Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		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	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
1p gain	6 (3%)	214	NA	NA	NA	NA	0.02718	1	0.11513	1	3.3857e-05	0.0105	0.10269	1	0.23369	1	0.20776	1
1q gain	8 (4%)	212	NA	NA	NA	NA	0.0012629	0.362	0.08985	1	0.031166	1	0.61823	1	0.85122	1	0.56891	1
6p gain	4 (2%)	216	NA	NA	NA	NA	0.21329	1	0.42643	1	0.051665	1	0.27942	1	0.092174	1	0.7166	1
7p gain	37 (17%)	183	0.17504	1	0.16171	1	1.8578e-17	6.17e-15	3.6514e-07	0.000118	8.1656e-12	2.65e-09	0.00020377	0.0615	0.00055153	0.164	0.0071003	1
7q gain	51 (23%)	169	0.28205	1	0.14444	1	6.782e-15	2.21e-12	6.0068e-06	0.00192	6.5645e-08	2.13e-05	0.0013934	0.396	0.0042319	1	0.12813	1
8p gain	14 (6%)	206	NA	NA	NA	NA	0.033689	1	0.25988	1	0.60632	1	0.46405	1	0.20451	1	0.45934	1
8q gain	17 (8%)	203	NA	NA	NA	NA	0.0046726	1	0.087245	1	0.37723	1	0.20267	1	0.12502	1	0.17222	1
9p gain	4 (2%)	216	NA	NA	NA	NA	0.21329	1	0.35496	1	0.071471	1	1	1	1	1	0.15881	1
9q gain	6 (3%)	214	NA	NA	NA	NA	0.02718	1	0.27449	1	0.0023081	0.642	0.51885	1	0.74735	1	0.36951	1
10p gain	21 (10%)	199	NA	NA	NA	NA	6.4093e-07	0.000206	2.8901e-05	0.00905	0.017501	1	0.094034	1	0.54002	1	0.93048	1
11p gain	9 (4%)	211	NA	NA	NA	NA	0.50028	1	0.19175	1	0.0039457	1	0.0026055	0.717	0.13765	1	0.42573	1
11q gain	14 (6%)	206	NA	NA	NA	NA	0.35309	1	0.30072	1	0.1716	1	0.10729	1	0.70762	1	0.52121	1
12p gain	11 (5%)	209	NA	NA	NA	NA	0.036807	1	0.17865	1	0.28595	1	0.17029	1	0.02988	1	0.050042	1
12q gain	5 (2%)	215	NA	NA	NA	NA	0.84818	1	0.88533	1	0.93405	1	0.34627	1	0.060541	1	0.15732	1
18p gain	4 (2%)	216	NA	NA	NA	NA	0.21329	1	0.50354	1	0.56941	1	0.27942	1	0.37038	1	0.095827	1
19p gain	11 (5%)	209	NA	NA	NA	NA	2.2549e-05	0.00708	0.0012353	0.356	0.0012203	0.353	0.010239	1	0.086058	1	0.059525	1
19q gain	9 (4%)	211	NA	NA	NA	NA	0.0003397	0.102	0.01033	1	0.00033593	0.101	0.021732	1	0.11504	1	0.16233	1
20p gain	17 (8%)	203	NA	NA	NA	NA	1.6641e-05	0.00528	0.002247	0.627	1.7004e-05	0.00537	0.25858	1	0.028147	1	0.26701	1
20q gain	16 (7%)	204	NA	NA	NA	NA	8.0385e-05	0.0247	0.0012818	0.365	7.3458e-08	2.37e-05	0.025208	1	0.0035627	0.966	0.046162	1
21q gain	3 (1%)	217	NA	NA	NA	NA	0.3283	1	0.70945	1	0.15818	1	0.08785	1	1	1	1	1
1p loss	67 (30%)	153	0.0036069	0.974	0.0086182	1	4.5646e-47	1.57e-44	1.4551e-42	4.96e-40	1.6058e-24	5.41e-22	1.3739e-30	4.66e-28	1.4141e-19	4.72e-17	3.0479e-05	0.00951
1q loss	9 (4%)	211	0.088889	1	0.097094	1	8.3814e-05	0.0256	3.2295e-05	0.01	0.0060313	1	0.00013044	0.0397	0.010621	1	0.71532	1
2p loss	4 (2%)	216	NA	NA	NA	NA	0.8251	1	1	1	0.46401	1	0.37036	1	0.37038	1	0.095827	1
2q loss	3 (1%)	217	NA	NA	NA	NA	0.79595	1	1	1	0.51312	1	0.25944	1	0.054301	1	0.38658	1
3p loss	4 (2%)	216	NA	NA	NA	NA	0.55287	1	0.50354	1	0.35637	1	0.27942	1	0.19069	1	0.24111	1
3q loss	9 (4%)	211	0.17504	1	1	1	0.12771	1	0.10937	1	0.54707	1	0.45331	1	0.96046	1	0.84908	1
4p loss	15 (7%)	205	0.41538	1	0.32872	1	0.00088221	0.259	0.00016931	0.0513	0.00010751	0.0328	0.00041817	0.125	4.9759e-06	0.00159	0.83298	1
4q loss	24 (11%)	196	0.83946	1	0.82832	1	0.0048973	1	0.00061295	0.181	0.0019954	0.56	0.0035527	0.966	6.6527e-05	0.0205	0.60027	1
5p loss	11 (5%)	209	1	1	0.38766	1	0.016243	1	0.031697	1	0.84671	1	0.35957	1	0.16116	1	0.76634	1
5q loss	9 (4%)	211	0.61538	1	0.097094	1	0.04528	1	0.073447	1	0.043898	1	0.021732	1	0.0050625	1	0.13851	1
6p loss	7 (3%)	213	NA	NA	NA	NA	0.12011	1	0.043149	1	0.13906	1	1	1	0.69288	1	0.15735	1
6q loss	21 (10%)	199	NA	NA	NA	NA	0.0043112	1	0.023697	1	0.36237	1	0.33233	1	0.052851	1	0.32027	1
8p loss	3 (1%)	217	NA	NA	NA	NA	0.17032	1	NA	NA	0.57083	1	1	1	0.1247	1	0.38658	1
9p loss	38 (17%)	182	0.38387	1	0.82832	1	0.0028858	0.791	0.055454	1	0.69245	1	0.24542	1	0.80352	1	0.91453	1
9q loss	6 (3%)	214	NA	NA	NA	NA	0.070248	1	0.054221	1	0.011059	1	0.00088239	0.259	0.0080647	1	0.79458	1
10p loss	31 (14%)	189	0.27077	1	0.24068	1	2.3011e-17	7.62e-15	7.9207e-17	2.61e-14	4.7878e-19	1.59e-16	0.0016029	0.454	0.019086	1	0.0066014	1
10q loss	32 (15%)	188	0.27077	1	0.24068	1	3.463e-16	1.14e-13	6.6251e-16	2.17e-13	3.8132e-20	1.28e-17	0.0010942	0.318	0.012788	1	0.017761	1
11p loss	20 (9%)	200	0.81538	1	0.52615	1	0.0019931	0.56	0.00047416	0.141	0.016205	1	0.0089692	1	0.011262	1	0.046944	1
11q loss	4 (2%)	216	NA	NA	NA	NA	0.0024251	0.669	0.23803	1	0.001869	0.527	0.27942	1	0.69666	1	0.095827	1
12q loss	8 (4%)	212	NA	NA	NA	NA	0.044397	1	0.15342	1	0.68631	1	0.61823	1	0.18201	1	0.83349	1
13q loss	28 (13%)	192	1	1	0.38766	1	0.63483	1	0.17102	1	0.85974	1	0.53653	1	0.91406	1	0.36429	1
14q loss	24 (11%)	196	NA	NA	NA	NA	0.0011119	0.322	0.018271	1	0.0012643	0.362	0.45188	1	0.012723	1	0.10253	1
15q loss	12 (5%)	208	NA	NA	NA	NA	0.0058203	1	0.016127	1	0.00097692	0.285	0.0050375	1	0.24827	1	0.88953	1
16q loss	6 (3%)	214	NA	NA	NA	NA	0.66175	1	0.11513	1	0.30188	1	0.51885	1	0.54941	1	1	1
18p loss	15 (7%)	205	0.34359	1	0.41333	1	0.14411	1	0.048449	1	0.11899	1	0.11708	1	0.075546	1	0.35361	1
18q loss	16 (7%)	204	0.088889	1	0.097094	1	0.0029558	0.807	0.0095303	1	0.002398	0.664	0.026375	1	0.011076	1	0.51049	1
19p loss	10 (5%)	210	0.30151	1	0.077258	1	0.06178	1	0.058098	1	0.074739	1	0.020379	1	0.01184	1	0.74391	1
19q loss	76 (35%)	144	0.24667	1	0.14491	1	1.4012e-45	4.79e-43	9.6253e-33	3.27e-30	9.5737e-22	3.22e-19	4.5028e-27	1.52e-24	3.0135e-17	9.94e-15	3.3212e-05	0.0103
21q loss	8 (4%)	212	NA	NA	NA	NA	0.58775	1	0.42313	1	0.46036	1	0.61823	1	0.32985	1	0.19737	1
22q loss	15 (7%)	205	1	1	0.76308	1	7.1522e-06	0.00227	0.00074956	0.221	1.9195e-05	0.00605	0.045058	1	0.14901	1	0.14874	1
Xq loss	6 (3%)	214	NA	NA	NA	NA	0.1322	1	0.20293	1	0.69752	1	0.10269	1	0.23369	1	0.20776	1