		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	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	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
1p gain	95 (10%)	818	1.3266e-05	0.00736	6.1959e-07	0.000384	3.7812e-07	0.000239	0.019752	1	2.1146e-05	0.0114	0.0001248	0.0603	2.4104e-06	0.00143	5.5263e-07	0.000343	1.7188e-05	0.00932	4.5212e-06	0.00262
1q gain	487 (53%)	426	7.0436e-05	0.0355	0.71422	1	3.0239e-08	2.03e-05	2.869e-15	2.19e-12	0.10293	1	0.18592	1	3.6671e-07	0.000232	0.15004	1	0.043468	1	0.049931	1
2p gain	48 (5%)	865	1.0607e-08	7.24e-06	3.5565e-11	2.54e-08	3.7043e-10	2.6e-07	4.6185e-05	0.0237	1.9734e-08	1.33e-05	3.137e-08	2.1e-05	2.4991e-11	1.8e-08	4.5145e-15	3.43e-12	9.6628e-12	7e-09	4.2614e-10	2.98e-07
2q gain	25 (3%)	888	0.0045812	1	1.9898e-05	0.0107	0.00012252	0.0593	0.0062489	1	1.536e-07	9.89e-05	0.00044367	0.196	0.00021201	0.099	1.2155e-07	7.89e-05	0.00028181	0.13	0.00013239	0.0637
3p gain	57 (6%)	856	0.34631	1	0.15266	1	6.601e-07	0.000408	0.53244	1	0.31488	1	0.15117	1	0.27306	1	0.012355	1	0.044649	1	0.21199	1
3q gain	99 (11%)	814	0.014582	1	0.0068508	1	2.3784e-09	1.64e-06	0.00032142	0.148	0.01494	1	0.11036	1	1.6209e-05	0.00886	2.259e-05	0.0121	1.4671e-05	0.00808	0.001155	0.465
4p gain	29 (3%)	884	1.3831e-06	0.00084	2.6595e-05	0.014	1.1243e-06	0.000685	4.1545e-05	0.0215	0.048524	1	0.039558	1	2.5259e-06	0.00149	8.477e-05	0.0423	0.00035896	0.163	0.28521	1
4q gain	27 (3%)	886	1.3831e-06	0.00084	2.6595e-05	0.014	1.2701e-08	8.65e-06	0.00038886	0.174	0.055143	1	0.012585	1	5.1467e-07	0.000322	0.00047091	0.206	0.0034555	1	0.11128	1
5p gain	172 (19%)	741	0.1562	1	0.42091	1	4.5561e-10	3.18e-07	0.15264	1	0.59267	1	0.45945	1	0.37198	1	0.17153	1	0.015339	1	0.60505	1
5q gain	108 (12%)	805	0.0055157	1	0.0058124	1	7.3121e-17	5.63e-14	0.0096536	1	0.0041972	1	0.006914	1	0.00062674	0.267	0.0010917	0.441	0.0067388	1	7.2783e-05	0.0366
6p gain	104 (11%)	809	0.00018465	0.0871	4.9234e-05	0.0251	1.0003e-14	7.53e-12	6.0362e-11	4.3e-08	0.0078475	1	0.042666	1	2.9566e-07	0.000187	2.124e-07	0.000136	2.7848e-11	2e-08	1.9333e-08	1.3e-05
6q gain	61 (7%)	852	0.001941	0.738	0.0047999	1	1.7167e-14	1.29e-11	0.0013108	0.524	0.00053548	0.231	0.027113	1	0.001448	0.571	6.8915e-06	0.00392	3.8556e-06	0.00224	2.4149e-06	0.00143
7p gain	158 (17%)	755	0.15063	1	0.2569	1	0.062147	1	0.01459	1	0.94671	1	0.51964	1	0.13895	1	0.16861	1	0.25567	1	0.041197	1
7q gain	118 (13%)	795	0.0027305	1	0.0093993	1	0.0089178	1	0.0018219	0.701	0.40402	1	0.27125	1	0.013298	1	0.0016481	0.641	0.1041	1	0.00035797	0.163
8p gain	175 (19%)	738	0.033407	1	0.079654	1	5.7146e-15	4.33e-12	0.00037023	0.167	0.19687	1	0.45747	1	0.0003811	0.171	0.0014415	0.569	0.0036128	1	0.95688	1
8q gain	381 (42%)	532	2.2851e-05	0.0122	0.00031466	0.145	1.329e-23	1.05e-20	8.1619e-13	6.02e-10	0.66836	1	0.50273	1	2.2629e-13	1.67e-10	7.0392e-07	0.000434	2.7499e-11	1.97e-08	0.0023091	0.868
9p gain	68 (7%)	845	1.3757e-08	9.34e-06	1.6045e-08	1.08e-05	1.7906e-08	1.21e-05	0.00084199	0.349	0.0088135	1	0.00010638	0.0519	3.3751e-11	2.42e-08	5.5877e-09	3.82e-06	2.5069e-06	0.00148	2.9472e-07	0.000187
9q gain	56 (6%)	857	0.45487	1	0.080467	1	0.00014819	0.0708	0.16121	1	1	1	0.48776	1	0.063058	1	0.0057313	1	0.049117	1	0.25578	1
10p gain	110 (12%)	803	7.3808e-11	5.25e-08	9.6198e-08	6.29e-05	5.0358e-15	3.82e-12	3.371e-15	2.57e-12	2.3919e-05	0.0127	1.4211e-06	0.00086	7.7525e-18	6e-15	6.2023e-16	4.77e-13	4.513e-14	3.37e-11	2.8876e-14	2.16e-11
10q gain	45 (5%)	868	0.011436	1	0.014421	1	0.00053303	0.231	0.015945	1	0.072987	1	0.047555	1	0.0019343	0.737	0.0015896	0.62	0.0010376	0.424	0.0070667	1
11p gain	67 (7%)	846	0.94322	1	0.60601	1	0.005067	1	0.034192	1	0.31819	1	0.15531	1	0.26939	1	0.46832	1	0.2677	1	0.28679	1
11q gain	46 (5%)	867	0.53749	1	0.77011	1	0.00013066	0.063	0.15287	1	0.90947	1	0.74498	1	0.65186	1	0.32013	1	0.17424	1	0.09217	1
12p gain	115 (13%)	798	0.0069147	1	0.0015365	0.601	8.9997e-14	6.7e-11	4.7581e-05	0.0244	0.24586	1	0.067941	1	3.5734e-05	0.0186	2.0352e-05	0.0109	3.7083e-06	0.00216	0.00040553	0.181
12q gain	87 (10%)	826	0.037187	1	0.063053	1	1.8127e-15	1.38e-12	8.7382e-05	0.0433	0.2749	1	0.39966	1	0.11309	1	0.0058539	1	0.0051051	1	0.38504	1
13q gain	47 (5%)	866	0.52498	1	0.6191	1	0.02835	1	0.030637	1	0.064214	1	0.25774	1	0.066824	1	0.030804	1	0.0073228	1	0.011233	1
14q gain	77 (8%)	836	0.00067392	0.286	0.011979	1	0.00097787	0.403	0.0068371	1	0.9487	1	0.31633	1	0.00044216	0.196	0.0076987	1	0.0012265	0.492	0.12998	1
15q gain	45 (5%)	868	0.72718	1	0.47411	1	0.68174	1	0.1448	1	0.81692	1	0.56066	1	0.49839	1	0.41948	1	0.47311	1	0.15256	1
16p gain	254 (28%)	659	1.0074e-05	0.00561	8.0704e-05	0.0404	0.011898	1	5.2651e-07	0.000329	0.00011863	0.0578	6.5848e-05	0.0333	7.1184e-07	0.000438	4.248e-05	0.022	0.00018636	0.0876	0.0093425	1
16q gain	56 (6%)	857	0.53114	1	0.21514	1	0.00084067	0.349	0.070477	1	0.13361	1	0.77536	1	0.10887	1	0.0094767	1	0.0096174	1	0.0046129	1
17p gain	47 (5%)	866	0.021743	1	0.39609	1	0.0018221	0.701	0.61853	1	0.18021	1	0.20026	1	0.022649	1	0.46199	1	0.41699	1	0.534	1
17q gain	123 (13%)	790	4.0095e-07	0.000252	0.0078159	1	2.6385e-18	2.05e-15	3.2739e-06	0.00192	0.46375	1	0.0091179	1	2.439e-11	1.76e-08	2.086e-07	0.000133	0.064	1	0.02115	1
18p gain	87 (10%)	826	0.002682	0.998	0.0041705	1	2.573e-07	0.000164	1.0305e-07	6.71e-05	0.01394	1	0.012594	1	5.057e-06	0.00291	1.4784e-05	0.00813	4.6782e-06	0.0027	2.9286e-05	0.0153
18q gain	77 (8%)	836	0.0011715	0.471	0.030021	1	6.6936e-06	0.00382	0.012716	1	0.31076	1	0.27447	1	1.9089e-05	0.0103	0.0019152	0.734	0.00023735	0.11	0.0079049	1
19p gain	69 (8%)	844	0.12511	1	0.029331	1	0.00038151	0.171	0.14068	1	0.037261	1	0.11438	1	0.0062081	1	0.00099889	0.411	0.011305	1	0.0010666	0.433
19q gain	86 (9%)	827	0.14191	1	0.037597	1	0.00041468	0.185	0.1113	1	0.1543	1	0.25142	1	0.023696	1	0.0026345	0.985	0.03615	1	0.012883	1
20p gain	239 (26%)	674	3.6557e-05	0.019	0.026902	1	3.0831e-23	2.43e-20	3.0604e-08	2.05e-05	0.021744	1	0.13273	1	0.00032461	0.149	0.00067523	0.286	1.7705e-06	0.00106	0.25621	1
20q gain	276 (30%)	637	1.4397e-05	0.00795	0.0088326	1	3.3245e-29	2.64e-26	2.3539e-14	1.77e-11	0.19855	1	0.79152	1	6.8217e-08	4.51e-05	3.6868e-06	0.00215	3.0898e-07	0.000196	0.1394	1
21q gain	104 (11%)	809	5.9732e-05	0.0303	0.00019028	0.0892	7.0951e-10	4.93e-07	4.6717e-09	3.2e-06	0.068398	1	0.0055358	1	5.019e-07	0.000315	1.7668e-11	1.27e-08	8.5887e-06	0.00484	1.5918e-05	0.00872
22q gain	43 (5%)	870	0.074917	1	0.0052285	1	3.7537e-08	2.5e-05	0.00099932	0.411	0.068455	1	0.15283	1	0.00465	1	8.3342e-07	0.000512	0.00034753	0.158	1.0503e-05	0.00584
Xq gain	21 (2%)	892	0.00073795	0.309	0.00016492	0.0783	0.00016631	0.0788	0.019256	1	0.075361	1	0.0072526	1	0.00010362	0.0507	8.7266e-06	0.0049	8.7095e-06	0.00489	9.2007e-05	0.0455
1p loss	123 (13%)	790	0.00022777	0.106	3.9755e-10	2.79e-07	2.44e-23	1.93e-20	1.8429e-06	0.0011	0.70203	1	0.17547	1	5.1384e-07	0.000322	3.6001e-18	2.79e-15	0.00050464	0.22	0.0010754	0.436
1q loss	22 (2%)	891	0.24282	1	0.033646	1	0.0041945	1	0.21088	1	0.27174	1	0.73938	1	0.12088	1	0.00035684	0.162	0.13702	1	0.32251	1
2p loss	75 (8%)	838	0.011578	1	3.095e-05	0.0162	2.5823e-12	1.89e-09	1.7191e-07	0.000111	0.036066	1	0.0042794	1	0.00019952	0.0934	3.7267e-08	2.48e-05	6.9193e-06	0.00393	0.0036957	1
2q loss	91 (10%)	822	0.11233	1	0.00044438	0.196	2.4802e-12	1.82e-09	4.0065e-06	0.00233	0.0688	1	0.028103	1	0.0070875	1	9.9432e-06	0.00555	1.584e-05	0.0087	0.42164	1
3p loss	92 (10%)	821	0.00069396	0.293	0.00091357	0.377	2.5776e-09	1.77e-06	3.4192e-05	0.0178	0.0023332	0.875	5.3125e-05	0.027	2.2841e-05	0.0122	0.00017756	0.084	1.4553e-07	9.39e-05	9.0603e-05	0.0448
3q loss	44 (5%)	869	0.01971	1	0.0058529	1	0.0010361	0.424	0.0041507	1	0.18482	1	0.065658	1	0.00057872	0.249	0.0083189	1	0.0019241	0.735	0.09896	1
4p loss	185 (20%)	728	4.4968e-12	3.27e-09	1.2357e-12	9.08e-10	9.9775e-28	7.92e-25	3.8655e-14	2.89e-11	0.00013974	0.0669	7.5719e-06	0.00429	2.9843e-18	2.32e-15	1.6299e-19	1.28e-16	5.2054e-15	3.95e-12	4.8264e-11	3.45e-08
4q loss	155 (17%)	758	1.793e-06	0.00107	2.1022e-08	1.41e-05	7.1716e-21	5.64e-18	1.188e-10	8.4e-08	0.016792	1	0.0017099	0.66	3.3517e-12	2.44e-09	1.2214e-15	9.34e-13	3.3339e-08	2.22e-05	7.4237e-08	4.88e-05
5p loss	73 (8%)	840	1.4864e-08	1.01e-05	4.1364e-06	0.0024	8.9663e-21	7.04e-18	4.0316e-12	2.93e-09	4.281e-05	0.022	6.7225e-06	0.00383	1.7733e-12	1.3e-09	5.2579e-10	3.67e-07	6.1687e-15	4.66e-12	2.9374e-12	2.14e-09
5q loss	124 (14%)	789	4.1442e-19	3.23e-16	9.9511e-15	7.5e-12	4.586e-45	3.67e-42	1.208e-32	9.64e-30	1.8608e-09	1.29e-06	6.9283e-11	4.93e-08	1.5537e-34	1.24e-31	4.7437e-24	3.75e-21	1.7462e-27	1.38e-24	2.2658e-30	1.8e-27
6p loss	109 (12%)	804	0.014226	1	9.3234e-05	0.046	1.0862e-09	7.52e-07	4.9649e-05	0.0253	0.013057	1	0.0060413	1	3.4586e-05	0.018	1.4363e-05	0.00794	8.5375e-05	0.0424	0.0044009	1
6q loss	171 (19%)	742	4.7111e-05	0.0242	9.1864e-07	0.000562	1.1984e-14	9.01e-12	6.4767e-08	4.29e-05	0.00054974	0.237	0.0051991	1	1.2064e-07	7.84e-05	8.3437e-08	5.48e-05	0.00015864	0.0755	5.0308e-06	0.0029
7p loss	48 (5%)	865	0.16748	1	0.023985	1	9.9283e-06	0.00555	0.0016964	0.657	0.37064	1	0.43816	1	0.0022515	0.849	0.00081902	0.341	0.0088846	1	0.0099266	1
7q loss	64 (7%)	849	0.32671	1	0.099562	1	0.00044344	0.196	0.20639	1	0.23573	1	0.42128	1	0.30328	1	0.0050929	1	0.019474	1	0.25384	1
8p loss	270 (30%)	643	0.00010329	0.0506	0.17767	1	2.5825e-15	1.97e-12	9.8353e-08	6.42e-05	0.6467	1	0.90862	1	2.0263e-07	0.00013	0.0035877	1	0.00074644	0.312	0.028013	1
8q loss	46 (5%)	867	0.50664	1	0.52563	1	0.20321	1	0.10264	1	0.68767	1	0.56647	1	0.77259	1	0.36925	1	0.064871	1	1	1
9p loss	190 (21%)	723	2.3909e-05	0.0127	0.0014752	0.578	5.0725e-19	3.95e-16	1.0838e-13	8.05e-11	0.038065	1	0.85818	1	1.7623e-07	0.000113	5.2837e-06	0.00302	7.5525e-07	0.000464	0.0063854	1
9q loss	147 (16%)	766	0.0074992	1	0.00061404	0.262	9.6053e-16	7.37e-13	1.7373e-12	1.28e-09	0.013473	1	0.18022	1	2.8778e-06	0.00169	7.0051e-06	0.00397	1.3584e-10	9.59e-08	0.000119	0.0578
10p loss	75 (8%)	838	0.024952	1	0.011863	1	2.5465e-06	0.0015	0.021294	1	0.71648	1	0.46013	1	0.016231	1	0.035204	1	0.011368	1	0.25839	1
10q loss	111 (12%)	802	0.00051224	0.223	0.0014653	0.576	4.3424e-14	3.24e-11	9.9541e-07	0.000608	0.0052379	1	0.11222	1	5.1425e-06	0.00295	0.0016835	0.653	0.003274	1	0.014416	1
11p loss	144 (16%)	769	0.034209	1	0.15638	1	8.4962e-15	6.41e-12	8.6051e-08	5.64e-05	0.092531	1	0.015069	1	0.0010469	0.426	0.0014132	0.561	0.00021743	0.101	0.38685	1
11q loss	229 (25%)	684	2.0071e-07	0.000129	0.00032741	0.15	2.0379e-31	1.62e-28	1.504e-11	1.09e-08	0.20843	1	0.19136	1	1.8795e-10	1.33e-07	1.0371e-06	0.000633	0.0053563	1	0.0035896	1
12p loss	67 (7%)	846	0.30487	1	0.097805	1	0.015838	1	1.5697e-06	0.000947	0.14925	1	0.27412	1	0.022163	1	0.00030159	0.139	0.0070049	1	0.022203	1
12q loss	52 (6%)	861	0.00070759	0.297	0.00024407	0.113	9.8806e-05	0.0486	4.1002e-09	2.82e-06	0.0048581	1	0.0026476	0.988	1.5108e-08	1.02e-05	1.3131e-07	8.5e-05	9.5568e-06	0.00535	1.651e-05	0.00898
13q loss	267 (29%)	646	0.00013384	0.0642	0.00061096	0.262	1.6163e-27	1.28e-24	2.8396e-10	2e-07	0.72674	1	0.48903	1	0.0041745	1	2.6285e-07	0.000167	2.4883e-09	1.71e-06	0.15748	1
14q loss	136 (15%)	777	1.0926e-10	7.74e-08	8.4996e-08	5.58e-05	2.5981e-22	2.04e-19	6.8291e-16	5.24e-13	0.0001846	0.0871	8.5203e-05	0.0424	3.5781e-19	2.79e-16	1.1509e-11	8.32e-09	1.0601e-12	7.8e-10	1.6184e-13	1.2e-10
15q loss	162 (18%)	751	0.0070087	1	0.00012076	0.0586	3.8542e-17	2.98e-14	4.9374e-07	0.00031	0.11743	1	0.005478	1	0.0055982	1	2.4121e-06	0.00143	1.0138e-07	6.61e-05	9.0808e-07	0.000557
16p loss	55 (6%)	858	0.0038466	1	0.020432	1	1.4165e-05	0.00785	2.4714e-05	0.0131	0.18381	1	0.28612	1	0.00075055	0.313	0.00042447	0.189	0.00051997	0.226	0.00062567	0.267
16q loss	390 (43%)	523	7.0792e-08	4.67e-05	1.749e-13	1.3e-10	9.634e-12	6.98e-09	6.0983e-17	4.7e-14	8.175e-06	0.00462	1.0185e-09	7.06e-07	3.3682e-19	2.63e-16	3.5808e-20	2.81e-17	5.4931e-17	4.24e-14	3.2659e-18	2.53e-15
17p loss	373 (41%)	540	8.2322e-06	0.00464	0.69364	1	6.1995e-14	4.62e-11	5.7983e-08	3.84e-05	0.0014162	0.561	0.1229	1	5.8072e-10	4.05e-07	0.071925	1	1.7715e-05	0.00958	0.027733	1
17q loss	143 (16%)	770	1.0823e-10	7.67e-08	1.7231e-06	0.00103	8.8754e-11	6.3e-08	7.4809e-05	0.0375	9.6879e-10	6.72e-07	6.3995e-07	0.000396	9.8745e-16	7.56e-13	1.2812e-08	8.71e-06	4.9715e-09	3.41e-06	1.6229e-06	0.000977
18p loss	175 (19%)	738	0.00037659	0.17	0.64532	1	6.1752e-10	4.3e-07	3.3209e-06	0.00194	0.89209	1	0.96226	1	4.8781e-08	3.24e-05	0.013524	1	0.042837	1	0.027515	1
18q loss	177 (19%)	736	0.0013265	0.529	0.64415	1	6.1054e-13	4.51e-10	7.0109e-08	4.63e-05	0.53469	1	0.82812	1	1.2581e-06	0.000765	0.01075	1	0.058135	1	0.18064	1
19p loss	67 (7%)	846	1.6501e-05	0.00898	0.0004615	0.203	7.7659e-13	5.73e-10	1.4259e-08	9.67e-06	0.42356	1	0.074143	1	2.1885e-06	0.0013	3.8212e-07	0.000241	0.00070475	0.297	0.18158	1
19q loss	53 (6%)	860	7.4107e-05	0.0372	0.0013843	0.551	3.6573e-10	2.57e-07	1.6203e-05	0.00886	0.10055	1	0.076715	1	5.1829e-06	0.00297	1.2263e-07	7.95e-05	0.011837	1	0.28857	1
20p loss	53 (6%)	860	0.056135	1	0.046337	1	1.4223e-06	0.00086	2.4246e-05	0.0129	0.36209	1	0.4304	1	0.013609	1	0.00014836	0.0708	2.7546e-05	0.0145	0.0020846	0.788
20q loss	29 (3%)	884	0.057931	1	0.10013	1	6.9738e-05	0.0352	2.824e-06	0.00166	0.49608	1	0.17222	1	0.0020028	0.759	0.00010156	0.0499	4.7794e-05	0.0244	2.2356e-05	0.012
21q loss	86 (9%)	827	0.023769	1	0.26929	1	1.6672e-06	0.001	0.057554	1	1	1	0.81202	1	0.44421	1	0.31608	1	0.034387	1	0.12879	1
22q loss	306 (34%)	607	4.2522e-05	0.022	1.4172e-07	9.16e-05	2.9691e-06	0.00174	5.3184e-07	0.000331	0.00047578	0.208	1.6369e-05	0.00892	4.9333e-06	0.00285	6.7542e-12	4.9e-09	1.0712e-08	7.31e-06	5.2693e-07	0.000329
Xq loss	31 (3%)	882	0.66774	1	0.073639	1	0.00061052	0.262	0.0045145	1	0.015385	1	0.2	1	0.028118	1	0.0004333	0.192	2.8814e-05	0.0151	0.013191	1
