Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		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	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	Chi-square test_P	Chi-square test_Q	Chi-square test_P	Chi-square 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
1p gain	4 (2%)	158	NA	NA	NA	NA	0.7078	1	0.48124	1	0.61573	1	0.10804	1	NA	NA	NA	NA	0.14978	1	0.74803	1
1q gain	27 (17%)	135	0.72447	1	0.92316	1	0.033243	1	0.1597	1	0.1693	1	0.40239	1	0.99844	1	0.035799	1	0.42954	1	0.76098	1
2p gain	20 (12%)	142	0.19685	1	0.42693	1	0.15693	1	0.69736	1	0.6788	1	0.70858	1	0.029218	1	0.099465	1	0.55319	1	0.34623	1
2q gain	21 (13%)	141	0.03046	1	0.078865	1	0.70065	1	0.79681	1	0.28795	1	0.88061	1	0.011845	1	0.13785	1	0.10802	1	0.72622	1
3p gain	17 (10%)	145	0.83343	1	0.67086	1	0.025198	1	0.60468	1	0.10942	1	0.7752	1	0.84563	1	1	1	0.34403	1	0.013752	1
3q gain	23 (14%)	139	1	1	0.80799	1	0.0083154	1	1	1	0.42814	1	0.32257	1	0.95476	1	1	1	0.51783	1	0.041012	1
4p gain	4 (2%)	158	NA	NA	NA	NA	0.3914	1	1	1	0.46275	1	0.58714	1	NA	NA	NA	NA	0.36628	1	0.50094	1
4q gain	3 (2%)	159	NA	NA	NA	NA	0.28558	1	NA	NA	0.47602	1	0.51514	1	NA	NA	NA	NA	0.7797	1	0.51232	1
5p gain	20 (12%)	142	0.83222	1	1	1	0.072042	1	0.1077	1	0.32624	1	0.86977	1	0.30594	1	1	1	0.33128	1	0.68016	1
5q gain	12 (7%)	150	0.54277	1	0.41842	1	0.056034	1	0.044364	1	0.066026	1	0.27065	1	0.18214	1	0.43099	1	0.39709	1	0.44731	1
6p gain	27 (17%)	135	0.43174	1	0.26258	1	3.0322e-05	0.0202	0.0082313	1	0.35328	1	0.14454	1	0.61439	1	1	1	0.74817	1	0.6941	1
6q gain	27 (17%)	135	0.43174	1	0.26258	1	7.7444e-05	0.0516	0.059697	1	0.35328	1	0.14454	1	0.44041	1	0.90347	1	0.8615	1	0.6941	1
7p gain	90 (56%)	72	0.0025599	1	0.0022159	1	1.2799e-06	0.000856	0.01546	1	0.5628	1	0.92247	1	0.6204	1	0.76314	1	0.15074	1	0.030206	1
7q gain	79 (49%)	83	0.0063052	1	0.0049446	1	6.4701e-07	0.000434	0.092591	1	0.29295	1	0.74169	1	0.41195	1	0.29255	1	0.65099	1	0.35359	1
8p gain	27 (17%)	135	0.6307	1	0.23804	1	0.0077538	1	0.66247	1	0.35776	1	0.054398	1	0.9088	1	0.88457	1	0.94036	1	0.49871	1
8q gain	72 (44%)	90	0.0087793	1	0.018987	1	3.133e-08	2.11e-05	0.52301	1	0.32593	1	0.4967	1	0.70875	1	0.81591	1	0.48799	1	0.28791	1
9p gain	35 (22%)	127	0.035396	1	0.20078	1	0.48174	1	0.049332	1	0.89381	1	0.17786	1	0.60815	1	0.074605	1	0.15273	1	0.71245	1
9q gain	26 (16%)	136	0.042568	1	0.27075	1	0.13481	1	0.43954	1	0.80291	1	0.21018	1	0.72172	1	0.66822	1	0.30562	1	0.46537	1
10p gain	8 (5%)	154	0.30865	1	0.51499	1	0.24476	1	0.48124	1	0.72729	1	0.55766	1	NA	NA	NA	NA	0.39067	1	0.8702	1
10q gain	4 (2%)	158	NA	NA	NA	NA	0.4435	1	NA	NA	1	1	0.9271	1	NA	NA	NA	NA	0.6308	1	0.7882	1
11p gain	21 (13%)	141	0.036255	1	0.060933	1	0.081297	1	0.33339	1	0.43614	1	0.71978	1	0.21588	1	0.083488	1	0.46379	1	0.1498	1
11q gain	17 (10%)	145	0.084838	1	0.13981	1	0.0013112	0.867	0.023985	1	0.78383	1	0.41956	1	0.32436	1	0.25315	1	0.93565	1	0.79649	1
12p gain	28 (17%)	134	0.58207	1	0.38134	1	0.020147	1	0.79681	1	0.3894	1	0.059794	1	0.64159	1	0.19093	1	0.29727	1	0.16384	1
12q gain	19 (12%)	143	1	1	1	1	0.31984	1	0.45776	1	0.45063	1	0.077811	1	0.50052	1	0.22953	1	0.34235	1	0.48477	1
13q gain	102 (63%)	60	0.22512	1	0.17484	1	1.2791e-07	8.6e-05	0.36189	1	0.97271	1	0.5515	1	0.30902	1	0.58452	1	0.031611	1	0.108	1
14q gain	4 (2%)	158	NA	NA	NA	NA	0.7078	1	0.17593	1	0.46275	1	0.49448	1	NA	NA	NA	NA	0.11123	1	0.18991	1
16p gain	29 (18%)	133	0.24532	1	0.35561	1	0.010133	1	0.45451	1	0.78442	1	0.681	1	0.94072	1	0.90347	1	0.44894	1	0.332	1
16q gain	30 (19%)	132	0.35578	1	0.47386	1	0.00011437	0.0761	0.53206	1	0.73343	1	0.7546	1	0.7863	1	0.58754	1	0.039697	1	0.096416	1
17p gain	3 (2%)	159	NA	NA	NA	NA	0.1107	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
17q gain	18 (11%)	144	0.18928	1	0.60576	1	0.039743	1	0.90886	1	0.57027	1	0.82522	1	0.20812	1	0.033388	1	0.40869	1	0.3104	1
18p gain	7 (4%)	155	0.28198	1	0.77371	1	0.11764	1	0.29861	1	1	1	0.79157	1	NA	NA	NA	NA	0.75669	1	1	1
18q gain	4 (2%)	158	NA	NA	NA	NA	0.7078	1	0.1132	1	1	1	0.79235	1	NA	NA	NA	NA	0.73544	1	0.50094	1
19p gain	20 (12%)	142	0.0072342	1	0.11525	1	0.0052367	1	0.70332	1	0.79853	1	0.60852	1	0.37733	1	0.43099	1	0.35735	1	0.23202	1
19q gain	23 (14%)	139	0.020151	1	0.082736	1	0.0056817	1	0.61355	1	0.25784	1	0.18075	1	0.47578	1	0.77898	1	0.40701	1	0.78836	1
20p gain	95 (59%)	67	0.71654	1	0.46562	1	0.14675	1	0.6191	1	0.071532	1	0.66234	1	0.27543	1	0.5802	1	0.57709	1	0.18954	1
20q gain	132 (81%)	30	0.085759	1	0.090897	1	0.00026508	0.176	0.22569	1	0.2768	1	0.5512	1	0.38337	1	0.71667	1	0.79121	1	0.465	1
21q gain	7 (4%)	155	0.50185	1	0.10675	1	0.46683	1	0.81846	1	0.72815	1	0.6103	1	0.49629	1	0.44745	1	0.30663	1	1	1
22q gain	5 (3%)	157	0.19132	1	0.10675	1	0.56273	1	NA	NA	0.31829	1	0.065396	1	NA	NA	NA	NA	0.6308	1	0.7882	1
Xq gain	7 (4%)	155	1	1	0.82857	1	0.59091	1	1	1	0.76234	1	0.70061	1	NA	NA	NA	NA	0.74396	1	0.8702	1
1p loss	21 (13%)	141	0.60422	1	1	1	0.023885	1	0.3946	1	0.47446	1	0.15447	1	0.45261	1	0.19093	1	0.38743	1	0.46324	1
1q loss	7 (4%)	155	0.83343	1	0.67086	1	0.53643	1	0.6221	1	0.57014	1	0.75237	1	NA	NA	NA	NA	0.5198	1	0.8702	1
2p loss	5 (3%)	157	0.42599	1	0.62048	1	0.41334	1	NA	NA	0.68197	1	0.12026	1	NA	NA	NA	NA	0.096523	1	0.074073	1
3p loss	8 (5%)	154	1	1	1	1	0.48585	1	0.46065	1	0.80667	1	0.7068	1	NA	NA	NA	NA	0.75425	1	0.77528	1
3q loss	4 (2%)	158	NA	NA	NA	NA	0.46336	1	NA	NA	1	1	0.29306	1	NA	NA	NA	NA	0.41347	1	1	1
4p loss	39 (24%)	123	0.36495	1	0.93959	1	0.0019968	1	0.86678	1	0.6332	1	0.46752	1	0.39486	1	0.018975	1	0.78348	1	1	1
4q loss	46 (28%)	116	0.59147	1	1	1	0.00085574	0.566	0.84097	1	0.42395	1	0.491	1	0.2766	1	0.047137	1	0.88508	1	0.81794	1
5p loss	11 (7%)	151	0.15108	1	0.24984	1	0.74525	1	0.36779	1	0.9027	1	0.71244	1	0.3764	1	0.77898	1	0.43828	1	0.12678	1
5q loss	23 (14%)	139	0.017342	1	0.060933	1	0.20374	1	0.10814	1	0.64258	1	0.81244	1	0.34446	1	0.34724	1	0.7735	1	0.15984	1
6p loss	8 (5%)	154	0.38022	1	0.82857	1	0.57174	1	0.013255	1	0.09715	1	0.70467	1	0.66813	1	1	1	0.75669	1	0.8702	1
6q loss	14 (9%)	148	1	1	0.60576	1	0.26916	1	0.2676	1	0.31048	1	0.84253	1	0.47918	1	0.53445	1	0.18574	1	0.13476	1
8p loss	56 (35%)	106	0.64159	1	0.37254	1	0.025841	1	0.69661	1	0.51133	1	0.60305	1	0.12304	1	0.93039	1	0.71576	1	0.10188	1
8q loss	3 (2%)	159	NA	NA	NA	NA	0.48599	1	NA	NA	0.78507	1	0.9271	1	NA	NA	NA	NA	0.52659	1	1	1
9p loss	12 (7%)	150	0.66155	1	0.75831	1	0.10082	1	0.8825	1	0.78383	1	0.59283	1	NA	NA	NA	NA	0.96481	1	1	1
9q loss	11 (7%)	151	0.60749	1	0.31511	1	0.26545	1	1	1	0.61444	1	0.69385	1	NA	NA	NA	NA	0.64533	1	0.31657	1
10p loss	17 (10%)	145	0.044717	1	0.014856	1	0.35303	1	0.61355	1	0.035097	1	0.11804	1	0.4851	1	1	1	0.91033	1	1	1
10q loss	21 (13%)	141	0.13555	1	0.31733	1	0.069234	1	0.58153	1	0.081421	1	0.28243	1	0.047644	1	0.66822	1	0.97004	1	0.89448	1
11p loss	19 (12%)	143	0.062832	1	0.13141	1	0.030298	1	0.043389	1	0.15789	1	0.072435	1	0.18703	1	0.065829	1	0.85595	1	0.66092	1
11q loss	23 (14%)	139	0.062832	1	0.13141	1	0.022142	1	0.11733	1	0.30391	1	0.12628	1	0.14045	1	0.0066599	1	0.10086	1	0.22141	1
12p loss	12 (7%)	150	0.73093	1	0.84835	1	0.33055	1	0.075339	1	0.40478	1	0.063848	1	NA	NA	NA	NA	0.8706	1	0.53527	1
12q loss	8 (5%)	154	1	1	0.62484	1	0.54141	1	1	1	0.36838	1	0.54054	1	NA	NA	NA	NA	0.48255	1	0.56962	1
13q loss	5 (3%)	157	NA	NA	NA	NA	0.091987	1	0.18583	1	0.13275	1	0.60805	1	0.85803	1	1	1	0.34494	1	0.84283	1
14q loss	51 (31%)	111	0.80522	1	0.25248	1	0.00040574	0.269	1	1	0.54531	1	0.17592	1	0.65887	1	0.56075	1	0.9648	1	0.37125	1
15q loss	58 (36%)	104	0.78482	1	0.22667	1	0.0022859	1	0.45026	1	0.15628	1	0.15265	1	0.63574	1	0.81044	1	0.56643	1	0.71444	1
16p loss	6 (4%)	156	0.19132	1	0.48788	1	0.22498	1	0.48124	1	0.87757	1	0.50543	1	0.85803	1	0.44745	1	0.56834	1	1	1
16q loss	10 (6%)	152	0.020236	1	0.11953	1	0.005393	1	0.44139	1	0.80667	1	0.50055	1	0.74652	1	0.17012	1	0.61167	1	0.60346	1
17p loss	89 (55%)	73	0.86593	1	1	1	0.25213	1	0.60638	1	0.7628	1	0.45764	1	0.14125	1	0.043692	1	0.61504	1	0.89322	1
17q loss	15 (9%)	147	0.61427	1	0.36217	1	0.30293	1	0.13403	1	0.61384	1	0.55484	1	0.66999	1	0.30504	1	0.33629	1	0.73555	1
18p loss	114 (70%)	48	0.018109	1	0.016255	1	1.1699e-05	0.00782	0.42546	1	0.37617	1	0.69093	1	0.14133	1	1	1	0.5823	1	0.40608	1
18q loss	126 (78%)	36	0.019531	1	0.014847	1	9.1647e-07	0.000614	0.37016	1	0.44785	1	0.70808	1	0.062803	1	0.53132	1	0.61255	1	0.66794	1
19p loss	7 (4%)	155	NA	NA	NA	NA	0.26545	1	0.36779	1	0.36838	1	0.42391	1	0.20907	1	1	1	0.1426	1	0.14073	1
19q loss	7 (4%)	155	NA	NA	NA	NA	0.49446	1	0.10489	1	0.57067	1	0.56803	1	0.37065	1	1	1	0.70089	1	0.35052	1
20p loss	18 (11%)	144	1	1	1	1	0.16195	1	0.64969	1	0.31942	1	0.77681	1	0.74652	1	0.53445	1	0.030547	1	0.091641	1
21q loss	43 (27%)	119	0.87864	1	0.67633	1	0.25011	1	0.59634	1	0.32782	1	0.62503	1	0.86655	1	0.54269	1	0.098961	1	0.6627	1
22q loss	42 (26%)	120	0.88664	1	0.73918	1	0.50033	1	0.31125	1	0.45508	1	0.45691	1	0.47536	1	0.36209	1	0.11911	1	0.78782	1
Xq loss	6 (4%)	156	0.77097	1	0.37002	1	0.28273	1	0.48124	1	0.85476	1	0.73886	1	NA	NA	NA	NA	0.84267	1	0.84283	1