		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	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
1p gain	0 (0%)	471	0.68266	1	0.1836	1	0.035042	1	0.66105	1	0.40106	1	1	1	0.18151	1	0.28962	1	0.0074301	1	0.075767	1
1q gain	0 (0%)	354	0.11087	1	0.63732	1	3.0433e-07	0.000174	0.005342	1	0.0012254	0.54	0.00071538	0.325	3.3148e-06	0.00182	9.2345e-07	0.000517	3.7404e-07	0.000213	0.017759	1
2p gain	0 (0%)	441	0.23344	1	0.29788	1	5.4103e-11	3.42e-08	0.058815	1	0.17655	1	0.8017	1	0.23768	1	0.43383	1	0.018437	1	0.16208	1
2q gain	0 (0%)	452	0.51784	1	0.76949	1	4.8278e-11	3.06e-08	0.175	1	0.065268	1	0.5746	1	0.30009	1	0.62396	1	0.015034	1	0.11652	1
3p gain	0 (0%)	464	NA	NA	NA	NA	4.1488e-19	2.82e-16	0.12145	1	0.52525	1	0.65189	1	0.014933	1	0.042907	1	0.3378	1	0.22479	1
3q gain	0 (0%)	442	0.17647	1	0.054256	1	3.4119e-22	2.34e-19	2.4886e-05	0.013	0.38821	1	0.30068	1	1.1907e-06	0.000666	5.1415e-05	0.0261	2.0651e-05	0.0109	0.00026258	0.126
4p gain	0 (0%)	486	NA	NA	NA	NA	0.0038953	1	0.12499	1	NA	NA	0.14038	1	0.039552	1	0.15399	1	0.022869	1	0.028095	1
5p gain	0 (0%)	460	0.86016	1	0.6235	1	3.0144e-09	1.83e-06	0.00013587	0.0674	0.031072	1	0.71241	1	3.9528e-06	0.00215	0.00041955	0.197	1.6554e-05	0.00884	5.2861e-05	0.0268
5q gain	0 (0%)	483	NA	NA	NA	NA	0.002863	1	0.42348	1	NA	NA	1	1	0.06786	1	0.28634	1	0.051953	1	0.20331	1
6p gain	0 (0%)	454	0.42965	1	0.2431	1	1.5228e-16	1.02e-13	0.034667	1	0.66066	1	1	1	0.0066461	1	0.0074982	1	0.01207	1	0.030239	1
6q gain	0 (0%)	462	0.42965	1	0.2431	1	1.5822e-13	1.04e-10	0.33135	1	0.40106	1	1	1	0.0083914	1	0.0079272	1	0.16776	1	0.27806	1
7p gain	0 (0%)	449	1	1	0.86704	1	8.6204e-19	5.85e-16	0.011813	1	0.73304	1	0.21665	1	1	1	0.47476	1	0.24414	1	0.60937	1
7q gain	0 (0%)	449	0.94364	1	0.77558	1	2.3979e-19	1.63e-16	0.024395	1	0.88873	1	0.055165	1	0.38457	1	0.033117	1	0.44003	1	0.42504	1
8p gain	0 (0%)	406	0.3955	1	1	1	7.4822e-18	5.05e-15	0.91294	1	0.13349	1	1	1	0.47386	1	0.43448	1	0.37993	1	0.0022026	0.947
8q gain	0 (0%)	374	0.0046103	1	0.042441	1	1.6503e-21	1.13e-18	0.36766	1	0.0049518	1	1	1	0.0059062	1	0.00029937	0.143	0.0018009	0.778	3.2674e-05	0.017
9p gain	0 (0%)	478	NA	NA	NA	NA	0.048355	1	0.078573	1	NA	NA	1	1	0.82159	1	0.07871	1	0.06993	1	0.029363	1
9q gain	0 (0%)	488	NA	NA	NA	NA	0.35164	1	0.36274	1	NA	NA	NA	NA	0.78103	1	0.36079	1	0.38666	1	0.12665	1
10p gain	0 (0%)	405	0.0035467	1	0.063958	1	0.00069957	0.318	0.20411	1	0.28359	1	0.13573	1	0.015488	1	0.25464	1	0.06389	1	0.017848	1
10q gain	0 (0%)	413	0.0015046	0.657	0.030274	1	9.3428e-05	0.0468	0.17582	1	0.38785	1	0.25211	1	0.026202	1	0.25647	1	0.012807	1	0.0025667	1
11p gain	0 (0%)	484	0.17647	1	0.054256	1	0.0099016	1	0.037261	1	0.10904	1	1	1	0.15748	1	0.44673	1	0.13017	1	0.23835	1
11q gain	0 (0%)	484	NA	NA	NA	NA	0.011078	1	0.46209	1	0.10904	1	0.29906	1	0.19408	1	0.39556	1	0.24246	1	0.36077	1
12p gain	0 (0%)	455	0.81541	1	0.82481	1	4.7807e-08	2.82e-05	0.0090941	1	0.9373	1	1	1	0.04547	1	0.090624	1	0.024128	1	0.016871	1
12q gain	0 (0%)	464	0.81541	1	0.82481	1	3.6845e-07	0.00021	0.12086	1	0.90119	1	1	1	0.081103	1	0.22715	1	0.12562	1	0.31102	1
13q gain	0 (0%)	472	NA	NA	NA	NA	9.5474e-08	5.56e-05	0.0055648	1	0.73455	1	0.36663	1	7.1356e-05	0.036	0.00046225	0.216	3.4545e-05	0.0178	4.2316e-05	0.0217
14q gain	0 (0%)	472	1	1	1	1	2.159e-05	0.0114	0.22681	1	0.2387	1	0.29227	1	0.40121	1	0.073693	1	0.048591	1	0.028108	1
15q gain	0 (0%)	486	NA	NA	NA	NA	0.0041566	1	0.84602	1	NA	NA	1	1	0.828	1	0.69879	1	0.88416	1	1	1
16p gain	0 (0%)	480	NA	NA	NA	NA	0.00079405	0.357	0.031322	1	0.24267	1	1	1	0.06786	1	0.07871	1	0.08308	1	0.33608	1
16q gain	0 (0%)	488	NA	NA	NA	NA	0.046028	1	1	1	NA	NA	1	1	NA	NA	NA	NA	1	1	0.86072	1
17p gain	0 (0%)	485	NA	NA	NA	NA	2.602e-05	0.0136	0.24392	1	NA	NA	1	1	0.31635	1	0.31542	1	0.070074	1	0.14496	1
17q gain	0 (0%)	479	NA	NA	NA	NA	0.00072729	0.329	0.0035743	1	0.053132	1	1	1	0.027619	1	0.28381	1	0.0088727	1	0.011039	1
18p gain	0 (0%)	455	0.059073	1	0.1325	1	4.9415e-14	3.26e-11	6.6366e-05	0.0336	0.092984	1	0.42867	1	3.3389e-05	0.0173	7.2822e-07	0.000411	4.2564e-09	2.58e-06	6.4699e-09	3.9e-06
18q gain	0 (0%)	472	0.17647	1	0.054256	1	8.2613e-06	0.00445	0.0056176	1	NA	NA	1	1	0.017254	1	0.0056462	1	0.00011073	0.0553	0.0004364	0.205
19p gain	0 (0%)	461	0.059073	1	0.015111	1	2.4038e-13	1.57e-10	0.0042875	1	0.52818	1	0.15057	1	4.7344e-06	0.00257	1.8393e-05	0.00979	9.1802e-07	0.000515	3.2364e-05	0.0168
19q gain	0 (0%)	464	NA	NA	NA	NA	4.2813e-13	2.8e-10	0.0014709	0.644	0.084981	1	1	1	4.7344e-06	0.00257	1.5912e-06	0.000886	8.1173e-07	0.000456	2.169e-05	0.0114
20p gain	0 (0%)	427	0.17647	1	0.054256	1	2.2767e-18	1.54e-15	3.4709e-05	0.0179	0.29078	1	1	1	9.0371e-05	0.0454	0.011949	1	1.8405e-08	1.1e-05	4.4015e-07	0.00025
20q gain	0 (0%)	414	0.059073	1	0.015111	1	3.6242e-24	2.49e-21	8.601e-08	5.03e-05	0.19154	1	0.58017	1	1.7451e-06	0.000967	0.00062065	0.285	1.6343e-11	1.05e-08	3.6456e-10	2.27e-07
21q gain	0 (0%)	467	NA	NA	NA	NA	1.1349e-08	6.82e-06	0.079381	1	0.2367	1	0.55767	1	0.00020408	0.0992	0.0094958	1	0.00041371	0.195	0.00037514	0.178
22q gain	0 (0%)	483	NA	NA	NA	NA	0.0047256	1	0.00053691	0.249	NA	NA	0.37629	1	0.11476	1	0.36079	1	0.0013204	0.581	0.0025879	1
Xq gain	0 (0%)	480	NA	NA	NA	NA	0.00025705	0.123	0.32236	1	NA	NA	0.37629	1	0.15748	1	0.44673	1	0.0087137	1	0.088767	1
1p loss	0 (0%)	479	NA	NA	NA	NA	1.8216e-08	1.09e-05	0.00095455	0.427	NA	NA	1	1	0.040252	1	0.088379	1	0.051655	1	0.0031776	1
1q loss	0 (0%)	488	NA	NA	NA	NA	0.03655	1	0.057423	1	NA	NA	NA	NA	0.11476	1	0.36079	1	0.099056	1	0.12665	1
2p loss	0 (0%)	486	NA	NA	NA	NA	0.019044	1	0.51798	1	NA	NA	0.14038	1	0.15748	1	0.087811	1	0.77312	1	0.19887	1
2q loss	0 (0%)	484	NA	NA	NA	NA	0.0063665	1	0.19926	1	NA	NA	0.14038	1	0.15748	1	0.087811	1	0.49273	1	0.19166	1
3p loss	0 (0%)	461	NA	NA	NA	NA	1.3351e-14	8.84e-12	0.00014128	0.0699	0.00052575	0.244	0.027968	1	1.7855e-07	0.000103	8.6312e-08	5.04e-05	4.2079e-05	0.0216	2.3725e-05	0.0124
3q loss	0 (0%)	480	NA	NA	NA	NA	4.3108e-05	0.022	0.05836	1	0.024047	1	0.55767	1	0.0047873	1	0.0027388	1	0.034692	1	0.073932	1
4p loss	0 (0%)	426	0.07289	1	0.013284	1	4.7865e-25	3.3e-22	7.079e-11	4.47e-08	0.033892	1	0.39315	1	2.45e-09	1.49e-06	1.2904e-07	7.48e-05	1.8764e-13	1.23e-10	4.4442e-12	2.88e-09
4q loss	0 (0%)	428	0.68266	1	0.37121	1	1.3603e-26	9.39e-24	2.656e-11	1.69e-08	0.13113	1	0.77642	1	2.643e-08	1.57e-05	2.4453e-08	1.45e-05	1.0419e-10	6.55e-08	1.3905e-10	8.69e-08
5p loss	0 (0%)	465	0.35228	1	0.1325	1	1.1633e-10	7.29e-08	0.00033435	0.159	0.16154	1	0.18109	1	0.0007823	0.353	0.00067185	0.307	0.00021616	0.105	0.0028051	1
5q loss	0 (0%)	447	0.07289	1	0.013284	1	1.1786e-18	7.99e-16	7.2617e-09	4.37e-06	0.04811	1	0.15296	1	6.2834e-08	3.69e-05	2.9609e-08	1.76e-05	2.8298e-09	1.72e-06	7.5812e-08	4.44e-05
6p loss	0 (0%)	482	0.68266	1	0.37121	1	0.00086192	0.386	0.096217	1	0.85846	1	0.55767	1	0.19389	1	0.24853	1	0.17221	1	0.01708	1
6q loss	0 (0%)	480	0.68266	1	0.37121	1	0.00023581	0.114	0.035408	1	0.85846	1	0.55767	1	0.015969	1	0.03837	1	0.13325	1	0.010299	1
7p loss	0 (0%)	463	0.17647	1	0.054256	1	9.8778e-10	6.09e-07	0.006562	1	0.15846	1	0.20053	1	0.00016195	0.0798	2.2672e-05	0.0119	0.00078279	0.353	0.003384	1
7q loss	0 (0%)	465	NA	NA	NA	NA	4.9115e-14	3.24e-11	0.00018012	0.0884	0.19732	1	0.012085	1	1.3201e-07	7.64e-05	1.5912e-06	0.000886	1.7667e-05	0.00942	1.2509e-05	0.0067
8p loss	0 (0%)	439	0.019107	1	0.0040321	1	4.0085e-24	2.75e-21	1.0774e-11	6.92e-09	0.165	1	0.18109	1	4.8415e-12	3.13e-09	6.9006e-10	4.28e-07	4.0129e-15	2.67e-12	7.1738e-17	4.82e-14
8q loss	0 (0%)	480	NA	NA	NA	NA	2.228e-05	0.0117	0.00095455	0.427	NA	NA	1	1	0.039552	1	0.15399	1	0.00030152	0.144	0.00044305	0.207
9p loss	0 (0%)	416	0.022668	1	0.0037915	1	2.631e-29	1.82e-26	2.341e-06	0.00129	0.011722	1	0.24436	1	2.1227e-12	1.38e-09	7.6036e-15	5.04e-12	1.3706e-09	8.42e-07	1.189e-08	7.13e-06
9q loss	0 (0%)	399	0.0015041	0.657	0.0002482	0.119	1.5312e-37	1.07e-34	5.863e-07	0.000332	0.0060055	1	0.37819	1	2.5645e-13	1.68e-10	2.816e-16	1.88e-13	2.0918e-12	1.36e-09	3.8291e-10	2.38e-07
10p loss	0 (0%)	469	0.17647	1	0.054256	1	3.9966e-11	2.54e-08	0.00033435	0.159	0.47447	1	0.63255	1	0.0004688	0.218	0.0015999	0.696	1.2481e-05	0.0067	0.0010795	0.477
10q loss	0 (0%)	468	NA	NA	NA	NA	2.9446e-10	1.83e-07	0.0001924	0.0939	0.45123	1	1	1	0.0004688	0.218	0.0056992	1	0.00021424	0.104	0.0019512	0.841
11p loss	0 (0%)	439	NA	NA	NA	NA	1.4445e-21	9.89e-19	7.4418e-07	0.000419	0.18182	1	0.75005	1	4.4598e-08	2.63e-05	2.5957e-07	0.000149	1.9861e-08	1.18e-05	1.9857e-06	0.0011
11q loss	0 (0%)	447	NA	NA	NA	NA	1.1505e-15	7.67e-13	7.5322e-05	0.0379	0.92479	1	0.71272	1	0.00039705	0.187	8.0744e-06	0.00436	2.5435e-06	0.0014	0.00018374	0.09
12p loss	0 (0%)	467	NA	NA	NA	NA	3.8618e-11	2.46e-08	0.0001924	0.0939	0.057656	1	1	1	3.6189e-05	0.0186	0.0056992	1	9.52e-08	5.55e-05	4.3437e-06	0.00236
12q loss	0 (0%)	474	NA	NA	NA	NA	1.23e-09	7.56e-07	0.00010017	0.0501	0.30993	1	0.42867	1	0.0010551	0.467	0.006701	1	1.2507e-06	0.000698	1.6661e-06	0.000925
13q loss	0 (0%)	432	0.68266	1	0.37121	1	2.4269e-18	1.64e-15	0.00011254	0.056	0.16118	1	0.39315	1	0.00039515	0.187	3.8892e-06	0.00212	7.271e-05	0.0366	0.00018788	0.0919
14q loss	0 (0%)	450	0.019107	1	0.0040321	1	8.9369e-17	6e-14	1.4782e-09	9.03e-07	0.084745	1	0.0051992	1	3.3753e-08	2e-05	1.9461e-07	0.000112	3.3396e-09	2.02e-06	9.8161e-12	6.33e-09
15q loss	0 (0%)	411	0.0067724	1	0.0010266	0.456	4.6791e-35	3.25e-32	1.6072e-13	1.06e-10	0.00259	1	0.26661	1	7.9229e-10	4.9e-07	1.0686e-10	6.71e-08	5.2164e-15	3.46e-12	1.0728e-16	7.19e-14
16p loss	0 (0%)	423	0.019107	1	0.0040321	1	2.8194e-31	1.95e-28	2.7681e-09	1.69e-06	0.19252	1	0.79627	1	7.5166e-10	4.65e-07	1.4726e-09	9.03e-07	1.4723e-09	9.03e-07	1.359e-10	8.51e-08
16q loss	0 (0%)	382	0.0068587	1	0.0017313	0.751	5.935e-40	4.14e-37	2.8603e-11	1.82e-08	0.23685	1	1	1	1.006e-11	6.48e-09	2.3407e-10	1.46e-07	1.068e-11	6.87e-09	1.9012e-11	1.22e-08
17p loss	0 (0%)	387	0.0068587	1	0.0017313	0.751	8.6624e-53	6.05e-50	8.1447e-13	5.31e-10	0.00057115	0.263	0.66522	1	1.6027e-20	1.09e-17	2.1472e-21	1.47e-18	4.8685e-17	3.28e-14	2.9242e-15	1.95e-12
17q loss	0 (0%)	424	0.019107	1	0.0040321	1	1.4783e-29	1.02e-26	3.4055e-05	0.0176	0.092362	1	0.61178	1	4.279e-09	2.58e-06	1.9474e-11	1.24e-08	2.7135e-07	0.000156	5.5038e-07	0.000313
18p loss	0 (0%)	456	NA	NA	NA	NA	3.1519e-12	2.05e-09	2.091e-05	0.0111	0.32575	1	0.74551	1	0.00065956	0.302	0.00017153	0.0844	0.0047178	1	0.00059413	0.273
18q loss	0 (0%)	443	NA	NA	NA	NA	9.7475e-18	6.57e-15	1.978e-06	0.00109	0.72497	1	1	1	3.8676e-06	0.00212	5.6503e-07	0.00032	3.0351e-06	0.00167	2.5908e-07	0.000149
19p loss	0 (0%)	458	NA	NA	NA	NA	4.6331e-12	3e-09	1.066e-07	6.19e-05	0.33053	1	1	1	1.8398e-05	0.00979	7.8364e-06	0.00424	1.0147e-05	0.00546	6.4116e-07	0.000362
19q loss	0 (0%)	464	NA	NA	NA	NA	1.787e-08	1.07e-05	4.6494e-05	0.0237	0.73417	1	0.71272	1	0.00071886	0.326	0.002828	1	0.00067643	0.308	1.4632e-05	0.00783
20p loss	0 (0%)	477	NA	NA	NA	NA	0.00012225	0.0608	0.10685	1	0.24267	1	0.63255	1	0.03678	1	0.046533	1	0.0063452	1	0.070239	1
20q loss	0 (0%)	485	NA	NA	NA	NA	0.010576	1	0.054039	1	NA	NA	0.52818	1	0.39137	1	0.47424	1	0.16373	1	0.078002	1
21q loss	0 (0%)	460	0.059073	1	0.015111	1	6.4739e-08	3.8e-05	0.0025241	1	0.09504	1	0.75005	1	0.00014817	0.0732	0.0013625	0.598	0.00096974	0.432	4.4287e-05	0.0226
22q loss	0 (0%)	405	0.019107	1	0.0040321	1	1.4075e-36	9.78e-34	4.2349e-08	2.5e-05	0.072103	1	1	1	4.876e-11	3.09e-08	3.2854e-14	2.17e-11	9.6434e-11	6.08e-08	1.0131e-09	6.24e-07
Xq loss	0 (0%)	474	NA	NA	NA	NA	2.9675e-07	0.00017	0.00056938	0.263	0.61718	1	0.63255	1	0.015969	1	0.006701	1	0.00023331	0.113	2.2718e-05	0.0119
