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	21 (4%)	449	4.6517e-06	0.00134	0.081812	1	0.015262	1	0.082642	1	0.032549	1	0.023329	1	0.19846	1	0.24237	1
4p gain	4 (1%)	466	2.3103e-05	0.00624	0.019481	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.073002	1	0.13714	1
4q gain	4 (1%)	466	2.3103e-05	0.00624	0.019481	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.073002	1	0.13714	1
5p gain	17 (4%)	453	1.7231e-19	5.39e-17	0.00076631	0.172	1	1	0.12522	1	0.0094529	1	0.010048	1	0.0056439	1	0.00066766	0.152
5q gain	14 (3%)	456	5.7488e-18	1.79e-15	3.2376e-05	0.00851	0.90108	1	0.02989	1	0.00081185	0.179	0.0009518	0.209	0.0010438	0.229	0.00013972	0.0351
7p gain	17 (4%)	453	4.1744e-22	1.31e-19	0.00019795	0.0489	1	1	0.01288	1	0.00070373	0.16	0.00060702	0.14	0.0017846	0.377	0.00041423	0.0965
7q gain	19 (4%)	451	4.8626e-23	1.53e-20	3.7227e-05	0.00968	0.68867	1	0.002983	0.6	0.00028636	0.0687	0.00017578	0.0438	0.00021389	0.0526	4.9377e-05	0.0127
11p gain	5 (1%)	465	0.0015058	0.321	0.0043706	0.874	NA	NA	NA	NA	0.01726	1	0.009332	1	0.002216	0.459	0.0015203	0.322
11q gain	4 (1%)	466	0.00024072	0.0587	0.019481	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0076107	1	0.0056372	1
12p gain	11 (2%)	459	1.791e-12	5.52e-10	3.2049e-06	0.000926	0.90108	1	0.02989	1	1.8261e-05	0.00506	1.9254e-05	0.00526	3.389e-05	0.00888	1.8733e-05	0.00515
12q gain	12 (3%)	458	2.2318e-12	6.85e-10	6.8351e-07	2e-04	0.90108	1	0.02989	1	7.7774e-06	0.00219	4.9094e-06	0.0014	1.0872e-05	0.00303	5.3226e-06	0.00151
13q gain	3 (1%)	467	0.00034804	0.0828	0.04959	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
14q gain	8 (2%)	462	7.3867e-09	2.21e-06	8.8463e-05	0.0226	1	1	0.25562	1	0.0021339	0.446	0.0012153	0.264	0.0029562	0.597	0.0024728	0.509
16p gain	12 (3%)	458	1.018e-13	3.17e-11	2.8946e-05	0.00764	1	1	0.044488	1	0.0002395	0.0587	0.00016713	0.0418	9.4641e-05	0.0239	7.7422e-05	0.0198
16q gain	10 (2%)	460	9.962e-13	3.08e-10	0.00025508	0.0615	0.85601	1	0.12945	1	0.0020425	0.429	0.0014646	0.313	0.001071	0.233	0.00070598	0.16
17p gain	12 (3%)	458	3.7346e-09	1.13e-06	6.8351e-07	2e-04	0.7724	1	0.017869	1	1.8261e-05	0.00506	1.9254e-05	0.00526	3.389e-05	0.00888	1.8733e-05	0.00515
17q gain	13 (3%)	457	5.9344e-09	1.78e-06	1.5271e-07	4.49e-05	0.79537	1	0.020579	1	7.7774e-06	0.00219	4.9094e-06	0.0014	1.0872e-05	0.00303	5.3226e-06	0.00151
18p gain	3 (1%)	467	0.0027299	0.56	0.04959	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
18q gain	3 (1%)	467	0.0027299	0.56	0.04959	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
19p gain	4 (1%)	466	2.3103e-05	0.00624	0.019481	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.025988	1	0.020769	1
19q gain	5 (1%)	465	1.4873e-06	0.000433	0.0043706	0.874	0.63557	1	0.055144	1	0.037083	1	0.034594	1	0.0076107	1	0.0056372	1
20p gain	9 (2%)	461	1.837e-11	5.6e-09	0.00078859	0.176	1	1	0.081715	1	0.013361	1	0.013593	1	0.01008	1	0.008043	1
20q gain	9 (2%)	461	1.837e-11	5.6e-09	0.00078859	0.176	1	1	0.081715	1	0.013361	1	0.013593	1	0.01008	1	0.008043	1
21q gain	3 (1%)	467	0.0027299	0.56	0.04959	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.025988	1	0.020769	1
1p loss	3 (1%)	467	0.00034804	0.0828	0.41174	1	NA	NA	NA	NA	0.48708	1	0.19475	1	0.20216	1	0.36686	1
2p loss	8 (2%)	462	7.3867e-09	2.21e-06	8.8463e-05	0.0226	1	1	0.081715	1	0.00073062	0.164	0.00033419	0.0799	5.2805e-05	0.0136	2.8672e-05	0.0076
2q loss	7 (1%)	463	5.5975e-09	1.68e-06	0.00037952	0.0892	0.83694	1	0.05495	1	0.0021339	0.446	0.0012153	0.264	0.0001846	0.0458	0.00010843	0.0273
3q loss	3 (1%)	467	0.00034804	0.0828	0.04959	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.025988	1	0.020769	1
6q loss	3 (1%)	467	0.023388	1	0.04959	1	NA	NA	NA	NA	0.10078	1	0.082084	1	0.025988	1	0.020769	1
8p loss	4 (1%)	466	2.3103e-05	0.00624	0.047358	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0076107	1	0.0056372	1
8q loss	4 (1%)	466	2.3103e-05	0.00624	0.047358	1	NA	NA	NA	NA	0.037083	1	0.034594	1	0.0076107	1	0.0056372	1
9p loss	11 (2%)	459	1.0438e-11	3.19e-09	0.36538	1	0.55913	1	0.2062	1	0.24879	1	0.5267	1	0.15141	1	0.19225	1
9q loss	16 (3%)	454	1.1002e-13	3.41e-11	0.28843	1	0.21009	1	0.0044095	0.874	0.44133	1	0.82326	1	0.1925	1	0.27411	1
10p loss	6 (1%)	464	9.2758e-08	2.75e-05	0.079316	1	NA	NA	NA	NA	0.12004	1	0.042664	1	0.025593	1	0.036075	1
10q loss	5 (1%)	465	1.4873e-06	0.000433	0.1771	1	NA	NA	NA	NA	0.2424	1	0.089285	1	0.073002	1	0.13714	1
11p loss	6 (1%)	464	9.2758e-08	2.75e-05	0.020218	1	0.49868	1	1	1	0.049471	1	0.16621	1	0.025593	1	0.036075	1
11q loss	8 (2%)	462	4.7917e-06	0.00137	0.027775	1	0.38774	1	0.79799	1	0.018602	1	0.067174	1	0.0087745	1	0.007978	1
13q loss	11 (2%)	459	0.01359	1	0.018448	1	0.077855	1	1	1	0.094075	1	0.116	1	0.0076904	1	0.014246	1
15q loss	6 (1%)	464	0.00042653	0.099	0.0054735	1	0.45787	1	0.25562	1	0.01726	1	0.009332	1	0.00064147	0.147	0.00040735	0.0953
17p loss	7 (1%)	463	0.0013417	0.288	1	1	1	1	1	1	0.82602	1	0.88579	1	0.40323	1	0.49547	1
18p loss	4 (1%)	466	0.00024072	0.0587	0.19136	1	1	1	0.36851	1	0.2424	1	0.089285	1	0.11087	1	0.041416	1
18q loss	4 (1%)	466	0.00024072	0.0587	0.19136	1	1	1	0.36851	1	0.2424	1	0.089285	1	0.11087	1	0.041416	1
19p loss	4 (1%)	466	0.13807	1	0.019481	1	0.28073	1	0.36851	1	0.037083	1	0.034594	1	0.0076107	1	0.0056372	1
21q loss	5 (1%)	465	1.9583e-05	0.00531	0.013161	1	0.38423	1	0.055144	1	0.049471	1	0.16621	1	0.025593	1	0.036075	1
22q loss	62 (13%)	408	7.0231e-54	2.22e-51	0.00052618	0.122	0.11409	1	0.083458	1	1.7863e-09	5.41e-07	1.216e-07	3.59e-05	4.7881e-05	0.0124	4.636e-06	0.00134