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	0 (0%)	476	3.2915e-06	0.000951	0.081157	1	0.015262	1	0.082642	1	0.014814	1	0.0013338	0.288	0.2243	1	0.20446	1
4p gain	0 (0%)	493	1.8464e-05	0.0051	0.019227	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.11167	1	0.097517	1
4q gain	0 (0%)	493	1.8464e-05	0.0051	0.019227	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.11167	1	0.097517	1
5p gain	0 (0%)	480	6.9657e-20	2.22e-17	0.00074659	0.166	1	1	0.12522	1	0.002469	0.499	0.00052218	0.119	0.0069104	1	0.0005414	0.123
5q gain	0 (0%)	483	2.602e-18	8.27e-16	3.1605e-05	0.00847	0.90108	1	0.02989	1	0.00016261	0.0408	4.2602e-05	0.0113	0.001456	0.309	0.00010604	0.0269
7p gain	0 (0%)	480	1.5893e-22	5.09e-20	0.00021843	0.0529	1	1	0.01288	1	0.00038891	0.0906	6.8994e-05	0.0178	0.0023192	0.478	0.00027181	0.0652
7q gain	0 (0%)	478	1.7604e-23	5.65e-21	3.6436e-05	0.00969	0.68867	1	0.002983	0.597	4.8672e-05	0.0128	6.2586e-06	0.00177	0.00028923	0.0691	2.8747e-05	0.00773
11p gain	0 (0%)	492	0.0013394	0.288	0.0043396	0.855	NA	NA	NA	NA	0.014702	1	0.0058722	1	0.0022796	0.474	0.0013163	0.286
11q gain	0 (0%)	493	0.0002043	0.0503	0.019227	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.007784	1	0.005026	0.965
12p gain	0 (0%)	486	1.0266e-12	3.22e-10	3.1352e-06	0.000912	0.90108	1	0.02989	1	1.5865e-05	0.00446	3.4259e-06	0.000987	5.1942e-05	0.0136	1.6978e-05	0.00472
12q gain	0 (0%)	485	1.27e-12	3.98e-10	6.8531e-07	0.000204	0.90108	1	0.02989	1	3.8773e-06	0.00111	7.938e-07	0.000235	1.638e-05	0.00459	4.848e-06	0.00138
13q gain	0 (0%)	494	0.00029424	0.07	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	NA	NA	NA	NA
14q gain	0 (0%)	489	5.0177e-09	1.53e-06	8.9354e-05	0.0229	1	1	0.25562	1	0.00049646	0.114	0.00016386	0.041	0.0046709	0.906	0.0022936	0.475
16p gain	0 (0%)	485	5.5123e-14	1.75e-11	2.8155e-05	0.0076	1	1	0.044488	1	0.00012774	0.0323	3.3671e-05	0.00899	0.00021395	0.052	5.8815e-05	0.0152
16q gain	0 (0%)	487	5.6685e-13	1.79e-10	0.00024685	0.0595	0.85601	1	0.12945	1	0.0014448	0.308	0.00042878	0.0995	0.0016904	0.355	0.00054668	0.124
17p gain	0 (0%)	485	1.9977e-09	6.13e-07	6.8531e-07	0.000204	0.7724	1	0.017869	1	3.8773e-06	0.00111	7.938e-07	0.000235	5.1942e-05	0.0136	1.6978e-05	0.00472
17q gain	0 (0%)	484	3.8322e-09	1.17e-06	1.5783e-07	4.73e-05	0.79537	1	0.020579	1	1.3635e-06	0.000398	1.9209e-07	5.74e-05	1.638e-05	0.00459	4.848e-06	0.00138
18p gain	0 (0%)	494	0.0024459	0.499	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	NA	NA	NA	NA
18q gain	0 (0%)	494	0.0024459	0.499	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	NA	NA	NA	NA
19p gain	0 (0%)	493	1.8464e-05	0.0051	0.019227	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.026428	1	0.019063	1
19q gain	0 (0%)	492	1.1236e-06	0.00033	0.0043396	0.855	0.63557	1	0.055144	1	0.014702	1	0.0058722	1	0.007784	1	0.005026	0.965
20p gain	0 (0%)	488	1.1065e-11	3.44e-09	0.00076668	0.17	1	1	0.081715	1	0.0039653	0.789	0.0012346	0.27	0.012444	1	0.0061924	1
20q gain	0 (0%)	488	1.1065e-11	3.44e-09	0.00076668	0.17	1	1	0.081715	1	0.0039653	0.789	0.0012346	0.27	0.012444	1	0.0061924	1
21q gain	0 (0%)	494	0.0024459	0.499	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	0.026428	1	0.019063	1
1p loss	0 (0%)	494	0.00029424	0.07	0.55924	1	NA	NA	NA	NA	0.49519	1	0.21374	1	0.2996	1	0.27592	1
2p loss	0 (0%)	489	5.0177e-09	1.53e-06	8.9354e-05	0.0229	1	1	0.081715	1	0.00049646	0.114	0.00016386	0.041	5.5292e-05	0.0144	2.2703e-05	0.00615
2q loss	0 (0%)	490	3.7767e-09	1.16e-06	0.00037781	0.0884	0.83694	1	0.05495	1	0.0014353	0.307	0.00065038	0.146	0.00019214	0.0475	8.8476e-05	0.0227
3q loss	0 (0%)	494	0.00029424	0.07	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	0.026428	1	0.019063	1
6q loss	0 (0%)	494	0.021827	1	0.049542	1	NA	NA	NA	NA	0.10052	1	0.076862	1	0.026428	1	0.019063	1
8p loss	0 (0%)	493	1.8464e-05	0.0051	0.047002	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.007784	1	0.005026	0.965
8q loss	0 (0%)	493	1.8464e-05	0.0051	0.047002	1	NA	NA	NA	NA	0.036567	1	0.018577	1	0.007784	1	0.005026	0.965
9p loss	0 (0%)	485	1.0764e-11	3.36e-09	0.27215	1	0.55913	1	0.2062	1	0.15685	1	0.20594	1	0.18481	1	0.15941	1
9q loss	0 (0%)	480	1.5806e-13	4.99e-11	0.2035	1	0.21009	1	0.0044095	0.86	0.26827	1	0.29487	1	0.2355	1	0.22795	1
10p loss	0 (0%)	491	6.6228e-08	2e-05	0.097863	1	NA	NA	NA	NA	0.046968	1	0.013536	1	0.039885	1	0.033299	1
10q loss	0 (0%)	492	1.1236e-06	0.00033	0.17547	1	NA	NA	NA	NA	0.10205	1	0.040531	1	0.11167	1	0.097517	1
11p loss	0 (0%)	490	7.7423e-08	2.33e-05	0.0094745	1	0.49868	1	1	1	0.014805	1	0.041902	1	0.039885	1	0.033299	1
11q loss	0 (0%)	488	3.2424e-06	0.00094	0.014871	1	0.38774	1	0.79799	1	0.044031	1	0.039	1	0.013813	1	0.0074995	1
13q loss	0 (0%)	486	0.012252	1	0.018235	1	0.077855	1	1	1	0.018246	1	0.0015394	0.325	0.0077405	1	0.016433	1
15q loss	0 (0%)	490	0.00046394	0.107	0.002412	0.494	0.45787	1	0.25562	1	0.0049121	0.948	0.0017549	0.367	0.00066375	0.149	0.00034244	0.0805
17p loss	0 (0%)	490	0.0011815	0.26	1	1	1	1	1	1	0.78983	1	0.81891	1	0.51802	1	0.49856	1
18p loss	0 (0%)	493	0.0002043	0.0503	0.19007	1	1	1	0.36851	1	0.22022	1	0.11979	1	0.074254	1	0.067089	1
18q loss	0 (0%)	493	0.0002043	0.0503	0.19007	1	1	1	0.36851	1	0.22022	1	0.11979	1	0.074254	1	0.067089	1
19p loss	0 (0%)	493	0.13197	1	0.019227	1	0.28073	1	0.36851	1	0.036567	1	0.018577	1	0.007784	1	0.005026	0.965
21q loss	0 (0%)	491	0.00019167	0.0475	0.097863	1	0.38423	1	0.055144	1	0.043939	1	0.11233	1	0.039885	1	0.033299	1
22q loss	0 (0%)	431	6.79e-58	2.19e-55	0.00013021	0.0328	0.11409	1	0.083458	1	8.4016e-11	2.6e-08	1.9826e-10	6.11e-08	4.327e-05	0.0114	9.5128e-06	0.00268