		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	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	0.40106	1	1	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	0.000173	0.005342	1	0.0012254	0.555	0.00071538	0.333	3.3148e-06	0.00182	9.2345e-07	0.000518	2.9429e-09	1.8e-06	7.7964e-06	0.00421
2p gain	51 (10%)	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	0.021466	1	0.02922	1
2q gain	40 (8%)	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	0.02411	1	0.0073024	1
3p gain	28 (6%)	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	0.87926	1	0.1055	1
3q gain	50 (10%)	442	0.17647	1	0.054256	1	3.4119e-22	2.34e-19	2.4886e-05	0.0131	0.38821	1	0.30068	1	1.1907e-06	0.000666	5.1415e-05	0.0265	0.0012499	0.565	1.0011e-06	0.000561
4p gain	6 (1%)	486	NA	NA	NA	NA	0.0038953	1	0.12499	1	NA	NA	0.14038	1	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	1.84e-06	0.00013587	0.0678	0.031072	1	0.71241	1	3.9528e-06	0.00216	0.00041955	0.201	1.6955e-05	0.00904	1.0385e-05	0.00556
5q gain	9 (2%)	483	NA	NA	NA	NA	0.002863	1	0.42348	1	NA	NA	1	1	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	1.02e-13	0.034667	1	0.66066	1	1	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	1.04e-10	0.33135	1	0.40106	1	1	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	5.85e-16	0.011813	1	0.73304	1	0.21665	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	1.63e-16	0.024395	1	0.88873	1	0.055165	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	5.05e-15	0.91294	1	0.13349	1	1	1	0.47386	1	0.43448	1	0.47978	1	0.0001072	0.0541
8q gain	118 (24%)	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	0.145	0.0029833	1	1.3738e-07	7.97e-05
9p gain	14 (3%)	478	NA	NA	NA	NA	0.048355	1	0.078573	1	NA	NA	1	1	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	0.326	0.20411	1	0.28359	1	0.13573	1	0.015488	1	0.25464	1	0.12699	1	0.01727	1
10q gain	79 (16%)	413	0.0015046	0.672	0.030274	1	9.3428e-05	0.0474	0.17582	1	0.38785	1	0.25211	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	0.10904	1	1	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	0.10904	1	0.29906	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	2.83e-05	0.0090941	1	0.9373	1	1	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	0.00021	0.12086	1	0.90119	1	1	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	5.58e-05	0.0055648	1	0.73455	1	0.36663	1	7.1356e-05	0.0365	0.00046225	0.22	0.0018201	0.797	0.00043361	0.207
14q gain	20 (4%)	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	0.045735	1	0.19871	1
15q gain	6 (1%)	486	NA	NA	NA	NA	0.0041566	1	0.84602	1	NA	NA	1	1	0.828	1	0.69879	1	1	1	0.90162	1
16p gain	12 (2%)	480	NA	NA	NA	NA	0.00079405	0.365	0.031322	1	0.24267	1	1	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	1	1	NA	NA	NA	NA	1	1	0.92013	1
17p gain	7 (1%)	485	NA	NA	NA	NA	2.602e-05	0.0136	0.24392	1	NA	NA	1	1	0.31635	1	0.31542	1	0.18625	1	0.043322	1
17q gain	13 (3%)	479	NA	NA	NA	NA	0.00072729	0.337	0.0035743	1	0.053132	1	1	1	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	3.27e-11	6.6366e-05	0.034	0.092984	1	0.42867	1	3.3389e-05	0.0175	7.2822e-07	0.000411	1.4011e-10	8.79e-08	2.362e-09	1.45e-06
18q gain	20 (4%)	472	0.17647	1	0.054256	1	8.2613e-06	0.00444	0.0056176	1	NA	NA	1	1	0.017254	1	0.0056462	1	1.6708e-05	0.00892	4.6256e-05	0.0239
19p gain	31 (6%)	461	0.059073	1	0.015111	1	2.4038e-13	1.58e-10	0.0042875	1	0.52818	1	0.15057	1	4.7344e-06	0.00258	1.8393e-05	0.00977	1.776e-05	0.00945	0.0013121	0.592
19q gain	28 (6%)	464	NA	NA	NA	NA	4.2813e-13	2.8e-10	0.0014709	0.659	0.084981	1	1	1	4.7344e-06	0.00258	1.5912e-06	0.000888	2.7243e-06	0.0015	0.0002309	0.113
20p gain	65 (13%)	427	0.17647	1	0.054256	1	2.2767e-18	1.54e-15	3.4709e-05	0.0181	0.29078	1	1	1	9.0371e-05	0.0459	0.011949	1	4.1797e-08	2.48e-05	8.4322e-08	4.95e-05
20q gain	78 (16%)	414	0.059073	1	0.015111	1	3.6242e-24	2.49e-21	8.601e-08	5.04e-05	0.19154	1	0.58017	1	1.7451e-06	0.00097	0.00062065	0.291	2.0002e-11	1.28e-08	2.8103e-11	1.8e-08
21q gain	25 (5%)	467	NA	NA	NA	NA	1.1349e-08	6.84e-06	0.079381	1	0.2367	1	0.55767	1	0.00020408	0.0998	0.0094958	1	0.00012253	0.0614	0.0071818	1
22q gain	9 (2%)	483	NA	NA	NA	NA	0.0047256	1	0.00053691	0.253	NA	NA	0.37629	1	0.11476	1	0.36079	1	0.00098888	0.451	0.0051804	1
Xq gain	12 (2%)	480	NA	NA	NA	NA	0.00025705	0.125	0.32236	1	NA	NA	0.37629	1	0.15748	1	0.44673	1	0.0065229	1	0.12795	1
1p loss	13 (3%)	479	NA	NA	NA	NA	1.8216e-08	1.09e-05	0.00095455	0.437	NA	NA	1	1	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	0.14038	1	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	0.14038	1	0.15748	1	0.087811	1	0.45184	1	0.04581	1
3p loss	31 (6%)	461	NA	NA	NA	NA	1.3351e-14	8.89e-12	0.00014128	0.0704	0.00052575	0.249	0.027968	1	1.7855e-07	0.000103	8.6312e-08	5.05e-05	5.4366e-05	0.0279	0.00011133	0.0561
3q loss	12 (2%)	480	NA	NA	NA	NA	4.3108e-05	0.0223	0.05836	1	0.024047	1	0.55767	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	3.3e-22	7.079e-11	4.47e-08	0.033892	1	0.39315	1	2.45e-09	1.5e-06	1.2904e-07	7.51e-05	1.5324e-13	1.01e-10	4.2932e-09	2.61e-06
4q loss	64 (13%)	428	0.68266	1	0.37121	1	1.3603e-26	9.39e-24	2.656e-11	1.7e-08	0.13113	1	0.77642	1	2.643e-08	1.58e-05	2.4453e-08	1.46e-05	1.2284e-10	7.71e-08	1.9382e-08	1.16e-05
5p loss	27 (5%)	465	0.35228	1	0.1325	1	1.1633e-10	7.32e-08	0.00033435	0.161	0.16154	1	0.18109	1	0.0007823	0.361	0.00067185	0.314	0.0015379	0.684	0.010391	1
5q loss	45 (9%)	447	0.07289	1	0.013284	1	1.1786e-18	7.99e-16	7.2617e-09	4.39e-06	0.04811	1	0.15296	1	6.2834e-08	3.7e-05	2.9609e-08	1.76e-05	2.5825e-07	0.000148	1.3766e-07	7.97e-05
6p loss	10 (2%)	482	0.68266	1	0.37121	1	0.00086192	0.396	0.096217	1	0.85846	1	0.55767	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	0.115	0.035408	1	0.85846	1	0.55767	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	6.11e-07	0.006562	1	0.15846	1	0.20053	1	0.00016195	0.0803	2.2672e-05	0.0119	0.0080538	1	0.011117	1
7q loss	27 (5%)	465	NA	NA	NA	NA	4.9115e-14	3.26e-11	0.00018012	0.0888	0.19732	1	0.012085	1	1.3201e-07	7.67e-05	1.5912e-06	0.000888	0.0015379	0.684	0.0001718	0.0849
8p loss	53 (11%)	439	0.019107	1	0.0040321	1	4.0085e-24	2.75e-21	1.0774e-11	6.95e-09	0.165	1	0.18109	1	4.8415e-12	3.13e-09	6.9006e-10	4.29e-07	2.8658e-14	1.91e-11	5.4483e-14	3.6e-11
8q loss	12 (2%)	480	NA	NA	NA	NA	2.228e-05	0.0117	0.00095455	0.437	NA	NA	1	1	0.039552	1	0.15399	1	0.0018038	0.792	0.021967	1
9p loss	76 (15%)	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	5.07e-12	5.7377e-09	3.48e-06	5.5232e-09	3.35e-06
9q loss	93 (19%)	399	0.0015041	0.672	0.0002482	0.121	1.5312e-37	1.07e-34	5.863e-07	0.000331	0.0060055	1	0.37819	1	2.5645e-13	1.68e-10	2.816e-16	1.89e-13	1.4294e-11	9.19e-09	1.3978e-07	8.08e-05
10p loss	23 (5%)	469	0.17647	1	0.054256	1	3.9966e-11	2.54e-08	0.00033435	0.161	0.47447	1	0.63255	1	0.0004688	0.223	0.0015999	0.709	2.6057e-06	0.00144	0.0067191	1
10q loss	24 (5%)	468	NA	NA	NA	NA	2.9446e-10	1.84e-07	0.0001924	0.0945	0.45123	1	1	1	0.0004688	0.223	0.0056992	1	7.0242e-05	0.036	0.0094157	1
11p loss	53 (11%)	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	2.64e-05	2.5957e-07	0.000149	5.5758e-10	3.47e-07	2.1416e-06	0.00119
11q loss	45 (9%)	447	NA	NA	NA	NA	1.1505e-15	7.7e-13	7.5322e-05	0.0384	0.92479	1	0.71272	1	0.00039705	0.191	8.0744e-06	0.00434	1.7438e-07	0.000101	7.756e-06	0.0042
12p loss	25 (5%)	467	NA	NA	NA	NA	3.8618e-11	2.46e-08	0.0001924	0.0945	0.057656	1	1	1	3.6189e-05	0.0188	0.0056992	1	1.6267e-08	9.79e-06	8.916e-06	0.00478
12q loss	18 (4%)	474	NA	NA	NA	NA	1.23e-09	7.6e-07	0.00010017	0.0507	0.30993	1	0.42867	1	0.0010551	0.479	0.006701	1	5.0797e-07	0.000288	0.00018142	0.0893
13q loss	60 (12%)	432	0.68266	1	0.37121	1	2.4269e-18	1.64e-15	0.00011254	0.0566	0.16118	1	0.39315	1	0.00039515	0.19	3.8892e-06	0.00213	8.5294e-05	0.0434	0.00492	1
14q loss	42 (9%)	450	0.019107	1	0.0040321	1	8.9369e-17	6.01e-14	1.4782e-09	9.11e-07	0.084745	1	0.0051992	1	3.3753e-08	2.01e-05	1.9461e-07	0.000112	4.3208e-07	0.000245	9.9414e-09	6e-06
15q loss	81 (16%)	411	0.0067724	1	0.0010266	0.467	4.6791e-35	3.25e-32	1.6072e-13	1.06e-10	0.00259	1	0.26661	1	7.9229e-10	4.91e-07	1.0686e-10	6.73e-08	2.159e-15	1.44e-12	2.7286e-12	1.77e-09
16p loss	69 (14%)	423	0.019107	1	0.0040321	1	2.8194e-31	1.95e-28	2.7681e-09	1.7e-06	0.19252	1	0.79627	1	7.5166e-10	4.67e-07	1.4726e-09	9.09e-07	4.3008e-09	2.61e-06	4.7729e-11	3.03e-08
16q loss	110 (22%)	382	0.0068587	1	0.0017313	0.765	5.935e-40	4.14e-37	2.8603e-11	1.82e-08	0.23685	1	1	1	1.006e-11	6.5e-09	2.3407e-10	1.47e-07	8.4138e-13	5.49e-10	1.532e-13	1.01e-10
17p loss	105 (21%)	387	0.0068587	1	0.0017313	0.765	8.6624e-53	6.05e-50	8.1447e-13	5.32e-10	0.00057115	0.268	0.66522	1	1.6027e-20	1.09e-17	2.1472e-21	1.47e-18	2.0101e-16	1.35e-13	1.4152e-11	9.11e-09
17q loss	68 (14%)	424	0.019107	1	0.0040321	1	1.4783e-29	1.02e-26	3.4055e-05	0.0178	0.092362	1	0.61178	1	4.279e-09	2.61e-06	1.9474e-11	1.25e-08	2.8675e-07	0.000164	4.2665e-05	0.0221
18p loss	36 (7%)	456	NA	NA	NA	NA	3.1519e-12	2.05e-09	2.091e-05	0.0111	0.32575	1	0.74551	1	0.00065956	0.309	0.00017153	0.0849	0.0034966	1	0.00013092	0.0655
18q loss	49 (10%)	443	NA	NA	NA	NA	9.7475e-18	6.57e-15	1.978e-06	0.0011	0.72497	1	1	1	3.8676e-06	0.00212	5.6503e-07	0.00032	8.8216e-07	0.000496	3.0061e-06	0.00165
19p loss	34 (7%)	458	NA	NA	NA	NA	4.6331e-12	3e-09	1.066e-07	6.21e-05	0.33053	1	1	1	1.8398e-05	0.00977	7.8364e-06	0.00422	5.7241e-06	0.0031	4.3371e-06	0.00236
19q loss	28 (6%)	464	NA	NA	NA	NA	1.787e-08	1.07e-05	4.6494e-05	0.024	0.73417	1	0.71272	1	0.00071886	0.334	0.002828	1	0.0014234	0.639	0.00049889	0.236
20p loss	15 (3%)	477	NA	NA	NA	NA	0.00012225	0.0614	0.10685	1	0.24267	1	0.63255	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	0.52818	1	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	3.81e-05	0.0025241	1	0.09504	1	0.75005	1	0.00014817	0.0736	0.0013625	0.613	0.0017744	0.781	0.0035712	1
22q loss	87 (18%)	405	0.019107	1	0.0040321	1	1.4075e-36	9.78e-34	4.2349e-08	2.51e-05	0.072103	1	1	1	4.876e-11	3.09e-08	3.2854e-14	2.18e-11	3.2041e-10	2e-07	5.6126e-08	3.31e-05
Xq loss	18 (4%)	474	NA	NA	NA	NA	2.9675e-07	0.000169	0.00056938	0.268	0.61718	1	0.63255	1	0.015969	1	0.006701	1	0.0007641	0.353	0.011299	1
