Molecular subtypes	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Chi-square test_P	Chi-square 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%)	118	0.0055266	1	0.00035264	0.141	0.0023236	0.89	0.0082681	1	0.4463	1	0.11208	1	0.81245	1	0.12818	1
2p gain	0 (0%)	114	0.060745	1	0.13248	1	0.58457	1	0.33789	1	0.78834	1	0.22671	1	0.041505	1	0.15515	1
2q gain	0 (0%)	112	0.030896	1	0.35395	1	0.32901	1	0.20533	1	0.87737	1	0.44111	1	0.26981	1	0.29052	1
3p gain	0 (0%)	98	7.9897e-15	3.49e-12	0.01319	1	0.00026832	0.108	3.6444e-07	0.000156	0.0068585	1	4.6384e-09	2.01e-06	0.23182	1	0.004252	1
3q gain	0 (0%)	94	1.9475e-12	8.49e-10	0.0073928	1	3.6453e-05	0.015	6.94e-06	0.00291	0.00067855	0.267	6.0663e-08	2.61e-05	0.19723	1	0.00024056	0.0969
4p gain	0 (0%)	123	0.38217	1	NA	NA	0.45704	1	1	1	0.75419	1	0.87393	1	NA	NA	NA	NA
4q gain	0 (0%)	124	0.57205	1	NA	NA	0.64474	1	0.60211	1	0.75908	1	0.60362	1	NA	NA	NA	NA
5p gain	0 (0%)	113	1.956e-08	8.45e-06	0.052112	1	0.15575	1	0.80008	1	0.83497	1	0.41132	1	0.4374	1	0.536	1
5q gain	0 (0%)	113	2.1846e-10	9.48e-08	0.052112	1	0.57862	1	0.80008	1	0.85113	1	0.41132	1	0.4374	1	0.536	1
6p gain	0 (0%)	123	0.50268	1	0.43969	1	0.11386	1	0.6766	1	0.28226	1	0.51438	1	0.27864	1	1	1
6q gain	0 (0%)	124	0.2129	1	NA	NA	0.40969	1	1	1	0.42889	1	0.51795	1	NA	NA	NA	NA
7p gain	0 (0%)	60	2.6924e-07	0.000115	2.6171e-06	0.00111	5.6531e-05	0.0231	2.0139e-05	0.00834	0.083428	1	0.0034113	1	0.15592	1	0.0070756	1
7q gain	0 (0%)	59	5.7917e-08	2.5e-05	9.3727e-06	0.00392	0.00018097	0.0735	3.7395e-05	0.0153	0.047434	1	0.004197	1	0.083169	1	0.0074083	1
8p gain	0 (0%)	118	0.3183	1	0.08702	1	0.73212	1	0.2325	1	0.50207	1	0.38949	1	0.4235	1	0.12818	1
8q gain	0 (0%)	116	0.0044568	1	0.013112	1	0.24306	1	0.06828	1	0.089866	1	0.39647	1	0.24619	1	0.076527	1
10p gain	0 (0%)	123	0.18407	1	NA	NA	0.64474	1	0.60211	1	0.13835	1	0.87393	1	NA	NA	NA	NA
10q gain	0 (0%)	124	0.39289	1	NA	NA	NA	NA	NA	NA	0.31656	1	0.44193	1	NA	NA	NA	NA
12p gain	0 (0%)	87	0.0005503	0.218	0.83267	1	0.16103	1	0.064767	1	0.093815	1	0.10335	1	0.4651	1	0.11034	1
12q gain	0 (0%)	87	0.0005503	0.218	0.83267	1	0.16103	1	0.064767	1	0.093815	1	0.10335	1	0.4651	1	0.11034	1
13q gain	0 (0%)	113	0.0066167	1	0.17939	1	0.32428	1	0.044459	1	0.63759	1	0.3069	1	0.92754	1	0.41392	1
16p gain	0 (0%)	67	4.1871e-06	0.00177	0.22101	1	0.0087431	1	0.00018232	0.0738	0.0074007	1	1.8925e-05	0.00787	0.099653	1	0.0040148	1
16q gain	0 (0%)	69	9.1728e-06	0.00384	0.052066	1	0.0041868	1	1.4611e-05	0.00609	0.0048905	1	1.7967e-06	0.000764	0.13431	1	0.0025398	0.968
17p gain	0 (0%)	61	9.5237e-08	4.09e-05	1.303e-06	0.000555	3.4862e-05	0.0144	2.2101e-06	0.000937	0.022768	1	7.7547e-05	0.0316	0.01971	1	0.011988	1
17q gain	0 (0%)	50	5.3976e-06	0.00227	0.0010394	0.404	0.014371	1	0.0009262	0.362	0.053601	1	0.013484	1	0.044165	1	0.050011	1
18p gain	0 (0%)	121	0.16019	1	0.32858	1	0.86321	1	1	1	0.88547	1	0.80392	1	0.18849	1	0.76099	1
18q gain	0 (0%)	123	0.022734	1	0.32858	1	0.76956	1	0.43158	1	0.8271	1	0.31988	1	0.18849	1	0.76099	1
20p gain	0 (0%)	88	0.018488	1	0.074275	1	0.00072212	0.284	0.015179	1	0.256	1	0.26746	1	0.079117	1	0.18907	1
20q gain	0 (0%)	87	0.010669	1	0.14225	1	0.00081338	0.319	0.038136	1	0.16645	1	0.52427	1	0.021301	1	0.25859	1
21q gain	0 (0%)	122	0.63705	1	0.46806	1	NA	NA	NA	NA	0.026677	1	0.19324	1	0.0052538	1	1	1
Xq gain	0 (0%)	122	0.12068	1	0.13651	1	0.45704	1	1	1	0.27766	1	0.75231	1	0.82706	1	0.20424	1
1p loss	0 (0%)	113	0.025597	1	0.32846	1	0.61111	1	0.58893	1	0.41715	1	0.28299	1	0.16188	1	0.47242	1
1q loss	0 (0%)	120	0.017063	1	0.19265	1	0.10312	1	0.43158	1	0.11149	1	0.0080272	1	0.37667	1	0.12339	1
3p loss	0 (0%)	119	0.0013844	0.536	0.001421	0.549	0.05796	1	0.014854	1	0.092257	1	0.073046	1	0.42633	1	0.0023927	0.914
3q loss	0 (0%)	124	0.24826	1	0.033451	1	0.028791	1	0.07623	1	0.10604	1	0.51795	1	0.77765	1	0.053919	1
4p loss	0 (0%)	116	0.0002471	0.0993	0.0044897	1	0.01289	1	0.17956	1	0.18053	1	0.65745	1	0.34551	1	0.040812	1
4q loss	0 (0%)	115	0.0010367	0.404	0.0015337	0.59	0.099931	1	0.06828	1	0.39413	1	0.8023	1	0.67113	1	0.16301	1
5p loss	0 (0%)	122	0.009317	1	0.24587	1	0.11386	1	0.062599	1	0.8046	1	0.83089	1	0.43816	1	0.84777	1
5q loss	0 (0%)	121	1.9632e-05	0.00815	0.22958	1	0.40969	1	0.21053	1	0.54714	1	0.6653	1	0.23859	1	0.61477	1
6p loss	0 (0%)	118	0.00043016	0.171	0.44293	1	0.4679	1	1	1	0.21379	1	0.5457	1	0.81245	1	1	1
6q loss	0 (0%)	115	0.0010706	0.415	0.066048	1	0.37371	1	0.5581	1	0.15128	1	0.8023	1	0.61827	1	0.16301	1
8p loss	0 (0%)	124	0.84646	1	NA	NA	NA	NA	NA	NA	1	1	0.60362	1	NA	NA	NA	NA
9p loss	0 (0%)	112	0.00016946	0.069	0.00031813	0.127	0.0078208	1	0.067805	1	0.11436	1	0.31429	1	1	1	0.024105	1
9q loss	0 (0%)	110	0.00044463	0.177	3.1693e-05	0.0131	0.025579	1	0.13122	1	0.075096	1	0.081397	1	1	1	0.0049313	1
10p loss	0 (0%)	120	0.017063	1	0.056021	1	0.26949	1	0.17956	1	0.27342	1	0.51038	1	0.43816	1	0.22238	1
10q loss	0 (0%)	119	0.0069639	1	0.036236	1	0.26949	1	0.087115	1	0.017067	1	0.13361	1	0.17057	1	0.066729	1
11p loss	0 (0%)	118	0.16736	1	0.11298	1	0.26949	1	0.14512	1	0.4463	1	0.58469	1	0.89901	1	0.36629	1
11q loss	0 (0%)	116	0.0051233	1	0.003541	1	0.29584	1	0.056335	1	0.35524	1	0.93637	1	0.67113	1	0.9112	1
13q loss	0 (0%)	115	0.019023	1	0.0015337	0.59	0.09099	1	0.40301	1	0.01595	1	0.070625	1	0.18604	1	0.0034223	1
14q loss	0 (0%)	104	1.5409e-11	6.7e-09	0.26683	1	0.13535	1	0.097727	1	0.75747	1	0.93371	1	1	1	0.45799	1
15q loss	0 (0%)	116	0.0040672	1	0.11903	1	0.57862	1	0.48748	1	0.72721	1	0.71432	1	0.77175	1	0.66708	1
16q loss	0 (0%)	124	0.63224	1	0.13911	1	NA	NA	NA	NA	0.87085	1	0.2199	1	0.49791	1	0.28297	1
17p loss	0 (0%)	122	0.75642	1	0.043589	1	0.028791	1	0.07623	1	0.30077	1	0.2674	1	0.30853	1	0.11572	1
18p loss	0 (0%)	108	0.086322	1	0.030625	1	0.077193	1	0.011421	1	0.54318	1	0.426	1	0.37338	1	0.94018	1
18q loss	0 (0%)	107	0.20869	1	0.015507	1	0.039207	1	0.0036251	1	0.75472	1	0.34886	1	0.62962	1	0.8357	1
19p loss	0 (0%)	123	0.051328	1	1	1	NA	NA	NA	NA	1	1	0.31988	1	0.5553	1	0.38041	1
19q loss	0 (0%)	123	0.051328	1	1	1	NA	NA	NA	NA	1	1	0.69691	1	0.5553	1	1	1
21q loss	0 (0%)	112	0.5038	1	0.23138	1	0.24646	1	0.72792	1	0.47198	1	0.37608	1	0.86251	1	0.17288	1
22q loss	0 (0%)	103	0.00023314	0.0942	0.0027113	1	0.67259	1	0.047716	1	0.017842	1	0.072131	1	0.088504	1	0.03309	1
Xq loss	0 (0%)	124	0.63224	1	NA	NA	NA	NA	NA	NA	0.6647	1	0.44193	1	NA	NA	NA	NA