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	Fisher's exact test_P	Fisher's exact test_Q
1q gain	16 (4%)	416	5.8203e-05	0.0148	0.25524	1	0.015262	1	0.082642	1	0.032549	1	0.023329	1	0.13611	1	0.051415	1
4p gain	4 (1%)	428	3.2405e-05	0.00862	0.021201	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.10851	1	0.098874	1
4q gain	4 (1%)	428	3.2405e-05	0.00862	0.021201	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.10851	1	0.098874	1
5p gain	16 (4%)	416	1.3955e-17	4.28e-15	0.0041133	0.806	1	1	0.12522	1	0.0094529	1	0.010048	1	0.00063334	0.14	0.0005439	0.122
5q gain	13 (3%)	419	3.7994e-16	1.16e-13	0.0001471	0.0363	0.90108	1	0.02989	1	0.00081185	0.176	0.0009518	0.206	0.00019233	0.0467	8.8366e-05	0.0222
7p gain	17 (4%)	415	1.7963e-21	5.53e-19	0.00039717	0.0917	1	1	0.01288	1	0.00070373	0.154	0.00060702	0.135	0.00027147	0.0652	0.00010317	0.0257
7q gain	19 (4%)	413	2.8437e-24	8.79e-22	7.6909e-05	0.0195	0.68867	1	0.002983	0.594	0.00028636	0.0682	0.00017578	0.0429	3.8445e-05	0.00996	9.6694e-06	0.00267
11p gain	5 (1%)	427	0.0018106	0.377	0.0050339	0.946	NA	NA	NA	NA	0.01726	1	0.009332	1	0.0020732	0.425	0.0012709	0.271
11q gain	4 (1%)	428	0.00030837	0.0731	0.021201	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0072204	1	0.0048899	0.944
12p gain	12 (3%)	420	5.2339e-12	1.59e-09	1.0077e-06	0.000292	0.90108	1	0.02989	1	7.7774e-06	0.00217	4.9094e-06	0.00138	1.4633e-05	0.00401	3.8879e-06	0.00111
12q gain	12 (3%)	420	5.2339e-12	1.59e-09	1.0077e-06	0.000292	0.90108	1	0.02989	1	7.7774e-06	0.00217	4.9094e-06	0.00138	1.4633e-05	0.00401	3.8879e-06	0.00111
14q gain	7 (2%)	425	1.7744e-07	5.18e-05	0.00047644	0.108	1	1	0.25562	1	0.0021339	0.433	0.0012153	0.261	0.0043737	0.853	0.0020895	0.426
16p gain	12 (3%)	420	2.5702e-13	7.84e-11	4.7022e-05	0.0121	1	1	0.044488	1	0.0002395	0.0577	0.00016713	0.0411	0.00013746	0.0341	5.082e-05	0.013
16q gain	10 (2%)	422	2.3345e-12	7.1e-10	0.00031395	0.0735	0.85601	1	0.12945	1	0.0020425	0.421	0.0014646	0.309	0.0016493	0.346	0.00064329	0.142
17p gain	11 (3%)	421	1.0417e-07	3.05e-05	4.2472e-06	0.0012	0.7724	1	0.017869	1	1.8261e-05	0.00495	1.9254e-05	0.0052	4.6727e-05	0.0121	1.4063e-05	0.00387
17q gain	12 (3%)	420	7.493e-08	2.2e-05	1.0077e-06	0.000292	0.79537	1	0.020579	1	7.7774e-06	0.00217	4.9094e-06	0.00138	1.4633e-05	0.00401	3.8879e-06	0.00111
19p gain	3 (1%)	429	0.00044845	0.103	0.055202	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.024994	1	0.018683	1
19q gain	4 (1%)	428	3.2405e-05	0.00862	0.021201	1	0.63557	1	0.055144	1	0.037083	1	0.034594	1	0.0072204	1	0.0048899	0.944
20p gain	8 (2%)	424	6.4415e-10	1.93e-07	0.0022115	0.445	1	1	0.081715	1	0.013361	1	0.013593	1	0.012193	1	0.0056239	1
20q gain	8 (2%)	424	6.4415e-10	1.93e-07	0.0022115	0.445	1	1	0.081715	1	0.013361	1	0.013593	1	0.012193	1	0.0056239	1
21q gain	3 (1%)	429	0.0032232	0.635	0.055202	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.024994	1	0.018683	1
1p loss	3 (1%)	429	0.00044845	0.103	0.72925	1	NA	NA	NA	NA	0.48708	1	0.19475	1	0.29474	1	0.35882	1
2p loss	8 (2%)	424	1.3241e-08	3.91e-06	0.00019749	0.0478	1	1	0.081715	1	0.00073062	0.159	0.00033419	0.0775	4.7276e-05	0.0121	2.1375e-05	0.00575
2q loss	7 (2%)	425	1.0139e-08	3e-06	0.00047644	0.108	0.83694	1	0.05495	1	0.0021339	0.433	0.0012153	0.261	0.00016777	0.0411	8.4033e-05	0.0212
3q loss	3 (1%)	429	0.00044845	0.103	0.055202	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.024994	1	0.018683	1
6q loss	3 (1%)	429	0.026076	1	0.055202	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.024994	1	0.018683	1
8p loss	4 (1%)	428	3.2405e-05	0.00862	0.053167	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0072204	1	0.0048899	0.944
8q loss	4 (1%)	428	3.2405e-05	0.00862	0.053167	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0072204	1	0.0048899	0.944
9p loss	10 (2%)	422	3.7399e-10	1.12e-07	0.60906	1	0.55913	1	0.2062	1	0.24879	1	0.5267	1	0.18235	1	0.143	1
9q loss	14 (3%)	418	8.2256e-11	2.48e-08	0.21201	1	0.21009	1	0.0044095	0.855	0.44133	1	0.82326	1	0.19349	1	0.25628	1
10p loss	4 (1%)	428	3.2405e-05	0.00862	0.4728	1	NA	NA	NA	NA	0.2424	1	0.089285	1	0.10851	1	0.098874	1
10q loss	4 (1%)	428	3.2405e-05	0.00862	0.4728	1	NA	NA	NA	NA	0.2424	1	0.089285	1	0.10851	1	0.098874	1
11p loss	5 (1%)	427	2.2714e-06	0.000652	0.068886	1	0.49868	1	1	1	0.049471	1	0.16621	1	0.038274	1	0.02248	1
11q loss	6 (1%)	426	2.3279e-05	0.00624	0.024002	1	0.38774	1	0.79799	1	0.018602	1	0.067174	1	0.013091	1	0.0069514	1
13q loss	11 (3%)	421	0.0019296	0.399	0.033671	1	0.077855	1	1	1	0.094075	1	0.116	1	0.016101	1	0.0029831	0.594
15q loss	6 (1%)	426	0.00055617	0.125	0.011212	1	0.45787	1	0.25562	1	0.01726	1	0.009332	1	0.0005916	0.132	0.00032797	0.0764
17p loss	7 (2%)	425	0.0016502	0.346	1	1	1	1	1	1	0.82602	1	0.88579	1	0.11234	1	0.49301	1
18p loss	4 (1%)	428	0.00030837	0.0731	0.20362	1	1	1	0.36851	1	0.2424	1	0.089285	1	0.10851	1	0.038863	1
18q loss	4 (1%)	428	0.00030837	0.0731	0.20362	1	1	1	0.36851	1	0.2424	1	0.089285	1	0.10851	1	0.038863	1
19p loss	4 (1%)	428	0.2303	1	0.021201	1	0.28073	1	0.36851	1	0.037083	1	0.034594	1	0.0072204	1	0.0048899	0.944
21q loss	5 (1%)	427	2.7257e-05	0.00728	0.022503	1	0.38423	1	0.055144	1	0.049471	1	0.16621	1	0.038274	1	0.02248	1
22q loss	54 (12%)	378	1.1754e-45	3.64e-43	0.0013484	0.286	0.11409	1	0.083458	1	3.6873e-09	1.1e-06	2.0658e-07	6.01e-05	0.0002843	0.0679	8.987e-05	0.0225