		Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_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	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
1p gain	0 (0%)	435	1	1	1	1	1.6258e-07	0.000141	0.015537	1	0.081519	1	0.024133	1	0.024329	1	0.30953	1	0.63509	1	0.76296	1	1	1	0.38636	1
1q gain	0 (0%)	302	0.46488	1	0.88479	1	0.033696	1	1.6666e-06	0.00143	0.13068	1	0.14618	1	0.00062963	0.486	0.64233	1	0.49354	1	0.60386	1	0.44385	1	0.074429	1
2p gain	0 (0%)	443	0.03123	1	0.015087	1	2.2832e-08	2.01e-05	1.2625e-06	0.00108	0.078071	1	0.030149	1	0.00016154	0.13	0.00076632	0.588	0.00040494	0.315	0.007648	1	0.0029477	1	0.038151	1
2q gain	0 (0%)	448	0.0302	1	0.025306	1	2.0907e-06	0.00178	1.7705e-08	1.56e-05	0.25214	1	0.27599	1	0.00018355	0.147	0.01826	1	0.00016153	0.13	0.0020987	1	0.00015216	0.123	0.0086937	1
3p gain	0 (0%)	480	NA	NA	NA	NA	0.016698	1	0.12028	1	0.13709	1	0.27068	1	0.0070266	1	0.0018011	1	0.87616	1	0.66359	1	0.75833	1	0.43603	1
3q gain	0 (0%)	463	NA	NA	NA	NA	0.0023546	1	0.010681	1	0.078299	1	0.022215	1	0.0045641	1	0.10727	1	0.042959	1	0.35803	1	0.089214	1	0.10493	1
4p gain	0 (0%)	463	0.55363	1	0.41815	1	0.00011374	0.0926	0.043956	1	0.094831	1	0.034726	1	0.85129	1	0.38226	1	0.56372	1	0.44707	1	0.63295	1	0.4418	1
4q gain	0 (0%)	483	NA	NA	NA	NA	0.022534	1	0.95542	1	0.32524	1	0.253	1	0.53234	1	0.34772	1	0.12888	1	0.22259	1	0.31273	1	0.036339	1
5p gain	0 (0%)	309	0.48692	1	0.4185	1	5.0329e-12	4.49e-09	0.042306	1	0.18205	1	0.61159	1	0.013032	1	0.021923	1	0.11856	1	0.081042	1	0.28853	1	0.20284	1
5q gain	0 (0%)	433	0.017738	1	0.64431	1	0.077382	1	0.0013211	0.996	0.49786	1	0.1641	1	0.0064444	1	0.037522	1	0.44655	1	0.14608	1	0.30612	1	0.24696	1
6p gain	0 (0%)	420	0.29183	1	0.05069	1	0.0091672	1	9.4758e-08	8.28e-05	0.0093568	1	0.26104	1	0.00282	1	0.26136	1	0.070268	1	0.34207	1	0.1541	1	0.096496	1
6q gain	0 (0%)	474	NA	NA	NA	NA	0.083495	1	0.0025837	1	0.10777	1	0.064469	1	0.11776	1	0.60543	1	0.1044	1	0.032667	1	0.28301	1	0.064737	1
7p gain	0 (0%)	334	0.75419	1	0.5228	1	3.5094e-21	3.14e-18	0.00038498	0.301	8.9258e-05	0.073	0.0094814	1	1.2361e-06	0.00106	4.9825e-07	0.000431	0.00028332	0.224	0.0026287	1	0.0016017	1	0.00077242	0.592
7q gain	0 (0%)	381	0.38828	1	0.70175	1	3.1278e-10	2.78e-07	0.020705	1	0.078881	1	0.29831	1	1.6806e-05	0.0141	1.2179e-05	0.0102	0.14224	1	0.23816	1	0.029347	1	0.1167	1
8p gain	0 (0%)	432	1	1	0.41815	1	7.738e-11	6.89e-08	0.0037094	1	0.44884	1	0.54197	1	4.6525e-05	0.0386	0.0056838	1	0.18863	1	0.10078	1	0.85016	1	0.064931	1
8q gain	0 (0%)	344	0.064056	1	0.19076	1	1.8352e-23	1.65e-20	1.26e-07	0.00011	0.027222	1	0.0040773	1	0.00091251	0.693	0.00077722	0.595	8.0527e-08	7.05e-05	1.6659e-07	0.000145	0.0016796	1	1.4619e-05	0.0123
9p gain	0 (0%)	477	NA	NA	NA	NA	0.1041	1	0.007058	1	1	1	0.84262	1	0.25296	1	0.21625	1	0.30284	1	0.15698	1	0.045361	1	0.23954	1
9q gain	0 (0%)	485	NA	NA	NA	NA	0.024189	1	0.27888	1	0.39223	1	0.26858	1	0.20058	1	1	1	0.26815	1	0.24873	1	0.032185	1	0.16712	1
10p gain	0 (0%)	442	NA	NA	NA	NA	0.002426	1	0.00030919	0.244	0.16869	1	0.16046	1	0.0033347	1	0.086687	1	0.061209	1	0.22031	1	0.0037604	1	0.075604	1
10q gain	0 (0%)	463	NA	NA	NA	NA	0.25067	1	0.00080604	0.615	0.50141	1	0.1573	1	7.0591e-06	0.00596	0.3155	1	0.78224	1	0.3634	1	0.49522	1	0.19551	1
11p gain	0 (0%)	457	NA	NA	NA	NA	0.015212	1	0.04555	1	0.18821	1	0.60176	1	0.061254	1	0.34922	1	0.031261	1	0.10884	1	0.03611	1	0.24678	1
11q gain	0 (0%)	442	0.11976	1	0.15726	1	0.00018712	0.15	0.020743	1	0.0015858	1	0.035395	1	0.0070532	1	0.002708	1	0.0046657	1	0.024322	1	0.0044733	1	0.05228	1
12p gain	0 (0%)	434	0.56496	1	0.13192	1	4.7366e-08	4.16e-05	3.9723e-05	0.033	0.17972	1	0.1154	1	0.00096369	0.73	0.00037483	0.294	0.00025698	0.204	0.0035673	1	0.00015413	0.125	0.018441	1
12q gain	0 (0%)	445	0.56496	1	0.13192	1	8.6192e-06	0.00727	0.00012545	0.102	0.15757	1	0.089273	1	0.0001892	0.151	0.0012316	0.931	0.0074355	1	0.075678	1	0.0054703	1	0.15804	1
13q gain	0 (0%)	477	0.19234	1	0.15726	1	0.56488	1	0.0048703	1	0.28818	1	0.19608	1	0.15092	1	0.10322	1	0.79196	1	0.20177	1	1	1	0.4422	1
14q gain	0 (0%)	434	NA	NA	NA	NA	5.1039e-07	0.000441	2.9826e-06	0.00254	0.12705	1	0.51774	1	0.00056561	0.439	0.018435	1	0.0071956	1	0.00035498	0.279	0.0023398	1	0.021128	1
15q gain	0 (0%)	479	NA	NA	NA	NA	0.72326	1	0.22085	1	0.81901	1	0.5781	1	0.20013	1	0.21241	1	0.54771	1	0.41528	1	0.69558	1	0.14972	1
16p gain	0 (0%)	422	0.35825	1	0.32152	1	0.0033257	1	0.00035677	0.28	0.064725	1	0.56106	1	0.00011064	0.0902	0.016273	1	0.21786	1	0.14852	1	0.16834	1	0.52673	1
16q gain	0 (0%)	450	0.19234	1	0.051411	1	0.017513	1	0.02678	1	0.031728	1	0.038258	1	0.0088049	1	0.23626	1	0.25406	1	0.13727	1	0.32983	1	0.79356	1
17p gain	0 (0%)	464	NA	NA	NA	NA	4.7633e-06	0.00403	8.4812e-05	0.0695	0.66456	1	0.53278	1	0.544	1	0.35624	1	0.041326	1	0.18362	1	0.23962	1	0.55788	1
17q gain	0 (0%)	413	0.044722	1	0.70175	1	4.6186e-10	4.1e-07	1.59e-07	0.000138	0.42297	1	0.19877	1	0.0057512	1	0.059537	1	0.021788	1	0.029841	1	0.077392	1	0.10904	1
18p gain	0 (0%)	449	NA	NA	NA	NA	3.5725e-07	0.00031	0.00015978	0.129	0.14832	1	0.33818	1	0.20887	1	0.051713	1	0.011177	1	0.019671	1	0.01507	1	0.0043999	1
18q gain	0 (0%)	466	NA	NA	NA	NA	2.2439e-06	0.00191	0.00094665	0.718	0.089952	1	0.037314	1	0.028423	1	0.0049668	1	0.085314	1	0.071568	1	0.051747	1	0.0070323	1
19p gain	0 (0%)	487	NA	NA	NA	NA	1	1	0.25383	1	0.7761	1	1	1	0.48209	1	1	1	0.5117	1	0.86194	1	1	1	1	1
19q gain	0 (0%)	469	NA	NA	NA	NA	0.0008179	0.623	0.062502	1	0.19818	1	0.0077234	1	0.0068897	1	0.019358	1	0.11202	1	0.042639	1	0.081862	1	0.19927	1
20p gain	0 (0%)	430	0.023526	1	0.012653	1	1.8783e-06	0.0016	2.2699e-06	0.00193	0.024914	1	0.68732	1	5.7439e-05	0.0475	0.00013508	0.11	0.018901	1	0.0077237	1	0.017868	1	0.067198	1
20q gain	0 (0%)	415	0.0023737	1	0.0021899	1	3.1081e-07	0.00027	4.307e-09	3.81e-06	0.00083915	0.639	0.091968	1	3.2623e-06	0.00276	3.9418e-05	0.0328	0.0019044	1	0.0026504	1	0.009365	1	0.011426	1
21q gain	0 (0%)	450	0.19234	1	0.15726	1	0.00022425	0.179	0.0026001	1	0.09138	1	0.052338	1	0.23005	1	0.16999	1	0.059583	1	0.3802	1	0.61919	1	0.67003	1
22q gain	0 (0%)	473	NA	NA	NA	NA	0.002945	1	0.085034	1	0.78173	1	0.17219	1	0.17515	1	0.39831	1	0.092872	1	0.056439	1	0.071418	1	0.2291	1
Xq gain	0 (0%)	476	0.7496	1	0.59113	1	8.3654e-05	0.0687	0.43971	1	0.63642	1	0.34512	1	0.28447	1	0.42097	1	0.45226	1	0.46539	1	0.13868	1	0.24777	1
1p loss	0 (0%)	464	NA	NA	NA	NA	2.163e-05	0.0181	0.00017477	0.141	0.11126	1	0.19883	1	0.1126	1	0.18866	1	0.78901	1	0.14613	1	0.29949	1	0.55744	1
1q loss	0 (0%)	483	NA	NA	NA	NA	0.00069286	0.533	0.092432	1	0.2221	1	0.015141	1	0.33996	1	0.21226	1	0.45228	1	0.16527	1	0.49964	1	0.1579	1
2p loss	0 (0%)	487	NA	NA	NA	NA	0.86677	1	0.56291	1	1	1	0.61732	1	0.54815	1	1	1	0.7577	1	0.86194	1	0.8462	1	1	1
2q loss	0 (0%)	489	NA	NA	NA	NA	0.042148	1	0.21774	1	NA	NA	NA	NA	0.8702	1	1	1	0.54389	1	0.79746	1	0.83146	1	0.77766	1
3p loss	0 (0%)	397	0.2081	1	0.17643	1	1.8567e-06	0.00159	3.2376e-06	0.00275	0.1244	1	0.25944	1	0.51276	1	0.038672	1	0.028759	1	0.018448	1	0.0038259	1	0.19041	1
3q loss	0 (0%)	437	0.55363	1	0.41815	1	0.00036809	0.289	0.00016615	0.134	0.34086	1	0.93304	1	0.16101	1	0.61206	1	0.43974	1	0.045132	1	0.0048821	1	0.34207	1
4p loss	0 (0%)	453	NA	NA	NA	NA	1.2191e-05	0.0102	0.0003758	0.294	0.19181	1	0.24819	1	0.00066842	0.515	4.1306e-05	0.0343	0.00010188	0.0831	0.0080962	1	0.007646	1	0.033606	1
4q loss	0 (0%)	446	0.0060484	1	0.0070565	1	1.2269e-10	1.09e-07	3.2591e-06	0.00276	0.46872	1	0.5783	1	9.0995e-05	0.0743	9.3857e-08	8.21e-05	0.00038576	0.301	0.00057878	0.449	0.0081031	1	0.0023469	1
5p loss	0 (0%)	482	NA	NA	NA	NA	0.026227	1	0.14576	1	0.83787	1	0.8808	1	0.35371	1	0.007677	1	0.014652	1	0.028626	1	0.023115	1	0.039126	1
5q loss	0 (0%)	433	0.023526	1	0.012653	1	1.8374e-06	0.00157	8.4794e-05	0.0695	0.038819	1	0.098574	1	0.00017648	0.142	0.046769	1	0.021245	1	0.010463	1	0.027814	1	0.043359	1
6p loss	0 (0%)	450	0.33468	1	0.30806	1	0.0014906	1	0.033385	1	0.10665	1	0.48792	1	0.1994	1	0.89633	1	0.35671	1	0.61156	1	0.15877	1	0.16788	1
6q loss	0 (0%)	381	0.80335	1	0.72164	1	0.037648	1	1.3262e-07	0.000116	0.15336	1	0.043674	1	0.0070471	1	0.19393	1	0.43113	1	0.87875	1	0.32646	1	0.016804	1
7p loss	0 (0%)	479	0.55363	1	0.41815	1	0.011896	1	0.41841	1	0.52239	1	0.93754	1	0.024383	1	0.066953	1	0.10006	1	0.80139	1	0.91722	1	0.89835	1
7q loss	0 (0%)	476	0.52998	1	0.18587	1	0.61431	1	0.4938	1	0.68724	1	0.82053	1	0.3147	1	0.27243	1	1	1	0.73423	1	0.3387	1	0.24563	1
8p loss	0 (0%)	371	0.10434	1	0.17288	1	1.7198e-20	1.54e-17	6.273e-05	0.0518	0.25853	1	0.054731	1	0.086793	1	0.0020934	1	0.018357	1	0.012558	1	0.01105	1	0.075207	1
8q loss	0 (0%)	472	NA	NA	NA	NA	0.00028483	0.225	0.64781	1	0.0025746	1	0.027501	1	0.052895	1	0.010872	1	0.63382	1	0.61901	1	0.50651	1	0.094709	1
9p loss	0 (0%)	351	0.05116	1	0.07018	1	5.5485e-05	0.046	9.9883e-06	0.00841	0.27214	1	0.038179	1	0.0059793	1	0.016775	1	0.81718	1	0.72156	1	0.6746	1	0.7734	1
9q loss	0 (0%)	373	0.20319	1	0.22214	1	1.0428e-06	0.000898	5.0546e-08	4.43e-05	0.39001	1	0.19775	1	0.026156	1	0.012701	1	0.12365	1	0.22246	1	0.1727	1	0.33301	1
10p loss	0 (0%)	455	0.90089	1	0.8178	1	2.067e-05	0.0173	0.0067739	1	0.052545	1	0.099122	1	0.083242	1	0.51045	1	0.045349	1	0.012846	1	0.00078395	0.599	0.00020133	0.161
10q loss	0 (0%)	444	0.7496	1	0.59113	1	0.00044747	0.348	0.00061339	0.474	0.015725	1	0.058513	1	0.022672	1	0.60065	1	0.29754	1	0.028813	1	0.11118	1	0.0059771	1
11p loss	0 (0%)	457	0.33468	1	0.10222	1	0.00030569	0.241	0.54596	1	0.0045403	1	0.026834	1	0.071156	1	0.024958	1	0.079834	1	0.051147	1	0.01592	1	0.15597	1
11q loss	0 (0%)	462	0.47379	1	0.15726	1	0.00075446	0.579	0.52625	1	0.010249	1	0.025131	1	0.39415	1	0.26201	1	0.28851	1	0.77332	1	0.45558	1	0.50535	1
12p loss	0 (0%)	453	0.7282	1	0.8178	1	0.7281	1	0.0023136	1	0.81934	1	0.53401	1	0.071998	1	0.59252	1	0.26859	1	0.7113	1	0.031541	1	0.96523	1
12q loss	0 (0%)	469	NA	NA	NA	NA	0.09558	1	0.43896	1	0.88633	1	0.30468	1	0.40413	1	0.92078	1	0.38626	1	0.82205	1	0.13619	1	0.9513	1
13q loss	0 (0%)	378	0.14244	1	0.14514	1	6.3744e-27	5.72e-24	0.00012216	0.0993	0.32241	1	0.01245	1	0.0012359	0.933	0.081915	1	0.0046765	1	0.040364	1	0.08794	1	0.071533	1
14q loss	0 (0%)	446	0.40121	1	0.41815	1	0.026006	1	0.1566	1	0.0087521	1	0.0080766	1	0.19454	1	0.55944	1	0.046328	1	0.22524	1	0.020227	1	0.70363	1
15q loss	0 (0%)	395	0.40454	1	0.21903	1	7.7536e-14	6.93e-11	3.7021e-08	3.25e-05	0.48115	1	0.018752	1	6.09e-05	0.0503	0.00041818	0.325	0.00026922	0.213	0.00023871	0.19	0.017675	1	0.0060547	1
16p loss	0 (0%)	454	NA	NA	NA	NA	7.15e-05	0.0588	0.016939	1	0.044709	1	0.28061	1	0.13474	1	0.11394	1	0.096874	1	0.08083	1	0.15407	1	0.22457	1
16q loss	0 (0%)	436	0.015881	1	1	1	6.7991e-09	6e-06	0.0043207	1	0.0092781	1	0.01119	1	0.0061184	1	0.17232	1	0.018202	1	0.29214	1	0.0091574	1	0.25497	1
17p loss	0 (0%)	375	0.3992	1	0.63133	1	3.3486e-08	2.95e-05	0.00059317	0.459	0.057179	1	0.20966	1	0.40028	1	0.56668	1	0.65563	1	0.52848	1	0.5423	1	0.348	1
17q loss	0 (0%)	474	NA	NA	NA	NA	0.10319	1	0.036517	1	0.049409	1	0.759	1	0.57235	1	0.077701	1	0.58678	1	0.0091024	1	0.72084	1	0.23133	1
18p loss	0 (0%)	413	0.41986	1	0.41218	1	5.9191e-09	5.23e-06	0.016265	1	0.90421	1	0.22827	1	0.036702	1	0.35269	1	0.58306	1	0.91983	1	0.022356	1	0.34506	1
18q loss	0 (0%)	381	0.41986	1	0.41218	1	9.9824e-13	8.91e-10	0.00086472	0.657	0.35082	1	0.12583	1	0.0002544	0.202	0.024221	1	0.1353	1	0.95043	1	0.040404	1	0.50401	1
19p loss	0 (0%)	374	0.64867	1	0.68791	1	5.566e-05	0.0461	5.9043e-07	0.00051	0.86711	1	0.68957	1	7.5294e-05	0.0619	0.1159	1	0.0060342	1	0.014327	1	0.023303	1	0.053491	1
19q loss	0 (0%)	421	0.71049	1	0.72164	1	0.00073188	0.563	0.033338	1	0.65849	1	0.35727	1	0.012351	1	0.36079	1	0.012888	1	0.051586	1	0.012633	1	0.06477	1
20p loss	0 (0%)	427	0.19188	1	0.41218	1	7.0237e-05	0.0579	0.014152	1	0.0039881	1	0.015782	1	0.15827	1	0.24341	1	0.79131	1	0.072532	1	0.7902	1	0.89075	1
20q loss	0 (0%)	468	NA	NA	NA	NA	0.087656	1	0.10568	1	0.32479	1	0.3064	1	0.41852	1	0.33318	1	0.63504	1	0.55499	1	0.72213	1	0.60535	1
21q loss	0 (0%)	425	NA	NA	NA	NA	1.3625e-09	1.21e-06	3.6534e-06	0.00309	0.10286	1	0.017555	1	1.4239e-06	0.00122	4.4379e-07	0.000384	3.1081e-05	0.0259	8.05e-07	0.000694	0.0076088	1	3.024e-05	0.0253
22q loss	0 (0%)	396	0.30751	1	0.32108	1	4.2283e-11	3.77e-08	0.00023443	0.187	0.0090911	1	0.010973	1	0.020166	1	0.0074711	1	0.00039775	0.31	0.00182	1	0.0081024	1	0.00034605	0.273
Xq loss	0 (0%)	482	NA	NA	NA	NA	0.47681	1	0.31608	1	0.7403	1	0.57183	1	0.055361	1	0.36283	1	0.79361	1	0.34957	1	0.41135	1	0.27543	1
