		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	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	11 (3%)	402	NA	NA	NA	NA	0.57626	1	0.90907	1	0.065623	1	0.20886	1	0.42521	1	0.68335	1	0.46021	1	1	1
1q gain	47 (11%)	366	0.053097	1	0.73195	1	0.078786	1	0.30743	1	0.61175	1	0.12518	1	0.11959	1	0.29923	1	0.4366	1	0.83658	1
2p gain	40 (10%)	373	0.156	1	0.037771	1	0.0040928	1	0.046011	1	0.1818	1	0.37275	1	0.00038556	0.249	0.019921	1	0.50846	1	0.35508	1
2q gain	39 (9%)	374	0.098461	1	0.035248	1	0.00017278	0.113	0.0023481	1	0.12194	1	0.46618	1	0.0010917	0.686	0.038358	1	0.52888	1	0.40458	1
3p gain	20 (5%)	393	0.39682	1	0.38241	1	0.071044	1	0.36719	1	0.70057	1	0.13684	1	0.97363	1	0.67551	1	0.62591	1	0.18436	1
3q gain	30 (7%)	383	0.48206	1	0.045848	1	0.00096864	0.611	0.22011	1	0.4628	1	0.35385	1	0.41476	1	0.63539	1	0.35718	1	0.82412	1
4p gain	3 (1%)	410	NA	NA	NA	NA	0.74635	1	0.47306	1	0.27053	1	0.34139	1	NA	NA	NA	NA	0.20776	1	0.033383	1
4q gain	5 (1%)	408	NA	NA	NA	NA	0.84236	1	1	1	1	1	1	1	NA	NA	NA	NA	0.5788	1	0.33452	1
5p gain	39 (9%)	374	0.28969	1	0.041804	1	0.002235	1	0.023566	1	0.5289	1	0.92241	1	0.61763	1	1	1	0.68528	1	0.53047	1
5q gain	21 (5%)	392	0.65716	1	0.56376	1	0.039106	1	0.18815	1	0.56622	1	0.64958	1	0.74855	1	0.57791	1	1	1	0.94763	1
6p gain	50 (12%)	363	0.17049	1	0.011561	1	0.026735	1	0.67498	1	0.55908	1	0.68372	1	0.036737	1	0.26847	1	0.51347	1	0.24624	1
6q gain	45 (11%)	368	0.31237	1	0.024817	1	0.031676	1	0.35198	1	0.71695	1	0.62265	1	0.15625	1	0.62058	1	0.44104	1	0.30861	1
7p gain	200 (48%)	213	0.0012376	0.775	0.0037522	1	1.9164e-15	1.37e-12	9.1419e-05	0.0599	0.19699	1	0.0047606	1	1.0881e-07	7.5e-05	2.8504e-05	0.019	0.42473	1	0.95791	1
7q gain	175 (42%)	238	0.0047588	1	0.023568	1	7.0474e-11	4.92e-08	0.0027808	1	0.5367	1	0.023278	1	3.0119e-06	0.00204	0.00018602	0.121	0.47424	1	0.75189	1
8p gain	80 (19%)	333	0.92471	1	0.78522	1	9.2183e-06	0.00619	0.056224	1	0.18398	1	0.22276	1	0.17509	1	0.032702	1	0.615	1	0.57107	1
8q gain	162 (39%)	251	0.75056	1	0.6124	1	9.3911e-12	6.6e-09	0.00066584	0.425	0.64798	1	0.21462	1	0.0071979	1	0.12747	1	0.098557	1	0.1543	1
9p gain	46 (11%)	367	0.033453	1	0.21301	1	0.28043	1	0.43276	1	0.23239	1	0.18632	1	0.87901	1	0.76037	1	0.76674	1	0.76256	1
9q gain	39 (9%)	374	0.091518	1	0.07755	1	0.064111	1	0.11304	1	0.018363	1	0.026965	1	0.36187	1	0.65886	1	0.058924	1	0.63487	1
10p gain	18 (4%)	395	0.64997	1	0.62538	1	0.10421	1	0.047659	1	0.84537	1	0.70524	1	0.90416	1	0.46649	1	0.76067	1	0.94138	1
10q gain	7 (2%)	406	NA	NA	NA	NA	0.11363	1	0.042029	1	0.67899	1	0.74596	1	0.93301	1	0.21941	1	0.20178	1	0.15076	1
11p gain	18 (4%)	395	0.15112	1	0.001355	0.847	0.00031424	0.203	0.00057549	0.369	0.49561	1	0.59587	1	0.87143	1	0.88902	1	0.63382	1	0.88213	1
11q gain	22 (5%)	391	0.030148	1	0.0022731	1	3.7234e-06	0.00251	0.0014127	0.881	0.12068	1	0.51658	1	0.1506	1	0.22004	1	0.38613	1	0.69294	1
12p gain	66 (16%)	347	0.24785	1	0.71014	1	0.0044169	1	0.014562	1	0.20485	1	0.80059	1	0.36103	1	0.68168	1	0.068987	1	0.21035	1
12q gain	60 (15%)	353	0.24785	1	0.54186	1	0.0018101	1	0.0029065	1	0.14198	1	0.75117	1	0.26963	1	0.69054	1	0.012051	1	0.26775	1
13q gain	211 (51%)	202	2.9524e-06	0.002	3.3163e-05	0.022	2.9518e-33	2.13e-30	0.00026706	0.173	0.24565	1	0.014638	1	1.7083e-06	0.00117	7.158e-05	0.0472	0.044991	1	0.46564	1
14q gain	15 (4%)	398	0.48458	1	0.4434	1	0.056649	1	0.27636	1	0.18897	1	0.43773	1	0.14473	1	0.12695	1	1	1	0.80535	1
15q gain	5 (1%)	408	NA	NA	NA	NA	0.073166	1	0.68257	1	0.12053	1	0.059239	1	0.78261	1	0.48055	1	0.47307	1	0.42668	1
16p gain	67 (16%)	346	0.012989	1	0.0037979	1	1.0833e-14	7.69e-12	0.13846	1	0.16256	1	0.025635	1	0.050958	1	0.17966	1	0.12636	1	0.047449	1
16q gain	66 (16%)	347	0.013862	1	0.0064365	1	1.4436e-16	1.03e-13	0.13607	1	0.13223	1	0.025635	1	0.050958	1	0.17966	1	0.31435	1	0.23221	1
17p gain	9 (2%)	404	NA	NA	NA	NA	0.61782	1	0.89252	1	0.20204	1	0.085973	1	0.031649	1	0.22465	1	0.73695	1	0.89132	1
17q gain	48 (12%)	365	0.092916	1	0.020216	1	0.00091327	0.578	0.0073931	1	0.23346	1	0.13015	1	1.1618e-05	0.00777	0.014993	1	0.058064	1	0.75324	1
18p gain	15 (4%)	398	0.11798	1	0.63749	1	0.0054775	1	0.013908	1	0.47625	1	0.61814	1	0.17065	1	0.058059	1	0.14412	1	0.3884	1
18q gain	9 (2%)	404	NA	NA	NA	NA	0.023231	1	0.030293	1	0.1283	1	0.069729	1	0.14202	1	0.26749	1	0.27437	1	0.32669	1
19p gain	34 (8%)	379	0.14153	1	0.23992	1	0.0055403	1	0.051177	1	0.74701	1	0.16527	1	0.32105	1	0.48103	1	0.58806	1	0.57289	1
19q gain	41 (10%)	372	0.071786	1	0.10441	1	0.43743	1	0.066588	1	0.14615	1	0.049292	1	0.14546	1	0.29663	1	0.92434	1	0.94219	1
20p gain	188 (46%)	225	0.001417	0.883	1.4709e-06	0.00101	4.2881e-20	3.07e-17	0.012719	1	0.11383	1	0.016779	1	3.3451e-05	0.0222	0.00019663	0.128	0.17412	1	0.075786	1
20q gain	267 (65%)	146	1.2389e-11	8.67e-09	1.886e-13	1.34e-10	9.4158e-47	6.81e-44	1.0617e-09	7.37e-07	0.010519	1	2.2689e-06	0.00155	2.6055e-13	1.84e-10	3.5822e-11	2.5e-08	0.10269	1	0.42883	1
21q gain	11 (3%)	402	0.19372	1	0.19462	1	0.085831	1	0.33915	1	0.071712	1	0.52322	1	0.28201	1	0.73007	1	0.70412	1	0.68448	1
Xq gain	12 (3%)	401	0.48687	1	0.77692	1	0.033071	1	0.63094	1	0.11053	1	0.23172	1	0.44618	1	0.76497	1	0.35201	1	0.40967	1
1p loss	51 (12%)	362	0.0048918	1	0.0007651	0.487	7.0876e-08	4.9e-05	0.0032853	1	0.51777	1	0.61108	1	0.098391	1	0.28609	1	0.18025	1	0.27379	1
1q loss	18 (4%)	395	0.45164	1	0.13542	1	0.01032	1	0.26876	1	0.47187	1	0.68704	1	0.1506	1	0.19603	1	0.94083	1	0.44046	1
2p loss	4 (1%)	409	0.57247	1	0.1105	1	0.43319	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.66171	1	0.13188	1
2q loss	6 (1%)	407	1	1	0.15638	1	0.60146	1	NA	NA	0.096581	1	0.22364	1	NA	NA	NA	NA	0.17503	1	0.0588	1
3p loss	27 (7%)	386	0.25348	1	0.10441	1	0.0025064	1	0.25233	1	0.55113	1	1	1	0.45836	1	0.55629	1	0.21162	1	0.14292	1
3q loss	12 (3%)	401	0.41487	1	0.56376	1	0.22379	1	1	1	0.17185	1	0.32301	1	0.2672	1	0.68335	1	0.42323	1	0.82207	1
4p loss	84 (20%)	329	0.0046945	1	0.052076	1	1.0515e-11	7.38e-09	0.0029908	1	0.24001	1	0.30901	1	0.00075446	0.481	0.00059947	0.384	0.08301	1	0.29045	1
4q loss	68 (16%)	345	0.007356	1	0.038081	1	2.2559e-10	1.57e-07	0.0022265	1	0.37204	1	0.33449	1	0.0034832	1	0.015793	1	0.0026607	1	0.035856	1
5p loss	25 (6%)	388	0.87467	1	0.17177	1	0.0017575	1	0.10207	1	0.64237	1	0.62482	1	0.12574	1	0.41591	1	0.84064	1	0.90748	1
5q loss	38 (9%)	375	0.12578	1	0.056322	1	1.1142e-05	0.00746	0.29312	1	0.53657	1	0.23424	1	0.0076323	1	0.10496	1	0.55089	1	0.47951	1
6p loss	12 (3%)	401	0.54027	1	0.25087	1	0.0028528	1	1	1	0.71917	1	1	1	0.66626	1	0.44955	1	0.64237	1	0.62386	1
6q loss	21 (5%)	392	0.94313	1	0.73195	1	0.074255	1	0.69654	1	0.23537	1	0.61741	1	1	1	0.84505	1	0.86383	1	1	1
8p loss	93 (23%)	320	0.0003169	0.205	0.0015632	0.972	7.7588e-17	5.55e-14	0.0010382	0.653	0.49858	1	0.013853	1	0.14082	1	0.066457	1	0.19995	1	0.35649	1
8q loss	8 (2%)	405	0.40267	1	0.77692	1	0.0096561	1	0.85153	1	0.21345	1	0.68625	1	1	1	1	1	0.19663	1	0.43569	1
9p loss	27 (7%)	386	0.87467	1	0.10976	1	4.3967e-05	0.0291	0.074568	1	0.42904	1	0.13443	1	0.042381	1	0.10496	1	0.5304	1	0.74427	1
9q loss	26 (6%)	387	0.34792	1	0.12399	1	2.5495e-06	0.00173	0.00061883	0.396	0.42904	1	0.13443	1	0.0008984	0.57	0.03599	1	0.11437	1	0.6754	1
10p loss	22 (5%)	391	0.66975	1	0.67198	1	0.00082829	0.526	0.28523	1	0.27906	1	0.975	1	0.51767	1	0.35247	1	0.23963	1	0.68136	1
10q loss	24 (6%)	389	0.60573	1	0.70978	1	0.00052594	0.338	0.15234	1	0.27906	1	1	1	0.29513	1	0.039998	1	0.69659	1	0.39298	1
11p loss	22 (5%)	391	0.47001	1	0.067421	1	8.336e-05	0.0548	0.00028101	0.182	0.80588	1	0.59969	1	0.048906	1	0.018363	1	0.040081	1	0.16178	1
11q loss	27 (7%)	386	0.37169	1	0.038707	1	7.9223e-06	0.00534	9.6071e-06	0.00645	0.91681	1	0.68704	1	0.2072	1	0.12893	1	0.35754	1	0.20161	1
12p loss	21 (5%)	392	0.090887	1	0.10976	1	7.1022e-05	0.0469	0.20684	1	0.67164	1	0.94732	1	0.080236	1	0.081727	1	0.71974	1	0.20758	1
12q loss	20 (5%)	393	0.16986	1	0.12399	1	0.00010141	0.0663	0.15257	1	0.68548	1	0.91336	1	0.016133	1	0.039998	1	0.41103	1	0.36188	1
13q loss	6 (1%)	407	NA	NA	NA	NA	0.020925	1	0.23224	1	0.035882	1	0.016259	1	0.42521	1	0.46356	1	0.86925	1	0.7227	1
14q loss	94 (23%)	319	2.0915e-07	0.000144	1.1836e-06	0.000812	1.5793e-22	1.13e-19	1.1969e-06	0.00082	0.00071669	0.457	0.0010247	0.646	1.4971e-06	0.00102	8.7803e-05	0.0576	0.53245	1	0.19414	1
15q loss	99 (24%)	314	0.01932	1	0.012231	1	9.291e-22	6.66e-19	0.0045786	1	0.13449	1	0.3143	1	4.0684e-05	0.0269	7.3474e-05	0.0483	0.48797	1	0.043531	1
16p loss	9 (2%)	404	0.2512	1	0.55383	1	0.30453	1	0.029781	1	0.73379	1	1	1	1	1	1	1	0.71093	1	1	1
16q loss	7 (2%)	406	0.46416	1	1	1	0.22757	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.17503	1	0.16959	1
17p loss	164 (40%)	249	1.7497e-05	0.0117	3.0491e-05	0.0203	4.4431e-23	3.19e-20	2.3112e-07	0.000159	0.13409	1	0.020681	1	2.6536e-06	0.0018	8.2008e-06	0.00552	0.14682	1	0.04636	1
17q loss	32 (8%)	381	0.11329	1	0.2246	1	0.0021573	1	0.21993	1	0.7314	1	0.36578	1	0.081268	1	0.10925	1	0.32156	1	0.29072	1
18p loss	209 (51%)	204	2.8122e-13	1.99e-10	2.9191e-10	2.03e-07	2.4423e-46	1.76e-43	5.149e-13	3.63e-10	0.0019121	1	3.1779e-05	0.0211	6.9843e-15	4.97e-12	5.8662e-09	4.07e-06	0.25052	1	0.49723	1
18q loss	225 (54%)	188	1.9205e-12	1.35e-09	3.831e-10	2.66e-07	8.8765e-46	6.4e-43	3.6165e-15	2.57e-12	0.023774	1	0.0001811	0.118	4.465e-14	3.17e-11	1.3634e-08	9.43e-06	0.061165	1	0.49873	1
19p loss	14 (3%)	399	1	1	0.31875	1	0.0027471	1	0.095687	1	0.19526	1	0.13399	1	0.0070759	1	0.078889	1	0.69276	1	0.087585	1
19q loss	13 (3%)	400	0.92159	1	0.38044	1	0.011541	1	0.095687	1	0.67899	1	0.18842	1	0.0070759	1	0.078889	1	0.56958	1	0.061113	1
20p loss	33 (8%)	380	0.013178	1	0.0071318	1	8.8788e-08	6.13e-05	0.051364	1	0.83945	1	0.63022	1	0.35278	1	0.30826	1	0.90557	1	0.52983	1
21q loss	71 (17%)	342	0.0026617	1	0.0048603	1	2.5982e-06	0.00176	0.25825	1	0.84825	1	0.64608	1	0.12188	1	0.34163	1	0.073098	1	0.60765	1
22q loss	81 (20%)	332	0.00091619	0.579	0.00045496	0.293	1.0613e-11	7.44e-09	0.089431	1	0.069953	1	0.020462	1	0.0097172	1	0.0011021	0.691	0.62418	1	0.12297	1
Xq loss	5 (1%)	408	NA	NA	NA	NA	0.84236	1	1	1	0.072635	1	0.68228	1	NA	NA	NA	NA	0.85062	1	0.14029	1
