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	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	Chi-square test_P	Chi-square test_Q
1p gain	0 (0%)	402	NA	NA	NA	NA	0.57626	1	0.83671	1	0.2752	1	0.38396	1	0.42521	1	0.68335	1	0.46021	1	1	1	0.4475	1	0.084715	1
1q gain	0 (0%)	366	0.040536	1	0.53602	1	0.078786	1	0.34651	1	0.3804	1	0.048087	1	0.11959	1	0.29923	1	0.4366	1	0.83658	1	0.5202	1	0.47341	1
2p gain	0 (0%)	373	0.124	1	0.074608	1	0.0040928	1	0.027822	1	0.049217	1	0.39257	1	0.00038556	0.299	0.019921	1	0.50846	1	0.35508	1	0.23571	1	0.01367	1
2q gain	0 (0%)	374	0.073705	1	0.050976	1	0.00017278	0.135	0.0029153	1	0.031071	1	0.39257	1	0.0010917	0.83	0.038358	1	0.52888	1	0.40458	1	0.14393	1	0.019848	1
3p gain	0 (0%)	393	0.29804	1	0.42991	1	0.071044	1	0.38696	1	0.6228	1	0.72105	1	0.97363	1	0.67551	1	0.62591	1	0.18436	1	0.87045	1	0.087685	1
3q gain	0 (0%)	383	0.37494	1	0.16405	1	0.00096864	0.739	0.21051	1	0.83316	1	0.75209	1	0.41476	1	0.63539	1	0.35718	1	0.82412	1	1	1	0.15002	1
4p gain	0 (0%)	410	NA	NA	NA	NA	0.74635	1	0.48011	1	0.24772	1	0.078815	1	NA	NA	NA	NA	0.20776	1	0.033383	1	0.51326	1	0.23148	1
4q gain	0 (0%)	408	NA	NA	NA	NA	0.84236	1	1	1	0.19909	1	0.49319	1	NA	NA	NA	NA	0.5788	1	0.33452	1	NA	NA	NA	NA
5p gain	0 (0%)	374	0.17363	1	0.05543	1	0.002235	1	0.049295	1	0.63078	1	0.88089	1	0.61763	1	1	1	0.68528	1	0.53047	1	0.4102	1	0.97762	1
5q gain	0 (0%)	392	0.54511	1	0.63094	1	0.039106	1	0.18804	1	0.42893	1	0.29256	1	0.74855	1	0.57791	1	1	1	0.94763	1	0.26086	1	0.68927	1
6p gain	0 (0%)	363	0.58873	1	0.013558	1	0.026735	1	0.67468	1	0.71061	1	0.44268	1	0.036737	1	0.26847	1	0.51347	1	0.24624	1	0.75822	1	0.39853	1
6q gain	0 (0%)	368	0.34847	1	0.027446	1	0.031676	1	0.31222	1	0.554	1	0.43338	1	0.15625	1	0.62058	1	0.44104	1	0.30861	1	0.15196	1	0.73667	1
7p gain	0 (0%)	213	0.00304	1	0.0022344	1	1.9164e-15	1.64e-12	0.00021481	0.168	0.37362	1	0.039715	1	1.0881e-07	9.01e-05	2.8504e-05	0.0228	0.42473	1	0.95791	1	0.003482	1	2.6894e-06	0.00219
7q gain	0 (0%)	238	0.014468	1	0.012963	1	7.0474e-11	5.93e-08	0.0053229	1	0.64991	1	0.071977	1	3.0119e-06	0.00245	0.00018602	0.146	0.47424	1	0.75189	1	0.03275	1	9.2547e-05	0.073
8p gain	0 (0%)	333	0.73847	1	0.42273	1	9.2183e-06	0.00744	0.038491	1	0.11726	1	0.38308	1	0.17509	1	0.032702	1	0.615	1	0.57107	1	0.2172	1	0.57211	1
8q gain	0 (0%)	251	0.72973	1	0.43213	1	9.3911e-12	7.95e-09	0.00057729	0.445	0.75062	1	0.020961	1	0.0071979	1	0.12747	1	0.098557	1	0.1543	1	0.1008	1	0.32976	1
9p gain	0 (0%)	367	0.0064524	1	0.19232	1	0.28043	1	0.39111	1	0.066363	1	0.17919	1	0.87901	1	0.76037	1	0.76674	1	0.76256	1	1	1	0.72817	1
9q gain	0 (0%)	374	0.011043	1	0.07296	1	0.064111	1	0.095288	1	0.017362	1	0.033971	1	0.36187	1	0.65886	1	0.058924	1	0.63487	1	0.51798	1	0.28925	1
10p gain	0 (0%)	395	0.69067	1	0.51996	1	0.10421	1	0.042928	1	0.42818	1	0.91721	1	0.90416	1	0.46649	1	0.76067	1	0.94138	1	0.049558	1	0.49344	1
10q gain	0 (0%)	406	NA	NA	NA	NA	0.11363	1	0.030833	1	0.8367	1	0.86126	1	0.93301	1	0.21941	1	0.20178	1	0.15076	1	0.87591	1	0.8712	1
11p gain	0 (0%)	395	0.13759	1	0.0013887	1	0.00031424	0.245	0.0011609	0.879	0.57499	1	0.80443	1	0.87143	1	0.88902	1	0.63382	1	0.88213	1	0.32208	1	0.41714	1
11q gain	0 (0%)	391	0.021447	1	0.0027657	1	3.7234e-06	0.00303	0.0017976	1	0.2646	1	0.80795	1	0.1506	1	0.22004	1	0.38613	1	0.69294	1	0.035264	1	0.16764	1
12p gain	0 (0%)	347	0.26725	1	0.38249	1	0.0044169	1	0.0096664	1	0.88769	1	0.8128	1	0.36103	1	0.68168	1	0.068987	1	0.21035	1	0.021588	1	0.15128	1
12q gain	0 (0%)	353	0.34121	1	0.54177	1	0.0018101	1	0.0016465	1	0.7908	1	0.66875	1	0.26963	1	0.69054	1	0.012051	1	0.26775	1	0.039357	1	0.24194	1
13q gain	0 (0%)	202	1.0588e-05	0.00852	1.6648e-05	0.0133	2.9518e-33	2.56e-30	0.00010123	0.0798	0.018773	1	0.0051019	1	1.7083e-06	0.0014	7.158e-05	0.0569	0.044991	1	0.46564	1	8.8754e-06	0.00717	1.3045e-06	0.00107
14q gain	0 (0%)	398	0.482	1	0.44276	1	0.056649	1	0.19841	1	0.22121	1	0.30896	1	0.14473	1	0.12695	1	1	1	0.80535	1	1	1	0.52667	1
15q gain	0 (0%)	408	NA	NA	NA	NA	0.073166	1	0.68453	1	0.069965	1	0.033319	1	0.78261	1	0.48055	1	0.47307	1	0.42668	1	0.68521	1	0.77924	1
16p gain	0 (0%)	346	0.0074852	1	0.00080364	0.616	1.0833e-14	9.26e-12	0.14957	1	0.64029	1	0.032865	1	0.050958	1	0.17966	1	0.12636	1	0.047449	1	0.25185	1	0.012386	1
16q gain	0 (0%)	347	0.0060209	1	0.0011609	0.879	1.4436e-16	1.24e-13	0.16929	1	0.64957	1	0.019909	1	0.050958	1	0.17966	1	0.31435	1	0.23221	1	0.055977	1	0.0029172	1
17p gain	0 (0%)	404	NA	NA	NA	NA	0.61782	1	0.89063	1	0.45381	1	0.23012	1	0.031649	1	0.22465	1	0.73695	1	0.89132	1	0.87591	1	0.33267	1
17q gain	0 (0%)	365	0.05312	1	0.054425	1	0.00091327	0.698	0.0047186	1	0.86593	1	0.19716	1	1.1618e-05	0.00933	0.014993	1	0.058064	1	0.75324	1	0.18734	1	0.0034125	1
18p gain	0 (0%)	398	0.1437	1	0.63479	1	0.0054775	1	0.011824	1	0.74961	1	0.96788	1	0.17065	1	0.058059	1	0.14412	1	0.3884	1	0.46786	1	0.31189	1
18q gain	0 (0%)	404	NA	NA	NA	NA	0.023231	1	0.023753	1	0.52043	1	0.15769	1	0.14202	1	0.26749	1	0.27437	1	0.32669	1	0.45218	1	0.072516	1
19p gain	0 (0%)	379	0.056278	1	0.20791	1	0.0055403	1	0.042198	1	0.29431	1	0.078152	1	0.32105	1	0.48103	1	0.58806	1	0.57289	1	0.080457	1	0.092641	1
19q gain	0 (0%)	372	0.047596	1	0.053692	1	0.43743	1	0.050981	1	0.12382	1	0.018291	1	0.14546	1	0.29663	1	0.92434	1	0.94219	1	0.74395	1	0.14747	1
20p gain	0 (0%)	225	0.0011286	0.855	4.9661e-07	0.00041	4.2881e-20	3.7e-17	0.012273	1	0.034359	1	0.037085	1	3.3451e-05	0.0267	0.00019663	0.154	0.17412	1	0.075786	1	0.0016413	1	5.774e-07	0.000476
20q gain	0 (0%)	146	6.3164e-12	5.36e-09	4.1783e-14	3.57e-11	9.4158e-47	8.18e-44	3.1306e-10	2.62e-07	0.00036176	0.281	1.5779e-06	0.0013	2.6055e-13	2.21e-10	3.5822e-11	3.02e-08	0.10269	1	0.42883	1	1.3143e-09	1.1e-06	3.8157e-17	3.29e-14
21q gain	0 (0%)	402	0.16982	1	0.19519	1	0.085831	1	0.33426	1	0.35839	1	0.27487	1	0.28201	1	0.73007	1	0.70412	1	0.68448	1	0.39779	1	0.43602	1
Xq gain	0 (0%)	401	0.065925	1	0.77725	1	0.033071	1	0.56818	1	0.17141	1	0.34424	1	0.44618	1	0.76497	1	0.35201	1	0.40967	1	0.22673	1	0.61825	1
1p loss	0 (0%)	362	0.0028289	1	0.00097194	0.741	7.0876e-08	5.88e-05	0.0028727	1	0.57577	1	0.69838	1	0.098391	1	0.28609	1	0.18025	1	0.27379	1	0.7975	1	0.02104	1
1q loss	0 (0%)	395	0.35571	1	0.13462	1	0.01032	1	0.29379	1	0.66027	1	0.79115	1	0.1506	1	0.19603	1	0.94083	1	0.44046	1	0.22673	1	0.37342	1
2p loss	0 (0%)	409	0.55938	1	0.11076	1	0.43319	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.66171	1	0.13188	1	NA	NA	NA	NA
2q loss	0 (0%)	407	1	1	0.15598	1	0.60146	1	NA	NA	0.29787	1	0.24525	1	NA	NA	NA	NA	0.17503	1	0.0588	1	NA	NA	NA	NA
3p loss	0 (0%)	386	0.413	1	0.18694	1	0.0025064	1	0.28355	1	0.20578	1	1	1	0.45836	1	0.55629	1	0.21162	1	0.14292	1	0.37034	1	0.039853	1
3q loss	0 (0%)	401	0.74475	1	0.63094	1	0.22379	1	1	1	0.015835	1	0.26143	1	0.2672	1	0.68335	1	0.42323	1	0.82207	1	1	1	0.95711	1
4p loss	0 (0%)	329	0.0027141	1	0.019893	1	1.0515e-11	8.9e-09	0.0039201	1	0.24117	1	0.70846	1	0.00075446	0.579	0.00059947	0.461	0.08301	1	0.29045	1	0.068318	1	0.013449	1
4q loss	0 (0%)	345	0.0036142	1	0.010724	1	2.2559e-10	1.89e-07	0.002239	1	0.17463	1	0.42703	1	0.0034832	1	0.015793	1	0.0026607	1	0.035856	1	0.12721	1	0.0062665	1
5p loss	0 (0%)	388	0.80979	1	0.18934	1	0.0017575	1	0.1259	1	0.47844	1	0.70393	1	0.12574	1	0.41591	1	0.84064	1	0.90748	1	0.29707	1	0.088116	1
5q loss	0 (0%)	375	0.092201	1	0.019189	1	1.1142e-05	0.00896	0.36908	1	0.19149	1	0.23421	1	0.0076323	1	0.10496	1	0.55089	1	0.47951	1	0.51733	1	0.10127	1
6p loss	0 (0%)	401	0.45647	1	0.24739	1	0.0028528	1	1	1	0.72246	1	0.94247	1	0.66626	1	0.44955	1	0.64237	1	0.62386	1	1	1	0.77924	1
6q loss	0 (0%)	392	0.91546	1	0.78906	1	0.074255	1	0.69709	1	0.33235	1	0.87128	1	1	1	0.84505	1	0.86383	1	1	1	1	1	0.91431	1
8p loss	0 (0%)	320	7.7924e-05	0.0618	0.0012216	0.922	7.7588e-17	6.67e-14	0.00051927	0.401	0.2821	1	0.041244	1	0.14082	1	0.066457	1	0.19995	1	0.35649	1	0.00036466	0.283	0.016678	1
8q loss	0 (0%)	405	0.33919	1	0.77725	1	0.0096561	1	0.85415	1	0.1412	1	0.66793	1	1	1	1	1	0.19663	1	0.43569	1	1	1	0.83275	1
9p loss	0 (0%)	386	0.80979	1	0.12326	1	4.3967e-05	0.035	0.089174	1	0.1331	1	0.33017	1	0.042381	1	0.10496	1	0.5304	1	0.74427	1	0.18724	1	0.034804	1
9q loss	0 (0%)	387	0.30814	1	0.13882	1	2.5495e-06	0.00209	0.0010084	0.767	0.1331	1	0.33017	1	0.0008984	0.687	0.03599	1	0.11437	1	0.6754	1	0.026076	1	0.0047369	1
10p loss	0 (0%)	391	0.69986	1	0.67266	1	0.00082829	0.634	0.4713	1	0.20059	1	0.96162	1	0.51767	1	0.35247	1	0.23963	1	0.68136	1	1	1	0.58283	1
10q loss	0 (0%)	389	0.59691	1	0.71065	1	0.00052594	0.406	0.15195	1	0.19656	1	1	1	0.29513	1	0.039998	1	0.69659	1	0.39298	1	0.37034	1	0.2433	1
11p loss	0 (0%)	391	0.44508	1	0.067986	1	8.336e-05	0.066	0.00040459	0.314	0.4393	1	0.2484	1	0.048906	1	0.018363	1	0.040081	1	0.16178	1	0.04838	1	0.046616	1
11q loss	0 (0%)	386	0.28782	1	0.038614	1	7.9223e-06	0.00642	9.2986e-06	0.00749	0.38374	1	0.59998	1	0.2072	1	0.12893	1	0.35754	1	0.20161	1	0.021016	1	0.051631	1
12p loss	0 (0%)	392	0.079183	1	0.12326	1	7.1022e-05	0.0565	0.22186	1	0.46277	1	0.92193	1	0.080236	1	0.081727	1	0.71974	1	0.20758	1	0.068894	1	0.25442	1
12q loss	0 (0%)	393	0.2078	1	0.13882	1	0.00010141	0.0798	0.15211	1	0.80482	1	0.87951	1	0.016133	1	0.039998	1	0.41103	1	0.36188	1	0.068894	1	0.25442	1
13q loss	0 (0%)	407	NA	NA	NA	NA	0.020925	1	0.29259	1	0.02379	1	0.093067	1	0.42521	1	0.46356	1	0.86925	1	0.7227	1	0.10698	1	0.077846	1
14q loss	0 (0%)	319	3.1842e-08	2.65e-05	2.1385e-06	0.00175	1.5793e-22	1.36e-19	2.1222e-06	0.00174	0.0083823	1	0.026613	1	1.4971e-06	0.00123	8.7803e-05	0.0694	0.53245	1	0.19414	1	8.4224e-05	0.0666	0.00011046	0.0868
15q loss	0 (0%)	314	0.010775	1	0.0027528	1	9.291e-22	8.02e-19	0.006905	1	0.080324	1	0.3927	1	4.0684e-05	0.0325	7.3474e-05	0.0583	0.48797	1	0.043531	1	0.012819	1	0.0014046	1
16p loss	0 (0%)	404	0.27385	1	0.5545	1	0.30453	1	0.031139	1	0.61004	1	0.90449	1	1	1	1	1	0.71093	1	1	1	0.6283	1	0.57484	1
16q loss	0 (0%)	406	0.51949	1	1	1	0.22757	1	NA	NA	0.19909	1	0.49319	1	NA	NA	NA	NA	0.17503	1	0.16959	1	NA	NA	NA	NA
17p loss	0 (0%)	249	1.454e-05	0.0117	8.7355e-06	0.00707	4.4431e-23	3.84e-20	1.3528e-07	0.000112	0.061475	1	0.039315	1	2.6536e-06	0.00217	8.2008e-06	0.00664	0.14682	1	0.04636	1	5.4226e-06	0.0044	0.00015363	0.121
17q loss	0 (0%)	381	0.091774	1	0.22668	1	0.0021573	1	0.30181	1	0.41234	1	0.15954	1	0.081268	1	0.10925	1	0.32156	1	0.29072	1	0.45116	1	0.23749	1
18p loss	0 (0%)	204	6.641e-14	5.65e-11	1.174e-09	9.83e-07	2.4423e-46	2.12e-43	4.3309e-14	3.69e-11	0.0016942	1	0.0004954	0.383	6.9843e-15	5.98e-12	5.8662e-09	4.89e-06	0.25052	1	0.49723	1	1.3167e-11	1.11e-08	9.7219e-11	8.17e-08
18q loss	0 (0%)	188	3.4196e-13	2.9e-10	8.7941e-11	7.4e-08	8.8765e-46	7.7e-43	4.4512e-15	3.81e-12	0.016169	1	0.0013775	1	4.465e-14	3.8e-11	1.3634e-08	1.13e-05	0.061165	1	0.49873	1	4.5049e-09	3.76e-06	1.2345e-09	1.03e-06
19p loss	0 (0%)	399	1	1	0.3199	1	0.0027471	1	0.13048	1	0.78288	1	0.36098	1	0.0070759	1	0.078889	1	0.69276	1	0.087585	1	0.62945	1	0.10659	1
19q loss	0 (0%)	400	0.92438	1	0.3813	1	0.011541	1	0.13048	1	0.90627	1	0.36307	1	0.0070759	1	0.078889	1	0.56958	1	0.061113	1	0.62945	1	0.10659	1
20p loss	0 (0%)	380	0.0091018	1	0.0094841	1	8.8788e-08	7.36e-05	0.067143	1	0.61445	1	0.47217	1	0.35278	1	0.30826	1	0.90557	1	0.52983	1	0.25191	1	0.42165	1
21q loss	0 (0%)	342	0.014096	1	0.0022745	1	2.5982e-06	0.00212	0.35776	1	0.52413	1	0.57198	1	0.12188	1	0.34163	1	0.073098	1	0.60765	1	0.45777	1	0.29993	1
22q loss	0 (0%)	332	0.00032035	0.25	0.0005809	0.447	1.0613e-11	8.97e-09	0.093922	1	0.34081	1	0.13829	1	0.0097172	1	0.0011021	0.837	0.62418	1	0.12297	1	0.003234	1	0.054083	1
Xq loss	0 (0%)	408	NA	NA	NA	NA	0.84236	1	1	1	0.15165	1	0.82096	1	NA	NA	NA	NA	0.85062	1	0.14029	1	0.64351	1	0.26016	1