Molecular subtypes	CN_CNMF		METHLYATION_CNMF		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
1p gain	9 (4%)	228	0.0047906	1	0.32335	1	1	1	0.38741	1	0.57668	1	0.6265	1
1q gain	30 (13%)	207	4.0882e-05	0.0159	0.063002	1	1	1	0.83965	1	0.0067498	1	0.037565	1
2p gain	13 (5%)	224	0.00093675	0.342	0.020271	1	0.48837	1	NA	NA	0.23027	1	0.0076582	1
2q gain	14 (6%)	223	0.00039943	0.15	0.0073966	1	0.23256	1	0.26829	1	0.43631	1	0.066984	1
3p gain	5 (2%)	232	0.83417	1	0.85796	1	0.48837	1	NA	NA	0.2482	1	0.38221	1
3q gain	17 (7%)	220	0.11108	1	0.19252	1	0.02114	1	0.11693	1	0.45295	1	0.14915	1
4p gain	4 (2%)	233	0.14523	1	NA	NA	1	1	NA	NA	0.83737	1	0.68892	1
5p gain	30 (13%)	207	2.6872e-05	0.0105	0.092275	1	0.28058	1	0.46435	1	0.10606	1	0.11723	1
5q gain	6 (3%)	231	0.047742	1	NA	NA	0.10777	1	0.10096	1	0.3338	1	0.76754	1
6p gain	15 (6%)	222	0.0019652	0.707	0.063571	1	1	1	1	1	0.026904	1	0.26326	1
6q gain	13 (5%)	224	0.0037444	1	0.02956	1	0.60692	1	0.74475	1	0.1015	1	0.25069	1
7p gain	64 (27%)	173	1.5454e-08	6.26e-06	0.0074207	1	1	1	0.52313	1	0.013739	1	0.013642	1
7q gain	56 (24%)	181	6.7386e-07	0.000271	0.031218	1	1	1	1	1	0.01557	1	0.30108	1
8p gain	61 (26%)	176	4.524e-16	1.88e-13	0.036984	1	0.54337	1	0.84003	1	0.008304	1	0.58958	1
8q gain	84 (35%)	153	1.3723e-15	5.7e-13	0.00013436	0.0516	0.36404	1	0.77946	1	0.0058146	1	0.10621	1
9p gain	13 (5%)	224	0.023931	1	0.58086	1	0.10777	1	0.16052	1	0.82281	1	0.44517	1
9q gain	17 (7%)	220	0.005643	1	0.97818	1	0.048497	1	0.039421	1	0.76928	1	0.52576	1
10p gain	29 (12%)	208	1.2772e-06	0.000512	0.010599	1	0.41206	1	0.55652	1	0.56814	1	0.064219	1
10q gain	17 (7%)	220	0.011512	1	0.067266	1	0.23256	1	0.26829	1	0.035748	1	0.55592	1
11p gain	7 (3%)	230	0.19789	1	0.47484	1	1	1	NA	NA	0.69972	1	0.54777	1
11q gain	12 (5%)	225	0.047984	1	0.16707	1	0.48837	1	NA	NA	0.41426	1	0.80493	1
12p gain	20 (8%)	217	0.00021491	0.0817	0.077384	1	0.23256	1	0.26829	1	0.10774	1	0.75878	1
12q gain	15 (6%)	222	0.0099156	1	0.25993	1	0.10777	1	0.2785	1	0.4909	1	0.55378	1
13q gain	42 (18%)	195	4.4323e-05	0.0172	0.0034546	1	0.72051	1	0.88507	1	0.50192	1	0.21933	1
15q gain	9 (4%)	228	0.00070696	0.262	0.37415	1	NA	NA	NA	NA	0.82723	1	0.027606	1
16p gain	13 (5%)	224	0.0063066	1	0.055996	1	0.60692	1	0.64265	1	0.61794	1	0.25069	1
16q gain	10 (4%)	227	0.010795	1	0.65819	1	0.60692	1	0.64265	1	0.84839	1	0.12309	1
17p gain	8 (3%)	229	0.0029301	1	0.54615	1	1	1	NA	NA	0.37435	1	1	1
17q gain	11 (5%)	226	0.00015053	0.0577	1	1	1	1	NA	NA	0.090565	1	0.79213	1
18p gain	16 (7%)	221	0.025031	1	0.048312	1	0.66403	1	0.83965	1	0.027039	1	0.60429	1
18q gain	8 (3%)	229	0.4035	1	0.25623	1	0.60692	1	1	1	0.070145	1	0.13187	1
19p gain	10 (4%)	227	0.90095	1	0.279	1	0.34487	1	0.35593	1	0.066044	1	0.26395	1
19q gain	21 (9%)	216	0.36245	1	0.29101	1	0.41206	1	0.22978	1	0.5918	1	0.45334	1
20p gain	91 (38%)	146	6.5901e-11	2.7e-08	0.0036657	1	0.12921	1	0.016484	1	0.11385	1	0.020802	1
20q gain	115 (49%)	122	2.6225e-17	1.09e-14	5.5981e-06	0.00222	0.22706	1	0.022695	1	0.0017368	0.629	0.0023619	0.846
22q gain	4 (2%)	233	0.14523	1	0.057329	1	NA	NA	NA	NA	0.45348	1	0.36858	1
1p loss	9 (4%)	228	0.00070696	0.262	0.8767	1	0.48837	1	NA	NA	0.28164	1	1	1
2p loss	4 (2%)	233	0.072224	1	0.85796	1	1	1	NA	NA	1	1	0.087047	1
2q loss	5 (2%)	232	0.03887	1	1	1	1	1	NA	NA	1	1	0.44749	1
3p loss	16 (7%)	221	2.1148e-06	0.000844	0.040087	1	0.23256	1	NA	NA	0.0036204	1	0.015498	1
3q loss	9 (4%)	228	0.00070696	0.262	0.05155	1	0.23256	1	NA	NA	0.00062939	0.235	0.013689	1
4p loss	38 (16%)	199	2.0708e-10	8.47e-08	0.0062092	1	0.45655	1	0.67439	1	0.0080325	1	6.4094e-07	0.000258
4q loss	34 (14%)	203	4.2642e-11	1.75e-08	0.0051876	1	0.41206	1	0.83965	1	0.006681	1	1.4013e-06	0.000561
5p loss	13 (5%)	224	3.6409e-05	0.0142	0.12062	1	0.48837	1	NA	NA	0.41426	1	0.16065	1
5q loss	25 (11%)	212	2.1079e-10	8.6e-08	0.0043972	1	1	1	1	1	0.015759	1	7.0508e-05	0.0272
6p loss	10 (4%)	227	0.062655	1	0.41335	1	0.48837	1	NA	NA	0.10595	1	0.45995	1
6q loss	16 (7%)	221	0.0052457	1	0.074193	1	0.60692	1	0.010493	1	0.30256	1	0.48595	1
7p loss	4 (2%)	233	0.072224	1	NA	NA	0.23256	1	NA	NA	0.45348	1	0.28331	1
7q loss	9 (4%)	228	0.00070696	0.262	0.05155	1	0.23256	1	NA	NA	0.0066673	1	0.027606	1
8p loss	17 (7%)	220	2.3593e-05	0.00925	0.52895	1	0.66403	1	0.72994	1	0.022824	1	0.015498	1
8q loss	5 (2%)	232	0.03887	1	0.6367	1	1	1	NA	NA	0.37206	1	0.017206	1
9p loss	38 (16%)	199	2.4182e-13	9.99e-11	0.00027736	0.105	1	1	1	1	0.0080325	1	0.0050169	1
9q loss	20 (8%)	217	1.4187e-05	0.00558	0.00063306	0.235	0.48837	1	NA	NA	0.13097	1	0.031303	1
10p loss	14 (6%)	223	9.6163e-06	0.0038	0.011041	1	1	1	0.20306	1	0.34251	1	0.33749	1
10q loss	14 (6%)	223	9.6163e-06	0.0038	0.011041	1	0.34487	1	0.481	1	0.24041	1	0.20856	1
11p loss	15 (6%)	222	0.0015497	0.564	0.0581	1	1	1	0.097365	1	0.059025	1	0.10556	1
11q loss	11 (5%)	226	0.0049143	1	0.25345	1	1	1	0.38741	1	0.068928	1	0.31994	1
12p loss	15 (6%)	222	0.00017379	0.0662	0.14284	1	0.10777	1	0.028361	1	0.1462	1	0.10556	1
12q loss	8 (3%)	229	0.0029301	1	0.036994	1	0.23256	1	NA	NA	0.37435	1	0.056145	1
13q loss	8 (3%)	229	0.0029301	1	0.29858	1	0.23256	1	0.26829	1	0.37435	1	0.73108	1
14q loss	19 (8%)	218	0.00042082	0.157	0.078153	1	0.34487	1	0.481	1	0.053477	1	0.067697	1
15q loss	15 (6%)	222	4.2894e-06	0.0017	0.023957	1	0.60692	1	0.74475	1	0.4909	1	0.21876	1
16p loss	11 (5%)	226	0.00015053	0.0577	0.54615	1	1	1	1	1	0.2002	1	0.16416	1
16q loss	17 (7%)	220	2.3593e-05	0.00925	0.1082	1	1	1	0.34856	1	0.038582	1	0.21468	1
17p loss	46 (19%)	191	5.0915e-14	2.11e-11	0.00011495	0.0443	0.28058	1	0.097262	1	0.0018648	0.673	0.00032826	0.123
17q loss	15 (6%)	222	0.00082001	0.301	0.89822	1	0.66403	1	1	1	0.07824	1	0.018515	1
18p loss	24 (10%)	213	0.0016224	0.589	0.051311	1	0.69808	1	0.86349	1	0.21881	1	0.12645	1
18q loss	37 (16%)	200	4.2339e-07	0.000171	0.16681	1	0.73604	1	1	1	0.13649	1	0.20781	1
19p loss	23 (10%)	214	1.2989e-09	5.29e-07	0.070409	1	0.0089009	1	0.010623	1	0.21881	1	0.0020268	0.728
19q loss	16 (7%)	221	2.1148e-06	0.000844	0.017548	1	0.02114	1	0.035756	1	0.10081	1	0.0032565	1
20p loss	7 (3%)	230	0.024623	1	0.053811	1	0.48837	1	NA	NA	0.34623	1	0.70251	1
21q loss	42 (18%)	195	3.5436e-09	1.44e-06	0.023817	1	0.28058	1	0.097262	1	0.0043004	1	0.45344	1
22q loss	30 (13%)	207	1.2616e-12	5.2e-10	0.00025861	0.0978	0.66403	1	1	1	0.0002384	0.0904	0.00090773	0.332
Xq loss	12 (5%)	225	0.062208	1	0.54116	1	0.60692	1	0.74475	1	0.35535	1	0.30776	1