		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	24 (6%)	373	0.8156	1	0.64165	1	0.48564	1	0.60704	1	0.86727	1	0.24709	1	0.55064	1	0.27035	1	0.28435	1	1	1
1q gain	83 (21%)	314	0.13272	1	0.10044	1	4.6141e-05	0.0341	0.014355	1	0.62657	1	0.47196	1	0.001946	1	0.0011154	0.781	0.040671	1	0.067329	1
2p gain	97 (24%)	300	0.0069813	1	0.010523	1	1.0079e-11	7.81e-09	6.9144e-05	0.051	0.065662	1	0.21632	1	0.0043593	1	0.00013131	0.096	1	1	0.14593	1
2q gain	43 (11%)	354	0.12585	1	0.018064	1	5.4084e-06	0.00403	0.0039887	1	0.1881	1	0.30626	1	0.0001769	0.129	0.00039677	0.285	0.85703	1	0.48899	1
3p gain	47 (12%)	350	0.53925	1	0.21493	1	0.012253	1	0.00037495	0.27	0.74148	1	0.48568	1	0.21818	1	0.10174	1	0.63757	1	0.27165	1
3q gain	180 (45%)	217	0.071969	1	0.6531	1	0.011381	1	0.037327	1	0.30122	1	0.40231	1	0.64727	1	0.64361	1	0.77194	1	0.38242	1
4p gain	14 (4%)	383	0.1484	1	0.14985	1	0.0062022	1	0.15643	1	0.13225	1	0.46423	1	0.012351	1	0.16277	1	1	1	0.9237	1
4q gain	7 (2%)	390	1	1	0.7151	1	0.063381	1	NA	NA	NA	NA	NA	NA	0.76682	1	0.024709	1	0.5933	1	1	1
5p gain	185 (47%)	212	0.85011	1	0.95357	1	1.8679e-06	0.00141	0.011327	1	0.21576	1	0.25047	1	0.16	1	0.61879	1	0.65807	1	0.32398	1
5q gain	43 (11%)	354	0.075361	1	0.27863	1	0.098474	1	0.14781	1	0.68738	1	0.65592	1	0.18727	1	0.47413	1	0.58067	1	0.072654	1
6p gain	36 (9%)	361	0.0021312	1	0.010633	1	0.00057352	0.408	0.5445	1	0.64273	1	0.27902	1	0.097999	1	0.0019888	1	0.80368	1	0.96756	1
6q gain	24 (6%)	373	0.0028901	1	0.073023	1	0.0002334	0.169	0.0013192	0.919	0.72331	1	0.59445	1	0.23375	1	0.0019723	1	0.70686	1	0.68864	1
7p gain	109 (27%)	288	0.17281	1	0.24789	1	2.7782e-06	0.00208	0.0012111	0.847	0.73142	1	0.9882	1	0.18577	1	0.062419	1	0.6387	1	0.015832	1
7q gain	101 (25%)	296	0.065972	1	0.097862	1	1.7193e-13	1.34e-10	5.6477e-07	0.000428	0.82541	1	0.84978	1	0.013571	1	0.016202	1	0.18803	1	0.0062929	1
8p gain	48 (12%)	349	0.12873	1	0.14267	1	0.03157	1	0.087495	1	0.75552	1	0.44108	1	0.070516	1	0.004551	1	0.34204	1	0.19374	1
8q gain	114 (29%)	283	0.032641	1	0.03107	1	0.013483	1	0.0043869	1	0.70845	1	0.61797	1	0.015035	1	0.0024332	1	0.038242	1	0.28242	1
9p gain	19 (5%)	378	0.28964	1	0.13856	1	0.14518	1	0.871	1	0.17173	1	0.00021605	0.157	0.0096746	1	0.017195	1	0.27368	1	0.043151	1
9q gain	32 (8%)	365	0.18569	1	0.074962	1	0.0043232	1	0.046996	1	0.074636	1	0.0021231	1	0.0014298	0.995	0.0049484	1	0.14105	1	0.079457	1
10p gain	22 (6%)	375	0.2079	1	1	1	0.4224	1	0.37172	1	0.5302	1	0.3894	1	0.27633	1	1	1	0.53622	1	0.79896	1
10q gain	8 (2%)	389	NA	NA	NA	NA	0.32748	1	1	1	0.16228	1	0.68423	1	0.53407	1	0.86497	1	0.7534	1	0.87503	1
11p gain	23 (6%)	374	1	1	0.92855	1	0.1362	1	0.12012	1	0.39773	1	0.27166	1	0.66208	1	0.76112	1	0.43691	1	0.86972	1
11q gain	26 (7%)	371	0.095959	1	0.49131	1	0.017092	1	0.034195	1	0.7732	1	0.37894	1	0.62997	1	0.062892	1	0.75115	1	1	1
12p gain	111 (28%)	286	0.014628	1	0.11889	1	1.0288e-06	0.000778	0.078419	1	0.19698	1	0.59275	1	0.15278	1	0.056541	1	0.73448	1	0.59253	1
12q gain	49 (12%)	348	0.04883	1	0.25761	1	1.15e-06	0.000868	0.033894	1	0.21615	1	0.77484	1	0.58251	1	0.015901	1	0.41165	1	0.56048	1
13q gain	10 (3%)	387	0.76867	1	1	1	0.0030647	1	0.58205	1	0.28874	1	0.34943	1	0.13224	1	0.083452	1	0.7534	1	0.76329	1
14q gain	41 (10%)	356	0.10256	1	0.81952	1	0.54851	1	0.29611	1	1	1	0.67612	1	0.34169	1	0.5218	1	0.041997	1	0.14353	1
15q gain	39 (10%)	358	0.20566	1	0.033363	1	0.0017337	1	0.017602	1	0.19324	1	0.11233	1	0.0093576	1	0.045652	1	0.058121	1	0.0049989	1
16p gain	17 (4%)	380	0.58909	1	1	1	0.00099342	0.697	0.3643	1	0.72331	1	0.34116	1	0.52116	1	0.2662	1	1	1	0.87631	1
16q gain	23 (6%)	374	0.23729	1	0.84377	1	3.9893e-05	0.0295	0.42857	1	0.4554	1	0.15359	1	0.34511	1	0.73497	1	0.19044	1	0.51433	1
17p gain	11 (3%)	386	0.29798	1	0.08809	1	0.00089051	0.627	0.1235	1	0.06691	1	0.34268	1	0.35357	1	0.025972	1	0.2774	1	0.029722	1
17q gain	44 (11%)	353	0.012958	1	0.028176	1	2.3598e-07	0.000179	0.0022885	1	0.41989	1	0.4197	1	0.003283	1	0.0061884	1	0.49941	1	0.1958	1
18p gain	67 (17%)	330	0.0023568	1	9.4497e-06	0.00704	1.6587e-07	0.000126	0.022592	1	0.17522	1	0.091672	1	0.037074	1	0.0041687	1	0.56126	1	0.1355	1
18q gain	44 (11%)	353	0.0078267	1	0.0004187	0.301	0.0028538	1	0.16515	1	0.13598	1	0.02853	1	0.0094068	1	0.010112	1	0.070587	1	0.027091	1
19p gain	40 (10%)	357	0.051591	1	0.16251	1	1.8649e-06	0.00141	0.0041479	1	0.00046844	0.335	0.0016581	1	0.069535	1	0.0086564	1	0.058121	1	0.33941	1
19q gain	58 (15%)	339	0.057664	1	0.7726	1	0.00036831	0.266	0.38073	1	0.059527	1	0.019025	1	0.26977	1	0.077472	1	0.71551	1	0.91132	1
20p gain	109 (27%)	288	0.13174	1	0.037917	1	5.0493e-08	3.85e-05	0.015861	1	0.68384	1	0.19449	1	0.32182	1	0.32208	1	0.2649	1	0.014209	1
20q gain	95 (24%)	302	0.67207	1	0.59929	1	1.6017e-08	1.23e-05	0.18368	1	0.88479	1	0.33121	1	0.2002	1	0.010684	1	0.9497	1	0.10393	1
21q gain	19 (5%)	378	0.96811	1	0.42462	1	0.83924	1	0.0018712	1	0.52434	1	0.93666	1	0.69725	1	0.35358	1	0.65908	1	0.20366	1
22q gain	97 (24%)	300	0.0036214	1	0.0085753	1	7.9548e-09	6.1e-06	0.0020699	1	0.22719	1	0.016673	1	0.070527	1	0.056273	1	1	1	0.014646	1
Xq gain	11 (3%)	386	0.76867	1	1	1	0.056703	1	0.072886	1	0.45078	1	0.58167	1	0.77288	1	0.15446	1	0.68163	1	0.24676	1
1p loss	59 (15%)	338	0.0024775	1	0.0004187	0.301	6.4218e-12	4.98e-09	2.3958e-06	0.0018	0.25081	1	0.039161	1	0.00076617	0.542	0.0070651	1	0.21209	1	0.01796	1
1q loss	9 (2%)	388	NA	NA	NA	NA	0.18254	1	0.24963	1	0.79944	1	0.32028	1	0.46077	1	0.57978	1	1	1	0.70869	1
2p loss	4 (1%)	393	NA	NA	NA	NA	0.076896	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.47708	1	0.56079	1
2q loss	11 (3%)	386	0.53216	1	1	1	0.013091	1	0.13147	1	0.73676	1	0.58167	1	0.6192	1	0.76548	1	0.62953	1	0.65435	1
3p loss	161 (41%)	236	0.050134	1	0.44773	1	4.1104e-06	0.00307	7.1917e-05	0.0529	0.49291	1	0.27534	1	0.51498	1	0.011759	1	0.87026	1	0.036622	1
3q loss	26 (7%)	371	0.26082	1	0.70138	1	0.041067	1	0.12012	1	0.70323	1	1	1	0.4964	1	0.13469	1	0.6144	1	0.87645	1
4p loss	164 (41%)	233	0.17085	1	0.031897	1	7.018e-10	5.42e-07	5.3601e-08	4.08e-05	0.053333	1	0.32731	1	0.34173	1	0.025484	1	0.16606	1	0.25682	1
4q loss	143 (36%)	254	0.0079594	1	0.00097462	0.685	5.5926e-11	4.33e-08	1.9919e-06	0.0015	0.0087604	1	0.11931	1	0.00819	1	0.0027315	1	0.073535	1	0.0036728	1
5p loss	24 (6%)	373	0.12193	1	0.25212	1	0.033148	1	0.14001	1	0.25524	1	0.20719	1	0.69411	1	0.26018	1	1	1	0.74827	1
5q loss	146 (37%)	251	0.23046	1	0.21301	1	1.3e-09	1e-06	6.6525e-09	5.11e-06	0.054301	1	0.089154	1	0.26732	1	0.24762	1	0.4318	1	0.098599	1
6p loss	35 (9%)	362	0.079844	1	0.016367	1	0.00011246	0.0824	0.008466	1	0.07526	1	0.029667	1	0.0037054	1	0.0092401	1	0.51612	1	0.30923	1
6q loss	40 (10%)	357	0.16555	1	0.026439	1	0.014138	1	0.066717	1	0.088271	1	0.15857	1	0.078526	1	0.16457	1	0.93283	1	0.69943	1
7p loss	23 (6%)	374	0.40774	1	0.83372	1	0.0020743	1	0.013071	1	0.50358	1	0.1136	1	0.46247	1	0.18677	1	0.088659	1	0.084713	1
7q loss	13 (3%)	384	0.47205	1	0.8485	1	0.078018	1	0.34049	1	1	1	0.69605	1	0.082478	1	0.044966	1	0.47396	1	0.45757	1
8p loss	117 (29%)	280	0.36687	1	0.55404	1	6.298e-08	4.79e-05	0.00078533	0.555	0.11457	1	0.82957	1	0.51376	1	0.87348	1	0.88921	1	0.5173	1
8q loss	12 (3%)	385	0.25403	1	0.039685	1	0.030261	1	0.025414	1	0.080133	1	0.28811	1	0.27981	1	0.0064886	1	0.16182	1	0.84287	1
9p loss	164 (41%)	233	0.11448	1	0.75117	1	2.7868e-16	2.17e-13	3.0404e-08	2.33e-05	0.9828	1	0.48695	1	0.93589	1	0.42371	1	0.70139	1	0.8704	1
9q loss	103 (26%)	294	0.0039378	1	0.0046861	1	5.6011e-14	4.36e-11	1.4944e-05	0.0111	1	1	0.3999	1	0.0012543	0.876	3.5289e-05	0.0261	0.13449	1	0.063716	1
10p loss	87 (22%)	310	0.054263	1	0.13391	1	9.5565e-10	7.37e-07	4.3954e-06	0.00328	1	1	0.13227	1	0.0033998	1	0.01083	1	0.091414	1	0.00029591	0.214
10q loss	91 (23%)	306	0.0091286	1	0.00015338	0.112	6.1909e-12	4.81e-09	6.3741e-05	0.047	0.26581	1	0.011788	1	0.00050315	0.36	0.00088588	0.625	0.064504	1	0.00037777	0.272
11p loss	59 (15%)	338	0.012908	1	0.18435	1	0.00017517	0.128	0.0033201	1	0.090483	1	0.041494	1	0.14683	1	0.099183	1	0.93382	1	0.64429	1
11q loss	42 (11%)	355	0.42033	1	0.48286	1	3.8127e-06	0.00286	0.008788	1	0.11893	1	0.31521	1	0.0058322	1	0.035025	1	0.12131	1	0.062649	1
12p loss	7 (2%)	390	NA	NA	NA	NA	0.13137	1	0.68385	1	NA	NA	NA	NA	0.22465	1	0.43092	1	0.76862	1	0.21388	1
12q loss	9 (2%)	388	NA	NA	NA	NA	0.34047	1	0.38289	1	0.29227	1	0.38118	1	0.77511	1	0.091656	1	0.84889	1	0.85924	1
13q loss	146 (37%)	251	0.22929	1	0.60914	1	3.8618e-08	2.95e-05	0.00023056	0.167	0.14906	1	0.43995	1	0.42035	1	0.57138	1	0.75231	1	0.081332	1
14q loss	70 (18%)	327	0.00058	0.412	0.021694	1	0.0022505	1	0.014843	1	0.04584	1	0.042167	1	0.00010097	0.0741	6.4037e-09	4.92e-06	0.33595	1	0.084627	1
15q loss	44 (11%)	353	0.76434	1	0.11493	1	0.15185	1	0.0024635	1	0.0080068	1	0.0017183	1	0.16922	1	0.011927	1	0.13283	1	0.32482	1
16p loss	60 (15%)	337	0.32905	1	0.38804	1	1.9622e-05	0.0146	0.024685	1	0.38783	1	0.3047	1	0.39769	1	0.020228	1	0.27756	1	0.0066987	1
16q loss	80 (20%)	317	0.065068	1	0.2372	1	0.00063885	0.453	0.0045279	1	0.17168	1	0.13181	1	0.15364	1	0.0005197	0.371	0.85501	1	0.00079001	0.558
17p loss	145 (37%)	252	0.10165	1	1	1	7.0992e-05	0.0523	0.00012271	0.0898	0.010684	1	0.069425	1	0.41745	1	0.40306	1	0.18801	1	0.0037375	1
17q loss	25 (6%)	372	0.27526	1	0.28227	1	0.052419	1	0.0049739	1	0.3043	1	0.94292	1	0.0035207	1	0.064107	1	0.55764	1	0.95616	1
18p loss	43 (11%)	354	0.48986	1	0.65252	1	0.0052736	1	0.063726	1	0.21284	1	0.86007	1	0.046398	1	0.27999	1	0.68568	1	0.91802	1
18q loss	76 (19%)	321	0.36302	1	0.9322	1	0.0010711	0.751	0.34146	1	0.25337	1	0.78978	1	0.20892	1	0.6582	1	0.24435	1	0.94817	1
19p loss	65 (16%)	332	0.016553	1	0.015173	1	0.00057158	0.408	0.098363	1	0.70796	1	0.86703	1	0.00060068	0.426	3.2182e-05	0.0239	0.0214	1	0.0044452	1
19q loss	43 (11%)	354	0.54085	1	0.2427	1	0.30708	1	0.051271	1	0.034579	1	0.10349	1	0.8114	1	0.13795	1	0.29226	1	0.41539	1
20p loss	17 (4%)	380	0.26792	1	0.023682	1	0.086842	1	0.2122	1	0.041193	1	0.55514	1	0.8022	1	0.59665	1	0.26952	1	0.33567	1
20q loss	22 (6%)	375	0.037591	1	0.020284	1	0.0349	1	0.083978	1	0.077354	1	0.42857	1	0.012559	1	0.010769	1	0.58591	1	0.18198	1
21q loss	122 (31%)	275	0.024673	1	0.016071	1	8.7138e-10	6.73e-07	9.2884e-07	0.000703	0.31758	1	0.24055	1	0.011505	1	0.015864	1	0.0060497	1	0.52711	1
22q loss	38 (10%)	359	0.05705	1	0.15715	1	0.46574	1	0.47858	1	0.48505	1	0.20159	1	0.45957	1	0.052444	1	0.090664	1	0.3828	1
Xq loss	15 (4%)	382	0.63366	1	1	1	0.43053	1	0.91432	1	0.27702	1	0.00026116	0.189	0.67435	1	0.85314	1	0.33303	1	0.27402	1
