Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_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	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	0.46675	1	0.49146	1	0.035042	1	0.66081	1	0.40106	1	1	1	0.18151	1	0.28962	1	0.0074301	1	0.075767	1	0.16649	1	0.1428	1
1q gain	0 (0%)	354	0.24994	1	0.29034	1	3.0433e-07	0.000222	0.0064607	1	0.0012254	0.687	0.00071538	0.415	3.3148e-06	0.00232	9.2345e-07	0.000661	3.7404e-07	0.000272	0.017759	1	0.27776	1	0.010236	1
2p gain	0 (0%)	441	0.42527	1	0.48132	1	5.4103e-11	4.27e-08	0.05499	1	0.17655	1	0.8017	1	0.23768	1	0.43383	1	0.018437	1	0.16208	1	0.14075	1	0.023584	1
2q gain	0 (0%)	452	0.34265	1	1	1	4.8278e-11	3.82e-08	0.16876	1	0.065268	1	0.5746	1	0.30009	1	0.62396	1	0.015034	1	0.11652	1	0.081879	1	0.031331	1
3p gain	0 (0%)	464	NA	NA	NA	NA	4.1488e-19	3.48e-16	0.11121	1	0.52525	1	0.65189	1	0.014933	1	0.042907	1	0.3378	1	0.22479	1	0.40447	1	0.41627	1
3q gain	0 (0%)	442	0.1372	1	0.27248	1	3.4119e-22	2.88e-19	2.3748e-05	0.0159	0.38821	1	0.30068	1	1.1907e-06	0.000849	5.1415e-05	0.0334	2.0651e-05	0.014	0.00026258	0.16	0.034239	1	0.018707	1
4p gain	0 (0%)	486	NA	NA	NA	NA	0.0038953	1	0.12338	1	NA	NA	0.14038	1	0.039552	1	0.15399	1	0.022869	1	0.028095	1	0.42457	1	0.44243	1
5p gain	0 (0%)	460	0.53641	1	0.27248	1	3.0144e-09	2.31e-06	0.00013768	0.0869	0.031072	1	0.71241	1	3.9528e-06	0.00276	0.00041955	0.252	1.6554e-05	0.0113	5.2861e-05	0.0343	0.0010957	0.616	7.2648e-05	0.0468
5q gain	0 (0%)	483	NA	NA	NA	NA	0.002863	1	0.42328	1	NA	NA	1	1	0.06786	1	0.28634	1	0.051953	1	0.20331	1	0.15129	1	0.071878	1
6p gain	0 (0%)	454	0.2533	1	0.09018	1	1.5228e-16	1.26e-13	0.031281	1	0.66066	1	1	1	0.0066461	1	0.0074982	1	0.01207	1	0.030239	1	0.20158	1	0.42461	1
6q gain	0 (0%)	462	0.2533	1	0.09018	1	1.5822e-13	1.29e-10	0.31801	1	0.40106	1	1	1	0.0083914	1	0.0079272	1	0.16776	1	0.27806	1	0.59945	1	0.70797	1
7p gain	0 (0%)	449	0.93531	1	0.86626	1	8.6204e-19	7.22e-16	0.012468	1	0.73304	1	0.21665	1	1	1	0.47476	1	0.24414	1	0.60937	1	0.79881	1	0.48112	1
7q gain	0 (0%)	449	0.85548	1	1	1	2.3979e-19	2.01e-16	0.025234	1	0.88873	1	0.055165	1	0.38457	1	0.033117	1	0.44003	1	0.42504	1	0.9089	1	0.76564	1
8p gain	0 (0%)	406	0.70442	1	0.6094	1	7.4822e-18	6.23e-15	0.94083	1	0.13349	1	1	1	0.47386	1	0.43448	1	0.37993	1	0.0022026	1	0.41567	1	0.0057505	1
8q gain	0 (0%)	374	0.033593	1	0.033888	1	1.6503e-21	1.39e-18	0.34509	1	0.0049518	1	1	1	0.0059062	1	0.00029937	0.182	0.0018009	0.996	3.2674e-05	0.0216	0.083364	1	0.0015118	0.841
9p gain	0 (0%)	478	NA	NA	NA	NA	0.048355	1	0.08413	1	NA	NA	1	1	0.82159	1	0.07871	1	0.06993	1	0.029363	1	0.12414	1	0.068364	1
9q gain	0 (0%)	488	NA	NA	NA	NA	0.35164	1	0.36111	1	NA	NA	NA	NA	0.78103	1	0.36079	1	0.38666	1	0.12665	1	0.42457	1	0.072812	1
10p gain	0 (0%)	405	0.0071379	1	0.047563	1	0.00069957	0.406	0.17063	1	0.28359	1	0.13573	1	0.015488	1	0.25464	1	0.06389	1	0.017848	1	0.053533	1	0.027044	1
10q gain	0 (0%)	413	0.0021162	1	0.026184	1	9.3428e-05	0.0597	0.1449	1	0.38785	1	0.25211	1	0.026202	1	0.25647	1	0.012807	1	0.0025667	1	0.044642	1	0.021687	1
11p gain	0 (0%)	484	0.1372	1	0.27248	1	0.0099016	1	0.036032	1	0.10904	1	1	1	0.15748	1	0.44673	1	0.13017	1	0.23835	1	0.82095	1	0.78427	1
11q gain	0 (0%)	484	NA	NA	NA	NA	0.011078	1	0.37429	1	0.10904	1	0.29906	1	0.19408	1	0.39556	1	0.24246	1	0.36077	1	1	1	1	1
12p gain	0 (0%)	455	0.64029	1	1	1	4.7807e-08	3.57e-05	0.0079353	1	0.9373	1	1	1	0.04547	1	0.090624	1	0.024128	1	0.016871	1	0.12714	1	0.11644	1
12q gain	0 (0%)	464	0.64029	1	1	1	3.6845e-07	0.000268	0.10586	1	0.90119	1	1	1	0.081103	1	0.22715	1	0.12562	1	0.31102	1	0.4118	1	0.30423	1
13q gain	0 (0%)	472	NA	NA	NA	NA	9.5474e-08	7.05e-05	0.0046501	1	0.73455	1	0.36663	1	7.1356e-05	0.0461	0.00046225	0.275	3.4545e-05	0.0228	4.2316e-05	0.0277	0.16924	1	0.11362	1
14q gain	0 (0%)	472	1	1	0.76885	1	2.159e-05	0.0146	0.21394	1	0.2387	1	0.29227	1	0.40121	1	0.073693	1	0.048591	1	0.028108	1	0.30286	1	0.41823	1
15q gain	0 (0%)	486	NA	NA	NA	NA	0.0041566	1	0.84577	1	NA	NA	1	1	0.828	1	0.69879	1	0.88416	1	1	1	0.3603	1	0.20845	1
16p gain	0 (0%)	480	NA	NA	NA	NA	0.00079405	0.456	0.030925	1	0.24267	1	1	1	0.06786	1	0.07871	1	0.08308	1	0.33608	1	0.58596	1	0.32942	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	0.78466	1	1	1
17p gain	0 (0%)	485	NA	NA	NA	NA	2.602e-05	0.0173	0.2415	1	NA	NA	1	1	0.31635	1	0.31542	1	0.070074	1	0.14496	1	0.855	1	0.82377	1
17q gain	0 (0%)	479	NA	NA	NA	NA	0.00072729	0.42	0.0034496	1	0.053132	1	1	1	0.027619	1	0.28381	1	0.0088727	1	0.011039	1	0.13984	1	0.085353	1
18p gain	0 (0%)	455	0.37937	1	0.09018	1	4.9415e-14	4.04e-11	6.0736e-05	0.0393	0.092984	1	0.42867	1	3.3389e-05	0.0221	7.2822e-07	0.000524	4.2564e-09	3.25e-06	6.4699e-09	4.92e-06	7.1761e-05	0.0463	0.00028469	0.174
18q gain	0 (0%)	472	0.1372	1	0.019423	1	8.2613e-06	0.00568	0.0050084	1	NA	NA	1	1	0.017254	1	0.0056462	1	0.00011073	0.0703	0.0004364	0.261	0.0013689	0.764	0.028029	1
19p gain	0 (0%)	461	0.039088	1	0.0046615	1	2.4038e-13	1.96e-10	0.0034528	1	0.52818	1	0.15057	1	4.7344e-06	0.00329	1.8393e-05	0.0125	9.1802e-07	0.000658	3.2364e-05	0.0215	0.10355	1	0.11644	1
19q gain	0 (0%)	464	NA	NA	NA	NA	4.2813e-13	3.47e-10	0.0014252	0.794	0.084981	1	1	1	4.7344e-06	0.00329	1.5912e-06	0.00113	8.1173e-07	0.000584	2.169e-05	0.0146	0.031318	1	0.065907	1
20p gain	0 (0%)	427	0.1372	1	0.019423	1	2.2767e-18	1.9e-15	3.2549e-05	0.0216	0.29078	1	1	1	9.0371e-05	0.0578	0.011949	1	1.8405e-08	1.39e-05	4.4015e-07	0.000319	0.0042526	1	0.00062748	0.367
20q gain	0 (0%)	414	0.039088	1	0.0046615	1	3.6242e-24	3.07e-21	8.0727e-08	5.99e-05	0.19154	1	0.58017	1	1.7451e-06	0.00124	0.00062065	0.364	1.6343e-11	1.31e-08	3.6456e-10	2.84e-07	0.00017804	0.111	3.4541e-05	0.0228
21q gain	0 (0%)	467	NA	NA	NA	NA	1.1349e-08	8.61e-06	0.075591	1	0.2367	1	0.55767	1	0.00020408	0.126	0.0094958	1	0.00041371	0.249	0.00037514	0.227	0.3138	1	0.11941	1
22q gain	0 (0%)	483	NA	NA	NA	NA	0.0047256	1	0.00052428	0.31	NA	NA	0.37629	1	0.11476	1	0.36079	1	0.0013204	0.739	0.0025879	1	0.053638	1	0.039078	1
Xq gain	0 (0%)	480	NA	NA	NA	NA	0.00025705	0.157	0.32091	1	NA	NA	0.37629	1	0.15748	1	0.44673	1	0.0087137	1	0.088767	1	0.08798	1	0.60017	1
1p loss	0 (0%)	479	NA	NA	NA	NA	1.8216e-08	1.38e-05	0.00091704	0.525	NA	NA	1	1	0.040252	1	0.088379	1	0.051655	1	0.0031776	1	0.17042	1	0.052189	1
1q loss	0 (0%)	488	NA	NA	NA	NA	0.03655	1	0.056194	1	NA	NA	NA	NA	0.11476	1	0.36079	1	0.099056	1	0.12665	1	0.42457	1	0.44243	1
2p loss	0 (0%)	486	NA	NA	NA	NA	0.019044	1	0.51674	1	NA	NA	0.14038	1	0.15748	1	0.087811	1	0.77312	1	0.19887	1	0.855	1	0.16073	1
2q loss	0 (0%)	484	NA	NA	NA	NA	0.0063665	1	0.19688	1	NA	NA	0.14038	1	0.15748	1	0.087811	1	0.49273	1	0.19166	1	0.68529	1	0.27699	1
3p loss	0 (0%)	461	NA	NA	NA	NA	1.3351e-14	1.09e-11	0.00012875	0.0814	0.00052575	0.311	0.027968	1	1.7855e-07	0.000131	8.6312e-08	6.4e-05	4.2079e-05	0.0276	2.3725e-05	0.0159	0.011358	1	0.0068495	1
3q loss	0 (0%)	480	NA	NA	NA	NA	4.3108e-05	0.0281	0.057357	1	0.024047	1	0.55767	1	0.0047873	1	0.0027388	1	0.034692	1	0.073932	1	0.077205	1	0.32942	1
4p loss	0 (0%)	426	0.051454	1	0.0075524	1	4.7865e-25	4.05e-22	6.032e-11	4.76e-08	0.033892	1	0.39315	1	2.45e-09	1.88e-06	1.2904e-07	9.51e-05	1.8764e-13	1.53e-10	4.4442e-12	3.58e-09	8.448e-05	0.0542	1.7807e-06	0.00126
4q loss	0 (0%)	428	0.6894	1	0.27248	1	1.3603e-26	1.15e-23	2.1509e-11	1.71e-08	0.13113	1	0.77642	1	2.643e-08	1.99e-05	2.4453e-08	1.84e-05	1.0419e-10	8.2e-08	1.3905e-10	1.09e-07	0.00018399	0.114	4.6761e-06	0.00325
5p loss	0 (0%)	465	0.37937	1	0.09018	1	1.1633e-10	9.13e-08	0.0003233	0.196	0.16154	1	0.18109	1	0.0007823	0.451	0.00067185	0.392	0.00021616	0.133	0.0028051	1	0.14942	1	0.061098	1
5q loss	0 (0%)	447	0.051454	1	0.0075524	1	1.1786e-18	9.85e-16	7.9237e-09	6.02e-06	0.04811	1	0.15296	1	6.2834e-08	4.68e-05	2.9609e-08	2.22e-05	2.8298e-09	2.17e-06	7.5812e-08	5.63e-05	0.0022027	1	0.00010749	0.0684
6p loss	0 (0%)	482	0.6894	1	0.27248	1	0.00086192	0.494	0.094454	1	0.85846	1	0.55767	1	0.19389	1	0.24853	1	0.17221	1	0.01708	1	0.27858	1	0.54755	1
6q loss	0 (0%)	480	0.6894	1	0.27248	1	0.00023581	0.145	0.034901	1	0.85846	1	0.55767	1	0.015969	1	0.03837	1	0.13325	1	0.010299	1	0.13553	1	0.2186	1
7p loss	0 (0%)	463	0.1372	1	0.019423	1	9.8778e-10	7.66e-07	0.0065237	1	0.15846	1	0.20053	1	0.00016195	0.102	2.2672e-05	0.0152	0.00078279	0.451	0.003384	1	0.18529	1	0.14149	1
7q loss	0 (0%)	465	NA	NA	NA	NA	4.9115e-14	4.02e-11	0.00017078	0.107	0.19732	1	0.012085	1	1.3201e-07	9.72e-05	1.5912e-06	0.00113	1.7667e-05	0.012	1.2509e-05	0.00857	0.024166	1	0.0075412	1
8p loss	0 (0%)	439	0.0080894	1	0.0010465	0.595	4.0085e-24	3.39e-21	3.6984e-11	2.94e-08	0.165	1	0.18109	1	4.8415e-12	3.89e-09	6.9006e-10	5.37e-07	4.0129e-15	3.3e-12	7.1738e-17	5.95e-14	9.3849e-07	0.000671	1.4642e-07	0.000108
8q loss	0 (0%)	480	NA	NA	NA	NA	2.228e-05	0.015	0.00091704	0.525	NA	NA	1	1	0.039552	1	0.15399	1	0.00030152	0.183	0.00044305	0.265	0.0029533	1	0.012796	1
9p loss	0 (0%)	416	0.012904	1	0.0019294	1	2.631e-29	2.23e-26	1.809e-06	0.00128	0.011722	1	0.24436	1	2.1227e-12	1.72e-09	7.6036e-15	6.24e-12	1.3706e-09	1.06e-06	1.189e-08	9.01e-06	0.026618	1	0.0091404	1
9q loss	0 (0%)	399	0.0005666	0.334	4.1747e-05	0.0274	1.5312e-37	1.31e-34	4.8425e-07	0.000351	0.0060055	1	0.37819	1	2.5645e-13	2.08e-10	2.816e-16	2.33e-13	2.0918e-12	1.69e-09	3.8291e-10	2.98e-07	0.0058645	1	0.0045399	1
10p loss	0 (0%)	469	0.1372	1	0.019423	1	3.9966e-11	3.17e-08	0.0003233	0.196	0.47447	1	0.63255	1	0.0004688	0.278	0.0015999	0.886	1.2481e-05	0.00856	0.0010795	0.608	0.077716	1	0.028382	1
10q loss	0 (0%)	468	NA	NA	NA	NA	2.9446e-10	2.3e-07	0.00016088	0.101	0.45123	1	1	1	0.0004688	0.278	0.0056992	1	0.00021424	0.132	0.0019512	1	0.12327	1	0.11206	1
11p loss	0 (0%)	439	NA	NA	NA	NA	1.4445e-21	1.22e-18	8.9041e-07	0.000639	0.18182	1	0.75005	1	4.4598e-08	3.33e-05	2.5957e-07	0.00019	1.9861e-08	1.5e-05	1.9857e-06	0.0014	0.0053705	1	0.0029584	1
11q loss	0 (0%)	447	NA	NA	NA	NA	1.1505e-15	9.49e-13	7.9034e-05	0.0507	0.92479	1	0.71272	1	0.00039705	0.239	8.0744e-06	0.00557	2.5435e-06	0.00179	0.00018374	0.114	0.018421	1	0.024194	1
12p loss	0 (0%)	467	NA	NA	NA	NA	3.8618e-11	3.07e-08	0.00016088	0.101	0.057656	1	1	1	3.6189e-05	0.0238	0.0056992	1	9.52e-08	7.04e-05	4.3437e-06	0.00303	0.0071629	1	0.00037368	0.226
12q loss	0 (0%)	474	NA	NA	NA	NA	1.23e-09	9.5e-07	9.438e-05	0.0602	0.30993	1	0.42867	1	0.0010551	0.595	0.006701	1	1.2507e-06	0.000891	1.6661e-06	0.00118	0.0062754	1	0.00078828	0.453
13q loss	0 (0%)	432	0.6894	1	0.27248	1	2.4269e-18	2.02e-15	0.00010658	0.0679	0.16118	1	0.39315	1	0.00039515	0.238	3.8892e-06	0.00272	7.271e-05	0.0468	0.00018788	0.117	0.2168	1	0.053866	1
14q loss	0 (0%)	450	0.0080894	1	0.0010465	0.595	8.9369e-17	7.41e-14	1.0632e-09	8.22e-07	0.084745	1	0.0051992	1	3.3753e-08	2.52e-05	1.9461e-07	0.000143	3.3396e-09	2.55e-06	9.8161e-12	7.88e-09	2.0294e-05	0.0137	4.8915e-05	0.0318
15q loss	0 (0%)	411	0.0020193	1	0.00021801	0.134	4.6791e-35	3.99e-32	2.9729e-13	2.41e-10	0.00259	1	0.26661	1	7.9229e-10	6.15e-07	1.0686e-10	8.4e-08	5.2164e-15	4.29e-12	1.0728e-16	8.88e-14	1.0464e-06	0.000747	3.035e-08	2.28e-05
16p loss	0 (0%)	423	0.0080894	1	0.0010465	0.595	2.8194e-31	2.4e-28	2.2701e-09	1.74e-06	0.19252	1	0.79627	1	7.5166e-10	5.84e-07	1.4726e-09	1.13e-06	1.4723e-09	1.13e-06	1.359e-10	1.07e-07	2.5554e-05	0.017	1.8195e-05	0.0124
16q loss	0 (0%)	382	0.0032363	1	0.0004537	0.271	5.935e-40	5.07e-37	2.1024e-11	1.68e-08	0.23685	1	1	1	1.006e-11	8.07e-09	2.3407e-10	1.83e-07	1.068e-11	8.55e-09	1.9012e-11	1.52e-08	5.3146e-06	0.00368	6.8959e-06	0.00477
17p loss	0 (0%)	387	0.0032363	1	0.0004537	0.271	8.6624e-53	7.41e-50	7.4287e-13	6.02e-10	0.00057115	0.336	0.66522	1	1.6027e-20	1.35e-17	2.1472e-21	1.81e-18	4.8685e-17	4.05e-14	2.9242e-15	2.41e-12	2.5068e-05	0.0167	2.0934e-05	0.0141
17q loss	0 (0%)	424	0.0080894	1	0.0010465	0.595	1.4783e-29	1.26e-26	3.366e-05	0.0222	0.092362	1	0.61178	1	4.279e-09	3.26e-06	1.9474e-11	1.55e-08	2.7135e-07	0.000198	5.5038e-07	0.000398	0.0043974	1	0.0018746	1
18p loss	0 (0%)	456	NA	NA	NA	NA	3.1519e-12	2.54e-09	1.8827e-05	0.0128	0.32575	1	0.74551	1	0.00065956	0.385	0.00017153	0.107	0.0047178	1	0.00059413	0.349	0.053315	1	0.021361	1
18q loss	0 (0%)	443	NA	NA	NA	NA	9.7475e-18	8.11e-15	1.9165e-06	0.00135	0.72497	1	1	1	3.8676e-06	0.00271	5.6503e-07	0.000408	3.0351e-06	0.00213	2.5908e-07	0.00019	0.01389	1	0.0031695	1
19p loss	0 (0%)	458	NA	NA	NA	NA	4.6331e-12	3.73e-09	9.1921e-08	6.8e-05	0.33053	1	1	1	1.8398e-05	0.0125	7.8364e-06	0.00541	1.0147e-05	0.00697	6.4116e-07	0.000462	8.1788e-06	0.00564	0.0020453	1
19q loss	0 (0%)	464	NA	NA	NA	NA	1.787e-08	1.35e-05	5.026e-05	0.0327	0.73417	1	0.71272	1	0.00071886	0.416	0.002828	1	0.00067643	0.394	1.4632e-05	0.01	0.00012447	0.0788	0.012218	1
20p loss	0 (0%)	477	NA	NA	NA	NA	0.00012225	0.0775	0.10599	1	0.24267	1	0.63255	1	0.03678	1	0.046533	1	0.0063452	1	0.070239	1	0.2406	1	0.14788	1
20q loss	0 (0%)	485	NA	NA	NA	NA	0.010576	1	0.052576	1	NA	NA	0.52818	1	0.39137	1	0.47424	1	0.16373	1	0.078002	1	0.12733	1	0.17147	1
21q loss	0 (0%)	460	0.039088	1	0.0046615	1	6.4739e-08	4.82e-05	0.0025898	1	0.09504	1	0.75005	1	0.00014817	0.0933	0.0013625	0.762	0.00096974	0.553	4.4287e-05	0.0289	0.00022013	0.135	0.00020258	0.126
22q loss	0 (0%)	405	0.0080894	1	0.0010465	0.595	1.4075e-36	1.2e-33	3.2331e-08	2.42e-05	0.072103	1	1	1	4.876e-11	3.86e-08	3.2854e-14	2.69e-11	9.6434e-11	7.6e-08	1.0131e-09	7.84e-07	0.0096991	1	0.001579	0.876
Xq loss	0 (0%)	474	NA	NA	NA	NA	2.9675e-07	0.000216	0.00054468	0.321	0.61718	1	0.63255	1	0.015969	1	0.006701	1	0.00023331	0.143	2.2718e-05	0.0152	0.0042543	1	0.002865	1