		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	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	Fisher's exact test_P	Fisher's exact test_Q
1p gain	15 (3%)	560	0.40567	1	0.10203	1	0.93194	1	0.49686	1	0.26047	1	0.11777	1	0.17804	1	0.33015	1	0.11131	1	0.91089	1
1q gain	80 (14%)	495	0.48395	1	0.8552	1	0.015823	1	0.92569	1	0.62534	1	0.73607	1	0.12824	1	0.075768	1	0.072884	1	0.97845	1
2p gain	60 (10%)	515	0.016908	1	0.0049882	1	0.0081555	1	0.00025563	0.172	0.07017	1	0.59599	1	0.00022405	0.152	0.00013733	0.0937	0.2161	1	0.020869	1
2q gain	59 (10%)	516	0.0036769	1	0.00391	1	0.0010069	0.666	5.8199e-06	0.00407	0.36308	1	0.79478	1	0.00023412	0.158	0.00082411	0.547	0.25079	1	0.050357	1
3p gain	36 (6%)	539	0.1259	1	0.43337	1	0.00018128	0.123	0.25722	1	0.29198	1	0.34557	1	0.2599	1	0.88499	1	0.20792	1	0.36632	1
3q gain	53 (9%)	522	0.22025	1	0.094667	1	2.4908e-06	0.00175	0.035341	1	0.016764	1	0.41726	1	0.074996	1	0.58768	1	0.11128	1	0.54357	1
4p gain	6 (1%)	569	NA	NA	NA	NA	0.062196	1	0.22614	1	0.20597	1	0.48497	1	NA	NA	NA	NA	0.13662	1	0.052496	1
4q gain	7 (1%)	568	0.70431	1	1	1	0.24967	1	0.787	1	1	1	0.61883	1	NA	NA	NA	NA	0.38271	1	0.80878	1
5p gain	60 (10%)	515	0.11285	1	0.7076	1	0.0015014	0.985	0.17846	1	0.27364	1	0.99002	1	0.40113	1	0.39993	1	0.7844	1	0.35435	1
5q gain	33 (6%)	542	0.45687	1	0.53436	1	0.0035603	1	0.35577	1	0.36743	1	0.76396	1	0.72984	1	0.44647	1	0.81846	1	0.48285	1
6p gain	77 (13%)	498	0.24622	1	0.0049188	1	1.5453e-06	0.00109	0.40135	1	0.2221	1	0.53897	1	0.02271	1	0.22684	1	0.84813	1	0.39161	1
6q gain	71 (12%)	504	0.37518	1	0.019854	1	7.4722e-07	0.000531	0.15877	1	0.34677	1	0.38279	1	0.06068	1	0.57524	1	0.74931	1	0.25108	1
7p gain	290 (50%)	285	0.00044346	0.298	0.0088723	1	1.8943e-21	1.42e-18	7.2886e-07	0.000518	0.24702	1	0.0087241	1	3.7185e-08	2.69e-05	9.5428e-05	0.0652	0.070344	1	0.030432	1
7q gain	255 (44%)	320	0.00064412	0.43	0.013397	1	6.9527e-16	5.14e-13	8.6118e-06	0.00601	0.29031	1	0.078548	1	8.7918e-07	0.000623	1.2379e-05	0.00862	0.24522	1	0.15535	1
8p gain	108 (19%)	467	0.94582	1	0.74582	1	1.0033e-08	7.27e-06	0.43331	1	0.58065	1	0.10124	1	0.18083	1	0.44035	1	0.49022	1	0.89065	1
8q gain	235 (41%)	340	0.069295	1	0.62149	1	1.0571e-33	7.98e-31	0.0094198	1	0.21686	1	0.41345	1	0.0010965	0.724	0.026497	1	0.45899	1	0.63306	1
9p gain	79 (14%)	496	0.41996	1	0.84253	1	0.17843	1	0.79019	1	0.70606	1	0.72977	1	0.53853	1	0.85475	1	0.78008	1	0.78126	1
9q gain	64 (11%)	511	0.47606	1	0.92298	1	0.214	1	0.43338	1	0.26228	1	0.49615	1	0.98879	1	0.69074	1	0.4082	1	0.73861	1
10p gain	28 (5%)	547	0.13658	1	0.8464	1	0.009811	1	0.012541	1	0.96177	1	0.97042	1	0.61731	1	0.044579	1	0.6164	1	0.49637	1
10q gain	13 (2%)	562	0.69094	1	0.58915	1	0.19283	1	0.043666	1	0.43377	1	0.08886	1	0.44811	1	0.076189	1	0.69363	1	0.90189	1
11p gain	39 (7%)	536	0.063043	1	0.654	1	1.7136e-05	0.0119	0.00021429	0.146	0.78095	1	0.73264	1	0.049079	1	0.00015336	0.104	0.24559	1	0.88201	1
11q gain	39 (7%)	536	0.10161	1	0.031637	1	1.3278e-06	0.000939	0.00091055	0.603	0.76461	1	0.50318	1	0.035611	1	0.0052563	1	0.55893	1	0.40622	1
12p gain	93 (16%)	482	0.36191	1	0.81826	1	0.25584	1	0.017053	1	0.63632	1	0.29191	1	0.023201	1	0.013443	1	0.21996	1	0.11247	1
12q gain	78 (14%)	497	0.31523	1	0.72067	1	0.098608	1	0.0019341	1	0.81221	1	0.28767	1	0.035315	1	0.01536	1	0.22169	1	0.16642	1
13q gain	314 (55%)	261	1.0021e-07	7.24e-05	2.4368e-05	0.0168	1.6222e-37	1.23e-34	1.7064e-08	1.24e-05	0.085458	1	0.026046	1	8.5412e-09	6.2e-06	6.3955e-07	0.000455	0.010037	1	0.44955	1
14q gain	19 (3%)	556	0.49483	1	0.55001	1	0.030087	1	0.70858	1	0.31348	1	0.51711	1	0.060477	1	0.047976	1	1	1	0.37109	1
15q gain	7 (1%)	568	NA	NA	NA	NA	0.51457	1	0.88163	1	1	1	0.14409	1	1	1	0.24372	1	0.86981	1	0.37371	1
16p gain	96 (17%)	479	0.097522	1	0.084417	1	1.2625e-16	9.37e-14	0.010804	1	0.29727	1	0.085783	1	0.022796	1	0.13645	1	0.57733	1	0.34666	1
16q gain	96 (17%)	479	0.043277	1	0.068344	1	3.0211e-18	2.25e-15	0.0039079	1	0.35052	1	0.068954	1	0.019816	1	0.060159	1	0.46459	1	0.27723	1
17p gain	13 (2%)	562	0.77999	1	0.0060489	1	1	1	0.84961	1	0.71452	1	0.67333	1	0.015683	1	0.0089989	1	0.69363	1	0.90189	1
17q gain	67 (12%)	508	0.045525	1	0.063861	1	0.00026856	0.181	0.0014284	0.938	0.17537	1	0.14176	1	1.4683e-05	0.0102	0.0019486	1	0.078543	1	0.35388	1
18p gain	21 (4%)	554	0.19204	1	0.01685	1	0.00061013	0.408	0.0095456	1	0.94878	1	0.79498	1	0.13285	1	0.39087	1	0.56836	1	0.39747	1
18q gain	12 (2%)	563	NA	NA	NA	NA	0.17246	1	0.0072864	1	0.32661	1	0.71088	1	0.12238	1	0.85815	1	0.10546	1	0.13438	1
19p gain	52 (9%)	523	0.16712	1	0.22776	1	5.843e-05	0.0401	0.023588	1	0.21528	1	0.25758	1	0.42326	1	0.47411	1	0.71797	1	0.74542	1
19q gain	61 (11%)	514	0.01235	1	0.02492	1	0.012239	1	0.071518	1	0.015545	1	0.049624	1	0.50709	1	0.51206	1	0.83213	1	0.49525	1
20p gain	288 (50%)	287	6.0603e-05	0.0415	6.7132e-09	4.88e-06	4.248e-22	3.19e-19	7.6737e-05	0.0525	0.029685	1	0.040306	1	3.1963e-07	0.000229	3.2029e-07	0.000229	0.62537	1	0.47156	1
20q gain	403 (70%)	172	1.2304e-18	9.18e-16	2.683e-17	1.99e-14	2.2246e-46	1.68e-43	9.0386e-13	6.64e-10	0.01099	1	2.2821e-05	0.0158	9.0343e-18	6.72e-15	1.1305e-13	8.32e-11	0.46311	1	0.10066	1
21q gain	19 (3%)	556	0.43625	1	0.38118	1	0.0026802	1	0.70858	1	0.55823	1	0.052266	1	0.61942	1	0.83363	1	0.68566	1	0.14321	1
22q gain	7 (1%)	568	0.69094	1	0.0060489	1	0.23406	1	0.46578	1	0.66888	1	0.032985	1	0.68907	1	0.49881	1	0.45861	1	0.59561	1
Xq gain	17 (3%)	558	0.14672	1	0.73499	1	0.016685	1	0.33848	1	0.0040371	1	0.4769	1	0.84629	1	1	1	0.48172	1	0.70461	1
1p loss	68 (12%)	507	0.078358	1	0.0032744	1	7.5476e-06	0.00528	3.8428e-05	0.0264	0.4806	1	0.82835	1	0.076382	1	0.0082272	1	0.19261	1	0.62049	1
1q loss	25 (4%)	550	0.55788	1	0.021479	1	0.082264	1	0.031495	1	0.60347	1	0.49802	1	0.1581	1	0.32381	1	0.42483	1	0.72532	1
2p loss	10 (2%)	565	1	1	0.43464	1	0.073513	1	NA	NA	0.44803	1	0.58521	1	NA	NA	NA	NA	0.015125	1	0.013286	1
2q loss	8 (1%)	567	0.74087	1	0.44409	1	0.54823	1	NA	NA	0.56996	1	0.58231	1	NA	NA	NA	NA	0.058427	1	0.045527	1
3p loss	35 (6%)	540	0.93812	1	0.53032	1	0.83112	1	0.83463	1	0.75751	1	0.79155	1	0.44134	1	0.15697	1	0.10485	1	0.72944	1
3q loss	17 (3%)	558	0.6182	1	0.81564	1	0.75688	1	0.015667	1	0.39473	1	0.59495	1	0.3845	1	0.18399	1	0.73957	1	0.7721	1
4p loss	122 (21%)	453	0.10576	1	0.105	1	5.4975e-11	4.01e-08	0.0035973	1	0.27388	1	0.72913	1	0.0061971	1	0.057158	1	0.045027	1	0.76936	1
4q loss	113 (20%)	462	0.096187	1	0.063801	1	3.1754e-12	2.33e-09	0.0016838	1	0.58887	1	0.44149	1	0.0021315	1	0.053451	1	0.012191	1	0.56362	1
5p loss	34 (6%)	541	0.2914	1	0.43337	1	0.00054432	0.365	0.034068	1	1	1	0.63006	1	0.23394	1	0.035241	1	0.96862	1	0.82879	1
5q loss	60 (10%)	515	0.016307	1	0.091686	1	5.5316e-07	0.000394	0.081603	1	0.73539	1	0.53871	1	0.021113	1	0.09854	1	0.96346	1	0.57856	1
6p loss	18 (3%)	557	0.11691	1	0.0742	1	0.026043	1	0.2767	1	0.76394	1	0.83592	1	0.88965	1	0.60116	1	0.60161	1	0.92285	1
6q loss	33 (6%)	542	0.4568	1	0.338	1	0.09827	1	1	1	0.025209	1	0.47045	1	0.73685	1	0.67654	1	0.26225	1	0.29769	1
7q loss	3 (1%)	572	NA	NA	NA	NA	0.21176	1	NA	NA	0.78716	1	0.73685	1	NA	NA	NA	NA	0.76387	1	1	1
8p loss	145 (25%)	430	0.011681	1	0.0046329	1	1.1426e-18	8.53e-16	0.00037323	0.251	0.47852	1	0.098448	1	0.11036	1	0.15185	1	0.51503	1	0.73021	1
8q loss	12 (2%)	563	0.60297	1	0.63949	1	0.082808	1	0.58001	1	0.052123	1	0.3299	1	1	1	0.8276	1	0.15853	1	0.27077	1
9p loss	39 (7%)	536	0.56409	1	0.12011	1	2.8967e-05	0.02	0.0015809	1	0.063458	1	0.15733	1	0.10225	1	0.022105	1	0.12745	1	1	1
9q loss	37 (6%)	538	0.048413	1	0.013528	1	1.9547e-06	0.00138	3.4176e-05	0.0235	0.093971	1	0.39851	1	0.021351	1	0.016716	1	0.049149	1	0.81952	1
10p loss	40 (7%)	535	0.70439	1	0.40096	1	0.00086224	0.572	0.41929	1	0.15082	1	0.15961	1	0.40869	1	0.53216	1	0.13213	1	0.59051	1
10q loss	46 (8%)	529	0.34014	1	0.56823	1	1.4367e-06	0.00101	0.15314	1	0.6091	1	0.27871	1	0.10225	1	0.2311	1	0.71404	1	0.81051	1
11p loss	40 (7%)	535	0.79678	1	1	1	0.0097676	1	0.70583	1	0.86742	1	0.56214	1	0.071558	1	0.083775	1	0.11333	1	0.35936	1
11q loss	51 (9%)	524	0.97545	1	0.85752	1	0.0016581	1	0.23178	1	0.83532	1	0.4532	1	0.099677	1	0.50904	1	0.12883	1	0.83548	1
12p loss	33 (6%)	542	0.11383	1	0.26366	1	5.424e-07	0.000387	0.25849	1	0.70196	1	0.6851	1	0.20105	1	0.46045	1	0.54148	1	0.22186	1
12q loss	28 (5%)	547	0.13127	1	0.052412	1	1.1071e-06	0.000784	0.52201	1	0.64801	1	0.69748	1	0.14256	1	0.18877	1	0.6164	1	0.6809	1
13q loss	12 (2%)	563	0.3244	1	0.10757	1	0.049459	1	0.22645	1	0.091511	1	0.16402	1	0.23575	1	0.66836	1	0.7263	1	0.40273	1
14q loss	143 (25%)	432	4.758e-06	0.00334	2.485e-07	0.000178	1.1184e-31	8.43e-29	1.9699e-07	0.000142	0.0012361	0.813	0.010377	1	1.7256e-07	0.000124	0.00070476	0.469	0.11445	1	0.70906	1
15q loss	156 (27%)	419	0.014365	1	0.011679	1	2.0874e-24	1.57e-21	0.015774	1	0.86073	1	0.61199	1	1.1894e-05	0.00829	0.00057188	0.383	0.3675	1	0.24605	1
16p loss	15 (3%)	560	0.25556	1	0.59763	1	0.09948	1	0.22645	1	0.51701	1	0.91027	1	0.58888	1	0.60116	1	1	1	0.91089	1
16q loss	17 (3%)	558	0.013057	1	0.50638	1	0.0022089	1	0.49228	1	0.71452	1	0.85154	1	0.091107	1	0.12148	1	0.13425	1	0.25684	1
17p loss	252 (44%)	323	0.00024224	0.164	0.0016454	1	5.4882e-22	4.12e-19	2.4395e-07	0.000175	0.7686	1	0.36683	1	3.2518e-06	0.00228	0.00079532	0.529	0.027	1	0.49718	1
17q loss	45 (8%)	530	0.76207	1	0.5585	1	0.0023038	1	0.85708	1	0.92076	1	0.75067	1	0.10108	1	0.10474	1	0.11572	1	0.63456	1
18p loss	324 (56%)	251	9.8728e-15	7.29e-12	8.5148e-12	6.23e-09	4.2634e-47	3.23e-44	4.3282e-19	3.24e-16	0.087657	1	0.0012275	0.809	5.387e-16	3.99e-13	2.735e-11	2e-08	0.065035	1	0.7872	1
18q loss	352 (61%)	223	1.4203e-12	1.04e-09	1.9645e-11	1.44e-08	6.8004e-51	5.16e-48	8.0336e-21	6.02e-18	0.13872	1	0.012816	1	3.958e-16	2.93e-13	3.6833e-09	2.68e-06	0.0093757	1	0.37782	1
19p loss	20 (3%)	555	0.49008	1	0.59763	1	1.4622e-05	0.0102	0.024428	1	1	1	0.18158	1	0.0015479	1	0.0028882	1	0.23499	1	0.37109	1
19q loss	18 (3%)	557	0.49008	1	0.59763	1	0.00023546	0.159	0.096499	1	0.77835	1	0.85927	1	0.0015479	1	0.0028882	1	0.42424	1	0.097617	1
20p loss	47 (8%)	528	0.16877	1	0.17976	1	4.5625e-07	0.000326	0.039019	1	0.92519	1	0.17183	1	0.57735	1	0.39072	1	0.55412	1	0.48621	1
21q loss	114 (20%)	461	0.058799	1	0.31932	1	3.6397e-05	0.025	0.055504	1	0.084084	1	0.47873	1	0.23518	1	0.3916	1	0.11838	1	0.3424	1
22q loss	122 (21%)	453	0.06793	1	0.003803	1	7.7977e-14	5.75e-11	0.35208	1	0.25688	1	0.40929	1	0.067555	1	0.064607	1	0.066218	1	0.10019	1
Xq loss	11 (2%)	564	0.76543	1	0.83939	1	0.33904	1	0.44599	1	0.81707	1	0.41009	1	0.01571	1	0.067381	1	0.51495	1	0.65187	1
