Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_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
1p gain	16 (11%)	134	0.0030324	1	0.17214	1	0.4661	1	0.74432	1	0.5185	1	0.38562	1	0.20167	1	0.25952	1
1q gain	32 (21%)	118	0.12704	1	0.47755	1	0.94061	1	0.63731	1	0.82168	1	0.65533	1	0.46285	1	0.70755	1
2p gain	28 (19%)	122	0.00011082	0.0617	0.0010228	0.557	0.21375	1	0.63731	1	0.28241	1	0.73848	1	0.057101	1	0.07208	1
2q gain	11 (7%)	139	0.058959	1	0.24148	1	0.6896	1	0.60471	1	0.34214	1	0.35869	1	0.18206	1	0.18713	1
3p gain	30 (20%)	120	3.509e-06	0.00198	0.044697	1	0.028711	1	0.014554	1	0.090936	1	0.0050015	1	0.025403	1	0.079318	1
3q gain	42 (28%)	108	0.00055894	0.308	0.2644	1	1	1	0.14212	1	0.58633	1	0.085692	1	0.21871	1	0.13381	1
4p gain	8 (5%)	142	0.44332	1	0.62452	1	1	1	1	1	1	1	0.6133	1	0.51974	1	0.386	1
4q gain	3 (2%)	147	0.29643	1	0.40509	1	NA	NA	NA	NA	0.78228	1	0.72698	1	0.32557	1	0.16274	1
5p gain	40 (27%)	110	0.08621	1	0.40206	1	0.028686	1	0.43569	1	0.35401	1	0.60097	1	0.22045	1	0.33004	1
5q gain	18 (12%)	132	0.090344	1	0.076924	1	0.22843	1	0.26132	1	0.70326	1	1	1	0.12219	1	0.33019	1
6p gain	8 (5%)	142	0.54496	1	0.18241	1	NA	NA	NA	NA	1	1	0.22693	1	0.46241	1	0.16862	1
6q gain	5 (3%)	145	0.40231	1	0.38169	1	NA	NA	NA	NA	NA	NA	NA	NA	0.11473	1	0.13054	1
7p gain	46 (31%)	104	0.0018774	1	0.0017241	0.931	0.83509	1	0.21142	1	0.96821	1	0.96295	1	0.017498	1	0.25679	1
7q gain	43 (29%)	107	0.0024946	1	0.050446	1	1	1	0.25837	1	0.96754	1	0.89057	1	0.40667	1	0.31087	1
8p gain	15 (10%)	135	0.10361	1	0.0033968	1	0.19229	1	0.25214	1	0.077555	1	1	1	0.53706	1	1	1
8q gain	39 (26%)	111	0.052333	1	0.088746	1	0.62304	1	0.45906	1	0.27836	1	0.88929	1	0.53265	1	0.88828	1
9p gain	15 (10%)	135	0.0033624	1	0.43663	1	0.18861	1	1	1	0.5185	1	0.098667	1	0.04336	1	0.89365	1
9q gain	11 (7%)	139	0.49401	1	0.32308	1	0.09789	1	0.66711	1	0.055614	1	0.03805	1	0.71681	1	0.71008	1
10p gain	28 (19%)	122	0.0011391	0.617	0.001915	1	0.38191	1	0.016951	1	0.52301	1	0.65128	1	0.38801	1	0.16198	1
10q gain	7 (5%)	143	0.34123	1	0.18804	1	0.51237	1	0.29442	1	0.55291	1	0.16366	1	0.61025	1	0.76889	1
11p gain	8 (5%)	142	0.050713	1	0.95649	1	NA	NA	NA	NA	0.72441	1	1	1	0.32322	1	0.49016	1
11q gain	8 (5%)	142	0.24705	1	0.51769	1	NA	NA	NA	NA	0.48279	1	0.35975	1	0.51974	1	0.386	1
12p gain	24 (16%)	126	0.0037783	1	0.62431	1	0.12992	1	0.19136	1	0.91391	1	0.49266	1	0.25244	1	0.77455	1
12q gain	17 (11%)	133	0.013898	1	0.30828	1	0.41907	1	0.55065	1	0.40861	1	0.75901	1	0.022613	1	0.23265	1
13q gain	25 (17%)	125	0.2181	1	0.8848	1	0.031759	1	0.084378	1	0.044184	1	0.045172	1	0.27355	1	0.66661	1
14q gain	11 (7%)	139	0.090272	1	0.8977	1	0.20595	1	0.57589	1	0.27781	1	0.17588	1	0.7025	1	0.69198	1
15q gain	5 (3%)	145	0.03821	1	0.031388	1	0.29599	1	0.32754	1	0.68264	1	1	1	1	1	1	1
16p gain	10 (7%)	140	0.049859	1	0.6091	1	0.63787	1	1	1	0.75115	1	0.71718	1	0.61768	1	1	1
16q gain	13 (9%)	137	0.0042973	1	0.26582	1	1	1	1	1	1	1	0.2557	1	0.73906	1	0.73338	1
17p gain	9 (6%)	141	0.19318	1	0.55098	1	NA	NA	NA	NA	0.72441	1	0.54474	1	0.51974	1	0.386	1
17q gain	25 (17%)	125	0.00038347	0.212	0.010316	1	0.49688	1	0.16783	1	0.023256	1	0.10759	1	0.12379	1	0.10702	1
18p gain	26 (17%)	124	4.8955e-06	0.00276	0.22066	1	0.9333	1	0.25366	1	0.06519	1	0.57862	1	0.38347	1	0.084829	1
18q gain	9 (6%)	141	0.033055	1	0.59851	1	0.46507	1	0.083649	1	0.4311	1	0.28944	1	0.80828	1	0.49016	1
19p gain	15 (10%)	135	0.033064	1	0.058455	1	NA	NA	NA	NA	0.10931	1	0.48909	1	0.32022	1	0.60999	1
19q gain	29 (19%)	121	0.00070008	0.384	0.11698	1	0.6325	1	1	1	0.046694	1	0.10528	1	0.31897	1	0.74998	1
20p gain	54 (36%)	96	0.033464	1	0.077142	1	0.41527	1	0.80463	1	0.47508	1	0.15112	1	0.40256	1	0.47663	1
20q gain	59 (39%)	91	0.020644	1	0.05109	1	0.43936	1	0.49442	1	0.07747	1	0.087981	1	0.026477	1	0.21365	1
21q gain	27 (18%)	123	0.0018655	1	0.0011049	0.601	0.59828	1	0.5386	1	0.19126	1	0.1023	1	0.27515	1	0.15234	1
22q gain	12 (8%)	138	0.000744	0.407	0.16458	1	0.53575	1	0.57199	1	0.45056	1	0.90252	1	0.021277	1	1	1
Xq gain	6 (4%)	144	0.11267	1	0.80129	1	NA	NA	NA	NA	0.76338	1	1	1	1	1	1	1
1p loss	4 (3%)	146	0.45572	1	0.050893	1	NA	NA	NA	NA	NA	NA	NA	NA	0.35826	1	0.22918	1
2p loss	8 (5%)	142	0.82789	1	0.02291	1	NA	NA	NA	NA	0.36811	1	0.16366	1	1	1	1	1
2q loss	17 (11%)	133	0.011189	1	0.47174	1	1	1	0.29442	1	0.4629	1	0.032343	1	0.75641	1	0.5717	1
3p loss	9 (6%)	141	0.063331	1	0.77287	1	0.34475	1	0.4667	1	0.085845	1	0.071884	1	0.1752	1	0.15681	1
4p loss	29 (19%)	121	0.00073887	0.405	0.29172	1	0.85302	1	0.76733	1	0.42513	1	0.34163	1	0.535	1	0.74998	1
4q loss	26 (17%)	124	0.077748	1	0.78022	1	0.67965	1	0.70858	1	0.59268	1	0.60125	1	0.72636	1	0.21002	1
5p loss	14 (9%)	136	0.00060734	0.334	0.6093	1	0.51704	1	0.86705	1	0.53222	1	0.72064	1	0.44241	1	0.58851	1
5q loss	36 (24%)	114	0.0011231	0.61	0.092333	1	0.76662	1	0.90556	1	0.8953	1	0.772	1	0.42646	1	0.30844	1
6p loss	18 (12%)	132	0.051694	1	0.23761	1	0.23336	1	0.45564	1	0.38443	1	0.8123	1	0.65316	1	0.90422	1
6q loss	29 (19%)	121	6.0493e-06	0.0034	0.0088271	1	0.24675	1	0.80167	1	0.26038	1	0.047743	1	0.77365	1	1	1
7q loss	3 (2%)	147	0.3754	1	0.2924	1	NA	NA	NA	NA	NA	NA	NA	NA	0.23281	1	0.26281	1
8p loss	49 (33%)	101	6.3969e-07	0.000362	3.0772e-05	0.0172	0.14267	1	0.28713	1	0.64311	1	0.4405	1	0.0071962	1	0.0027731	1
8q loss	5 (3%)	145	0.28492	1	0.19193	1	NA	NA	NA	NA	0.78228	1	1	1	0.15053	1	0.019146	1
9p loss	43 (29%)	107	0.00020006	0.111	0.0065168	1	0.037356	1	0.36287	1	0.034134	1	0.00081284	0.444	0.89411	1	0.61175	1
9q loss	41 (27%)	109	7.8247e-05	0.0437	0.005446	1	0.001208	0.654	0.0083329	1	0.0027444	1	0.00011491	0.0639	0.84105	1	0.7185	1
10p loss	19 (13%)	131	0.76299	1	0.8782	1	0.18861	1	0.52816	1	0.25174	1	0.275	1	0.29053	1	0.069099	1
10q loss	30 (20%)	120	0.11818	1	0.053763	1	0.92133	1	0.84318	1	0.20859	1	0.040607	1	0.047541	1	0.010437	1
11p loss	48 (32%)	102	1.3616e-06	0.000769	0.0019012	1	0.23202	1	0.66244	1	0.073907	1	0.0024832	1	0.17765	1	0.72778	1
11q loss	35 (23%)	115	0.00018792	0.104	0.029811	1	0.3002	1	0.55563	1	0.21099	1	0.42423	1	0.27585	1	0.6778	1
12p loss	6 (4%)	144	0.15909	1	0.16112	1	NA	NA	NA	NA	0.32493	1	0.28446	1	0.66558	1	1	1
12q loss	9 (6%)	141	0.15867	1	1	1	NA	NA	NA	NA	0.15025	1	0.35975	1	0.40452	1	0.52571	1
13q loss	20 (13%)	130	0.015746	1	0.31107	1	0.10353	1	0.14141	1	0.11089	1	0.41842	1	0.7106	1	0.3692	1
14q loss	25 (17%)	125	0.00037396	0.207	0.027225	1	0.81766	1	0.31672	1	0.74575	1	0.47021	1	0.039025	1	0.18057	1
15q loss	19 (13%)	131	0.16825	1	0.094986	1	0.12078	1	0.41094	1	0.077555	1	0.057567	1	0.19177	1	0.015563	1
16p loss	17 (11%)	133	0.01789	1	0.27557	1	0.6034	1	1	1	0.34313	1	0.86361	1	0.15836	1	0.0021656	1
16q loss	17 (11%)	133	0.0047746	1	0.3993	1	0.74957	1	1	1	0.73473	1	0.80619	1	0.71244	1	0.013221	1
17p loss	42 (28%)	108	0.0020831	1	0.10811	1	0.54073	1	0.80463	1	0.0062607	1	0.16064	1	0.05165	1	0.035004	1
17q loss	6 (4%)	144	0.71977	1	0.039355	1	NA	NA	NA	NA	0.85704	1	0.8447	1	0.235	1	0.52657	1
18p loss	22 (15%)	128	0.004995	1	0.033528	1	0.50728	1	0.58438	1	1	1	0.17159	1	0.45981	1	0.0093524	1
18q loss	39 (26%)	111	1.5386e-05	0.00863	0.70891	1	0.81334	1	0.18904	1	0.18208	1	0.5589	1	0.42002	1	0.1557	1
19p loss	9 (6%)	141	0.29996	1	0.93289	1	0.25229	1	0.14046	1	0.41537	1	0.35616	1	0.44477	1	0.073747	1
19q loss	4 (3%)	146	0.54538	1	0.70202	1	NA	NA	NA	NA	0.48026	1	0.72698	1	0.14823	1	0.14401	1
20p loss	7 (5%)	143	0.31279	1	0.25113	1	NA	NA	NA	NA	1	1	1	1	0.68975	1	0.05772	1
21q loss	17 (11%)	133	0.55556	1	0.53304	1	0.4661	1	0.21582	1	0.6739	1	0.58428	1	0.84763	1	0.26656	1
22q loss	29 (19%)	121	6.2976e-05	0.0352	0.66937	1	0.070593	1	0.12643	1	0.068631	1	0.12033	1	0.77029	1	0.013814	1
Xq loss	4 (3%)	146	0.25181	1	0.28538	1	NA	NA	NA	NA	0.48026	1	0.5623	1	0.6891	1	0.65934	1