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
1p gain	20 (14%)	127	0.79862	1	0.54032	1	0.59477	1	0.25548	1	0.10947	1	0.3004	1	1	1	1	1
1q gain	48 (33%)	99	0.00048994	0.269	0.025917	1	0.43897	1	0.26627	1	0.13811	1	0.94766	1	0.71745	1	0.48101	1
2p gain	16 (11%)	131	0.16715	1	0.53073	1	0.29838	1	0.23394	1	0.71022	1	0.94371	1	0.88154	1	0.46025	1
2q gain	15 (10%)	132	0.12707	1	0.69741	1	0.29838	1	0.23394	1	0.88748	1	0.72972	1	0.81546	1	0.33895	1
3p gain	12 (8%)	135	0.0016496	0.884	0.19095	1	0.25004	1	0.75191	1	0.080896	1	0.48008	1	0.92507	1	1	1
3q gain	15 (10%)	132	0.0047683	1	0.33129	1	0.047044	1	0.52894	1	0.00094359	0.511	0.256	1	0.59593	1	0.46025	1
4p gain	14 (10%)	133	0.022139	1	0.10281	1	0.26184	1	0.59337	1	1	1	0.23187	1	0.31221	1	0.76608	1
4q gain	12 (8%)	135	0.0044583	1	0.043216	1	0.18199	1	0.86123	1	0.55296	1	0.22082	1	0.17726	1	0.81244	1
5p gain	13 (9%)	134	0.00067765	0.37	0.54327	1	0.76805	1	0.80537	1	0.87354	1	0.81085	1	0.26035	1	0.90974	1
5q gain	5 (3%)	142	0.058782	1	0.62741	1	0.73448	1	0.70434	1	0.7394	1	0.61434	1	0.6273	1	1	1
6p gain	45 (31%)	102	0.00082185	0.447	0.19103	1	0.39495	1	0.92724	1	0.74515	1	0.92141	1	0.28538	1	0.068395	1
6q gain	9 (6%)	138	0.93035	1	0.05213	1	0.60497	1	1	1	0.62787	1	0.24394	1	0.73935	1	0.87213	1
7p gain	63 (43%)	84	8.3073e-05	0.0461	0.51314	1	0.15877	1	0.15308	1	0.061526	1	0.42801	1	0.52591	1	0.82216	1
7q gain	62 (42%)	85	4.1634e-06	0.00237	0.89105	1	0.092755	1	0.066148	1	0.058376	1	0.29013	1	0.075837	1	0.24174	1
8p gain	29 (20%)	118	1.0046e-05	0.00569	0.0049171	1	0.24801	1	0.051021	1	0.00055966	0.307	0.0019307	1	0.086108	1	0.10308	1
8q gain	46 (31%)	101	2.7743e-06	0.00158	4.854e-05	0.0271	0.23836	1	0.1328	1	3.4277e-05	0.0192	0.0088627	1	0.16556	1	0.22426	1
9p gain	3 (2%)	144	0.022751	1	0.18845	1	NA	NA	NA	NA	NA	NA	NA	NA	1	1	0.43794	1
9q gain	3 (2%)	144	0.41993	1	1	1	NA	NA	NA	NA	0.36302	1	0.45676	1	NA	NA	NA	NA
11p gain	9 (6%)	138	0.059753	1	0.12402	1	0.062561	1	0.55522	1	0.056541	1	0.68693	1	0.15218	1	0.0051364	1
11q gain	6 (4%)	141	0.010106	1	0.010003	1	0.22024	1	0.63201	1	0.058558	1	0.76329	1	0.56941	1	0.054663	1
12p gain	16 (11%)	131	1.3102e-05	0.00739	0.29832	1	0.76805	1	0.67665	1	0.0013625	0.734	0.05403	1	0.10102	1	0.11735	1
12q gain	7 (5%)	140	0.0011465	0.62	0.70422	1	0.63417	1	0.12855	1	0.69965	1	0.2432	1	0.21052	1	0.062605	1
13q gain	21 (14%)	126	7.2278e-05	0.0402	0.00030047	0.166	0.19631	1	0.31183	1	0.094729	1	0.21542	1	0.86616	1	0.93996	1
14q gain	12 (8%)	135	0.0067629	1	0.12536	1	0.20926	1	0.29196	1	0.6965	1	0.73651	1	0.92507	1	1	1
15q gain	21 (14%)	126	6.5096e-05	0.0363	0.76182	1	0.048284	1	0.48772	1	0.91318	1	0.6836	1	0.44789	1	0.13619	1
16p gain	12 (8%)	135	0.071002	1	0.12536	1	0.25004	1	0.52115	1	0.035221	1	0.046209	1	0.58252	1	0.24365	1
16q gain	10 (7%)	137	0.018991	1	0.70718	1	0.18495	1	0.47302	1	0.16186	1	0.25222	1	0.076374	1	0.029447	1
17p gain	13 (9%)	134	0.014928	1	0.10727	1	0.3987	1	0.16398	1	0.30591	1	0.27134	1	0.26035	1	0.1949	1
17q gain	21 (14%)	126	0.025104	1	0.4578	1	0.31899	1	0.22832	1	0.45905	1	0.91035	1	0.19643	1	1	1
18p gain	19 (13%)	128	0.11348	1	0.2132	1	0.87	1	0.32485	1	0.10947	1	0.13443	1	0.051085	1	0.43257	1
18q gain	10 (7%)	137	0.01195	1	0.42397	1	0.88955	1	0.8227	1	0.26032	1	0.12563	1	0.91157	1	0.62215	1
19p gain	7 (5%)	140	0.42346	1	0.035694	1	0.60497	1	0.29318	1	0.048839	1	0.0037891	1	0.88104	1	0.85608	1
19q gain	11 (7%)	136	0.063092	1	0.032608	1	0.45012	1	0.86352	1	0.002325	1	0.021446	1	0.32826	1	0.35109	1
20p gain	43 (29%)	104	0.00038057	0.209	0.0037672	1	0.52236	1	0.7276	1	0.0062168	1	0.20244	1	0.046459	1	0.62964	1
20q gain	53 (36%)	94	3.7871e-05	0.0212	0.0053604	1	0.42954	1	0.62192	1	0.023844	1	0.27116	1	0.16502	1	0.4173	1
21q gain	17 (12%)	130	0.094419	1	0.0015517	0.833	0.26338	1	0.4847	1	0.28186	1	0.0064878	1	0.94419	1	1	1
22q gain	37 (25%)	110	4.5358e-05	0.0254	0.1984	1	0.35	1	0.54437	1	0.4798	1	0.38436	1	0.38972	1	0.62801	1
1p loss	12 (8%)	135	0.0077068	1	0.005523	1	0.80922	1	0.55013	1	0.070144	1	0.01868	1	0.92507	1	0.90409	1
1q loss	4 (3%)	143	0.0013698	0.737	0.18816	1	NA	NA	NA	NA	0.56383	1	0.81924	1	1	1	0.28579	1
2p loss	14 (10%)	133	0.19293	1	0.33338	1	0.63134	1	0.034383	1	0.42892	1	0.47571	1	0.029599	1	0.050854	1
2q loss	13 (9%)	134	0.14055	1	0.1588	1	0.81731	1	0.26305	1	0.37443	1	0.56372	1	0.0054728	1	0.059444	1
3p loss	10 (7%)	137	0.012343	1	0.093637	1	0.37312	1	0.66263	1	0.002325	1	0.0065164	1	0.24656	1	1	1
3q loss	12 (8%)	135	0.036209	1	0.060496	1	0.073384	1	0.14189	1	0.064968	1	0.3143	1	1	1	0.18712	1
4p loss	15 (10%)	132	0.0035253	1	0.4306	1	0.76805	1	0.69683	1	0.022593	1	0.11299	1	0.31228	1	0.84734	1
4q loss	16 (11%)	131	0.005224	1	0.84147	1	0.71227	1	0.45808	1	0.13471	1	0.20534	1	0.61589	1	0.92384	1
5p loss	18 (12%)	129	0.064147	1	0.045883	1	0.48635	1	0.31883	1	0.12251	1	0.0021333	1	0.13796	1	0.32451	1
5q loss	31 (21%)	116	0.43304	1	0.01859	1	0.26408	1	0.70749	1	0.13978	1	0.083851	1	0.31384	1	0.68283	1
6p loss	11 (7%)	136	0.070408	1	0.080819	1	0.076329	1	0.79337	1	0.41846	1	0.48008	1	0.84465	1	0.27647	1
6q loss	53 (36%)	94	0.00076187	0.415	0.0028544	1	0.51423	1	0.87885	1	0.055327	1	0.28494	1	0.35939	1	0.43633	1
8p loss	16 (11%)	131	0.74703	1	0.47117	1	0.35297	1	0.78325	1	0.31268	1	0.94371	1	0.014542	1	0.0047818	1
9p loss	82 (56%)	65	5.6433e-06	0.0032	0.00016047	0.0887	0.4522	1	0.28762	1	0.0062448	1	0.020627	1	0.45425	1	0.2055	1
9q loss	61 (41%)	86	0.0092005	1	0.00016615	0.0917	0.62191	1	0.4741	1	0.34447	1	0.33282	1	0.054024	1	0.23752	1
10p loss	64 (44%)	83	4.2977e-06	0.00244	0.00066654	0.365	0.47625	1	0.25872	1	0.00010266	0.0569	0.0012478	0.674	0.52634	1	0.16231	1
10q loss	71 (48%)	76	1.2599e-06	0.000721	0.0044017	1	0.60668	1	0.75669	1	1.4662e-05	0.00825	0.0022821	1	0.53086	1	0.54267	1
11p loss	35 (24%)	112	2.2235e-06	0.00127	0.00084351	0.458	0.66397	1	0.91036	1	0.016237	1	0.7991	1	0.47728	1	0.73461	1
11q loss	39 (27%)	108	1.1256e-05	0.00636	0.0052986	1	0.68321	1	1	1	0.013017	1	0.83496	1	0.44852	1	0.6651	1
12p loss	8 (5%)	139	0.064755	1	0.19262	1	0.36116	1	0.35854	1	0.30843	1	0.8094	1	0.71346	1	1	1
12q loss	15 (10%)	132	0.0024111	1	0.012833	1	0.80922	1	0.95622	1	0.37694	1	0.88382	1	1	1	0.71016	1
13q loss	23 (16%)	124	0.11336	1	0.46342	1	1	1	0.94725	1	0.22955	1	0.91575	1	0.15977	1	0.48979	1
14q loss	35 (24%)	112	3.2286e-05	0.0181	0.092032	1	0.73527	1	0.21268	1	0.017337	1	0.082489	1	0.79061	1	0.081699	1
15q loss	12 (8%)	135	0.024734	1	0.043216	1	0.80922	1	0.91731	1	0.12203	1	0.5037	1	0.92507	1	0.90409	1
16p loss	9 (6%)	138	0.55447	1	0.18755	1	0.32045	1	0.49938	1	0.12323	1	0.75755	1	0.010906	1	0.095947	1
16q loss	20 (14%)	127	0.072482	1	0.62331	1	0.26592	1	0.23	1	0.0061677	1	0.61308	1	0.015363	1	0.0041082	1
17p loss	33 (22%)	114	0.13277	1	0.1277	1	0.78347	1	0.82611	1	0.092608	1	0.24265	1	0.17095	1	0.074358	1
17q loss	12 (8%)	135	0.48928	1	1	1	0.90729	1	0.86352	1	0.55296	1	0.26627	1	0.51165	1	0.46389	1
18p loss	26 (18%)	121	0.025473	1	0.014776	1	0.87874	1	0.56731	1	0.0022493	1	0.08943	1	0.25564	1	0.947	1
18q loss	24 (16%)	123	0.0070131	1	0.035589	1	0.76001	1	0.033669	1	0.11225	1	0.31499	1	0.26939	1	0.8437	1
19p loss	14 (10%)	133	0.020857	1	0.088319	1	0.55864	1	0.64657	1	0.2203	1	0.62843	1	0.072347	1	1	1
19q loss	15 (10%)	132	0.012931	1	0.022844	1	0.92327	1	0.63924	1	0.32934	1	0.7791	1	0.15576	1	1	1
20p loss	6 (4%)	141	0.65055	1	1	1	NA	NA	NA	NA	0.66088	1	0.6643	1	0.31427	1	0.35295	1
21q loss	18 (12%)	129	0.52271	1	0.12379	1	0.32978	1	0.67745	1	0.90225	1	0.37454	1	0.056058	1	0.69856	1
22q loss	12 (8%)	135	0.67719	1	0.55426	1	0.91107	1	0.90515	1	0.35265	1	0.11816	1	0.35901	1	0.5411	1
Xq loss	4 (3%)	143	0.56175	1	0.13699	1	0.78829	1	0.27301	1	0.56383	1	0.81924	1	0.83825	1	0.75031	1