714	1	0.51432	1	0.64423	1	0.24528	1
22q gain	0 (0%)	300	0.0036214	1	0.0085753	1	7.9548e-09	6.13e-06	0.0020699	1	0.22719	1	0.016673	1	0.010268	1	0.011171	1	0.43357	1	0.0033483	1
Xq gain	0 (0%)	386	0.76867	1	1	1	0.056703	1	0.072886	1	0.45078	1	0.58167	1	0.85819	1	0.12968	1	0.25108	1	0.20352	1
1p loss	0 (0%)	338	0.0024775	1	0.0004187	0.299	6.4218e-12	5e-09	2.3958e-06	0.0018	0.25081	1	0.039161	1	1.1539e-06	0.00087	1.0166e-06	0.00077	0.48351	1	0.018669	1
1q loss	0 (0%)	388	NA	NA	NA	NA	0.18254	1	0.24963	1	0.79944	1	0.32028	1	0.54654	1	1	1	0.82593	1	0.14749	1
2p loss	0 (0%)	393	NA	NA	NA	NA	0.076896	1	NA	NA	NA	NA	NA	NA	1	1	1	1	0.77709	1	0.592	1
2q loss	0 (0%)	386	0.53216	1	1	1	0.013091	1	0.13147	1	0.73676	1	0.58167	1	0.25865	1	0.25259	1	0.18828	1	0.44629	1
3p loss	0 (0%)	236	0.050134	1	0.44773	1	4.1104e-06	0.00307	7.1917e-05	0.0524	0.49291	1	0.27534	1	0.43903	1	0.016515	1	0.91185	1	0.53847	1
3q loss	0 (0%)	371	0.26082	1	0.70138	1	0.041067	1	0.12012	1	0.70323	1	1	1	0.6912	1	0.12792	1	0.54718	1	1	1
4p loss	0 (0%)	233	0.17085	1	0.031897	1	7.018e-10	5.44e-07	5.3601e-08	4.1e-05	0.053333	1	0.32731	1	0.023376	1	0.0073667	1	0.19208	1	0.18191	1
4q loss	0 (0%)	254	0.0079594	1	0.00097462	0.679	5.5926e-11	4.34e-08	1.9919e-06	0.0015	0.0087604	1	0.11931	1	3.8535e-05	0.0284	3.9715e-05	0.0292	0.19456	1	0.026895	1
5p loss	0 (0%)	373	0.12193	1	0.25212	1	0.033148	1	0.14001	1	0.25524	1	0.20719	1	0.84129	1	1	1	0.77211	1	0.91794	1
5q loss	0 (0%)	251	0.23046	1	0.21301	1	1.3e-09	1e-06	6.6525e-09	5.13e-06	0.054301	1	0.089154	1	0.063664	1	0.2927	1	0.25879	1	0.019677	1
6p loss	0 (0%)	362	0.079844	1	0.016367	1	0.00011246	0.0819	0.008466	1	0.07526	1	0.029667	1	0.0026111	1	0.00019486	0.141	0.93744	1	0.82168	1
6q loss	0 (0%)	357	0.16555	1	0.026439	1	0.014138	1	0.066717	1	0.088271	1	0.15857	1	0.1117	1	0.046358	1	1	1	0.53207	1
7p loss	0 (0%)	374	0.40774	1	0.83372	1	0.0020743	1	0.013071	1	0.50358	1	0.1136	1	0.68925	1	0.70979	1	0.23398	1	0.64995	1
7q loss	0 (0%)	384	0.47205	1	0.8485	1	0.078018	1	0.34049	1	1	1	0.69605	1	0.05922	1	0.023448	1	0.19878	1	0.12059	1
8p loss	0 (0%)	280	0.36687	1	0.55404	1	6.298e-08	4.81e-05	0.00078533	0.551	0.11457	1	0.82957	1	0.4745	1	0.23144	1	0.40231	1	0.63374	1
8q loss	0 (0%)	385	0.25403	1	0.039685	1	0.030261	1	0.025414	1	0.080133	1	0.28811	1	0.39234	1	0.0040961	1	0.64243	1	0.58905	1
9p loss	0 (0%)	233	0.11448	1	0.75117	1	2.7868e-16	2.18e-13	3.0404e-08	2.34e-05	0.9828	1	0.48695	1	0.29288	1	0.20747	1	0.38687	1	0.42722	1
9q loss	0 (0%)	294	0.0039378	1	0.0046861	1	5.6011e-14	4.37e-11	1.4944e-05	0.0111	1	1	0.3999	1	3.3785e-05	0.0249	1.6829e-05	0.0124	0.066524	1	0.0083648	1
10p loss	0 (0%)	310	0.054263	1	0.13391	1	9.5565e-10	7.39e-07	4.3954e-06	0.00328	1	1	0.13227	1	0.00081293	0.569	0.00013093	0.0949	0.061627	1	0.00043234	0.307
10q loss	0 (0%)	306	0.0091286	1	0.00015338	0.111	6.1909e-12	4.82e-09	6.3741e-05	0.0467	0.26581	1	0.011788	1	0.00023262	0.167	8.8623e-06	0.00658	0.0067557	1	0.00059101	0.417
11p loss	0 (0%)	338	0.012908	1	0.18435	1	0.00017517	0.127	0.0033201	1	0.090483	1	0.041494	1	0.032405	1	0.15532	1	0.25254	1	0.49271	1
11q loss	0 (0%)	355	0.42033	1	0.48286	1	3.8127e-06	0.00285	0.008788	1	0.11893	1	0.31521	1	0.018237	1	0.057284	1	0.043408	1	0.14517	1
12p loss	0 (0%)	390	NA	NA	NA	NA	0.13137	1	0.68385	1	NA	NA	NA	NA	0.31859	1	0.32991	1	0.34717	1	0.71209	1
12q loss	0 (0%)	388	NA	NA	NA	NA	0.34047	1	0.38289	1	0.29227	1	0.38118	1	0.93334	1	0.038461	1	0.2244	1	0.51374	1
13q loss	0 (0%)	251	0.22929	1	0.60914	1	3.8618e-08	2.96e-05	0.00023056	0.166	0.14906	1	0.43995	1	0.58206	1	0.59895	1	0.85327	1	0.12301	1
14q loss	0 (0%)	327	0.00058	0.41	0.021694	1	0.0022505	1	0.014843	1	0.04584	1	0.042167	1	1.0053e-06	0.000762	9.8255e-08	7.5e-05	0.41247	1	0.27999	1
15q loss	0 (0%)	353	0.76434	1	0.11493	1	0.15185	1	0.0024635	1	0.0080068	1	0.0017183	1	0.42951	1	0.01301	1	0.19694	1	0.41908	1
16p loss	0 (0%)	337	0.32905	1	0.38804	1	1.9622e-05	0.0145	0.024685	1	0.38783	1	0.3047	1	0.077153	1	0.14277	1	0.72024	1	0.096535	1
16q loss	0 (0%)	317	0.065068	1	0.2372	1	0.00063885	0.45	0.0045279	1	0.17168	1	0.13181	1	0.072	1	0.0070809	1	0.92487	1	0.0060224	1
17p loss	0 (0%)	252	0.10165	1	1	1	7.0992e-05	0.0518	0.00012271	0.0892	0.010684	1	0.069425	1	0.20419	1	0.18418	1	0.21508	1	0.31641	1
17q loss	0 (0%)	372	0.27526	1	0.28227	1	0.052419	1	0.0049739	1	0.3043	1	0.94292	1	0.031504	1	0.055007	1	0.73763	1	0.70563	1
18p loss	0 (0%)	354	0.48986	1	0.65252	1	0.0052736	1	0.063726	1	0.21284	1	0.86007	1	0.25629	1	0.22177	1	0.60303	1	0.45555	1
18q loss	0 (0%)	321	0.36302	1	0.9322	1	0.0010711	0.744	0.34146	1	0.25337	1	0.78978	1	0.27725	1	0.013882	1	0.32934	1	0.31765	1
19p loss	0 (0%)	332	0.016553	1	0.015173	1	0.00057158	0.405	0.098363	1	0.70796	1	0.86703	1	0.0025224	1	0.016008	1	0.00091716	0.64	0.0027547	1
19q loss	0 (0%)	354	0.54085	1	0.2427	1	0.30708	1	0.051271	1	0.034579	1	0.10349	1	1	1	0.97431	1	0.10102	1	0.50257	1
20p loss	0 (0%)	380	0.26792	1	0.023682	1	0.086842	1	0.2122	1	0.041193	1	0.55514	1	0.58814	1	0.51432	1	0.31053	1	0.43491	1
20q loss	0 (0%)	375	0.037591	1	0.020284	1	0.0349	1	0.083978	1	0.077354	1	0.42857	1	0.0018684	1	0.001497	1	0.54539	1	0.59341	1
21q loss	0 (0%)	275	0.024673	1	0.016071	1	8.7138e-10	6.74e-07	9.2884e-07	0.000705	0.31758	1	0.24055	1	0.010769	1	0.013352	1	0.10942	1	0.21402	1
22q loss	0 (0%)	359	0.05705	1	0.15715	1	0.46574	1	0.47858	1	0.48505	1	0.20159	1	0.65218	1	0.11473	1	0.047787	1	0.090484	1
Xq loss	0 (0%)	382	0.63366	1	1	1	0.43053	1	0.91432	1	0.27702	1	0.00026116	0.187	0.60775	1	0.34665	1	0.087759	1	0.42054	1
