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	0.86943	1	0.5185	1	0.38562	1	0.27894	1	0.81579	1
1q gain	32 (21%)	118	0.12704	1	0.47755	1	0.94061	1	0.58963	1	0.82168	1	0.65533	1	0.34011	1	0.46693	1
2p gain	28 (19%)	122	0.00011082	0.0615	0.0010228	0.555	0.21375	1	0.52776	1	0.28241	1	0.73848	1	0.017129	1	0.060462	1
2q gain	11 (7%)	139	0.058959	1	0.24148	1	0.6896	1	0.77714	1	0.34214	1	0.35869	1	0.20121	1	0.27382	1
3p gain	30 (20%)	120	3.509e-06	0.00197	0.044697	1	0.028711	1	0.15886	1	0.090936	1	0.0050015	1	0.045374	1	0.26081	1
3q gain	42 (28%)	108	0.00055894	0.307	0.2644	1	1	1	0.57574	1	0.58633	1	0.085692	1	0.22817	1	0.062778	1
4p gain	8 (5%)	142	0.44332	1	0.62452	1	1	1	0.64266	1	1	1	0.6133	1	0.1497	1	1	1
4q gain	3 (2%)	147	0.29643	1	0.40509	1	NA	NA	NA	NA	0.78228	1	0.72698	1	0.43491	1	1	1
5p gain	40 (27%)	110	0.08621	1	0.40206	1	0.028686	1	0.26358	1	0.35401	1	0.60097	1	0.45898	1	0.15833	1
5q gain	18 (12%)	132	0.090344	1	0.076924	1	0.22843	1	0.66571	1	0.70326	1	1	1	0.19137	1	0.25169	1
6p gain	8 (5%)	142	0.54496	1	0.18241	1	NA	NA	NA	NA	1	1	0.22693	1	0.75321	1	0.82969	1
6q gain	5 (3%)	145	0.40231	1	0.38169	1	NA	NA	NA	NA	NA	NA	NA	NA	0.20609	1	0.19364	1
7p gain	46 (31%)	104	0.0018774	1	0.0017241	0.926	0.83509	1	0.38008	1	0.96821	1	0.96295	1	0.075255	1	0.55378	1
7q gain	43 (29%)	107	0.0024946	1	0.050446	1	1	1	0.52334	1	0.96754	1	0.89057	1	0.50958	1	1	1
8p gain	15 (10%)	135	0.10361	1	0.0033968	1	0.19229	1	0.62518	1	0.077555	1	1	1	0.091082	1	0.27937	1
8q gain	39 (26%)	111	0.052333	1	0.088746	1	0.62304	1	0.92829	1	0.27836	1	0.88929	1	0.19891	1	0.29742	1
9p gain	15 (10%)	135	0.0033624	1	0.43663	1	0.18861	1	0.64266	1	0.5185	1	0.098667	1	0.13378	1	0.32051	1
9q gain	11 (7%)	139	0.49401	1	0.32308	1	0.09789	1	0.39376	1	0.055614	1	0.03805	1	0.77743	1	0.88645	1
10p gain	28 (19%)	122	0.0011391	0.614	0.001915	1	0.38191	1	0.020278	1	0.52301	1	0.65128	1	0.66396	1	0.26124	1
10q gain	7 (5%)	143	0.34123	1	0.18804	1	0.51237	1	0.34742	1	0.55291	1	0.16366	1	0.88663	1	0.14941	1
11p gain	8 (5%)	142	0.050713	1	0.95649	1	NA	NA	NA	NA	0.72441	1	1	1	0.4446	1	0.72543	1
11q gain	8 (5%)	142	0.24705	1	0.51769	1	NA	NA	NA	NA	0.48279	1	0.35975	1	0.64167	1	0.52213	1
12p gain	24 (16%)	126	0.0037783	1	0.62431	1	0.12992	1	0.26379	1	0.91391	1	0.49266	1	0.04501	1	0.36927	1
12q gain	17 (11%)	133	0.013898	1	0.30828	1	0.41907	1	0.4352	1	0.40861	1	0.75901	1	0.036274	1	0.4977	1
13q gain	25 (17%)	125	0.2181	1	0.8848	1	0.031759	1	0.035064	1	0.044184	1	0.045172	1	0.39877	1	0.81927	1
14q gain	11 (7%)	139	0.090272	1	0.8977	1	0.20595	1	0.28663	1	0.27781	1	0.17588	1	0.35677	1	0.37916	1
15q gain	5 (3%)	145	0.03821	1	0.031388	1	0.29599	1	0.77714	1	0.68264	1	1	1	0.45482	1	0.51875	1
16p gain	10 (7%)	140	0.049859	1	0.6091	1	0.63787	1	0.81429	1	0.75115	1	0.71718	1	1	1	0.11532	1
16q gain	13 (9%)	137	0.0042973	1	0.26582	1	1	1	1	1	1	1	0.2557	1	0.92468	1	0.19713	1
17p gain	9 (6%)	141	0.19318	1	0.55098	1	NA	NA	NA	NA	0.72441	1	0.54474	1	0.1497	1	0.43237	1
17q gain	25 (17%)	125	0.00038347	0.211	0.010316	1	0.49688	1	0.333	1	0.023256	1	0.10759	1	0.14733	1	0.062698	1
18p gain	26 (17%)	124	4.8955e-06	0.00275	0.22066	1	0.9333	1	0.30253	1	0.06519	1	0.57862	1	0.2139	1	0.66511	1
18q gain	9 (6%)	141	0.033055	1	0.59851	1	0.46507	1	0.33748	1	0.4311	1	0.28944	1	1	1	1	1
19p gain	15 (10%)	135	0.033064	1	0.058455	1	NA	NA	NA	NA	0.10931	1	0.48909	1	0.51252	1	0.63952	1
19q gain	29 (19%)	121	0.00070008	0.383	0.11698	1	0.6325	1	0.82195	1	0.046694	1	0.10528	1	0.58849	1	1	1
20p gain	54 (36%)	96	0.033464	1	0.077142	1	0.41527	1	0.36951	1	0.47508	1	0.15112	1	0.26457	1	0.30948	1
20q gain	59 (39%)	91	0.020644	1	0.05109	1	0.43936	1	0.66173	1	0.07747	1	0.087981	1	0.056424	1	0.22935	1
21q gain	27 (18%)	123	0.0018655	1	0.0011049	0.599	0.59828	1	1	1	0.19126	1	0.1023	1	0.27321	1	0.10307	1
22q gain	12 (8%)	138	0.000744	0.405	0.16458	1	0.53575	1	0.44	1	0.45056	1	0.90252	1	0.042445	1	0.23221	1
Xq gain	6 (4%)	144	0.11267	1	0.80129	1	NA	NA	NA	NA	0.76338	1	1	1	1	1	0.29272	1
1p loss	4 (3%)	146	0.45572	1	0.050893	1	NA	NA	NA	NA	NA	NA	NA	NA	0.60451	1	1	1
2p loss	8 (5%)	142	0.82789	1	0.02291	1	NA	NA	NA	NA	0.36811	1	0.16366	1	1	1	0.43237	1
2q loss	17 (11%)	133	0.011189	1	0.47174	1	1	1	0.42442	1	0.4629	1	0.032343	1	0.77938	1	0.91069	1
3p loss	9 (6%)	141	0.063331	1	0.77287	1	0.34475	1	0.66571	1	0.085845	1	0.071884	1	0.14801	1	0.27318	1
4p loss	29 (19%)	121	0.00073887	0.403	0.29172	1	0.85302	1	0.68038	1	0.42513	1	0.34163	1	0.4246	1	0.51733	1
4q loss	26 (17%)	124	0.077748	1	0.78022	1	0.67965	1	0.333	1	0.59268	1	0.60125	1	0.32611	1	0.6753	1
5p loss	14 (9%)	136	0.00060734	0.333	0.6093	1	0.51704	1	1	1	0.53222	1	0.72064	1	0.27894	1	0.26233	1
5q loss	36 (24%)	114	0.0011231	0.608	0.092333	1	0.76662	1	0.82195	1	0.8953	1	0.772	1	0.1513	1	0.41549	1
6p loss	18 (12%)	132	0.051694	1	0.23761	1	0.23336	1	0.35275	1	0.38443	1	0.8123	1	0.75943	1	0.51948	1
6q loss	29 (19%)	121	6.0493e-06	0.00339	0.0088271	1	0.24675	1	0.52114	1	0.26038	1	0.047743	1	0.82472	1	0.75243	1
7q loss	3 (2%)	147	0.3754	1	0.2924	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
8p loss	49 (33%)	101	6.3969e-07	0.000361	3.0772e-05	0.0172	0.14267	1	0.12335	1	0.64311	1	0.4405	1	0.047974	1	0.074499	1
8q loss	5 (3%)	145	0.28492	1	0.19193	1	NA	NA	NA	NA	0.78228	1	1	1	0.3487	1	0.068818	1
9p loss	43 (29%)	107	0.00020006	0.11	0.0065168	1	0.037356	1	0.12478	1	0.034134	1	0.00081284	0.442	0.88286	1	0.1145	1
9q loss	41 (27%)	109	7.8247e-05	0.0435	0.005446	1	0.001208	0.65	0.0011335	0.612	0.0027444	1	0.00011491	0.0637	0.79808	1	0.34751	1
10p loss	19 (13%)	131	0.76299	1	0.8782	1	0.18861	1	0.40944	1	0.25174	1	0.275	1	0.18277	1	0.41951	1
10q loss	30 (20%)	120	0.11818	1	0.053763	1	0.92133	1	0.71682	1	0.20859	1	0.040607	1	0.030837	1	0.35878	1
11p loss	48 (32%)	102	1.3616e-06	0.000767	0.0019012	1	0.23202	1	0.36481	1	0.073907	1	0.0024832	1	0.20612	1	0.64725	1
11q loss	35 (23%)	115	0.00018792	0.104	0.029811	1	0.3002	1	0.6971	1	0.21099	1	0.42423	1	0.20111	1	0.24569	1
12p loss	6 (4%)	144	0.15909	1	0.16112	1	NA	NA	NA	NA	0.32493	1	0.28446	1	1	1	0.43881	1
12q loss	9 (6%)	141	0.15867	1	1	1	NA	NA	NA	NA	0.15025	1	0.35975	1	0.1497	1	1	1
13q loss	20 (13%)	130	0.015746	1	0.31107	1	0.10353	1	0.17348	1	0.11089	1	0.41842	1	0.04903	1	0.66235	1
14q loss	25 (17%)	125	0.00037396	0.206	0.027225	1	0.81766	1	0.36398	1	0.74575	1	0.47021	1	0.05732	1	0.11684	1
15q loss	19 (13%)	131	0.16825	1	0.094986	1	0.12078	1	0.56056	1	0.077555	1	0.057567	1	0.051531	1	0.24644	1
16p loss	17 (11%)	133	0.01789	1	0.27557	1	0.6034	1	0.47129	1	0.34313	1	0.86361	1	0.32565	1	0.6862	1
16q loss	17 (11%)	133	0.0047746	1	0.3993	1	0.74957	1	0.50344	1	0.73473	1	0.80619	1	0.82262	1	0.82808	1
17p loss	42 (28%)	108	0.0020831	1	0.10811	1	0.54073	1	0.86908	1	0.0062607	1	0.16064	1	0.21744	1	0.32334	1
17q loss	6 (4%)	144	0.71977	1	0.039355	1	NA	NA	NA	NA	0.85704	1	0.8447	1	0.26621	1	0.5098	1
18p loss	22 (15%)	128	0.004995	1	0.033528	1	0.50728	1	0.19496	1	1	1	0.17159	1	0.58127	1	0.011257	1
18q loss	39 (26%)	111	1.5386e-05	0.0086	0.70891	1	0.81334	1	0.48891	1	0.18208	1	0.5589	1	0.55267	1	0.21848	1
19p loss	9 (6%)	141	0.29996	1	0.93289	1	0.25229	1	0.11006	1	0.41537	1	0.35616	1	0.1497	1	1	1
19q loss	4 (3%)	146	0.54538	1	0.70202	1	NA	NA	NA	NA	0.48026	1	0.72698	1	0.18259	1	1	1
20p loss	7 (5%)	143	0.31279	1	0.25113	1	NA	NA	NA	NA	1	1	1	1	0.86838	1	0.66308	1
21q loss	17 (11%)	133	0.55556	1	0.53304	1	0.4661	1	0.47129	1	0.6739	1	0.58428	1	0.46745	1	0.90405	1
22q loss	29 (19%)	121	6.2976e-05	0.0351	0.66937	1	0.070593	1	0.0044353	1	0.068631	1	0.12033	1	0.88464	1	0.41535	1
Xq loss	4 (3%)	146	0.25181	1	0.28538	1	NA	NA	NA	NA	0.48026	1	0.5623	1	0.8084	1	1	1