		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	0.036544	1	0.23445	1	1	1	0.078307	1	0.46021	1	1	1
1q gain	47 (11%)	366	0.052661	1	0.60421	1	0.078786	1	0.30743	1	0.56747	1	0.18103	1	0.094316	1	0.93101	1	0.4366	1	0.83658	1
2p gain	40 (10%)	373	0.097532	1	0.056629	1	0.0040928	1	0.046011	1	0.14097	1	0.48836	1	0.0058999	1	0.004329	1	0.50846	1	0.35508	1
2q gain	39 (9%)	374	0.057657	1	0.051225	1	0.00017278	0.112	0.0023481	1	0.12056	1	0.58893	1	0.0029376	1	0.0026079	1	0.52888	1	0.40458	1
3p gain	20 (5%)	393	0.37803	1	0.42959	1	0.071044	1	0.36719	1	0.71452	1	0.17462	1	0.46373	1	0.85973	1	0.62591	1	0.18436	1
3q gain	30 (7%)	383	0.45805	1	0.055068	1	0.00096864	0.607	0.22011	1	0.39276	1	0.4438	1	0.17821	1	0.58538	1	0.35718	1	0.82412	1
4p gain	3 (1%)	410	NA	NA	NA	NA	0.74635	1	0.47306	1	0.22537	1	0.21377	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	0.8316	1	NA	NA	NA	NA	0.5788	1	0.33452	1
5p gain	39 (9%)	374	0.28556	1	0.047911	1	0.002235	1	0.023566	1	0.51263	1	0.98717	1	0.34051	1	0.33796	1	0.68528	1	0.53047	1
5q gain	21 (5%)	392	0.65619	1	0.31874	1	0.039106	1	0.18815	1	0.3688	1	0.34548	1	1	1	0.42704	1	1	1	0.94763	1
6p gain	50 (12%)	363	0.51572	1	0.010749	1	0.026735	1	0.67498	1	0.61856	1	0.95465	1	0.29911	1	0.73156	1	0.51347	1	0.24624	1
6q gain	45 (11%)	368	0.33408	1	0.026664	1	0.031676	1	0.35198	1	0.87734	1	0.84738	1	0.4433	1	0.94325	1	0.44104	1	0.30861	1
7p gain	200 (48%)	213	0.0011955	0.745	0.0014094	0.877	1.9164e-15	1.35e-12	9.1419e-05	0.0599	0.31648	1	0.019937	1	1.221e-06	0.000829	7.1941e-05	0.0473	0.42473	1	0.95791	1
7q gain	175 (42%)	238	0.004193	1	0.014622	1	7.0474e-11	4.88e-08	0.0027808	1	0.66662	1	0.075137	1	0.0001633	0.106	0.00045347	0.291	0.47424	1	0.75189	1
8p gain	80 (19%)	333	1	1	0.98822	1	9.2183e-06	0.00616	0.056224	1	0.2496	1	0.16168	1	0.47019	1	0.84908	1	0.615	1	0.57107	1
8q gain	162 (39%)	251	0.79277	1	0.15105	1	9.3911e-12	6.55e-09	0.00066584	0.421	0.65042	1	0.056547	1	0.15048	1	0.13618	1	0.098557	1	0.1543	1
9p gain	46 (11%)	367	0.03165	1	0.26151	1	0.28043	1	0.43276	1	0.08168	1	0.12969	1	0.078335	1	0.34981	1	0.76674	1	0.76256	1
9q gain	39 (9%)	374	0.056767	1	0.3046	1	0.064111	1	0.11304	1	0.01704	1	0.025352	1	0.59499	1	0.8746	1	0.058924	1	0.63487	1
10p gain	18 (4%)	395	0.66898	1	0.55036	1	0.10421	1	0.047659	1	0.95066	1	0.69641	1	0.82579	1	0.45037	1	0.76067	1	0.94138	1
10q gain	7 (2%)	406	NA	NA	NA	NA	0.11363	1	0.042029	1	0.877	1	0.61513	1	NA	NA	NA	NA	0.20178	1	0.15076	1
11p gain	18 (4%)	395	0.14977	1	0.0018981	1	0.00031424	0.203	0.00057549	0.367	1	1	0.60504	1	0.0055855	1	0.042103	1	0.63382	1	0.88213	1
11q gain	22 (5%)	391	0.029722	1	0.0039665	1	3.7234e-06	0.00251	0.0014127	0.877	0.29898	1	0.67656	1	0.00061975	0.394	0.0098033	1	0.38613	1	0.69294	1
12p gain	66 (16%)	347	0.36141	1	0.091238	1	0.0044169	1	0.014562	1	0.53678	1	0.57397	1	0.14612	1	0.56123	1	0.068987	1	0.21035	1
12q gain	60 (15%)	353	0.24467	1	0.18956	1	0.0018101	1	0.0029065	1	0.41709	1	0.54594	1	0.20803	1	0.8739	1	0.012051	1	0.26775	1
13q gain	211 (51%)	202	1.076e-05	0.00717	4.1393e-05	0.0274	2.9518e-33	2.11e-30	0.00026706	0.173	0.10109	1	0.021236	1	8.394e-07	0.000572	8.4619e-06	0.00567	0.044991	1	0.46564	1
14q gain	15 (4%)	398	0.48354	1	0.44965	1	0.056649	1	0.27636	1	0.049926	1	0.367	1	0.30633	1	0.50251	1	1	1	0.80535	1
15q gain	5 (1%)	408	NA	NA	NA	NA	0.073166	1	0.68257	1	0.037418	1	0.063649	1	NA	NA	NA	NA	0.47307	1	0.42668	1
16p gain	67 (16%)	346	0.012748	1	0.011082	1	1.0833e-14	7.62e-12	0.13846	1	0.25803	1	0.048753	1	0.0098556	1	9.9365e-05	0.065	0.12636	1	0.047449	1
16q gain	66 (16%)	347	0.013846	1	0.018495	1	1.4436e-16	1.02e-13	0.13607	1	0.18116	1	0.048753	1	0.0028546	1	0.00040845	0.263	0.31435	1	0.23221	1
17p gain	9 (2%)	404	NA	NA	NA	NA	0.61782	1	0.89252	1	0.62638	1	0.099646	1	NA	NA	NA	NA	0.73695	1	0.89132	1
17q gain	48 (12%)	365	0.089782	1	0.021785	1	0.00091327	0.574	0.0073931	1	0.24997	1	0.18533	1	0.00047514	0.304	0.0060503	1	0.058064	1	0.75324	1
18p gain	15 (4%)	398	0.11676	1	0.82845	1	0.0054775	1	0.013908	1	0.33447	1	0.60323	1	0.21552	1	0.023418	1	0.14412	1	0.3884	1
18q gain	9 (2%)	404	NA	NA	NA	NA	0.023231	1	0.030293	1	0.074678	1	0.066625	1	NA	NA	NA	NA	0.27437	1	0.32669	1
19p gain	34 (8%)	379	0.074386	1	0.22249	1	0.0055403	1	0.051177	1	0.22917	1	0.23327	1	0.75047	1	0.10412	1	0.58806	1	0.57289	1
19q gain	41 (10%)	372	0.067592	1	0.093476	1	0.43743	1	0.066588	1	0.026239	1	0.072086	1	0.0050557	1	0.41898	1	0.92434	1	0.94219	1
20p gain	188 (46%)	225	0.0022252	1	5.9198e-06	0.00398	4.2881e-20	3.05e-17	0.012719	1	0.022913	1	0.064848	1	8.669e-06	0.0058	3.5462e-07	0.000242	0.17412	1	0.075786	1
20q gain	267 (65%)	146	1.1841e-11	8.21e-09	9.6884e-15	6.82e-12	9.4158e-47	6.77e-44	1.0617e-09	7.32e-07	0.0010368	0.649	1.2438e-05	0.00826	3.9537e-16	2.8e-13	5.9833e-18	4.25e-15	0.10269	1	0.42883	1
21q gain	11 (3%)	402	0.1916	1	0.29494	1	0.085831	1	0.33915	1	0.19318	1	0.48036	1	0.59137	1	1	1	0.70412	1	0.68448	1
Xq gain	12 (3%)	401	0.068912	1	0.7347	1	0.033071	1	0.63094	1	0.13267	1	0.35201	1	0.89179	1	0.22526	1	0.35201	1	0.40967	1
1p loss	51 (12%)	362	0.0024918	1	0.00092707	0.582	7.0876e-08	4.87e-05	0.0032853	1	0.71035	1	0.59716	1	0.0043209	1	0.001443	0.895	0.18025	1	0.27379	1
1q loss	18 (4%)	395	0.27063	1	0.11239	1	0.01032	1	0.26876	1	0.40053	1	0.59388	1	0.34513	1	0.029812	1	0.94083	1	0.44046	1
2p loss	4 (1%)	409	0.56945	1	0.14186	1	0.43319	1	NA	NA	NA	NA	NA	NA	0.15974	1	1	1	0.66171	1	0.13188	1
2q loss	6 (1%)	407	1	1	0.06611	1	0.60146	1	NA	NA	0.070954	1	0.2687	1	0.081605	1	1	1	0.17503	1	0.0588	1
3p loss	27 (7%)	386	0.52785	1	0.19969	1	0.0025064	1	0.25233	1	0.42718	1	0.97191	1	0.77166	1	0.19506	1	0.21162	1	0.14292	1
3q loss	12 (3%)	401	0.81607	1	0.69182	1	0.22379	1	1	1	0.12364	1	0.30616	1	1	1	0.18315	1	0.42323	1	0.82207	1
4p loss	84 (20%)	329	0.0019927	1	0.036897	1	1.0515e-11	7.31e-09	0.0029908	1	0.15706	1	0.25508	1	0.0087489	1	0.023375	1	0.08301	1	0.29045	1
4q loss	68 (16%)	345	0.0046998	1	0.016105	1	2.2559e-10	1.56e-07	0.0022265	1	0.10969	1	0.23051	1	0.038839	1	0.21707	1	0.0026607	1	0.035856	1
5p loss	25 (6%)	388	0.65913	1	0.17195	1	0.0017575	1	0.10207	1	0.72509	1	0.69984	1	0.43384	1	0.47736	1	0.84064	1	0.90748	1
5q loss	38 (9%)	375	0.092594	1	0.12247	1	1.1142e-05	0.00741	0.29312	1	0.38129	1	0.28369	1	0.029736	1	0.074251	1	0.55089	1	0.47951	1
6p loss	12 (3%)	401	0.53811	1	0.050029	1	0.0028528	1	1	1	0.75455	1	1	1	0.17551	1	0.34006	1	0.64237	1	0.62386	1
6q loss	21 (5%)	392	0.94266	1	0.5294	1	0.074255	1	0.69654	1	0.16536	1	0.71098	1	0.57506	1	0.31397	1	0.86383	1	1	1
8p loss	93 (23%)	320	0.0002927	0.189	0.0082312	1	7.7588e-17	5.51e-14	0.0010382	0.649	0.22938	1	0.033727	1	0.00021835	0.142	0.0024981	1	0.19995	1	0.35649	1
8q loss	8 (2%)	405	0.40248	1	0.7347	1	0.0096561	1	0.85153	1	0.27311	1	0.72636	1	0.051432	1	0.038103	1	0.19663	1	0.43569	1
9p loss	27 (7%)	386	0.87438	1	0.19679	1	4.3967e-05	0.0291	0.074568	1	0.24082	1	0.17721	1	0.30078	1	0.80652	1	0.5304	1	0.74427	1
9q loss	26 (6%)	387	0.35849	1	0.17139	1	2.5495e-06	0.00172	0.00061883	0.394	0.24082	1	0.17721	1	0.0587	1	0.37149	1	0.11437	1	0.6754	1
10p loss	22 (5%)	391	0.63045	1	0.69182	1	0.00082829	0.522	0.28523	1	0.10864	1	0.63752	1	0.25538	1	0.084192	1	0.23963	1	0.68136	1
10q loss	24 (6%)	389	0.37283	1	0.5689	1	0.00052594	0.336	0.15234	1	0.13532	1	0.94907	1	0.30346	1	0.029714	1	0.69659	1	0.39298	1
11p loss	22 (5%)	391	0.49363	1	0.10558	1	8.336e-05	0.0547	0.00028101	0.182	0.72668	1	0.51436	1	0.92902	1	0.64029	1	0.040081	1	0.16178	1
11q loss	27 (7%)	386	0.36458	1	0.06658	1	7.9223e-06	0.00532	9.6071e-06	0.00641	0.65207	1	0.59388	1	0.66348	1	1	1	0.35754	1	0.20161	1
12p loss	21 (5%)	392	0.096973	1	0.12566	1	7.1022e-05	0.0468	0.20684	1	0.52971	1	0.97191	1	0.28183	1	0.76211	1	0.71974	1	0.20758	1
12q loss	20 (5%)	393	0.18953	1	0.15428	1	0.00010141	0.0662	0.15257	1	0.70572	1	0.93933	1	0.44563	1	0.8183	1	0.41103	1	0.36188	1
13q loss	6 (1%)	407	NA	NA	NA	NA	0.020925	1	0.23224	1	0.037998	1	0.021419	1	NA	NA	NA	NA	0.86925	1	0.7227	1
14q loss	94 (23%)	319	9.7545e-08	6.68e-05	2.1017e-06	0.00142	1.5793e-22	1.13e-19	1.1969e-06	0.000814	0.00025118	0.163	0.0030768	1	1.5378e-07	0.000105	1.7591e-06	0.00119	0.53245	1	0.19414	1
15q loss	99 (24%)	314	0.007525	1	0.0087304	1	9.291e-22	6.62e-19	0.0045786	1	0.054069	1	0.59654	1	0.043741	1	0.00045086	0.289	0.48797	1	0.043531	1
16p loss	9 (2%)	404	0.24922	1	0.57054	1	0.30453	1	0.029781	1	0.52758	1	1	1	0.3831	1	0.31721	1	0.71093	1	1	1
16q loss	7 (2%)	406	0.46196	1	0.91698	1	0.22757	1	NA	NA	NA	NA	NA	NA	0.64877	1	0.55777	1	0.17503	1	0.16959	1
17p loss	164 (40%)	249	4.4375e-06	0.00299	5.8826e-05	0.0388	4.4431e-23	3.18e-20	2.3112e-07	0.000158	0.027963	1	0.033637	1	0.00041042	0.264	5.09e-05	0.0336	0.14682	1	0.04636	1
17q loss	32 (8%)	381	0.11563	1	0.13434	1	0.0021573	1	0.21993	1	0.6218	1	0.41148	1	0.90299	1	0.36721	1	0.32156	1	0.29072	1
18p loss	209 (51%)	204	2.0412e-14	1.43e-11	6.4706e-10	4.46e-07	2.4423e-46	1.75e-43	5.149e-13	3.6e-10	0.00081037	0.511	8.2397e-05	0.0541	5.9168e-13	4.13e-10	4.6025e-14	3.23e-11	0.25052	1	0.49723	1
18q loss	225 (54%)	188	1.4041e-13	9.83e-11	1.6231e-09	1.12e-06	8.8765e-46	6.36e-43	3.6165e-15	2.55e-12	0.0097463	1	0.00066206	0.419	1.0128e-11	7.05e-09	1.7366e-15	1.23e-12	0.061165	1	0.49873	1
19p loss	14 (3%)	399	1	1	0.3385	1	0.0027471	1	0.095687	1	0.12747	1	0.12335	1	0.46373	1	0.34006	1	0.69276	1	0.087585	1
19q loss	13 (3%)	400	0.92198	1	0.43529	1	0.011541	1	0.095687	1	0.58354	1	0.19581	1	0.42825	1	0.55777	1	0.56958	1	0.061113	1
20p loss	33 (8%)	380	0.013465	1	0.0081801	1	8.8788e-08	6.09e-05	0.051364	1	0.75633	1	0.64487	1	0.063138	1	0.039273	1	0.90557	1	0.52983	1
21q loss	71 (17%)	342	0.010314	1	0.006929	1	2.5982e-06	0.00175	0.25825	1	0.60461	1	0.82672	1	0.10341	1	0.024492	1	0.073098	1	0.60765	1
22q loss	81 (20%)	332	0.0004731	0.303	0.0006228	0.395	1.0613e-11	7.37e-09	0.089431	1	0.062327	1	0.015201	1	0.06208	1	0.0011002	0.687	0.62418	1	0.12297	1
Xq loss	5 (1%)	408	NA	NA	NA	NA	0.84236	1	1	1	0.38896	1	0.67311	1	NA	NA	NA	NA	0.85062	1	0.14029	1
