		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	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	Chi-square test_P	Chi-square test_Q
1p gain	21 (4%)	471	0.68266	1	0.1836	1	0.035042	1	0.66105	1	0.053216	1	0.58903	1	0.18151	1	0.28962	1	0.032045	1	0.043001	1
1q gain	138 (28%)	354	0.11087	1	0.63732	1	3.0433e-07	0.000169	0.005342	1	0.0023621	0.99	0.00042747	0.197	3.3148e-06	0.00177	9.2345e-07	0.000505	2.9429e-09	1.76e-06	7.7964e-06	0.0041
2p gain	51 (10%)	441	0.23344	1	0.29788	1	5.4103e-11	3.34e-08	0.058815	1	0.30877	1	0.76195	1	0.23768	1	0.43383	1	0.021466	1	0.02922	1
2q gain	40 (8%)	452	0.51784	1	0.76949	1	4.8278e-11	2.99e-08	0.175	1	0.12729	1	0.40662	1	0.30009	1	0.62396	1	0.02411	1	0.0073024	1
3p gain	28 (6%)	464	NA	NA	NA	NA	4.1488e-19	2.76e-16	0.12145	1	0.63226	1	0.26551	1	0.014933	1	0.042907	1	0.87926	1	0.1055	1
3q gain	50 (10%)	442	0.17647	1	0.054256	1	3.4119e-22	2.29e-19	2.4886e-05	0.0127	0.41161	1	0.2205	1	1.1907e-06	0.000649	5.1415e-05	0.0257	0.0012499	0.545	1.0011e-06	0.000547
4p gain	6 (1%)	486	NA	NA	NA	NA	0.0038953	1	0.12499	1	NA	NA	NA	NA	0.039552	1	0.15399	1	0.0091217	1	0.01315	1
5p gain	32 (7%)	460	0.86016	1	0.6235	1	3.0144e-09	1.8e-06	0.00013587	0.0656	0.028371	1	0.87879	1	3.9528e-06	0.0021	0.00041955	0.193	1.6955e-05	0.0088	1.0385e-05	0.00541
5q gain	9 (2%)	483	NA	NA	NA	NA	0.002863	1	0.42348	1	NA	NA	NA	NA	0.06786	1	0.28634	1	0.031436	1	0.046709	1
6p gain	38 (8%)	454	0.42965	1	0.2431	1	1.5228e-16	1e-13	0.034667	1	0.75229	1	0.76092	1	0.0066461	1	0.0074982	1	0.0069553	1	0.014363	1
6q gain	30 (6%)	462	0.42965	1	0.2431	1	1.5822e-13	1.02e-10	0.33135	1	0.48834	1	0.88323	1	0.0083914	1	0.0079272	1	0.12999	1	0.28213	1
7p gain	43 (9%)	449	1	1	0.86704	1	8.6204e-19	5.73e-16	0.011813	1	0.75143	1	0.45454	1	1	1	0.47476	1	0.42962	1	0.29736	1
7q gain	43 (9%)	449	0.94364	1	0.77558	1	2.3979e-19	1.6e-16	0.024395	1	0.77476	1	0.327	1	0.38457	1	0.033117	1	0.7338	1	0.18791	1
8p gain	86 (17%)	406	0.3955	1	1	1	7.4822e-18	4.95e-15	0.91294	1	0.26286	1	0.63163	1	0.47386	1	0.43448	1	0.47978	1	0.0001072	0.0524
8q gain	118 (24%)	374	0.0046103	1	0.042441	1	1.6503e-21	1.11e-18	0.36766	1	0.0015867	0.676	0.44891	1	0.0059062	1	0.00029937	0.14	0.0029833	1	1.3738e-07	7.78e-05
9p gain	14 (3%)	478	NA	NA	NA	NA	0.048355	1	0.078573	1	NA	NA	NA	NA	0.82159	1	0.07871	1	0.043203	1	0.11926	1
9q gain	4 (1%)	488	NA	NA	NA	NA	0.35164	1	0.36274	1	NA	NA	NA	NA	0.78103	1	0.36079	1	0.31228	1	0.17268	1
10p gain	87 (18%)	405	0.0035467	1	0.063958	1	0.00069957	0.313	0.20411	1	0.26564	1	0.54392	1	0.015488	1	0.25464	1	0.12699	1	0.01727	1
10q gain	79 (16%)	413	0.0015046	0.648	0.030274	1	9.3428e-05	0.0459	0.17582	1	0.29058	1	0.71619	1	0.026202	1	0.25647	1	0.019238	1	0.0085046	1
11p gain	8 (2%)	484	0.17647	1	0.054256	1	0.0099016	1	0.037261	1	0.10432	1	0.22164	1	0.15748	1	0.44673	1	0.90991	1	0.22728	1
11q gain	8 (2%)	484	NA	NA	NA	NA	0.011078	1	0.46209	1	0.10432	1	0.02839	1	0.19408	1	0.39556	1	0.67031	1	0.39759	1
12p gain	37 (8%)	455	0.81541	1	0.82481	1	4.7807e-08	2.76e-05	0.0090941	1	0.99258	1	0.21908	1	0.04547	1	0.090624	1	0.026256	1	0.013493	1
12q gain	28 (6%)	464	0.81541	1	0.82481	1	3.6845e-07	0.000204	0.12086	1	0.86847	1	0.060223	1	0.081103	1	0.22715	1	0.19182	1	0.12342	1
13q gain	20 (4%)	472	NA	NA	NA	NA	9.5474e-08	5.44e-05	0.0055648	1	0.7006	1	0.6848	1	7.1356e-05	0.0353	0.00046225	0.212	0.0018201	0.764	0.00043361	0.199
14q gain	20 (4%)	472	1	1	1	1	2.159e-05	0.0111	0.22681	1	0.36492	1	0.63645	1	0.40121	1	0.073693	1	0.045735	1	0.19871	1
15q gain	6 (1%)	486	NA	NA	NA	NA	0.0041566	1	0.84602	1	NA	NA	NA	NA	0.828	1	0.69879	1	1	1	0.90162	1
16p gain	12 (2%)	480	NA	NA	NA	NA	0.00079405	0.352	0.031322	1	0.23219	1	0.91448	1	0.06786	1	0.07871	1	0.060853	1	0.23388	1
16q gain	4 (1%)	488	NA	NA	NA	NA	0.046028	1	1	1	NA	NA	NA	NA	NA	NA	NA	NA	1	1	0.92013	1
17p gain	7 (1%)	485	NA	NA	NA	NA	2.602e-05	0.0133	0.24392	1	NA	NA	NA	NA	0.31635	1	0.31542	1	0.18625	1	0.043322	1
17q gain	13 (3%)	479	NA	NA	NA	NA	0.00072729	0.324	0.0035743	1	0.071012	1	6.6387e-05	0.0331	0.027619	1	0.28381	1	0.072583	1	0.024343	1
18p gain	37 (8%)	455	0.059073	1	0.1325	1	4.9415e-14	3.2e-11	6.6366e-05	0.0331	0.087733	1	0.051394	1	3.3389e-05	0.017	7.2822e-07	0.000401	1.4011e-10	8.59e-08	2.362e-09	1.42e-06
18q gain	20 (4%)	472	0.17647	1	0.054256	1	8.2613e-06	0.00432	0.0056176	1	NA	NA	NA	NA	0.017254	1	0.0056462	1	1.6708e-05	0.00869	4.6256e-05	0.0232
19p gain	31 (6%)	461	0.059073	1	0.015111	1	2.4038e-13	1.54e-10	0.0042875	1	0.50613	1	0.43066	1	4.7344e-06	0.00251	1.8393e-05	0.00951	1.776e-05	0.0092	0.0013121	0.571
19q gain	28 (6%)	464	NA	NA	NA	NA	4.2813e-13	2.74e-10	0.0014709	0.635	0.08343	1	0.084981	1	4.7344e-06	0.00251	1.5912e-06	0.000866	2.7243e-06	0.00146	0.0002309	0.109
20p gain	65 (13%)	427	0.17647	1	0.054256	1	2.2767e-18	1.51e-15	3.4709e-05	0.0176	0.27385	1	0.69333	1	9.0371e-05	0.0445	0.011949	1	4.1797e-08	2.42e-05	8.4322e-08	4.83e-05
20q gain	78 (16%)	414	0.059073	1	0.015111	1	3.6242e-24	2.44e-21	8.601e-08	4.92e-05	0.17078	1	0.45589	1	1.7451e-06	0.000946	0.00062065	0.28	2.0002e-11	1.25e-08	2.8103e-11	1.76e-08
21q gain	25 (5%)	467	NA	NA	NA	NA	1.1349e-08	6.68e-06	0.079381	1	0.22156	1	0.67703	1	0.00020408	0.0965	0.0094958	1	0.00012253	0.0594	0.0071818	1
22q gain	9 (2%)	483	NA	NA	NA	NA	0.0047256	1	0.00053691	0.244	NA	NA	NA	NA	0.11476	1	0.36079	1	0.00098888	0.434	0.0051804	1
Xq gain	12 (2%)	480	NA	NA	NA	NA	0.00025705	0.121	0.32236	1	NA	NA	NA	NA	0.15748	1	0.44673	1	0.0065229	1	0.12795	1
1p loss	13 (3%)	479	NA	NA	NA	NA	1.8216e-08	1.07e-05	0.00095455	0.421	NA	NA	NA	NA	0.040252	1	0.088379	1	0.0097374	1	0.0083303	1
1q loss	4 (1%)	488	NA	NA	NA	NA	0.03655	1	0.057423	1	NA	NA	NA	NA	0.11476	1	0.36079	1	0.041673	1	0.2426	1
2p loss	6 (1%)	486	NA	NA	NA	NA	0.019044	1	0.51798	1	NA	NA	NA	NA	0.15748	1	0.087811	1	0.77465	1	0.024413	1
2q loss	8 (2%)	484	NA	NA	NA	NA	0.0063665	1	0.19926	1	NA	NA	NA	NA	0.15748	1	0.087811	1	0.45184	1	0.04581	1
3p loss	31 (6%)	461	NA	NA	NA	NA	1.3351e-14	8.7e-12	0.00014128	0.0681	0.00036283	0.168	0.014083	1	1.7855e-07	1e-04	8.6312e-08	4.93e-05	5.4366e-05	0.0271	0.00011133	0.0543
3q loss	12 (2%)	480	NA	NA	NA	NA	4.3108e-05	0.0217	0.05836	1	0.020119	1	0.33257	1	0.0047873	1	0.0027388	1	0.022642	1	0.29666	1
4p loss	66 (13%)	426	0.07289	1	0.013284	1	4.7865e-25	3.23e-22	7.079e-11	4.37e-08	0.029521	1	0.20974	1	2.45e-09	1.47e-06	1.2904e-07	7.33e-05	1.5324e-13	9.9e-11	4.2932e-09	2.55e-06
4q loss	64 (13%)	428	0.68266	1	0.37121	1	1.3603e-26	9.2e-24	2.656e-11	1.66e-08	0.12432	1	0.075139	1	2.643e-08	1.54e-05	2.4453e-08	1.43e-05	1.2284e-10	7.54e-08	1.9382e-08	1.13e-05
5p loss	27 (5%)	465	0.35228	1	0.1325	1	1.1633e-10	7.15e-08	0.00033435	0.156	0.16545	1	0.14444	1	0.0007823	0.347	0.00067185	0.302	0.0015379	0.658	0.010391	1
5q loss	45 (9%)	447	0.07289	1	0.013284	1	1.1786e-18	7.83e-16	7.2617e-09	4.29e-06	0.0048669	1	0.035896	1	6.2834e-08	3.61e-05	2.9609e-08	1.72e-05	2.5825e-07	0.000145	1.3766e-07	7.78e-05
6p loss	10 (2%)	482	0.68266	1	0.37121	1	0.00086192	0.381	0.096217	1	0.82832	1	0.38638	1	0.19389	1	0.24853	1	0.030919	1	0.046053	1
6q loss	12 (2%)	480	0.68266	1	0.37121	1	0.00023581	0.111	0.035408	1	0.82832	1	0.38638	1	0.015969	1	0.03837	1	0.047625	1	0.23949	1
7p loss	29 (6%)	463	0.17647	1	0.054256	1	9.8778e-10	5.98e-07	0.006562	1	0.18147	1	0.71391	1	0.00016195	0.0777	2.2672e-05	0.0116	0.0080538	1	0.011117	1
7q loss	27 (5%)	465	NA	NA	NA	NA	4.9115e-14	3.19e-11	0.00018012	0.0859	0.18014	1	0.38489	1	1.3201e-07	7.48e-05	1.5912e-06	0.000866	0.0015379	0.658	0.0001718	0.0822
8p loss	53 (11%)	439	0.019107	1	0.0040321	1	4.0085e-24	2.7e-21	1.0774e-11	6.8e-09	0.018756	1	0.48121	1	4.8415e-12	3.06e-09	6.9006e-10	4.2e-07	2.8658e-14	1.87e-11	5.4483e-14	3.53e-11
8q loss	12 (2%)	480	NA	NA	NA	NA	2.228e-05	0.0114	0.00095455	0.421	NA	NA	NA	NA	0.039552	1	0.15399	1	0.0018038	0.759	0.021967	1
9p loss	76 (15%)	416	0.022668	1	0.0037915	1	2.631e-29	1.78e-26	2.341e-06	0.00126	0.00055245	0.25	0.44742	1	2.1227e-12	1.35e-09	7.6036e-15	4.97e-12	5.7377e-09	3.4e-06	5.5232e-09	3.28e-06
9q loss	93 (19%)	399	0.0015041	0.648	0.0002482	0.117	1.5312e-37	1.04e-34	5.863e-07	0.000323	0.00033368	0.156	0.84614	1	2.5645e-13	1.64e-10	2.816e-16	1.85e-13	1.4294e-11	8.99e-09	1.3978e-07	7.88e-05
10p loss	23 (5%)	469	0.17647	1	0.054256	1	3.9966e-11	2.49e-08	0.00033435	0.156	0.45106	1	0.46628	1	0.0004688	0.214	0.0015999	0.68	2.6057e-06	0.0014	0.0067191	1
10q loss	24 (5%)	468	NA	NA	NA	NA	2.9446e-10	1.8e-07	0.0001924	0.0914	0.42387	1	0.71033	1	0.0004688	0.214	0.0056992	1	7.0242e-05	0.0348	0.0094157	1
11p loss	53 (11%)	439	NA	NA	NA	NA	1.4445e-21	9.69e-19	7.4418e-07	0.000409	0.27517	1	0.45929	1	4.4598e-08	2.58e-05	2.5957e-07	0.000145	5.5758e-10	3.4e-07	2.1416e-06	0.00116
11q loss	45 (9%)	447	NA	NA	NA	NA	1.1505e-15	7.54e-13	7.5322e-05	0.0372	0.71251	1	0.36952	1	0.00039705	0.183	8.0744e-06	0.00423	1.7438e-07	9.82e-05	7.756e-06	0.00409
12p loss	25 (5%)	467	NA	NA	NA	NA	3.8618e-11	2.41e-08	0.0001924	0.0914	0.0060418	1	0.32785	1	3.6189e-05	0.0183	0.0056992	1	1.6267e-08	9.57e-06	8.916e-06	0.00465
12q loss	18 (4%)	474	NA	NA	NA	NA	1.23e-09	7.43e-07	0.00010017	0.0491	0.043548	1	0.31162	1	0.0010551	0.461	0.006701	1	5.0797e-07	0.000281	0.00018142	0.0864
13q loss	60 (12%)	432	0.68266	1	0.37121	1	2.4269e-18	1.61e-15	0.00011254	0.0548	0.08043	1	0.21144	1	0.00039515	0.183	3.8892e-06	0.00207	8.5294e-05	0.0421	0.00492	1
14q loss	42 (9%)	450	0.019107	1	0.0040321	1	8.9369e-17	5.89e-14	1.4782e-09	8.9e-07	0.068262	1	0.011705	1	3.3753e-08	1.96e-05	1.9461e-07	0.000109	4.3208e-07	0.000239	9.9414e-09	5.87e-06
15q loss	81 (16%)	411	0.0067724	1	0.0010266	0.45	4.6791e-35	3.18e-32	1.6072e-13	1.03e-10	0.0015087	0.648	0.0091403	1	7.9229e-10	4.8e-07	1.0686e-10	6.58e-08	2.159e-15	1.41e-12	2.7286e-12	1.74e-09
16p loss	69 (14%)	423	0.019107	1	0.0040321	1	2.8194e-31	1.91e-28	2.7681e-09	1.66e-06	0.29321	1	0.84381	1	7.5166e-10	4.56e-07	1.4726e-09	8.88e-07	4.3008e-09	2.55e-06	4.7729e-11	2.96e-08
16q loss	110 (22%)	382	0.0068587	1	0.0017313	0.734	5.935e-40	4.05e-37	2.8603e-11	1.78e-08	0.40044	1	0.76552	1	1.006e-11	6.36e-09	2.3407e-10	1.43e-07	8.4138e-13	5.37e-10	1.532e-13	9.9e-11
17p loss	105 (21%)	387	0.0068587	1	0.0017313	0.734	8.6624e-53	5.93e-50	8.1447e-13	5.2e-10	4.5061e-05	0.0227	0.11928	1	1.6027e-20	1.07e-17	2.1472e-21	1.44e-18	2.0101e-16	1.32e-13	1.4152e-11	8.92e-09
17q loss	68 (14%)	424	0.019107	1	0.0040321	1	1.4783e-29	1e-26	3.4055e-05	0.0173	0.024551	1	0.19677	1	4.279e-09	2.55e-06	1.9474e-11	1.22e-08	2.8675e-07	0.00016	4.2665e-05	0.0215
18p loss	36 (7%)	456	NA	NA	NA	NA	3.1519e-12	2e-09	2.091e-05	0.0108	0.12861	1	0.64888	1	0.00065956	0.297	0.00017153	0.0822	0.0034966	1	0.00013092	0.0634
18q loss	49 (10%)	443	NA	NA	NA	NA	9.7475e-18	6.43e-15	1.978e-06	0.00107	0.41411	1	0.46384	1	3.8676e-06	0.00207	5.6503e-07	0.000312	8.8216e-07	0.000483	3.0061e-06	0.00161
19p loss	34 (7%)	458	NA	NA	NA	NA	4.6331e-12	2.94e-09	1.066e-07	6.07e-05	0.31793	1	0.61809	1	1.8398e-05	0.00951	7.8364e-06	0.00411	5.7241e-06	0.00302	4.3371e-06	0.0023
19q loss	28 (6%)	464	NA	NA	NA	NA	1.787e-08	1.05e-05	4.6494e-05	0.0233	0.71251	1	0.95813	1	0.00071886	0.321	0.002828	1	0.0014234	0.616	0.00049889	0.227
20p loss	15 (3%)	477	NA	NA	NA	NA	0.00012225	0.0594	0.10685	1	0.23219	1	0.51636	1	0.03678	1	0.046533	1	0.0026484	1	0.040187	1
20q loss	7 (1%)	485	NA	NA	NA	NA	0.010576	1	0.054039	1	NA	NA	NA	NA	0.39137	1	0.47424	1	0.094326	1	0.039563	1
21q loss	32 (7%)	460	0.059073	1	0.015111	1	6.4739e-08	3.72e-05	0.0025241	1	0.011504	1	0.63835	1	0.00014817	0.0713	0.0013625	0.591	0.0017744	0.749	0.0035712	1
22q loss	87 (18%)	405	0.019107	1	0.0040321	1	1.4075e-36	9.58e-34	4.2349e-08	2.45e-05	0.017277	1	0.77242	1	4.876e-11	3.02e-08	3.2854e-14	2.14e-11	3.2041e-10	1.95e-07	5.6126e-08	3.23e-05
Xq loss	18 (4%)	474	NA	NA	NA	NA	2.9675e-07	0.000165	0.00056938	0.257	0.87203	1	0.79099	1	0.015969	1	0.006701	1	0.0007641	0.34	0.011299	1
