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	15 (5%)	291	3.443e-05	0.0134	0.92402	1	1	1	0.64265	1	0.62695	1	0.92566	1
1q gain	41 (13%)	265	2.9573e-11	1.24e-08	0.0049948	1	1	1	0.72994	1	0.0020917	0.732	0.031842	1
2p gain	21 (7%)	285	4.423e-06	0.00177	0.0022468	0.782	0.48837	1	NA	NA	0.23027	1	0.0076582	1
2q gain	22 (7%)	284	6.4007e-05	0.0246	0.0022468	0.782	0.23256	1	0.26829	1	0.43631	1	0.066984	1
3p gain	9 (3%)	297	0.43277	1	0.22517	1	0.48837	1	NA	NA	0.36477	1	0.5772	1
3q gain	26 (8%)	280	0.0013399	0.482	0.25582	1	0.02114	1	0.11693	1	0.45295	1	0.14915	1
4p gain	5 (2%)	301	0.03958	1	0.28586	1	1	1	NA	NA	0.83737	1	0.68892	1
5p gain	36 (12%)	270	8.4999e-08	3.47e-05	0.020843	1	0.28058	1	0.46435	1	0.10606	1	0.11723	1
5q gain	9 (3%)	297	0.0020176	0.71	1	1	0.10777	1	0.10096	1	0.19956	1	0.53498	1
6p gain	23 (8%)	283	1.5739e-05	0.00619	0.0041041	1	1	1	1	1	0.0064355	1	0.25668	1
6q gain	20 (7%)	286	5.05e-05	0.0194	0.002351	0.813	1	1	1	1	0.015911	1	0.13938	1
7p gain	89 (29%)	217	1.2146e-18	5.19e-16	0.00014836	0.0564	1	1	0.52313	1	0.0066361	1	0.01321	1
7q gain	72 (24%)	234	1.5888e-16	6.72e-14	0.0038388	1	1	1	1	1	0.01563	1	0.22599	1
8p gain	81 (26%)	225	4.1181e-05	0.0159	0.0023791	0.821	0.54337	1	0.84003	1	0.012069	1	0.65698	1
8q gain	108 (35%)	198	4.086e-05	0.0158	1.5172e-05	0.00598	0.36404	1	0.77946	1	0.0076833	1	0.11578	1
9p gain	20 (7%)	286	0.14036	1	0.49337	1	0.34487	1	0.481	1	0.93967	1	0.3592	1
9q gain	25 (8%)	281	0.014557	1	0.47111	1	0.18528	1	0.21877	1	0.7397	1	0.63753	1
10p gain	42 (14%)	264	3.1389e-10	1.3e-07	0.0017011	0.604	0.41206	1	0.55652	1	0.72341	1	0.05942	1
10q gain	25 (8%)	281	8.6555e-06	0.00344	0.0622	1	0.60692	1	0.64265	1	0.31567	1	0.69217	1
11p gain	11 (4%)	295	0.51149	1	0.11239	1	1	1	NA	NA	0.69972	1	0.54777	1
11q gain	18 (6%)	288	0.10074	1	0.029957	1	0.48837	1	NA	NA	0.266	1	0.8216	1
12p gain	30 (10%)	276	0.002591	0.891	0.066433	1	0.23256	1	0.26829	1	0.10774	1	0.75878	1
12q gain	23 (8%)	283	0.2956	1	0.27852	1	0.10777	1	0.2785	1	0.24041	1	0.3592	1
13q gain	62 (20%)	244	2.5829e-08	1.07e-05	0.00067707	0.249	0.72051	1	0.88507	1	0.39854	1	0.13519	1
14q gain	4 (1%)	302	0.083383	1	0.77565	1	1	1	NA	NA	NA	NA	NA	NA
15q gain	10 (3%)	296	0.01591	1	0.2735	1	NA	NA	NA	NA	0.69972	1	0.052688	1
16p gain	14 (5%)	292	0.00063728	0.236	0.056938	1	0.60692	1	0.64265	1	0.61794	1	0.25069	1
16q gain	11 (4%)	295	0.0014727	0.526	0.87004	1	0.60692	1	0.64265	1	0.84839	1	0.12309	1
17p gain	7 (2%)	299	0.010888	1	0.8028	1	1	1	NA	NA	0.34623	1	1	1
17q gain	13 (4%)	293	0.0027234	0.934	0.97641	1	1	1	NA	NA	0.090565	1	0.79213	1
18p gain	21 (7%)	285	0.0037587	1	0.00084892	0.31	0.66403	1	0.83965	1	0.030282	1	0.77679	1
18q gain	13 (4%)	293	0.055769	1	0.093414	1	0.60692	1	1	1	0.070145	1	0.13187	1
19p gain	12 (4%)	294	0.36209	1	0.079678	1	0.34487	1	0.35593	1	0.066044	1	0.26395	1
19q gain	28 (9%)	278	0.0159	1	0.10032	1	0.41206	1	0.22978	1	0.5918	1	0.45334	1
20p gain	122 (40%)	184	2.7104e-19	1.16e-16	7.8956e-05	0.0302	0.12921	1	0.016484	1	0.16964	1	0.017395	1
20q gain	149 (49%)	157	2.5877e-29	1.11e-26	4.1767e-08	1.71e-05	0.22706	1	0.022695	1	0.0080909	1	0.0011846	0.429
22q gain	6 (2%)	300	0.019871	1	0.19035	1	NA	NA	NA	NA	0.45348	1	0.36858	1
Xq gain	4 (1%)	302	0.083383	1	0.12276	1	1	1	NA	NA	NA	NA	NA	NA
1p loss	14 (5%)	292	4.1173e-06	0.00166	0.54258	1	0.48837	1	NA	NA	0.13124	1	1	1
1q loss	4 (1%)	302	0.057303	1	0.74963	1	NA	NA	NA	NA	0.22702	1	0.68892	1
2p loss	4 (1%)	302	0.057303	1	0.54151	1	1	1	NA	NA	1	1	0.17322	1
2q loss	5 (2%)	301	0.027166	1	0.22307	1	1	1	NA	NA	1	1	0.087047	1
3p loss	26 (8%)	280	4.4242e-08	1.81e-05	0.0075935	1	0.23256	1	NA	NA	0.0036204	1	0.015498	1
3q loss	15 (5%)	291	9.7288e-06	0.00384	0.017405	1	0.23256	1	NA	NA	0.00062939	0.234	0.013689	1
4p loss	49 (16%)	257	7.2541e-11	3.02e-08	0.00070595	0.259	0.45655	1	0.67439	1	0.0064642	1	2.8827e-07	0.000116
4q loss	47 (15%)	259	1.1697e-14	4.94e-12	0.00017329	0.0653	0.66403	1	0.5495	1	0.0029073	0.991	1.561e-07	6.32e-05
5p loss	15 (5%)	291	1.6737e-05	0.00654	0.097882	1	0.48837	1	NA	NA	0.84839	1	0.19887	1
5q loss	34 (11%)	272	2.593e-12	1.09e-09	0.0016646	0.593	1	1	1	1	0.028896	1	0.00021867	0.0822
6p loss	14 (5%)	292	0.0060665	1	0.55215	1	0.48837	1	NA	NA	0.19126	1	0.25406	1
6q loss	18 (6%)	288	0.001981	0.699	0.27171	1	0.60692	1	0.010493	1	0.43113	1	0.40498	1
7p loss	5 (2%)	301	0.027166	1	0.8606	1	0.23256	1	NA	NA	0.45348	1	0.28331	1
7q loss	12 (4%)	294	2.8968e-05	0.0113	0.067404	1	0.23256	1	NA	NA	0.017858	1	0.017946	1
8p loss	27 (9%)	279	1.1944e-06	0.000481	0.1207	1	0.66403	1	0.72994	1	0.014182	1	0.030061	1
8q loss	8 (3%)	298	0.0012997	0.469	0.33701	1	1	1	NA	NA	0.51283	1	0.055916	1
9p loss	47 (15%)	259	4.5383e-17	1.93e-14	0.00029083	0.109	0.69808	1	0.86349	1	0.0064642	1	0.0045268	1
9q loss	25 (8%)	281	3.151e-08	1.3e-05	0.00141	0.506	1	1	NA	NA	0.16338	1	0.030061	1
10p loss	17 (6%)	289	0.00010773	0.0412	0.01025	1	1	1	0.20306	1	0.34251	1	0.33749	1
10q loss	17 (6%)	289	8.388e-06	0.00335	0.0057639	1	0.34487	1	0.481	1	0.24041	1	0.20856	1
11p loss	19 (6%)	287	1.6279e-05	0.00638	0.0017249	0.611	1	1	0.097365	1	0.059025	1	0.10556	1
11q loss	17 (6%)	289	9.49e-06	0.00376	0.0050269	1	1	1	0.38741	1	0.068928	1	0.31994	1
12p loss	19 (6%)	287	0.00014011	0.0534	0.0078401	1	0.10777	1	0.028361	1	0.24041	1	0.090668	1
12q loss	11 (4%)	295	0.005932	1	0.0014669	0.525	0.23256	1	NA	NA	0.37435	1	0.056145	1
13q loss	9 (3%)	297	0.00041925	0.156	0.22517	1	0.48837	1	NA	NA	0.38914	1	0.4859	1
14q loss	25 (8%)	281	8.6555e-06	0.00344	0.062178	1	0.34487	1	0.481	1	0.053477	1	0.067697	1
15q loss	22 (7%)	284	1.0871e-07	4.42e-05	0.0066583	1	0.60692	1	0.74475	1	0.57134	1	0.11439	1
16p loss	24 (8%)	282	1.0052e-10	4.18e-08	0.0073353	1	1	1	1	1	0.11531	1	0.31994	1
16q loss	26 (8%)	280	7.495e-10	3.1e-07	0.00050205	0.187	1	1	0.34856	1	0.038582	1	0.21468	1
17p loss	58 (19%)	248	3.4544e-18	1.47e-15	0.00015749	0.0597	0.28058	1	0.097262	1	0.0028521	0.975	0.00067037	0.247
17q loss	19 (6%)	287	2.1666e-05	0.00845	0.32272	1	0.66403	1	1	1	0.049144	1	0.0071321	1
18p loss	36 (12%)	270	0.00078069	0.286	0.10213	1	0.69808	1	0.86349	1	0.21881	1	0.12645	1
18q loss	51 (17%)	255	1.1334e-07	4.6e-05	0.030592	1	0.73604	1	1	1	0.12709	1	0.18694	1
19p loss	30 (10%)	276	1.8728e-12	7.88e-10	0.012239	1	0.0089009	1	0.010623	1	0.21881	1	0.0020268	0.711
19q loss	21 (7%)	285	3.3229e-08	1.37e-05	0.0054814	1	0.02114	1	0.035756	1	0.10081	1	0.0032565	1
20p loss	10 (3%)	296	0.00017054	0.0645	0.0022227	0.776	0.48837	1	NA	NA	0.37435	1	1	1
21q loss	53 (17%)	253	1.7293e-11	7.25e-09	0.020886	1	0.28058	1	0.097262	1	0.0035369	1	0.45246	1
22q loss	39 (13%)	267	9.2635e-17	3.93e-14	8.171e-06	0.00327	0.66403	1	1	1	0.0002384	0.0894	0.00090773	0.33
Xq loss	13 (4%)	293	0.00107	0.388	0.051563	1	0.60692	1	0.74475	1	0.25669	1	0.38333	1