		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	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	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q
1p gain	89 (10%)	802	0.00041183	0.192	1.6001e-06	0.000997	2.8331e-07	0.000184	0.019094	1	5.4527e-05	0.0292	0.00029752	0.144	7.7807e-07	0.000494	3.1045e-05	0.0171	2.8048e-05	0.0156	2.212e-05	0.0124
1q gain	473 (53%)	418	0.16279	1	0.70397	1	1.1187e-09	7.89e-07	4.0163e-14	3.04e-11	0.11973	1	0.15747	1	0.10475	1	0.017219	1	0.024847	1	0.026122	1
2p gain	48 (5%)	843	7.7602e-12	5.74e-09	2.8807e-11	2.1e-08	2.4676e-10	1.76e-07	4.9675e-05	0.0267	2.709e-08	1.84e-05	4.8889e-08	3.28e-05	1.0645e-11	7.86e-09	6.5987e-13	4.92e-10	1.3615e-11	1e-08	5.4518e-10	3.87e-07
2q gain	25 (3%)	866	2.6595e-07	0.000173	1.8498e-05	0.0105	0.00033435	0.159	0.0061211	1	1.6454e-07	0.000108	0.00052147	0.237	3.1477e-06	0.00191	7.9932e-06	0.00474	0.00029555	0.143	0.00016323	0.0816
3p gain	52 (6%)	839	0.83485	1	0.038142	1	1.3674e-06	0.000856	0.18135	1	0.52754	1	0.2161	1	0.043186	1	0.046571	1	0.025029	1	0.16994	1
3q gain	98 (11%)	793	0.015343	1	0.0025018	0.991	1.9081e-09	1.34e-06	0.00054011	0.245	0.026598	1	0.17145	1	0.00016047	0.0806	0.00040896	0.191	3.1332e-05	0.0172	0.00105	0.455
4p gain	29 (3%)	862	0.11607	1	4.2543e-05	0.0231	1.6722e-07	0.00011	0.0015606	0.662	0.044743	1	0.039867	1	0.015957	1	0.0017774	0.736	0.00029727	0.144	0.25765	1
4q gain	27 (3%)	864	0.23598	1	0.00043835	0.203	3.7799e-09	2.64e-06	0.00517	1	0.055083	1	0.010507	1	0.010657	1	0.0057554	1	0.003197	1	0.11261	1
5p gain	166 (19%)	725	0.51355	1	0.38612	1	2.3974e-09	1.68e-06	0.18102	1	0.54074	1	0.3146	1	0.70701	1	0.31485	1	0.02131	1	0.63199	1
5q gain	102 (11%)	789	0.025127	1	0.0045266	1	1.362e-15	1.05e-12	0.0034935	1	0.0013424	0.573	0.0022623	0.905	0.00057674	0.26	1.1465e-05	0.00666	0.0048763	1	2.1781e-05	0.0123
6p gain	101 (11%)	790	2.8697e-05	0.016	2.0027e-05	0.0113	1.0304e-14	7.89e-12	4.2649e-07	0.000274	0.0041532	1	0.050851	1	7.8559e-09	5.44e-06	2.6682e-08	1.82e-05	1.5057e-11	1.11e-08	1.1299e-08	7.79e-06
6q gain	59 (7%)	832	0.00013505	0.0687	0.0051332	1	2.2325e-15	1.73e-12	0.0043839	1	0.00036343	0.171	0.027849	1	6.4341e-06	0.00383	2.1519e-06	0.00133	3.2157e-07	0.000208	1.4816e-06	0.000925
7p gain	153 (17%)	738	0.39196	1	0.38813	1	0.00030163	0.145	0.0045603	1	0.98598	1	0.51259	1	0.030205	1	0.11517	1	0.19577	1	0.039334	1
7q gain	111 (12%)	780	0.15923	1	0.015985	1	1.52e-05	0.00871	0.00043697	0.203	0.31248	1	0.19889	1	0.0057434	1	0.00043837	0.203	0.077275	1	0.00029511	0.143
8p gain	169 (19%)	722	0.13442	1	0.013389	1	5.5999e-13	4.19e-10	0.0027677	1	0.14258	1	0.39121	1	0.00019214	0.0951	0.00011276	0.0583	0.0031716	1	0.89318	1
8q gain	366 (41%)	525	0.0064552	1	4.3715e-05	0.0236	3.1459e-23	2.49e-20	4.6562e-09	3.25e-06	0.66766	1	0.55936	1	8.4036e-08	5.57e-05	4.6276e-06	0.00278	1.1942e-10	8.6e-08	0.003086	1
9p gain	67 (8%)	824	0.00031738	0.152	6.9971e-08	4.67e-05	1.1496e-09	8.09e-07	0.00055777	0.252	0.011288	1	0.00013812	0.0702	1.2997e-07	8.58e-05	2.6335e-08	1.8e-05	3.2337e-06	0.00196	3.8982e-07	0.000251
9q gain	54 (6%)	837	0.33599	1	0.042779	1	9.788e-05	0.0514	0.33813	1	0.96765	1	0.5434	1	0.043389	1	0.0068317	1	0.049146	1	0.24324	1
10p gain	109 (12%)	782	6.6062e-09	4.58e-06	7.1906e-08	4.79e-05	2.6216e-18	2.04e-15	1.2132e-13	9.12e-11	1.3235e-05	0.00764	1.1027e-06	0.000696	3.5934e-15	2.77e-12	1.138e-14	8.71e-12	1.4057e-14	1.07e-11	4.471e-14	3.38e-11
10q gain	44 (5%)	847	0.0017412	0.724	0.012595	1	1.225e-05	0.00709	0.021889	1	0.082237	1	0.051488	1	0.0039073	1	0.0026556	1	0.0011418	0.492	0.0080131	1
11p gain	64 (7%)	827	0.61314	1	0.61078	1	0.011606	1	0.23222	1	0.38412	1	0.16348	1	0.63686	1	0.81876	1	0.42822	1	0.30411	1
11q gain	45 (5%)	846	0.17445	1	0.80905	1	0.00058211	0.261	0.28581	1	0.93543	1	0.68705	1	0.32969	1	0.43331	1	0.23128	1	0.09402	1
12p gain	110 (12%)	781	0.0024015	0.958	0.00056345	0.254	1.712e-14	1.3e-11	0.00014189	0.0717	0.37444	1	0.09137	1	7.3752e-05	0.0389	0.00039696	0.186	5.5292e-06	0.00331	0.00053221	0.242
12q gain	83 (9%)	808	0.020805	1	0.0047963	1	1.2083e-14	9.23e-12	0.00035673	0.169	0.25556	1	0.5139	1	0.0016465	0.69	0.039445	1	0.007561	1	0.42127	1
13q gain	45 (5%)	846	0.047319	1	0.086497	1	0.051872	1	0.045766	1	0.019638	1	0.13422	1	0.00042436	0.198	0.0405	1	0.0069335	1	0.0081042	1
14q gain	77 (9%)	814	0.076363	1	0.021394	1	0.00012149	0.0624	0.0059435	1	0.94883	1	0.28235	1	1.9379e-05	0.011	0.0011139	0.481	0.00079108	0.35	0.11029	1
15q gain	46 (5%)	845	0.60422	1	0.33882	1	0.29003	1	0.34458	1	0.91828	1	0.48039	1	0.21552	1	0.18094	1	0.2447	1	0.096373	1
16p gain	239 (27%)	652	0.0014652	0.623	0.0016191	0.682	0.0075427	1	8.8043e-06	0.0052	0.0006973	0.312	0.00060828	0.273	0.00015648	0.0787	3.6364e-06	0.0022	0.00071349	0.318	0.02698	1
16q gain	53 (6%)	838	0.5052	1	0.34428	1	0.0018371	0.757	0.16822	1	0.14259	1	0.77542	1	0.11138	1	0.1088	1	0.0079273	1	0.0035147	1
17p gain	46 (5%)	845	0.090621	1	0.30851	1	0.00076596	0.34	0.83153	1	0.17785	1	0.23448	1	0.57491	1	0.72055	1	0.4741	1	0.52846	1
17q gain	122 (14%)	769	0.036811	1	0.0074553	1	2.3038e-22	1.82e-19	6.1651e-05	0.0329	0.36961	1	0.0094374	1	3.5701e-05	0.0195	4.6193e-06	0.00278	0.091405	1	0.018495	1
18p gain	86 (10%)	805	0.0071903	1	0.00017244	0.0859	1.7738e-07	0.000116	2.5571e-06	0.00157	0.0037556	1	0.0032577	1	3.0526e-06	0.00186	3.8145e-08	2.57e-05	2.1937e-06	0.00135	9.6543e-06	0.00566
18q gain	74 (8%)	817	0.17571	1	0.0020606	0.832	8.8307e-06	0.00521	0.032099	1	0.20784	1	0.20009	1	0.00024136	0.119	9.7985e-05	0.0514	8.5626e-05	0.045	0.0060251	1
19p gain	67 (8%)	824	0.095288	1	0.014741	1	0.00010206	0.0532	0.15344	1	0.07517	1	0.10261	1	0.013878	1	0.00044371	0.204	0.020514	1	0.00087662	0.383
19q gain	83 (9%)	808	0.46741	1	0.038377	1	0.00011368	0.0587	0.072239	1	0.19949	1	0.1603	1	0.045849	1	0.0012733	0.545	0.0504	1	0.0084167	1
20p gain	236 (26%)	655	1.4129e-05	0.00811	0.0018439	0.758	5.704e-26	4.53e-23	2.6075e-05	0.0146	0.03103	1	0.10839	1	0.0015927	0.674	0.065	1	1.9841e-06	0.00123	0.27025	1
20q gain	272 (31%)	619	0.00031069	0.149	0.00084315	0.371	1.2169e-33	9.72e-31	2.7663e-10	1.97e-07	0.23809	1	0.75205	1	1.2395e-05	0.00716	0.0067279	1	3.7779e-07	0.000244	0.13901	1
21q gain	101 (11%)	790	0.001992	0.811	6.9421e-05	0.0369	5.0024e-09	3.48e-06	2.1184e-06	0.00131	0.11295	1	0.012655	1	1.6526e-10	1.18e-07	6.6345e-10	4.7e-07	1.0763e-05	0.00627	1.9661e-05	0.0112
22q gain	42 (5%)	849	0.012766	1	0.0047833	1	5.2679e-11	3.81e-08	0.015341	1	0.133	1	0.14754	1	3.0234e-06	0.00185	1.4095e-05	0.0081	0.00030084	0.145	6.3219e-06	0.00377
Xq gain	20 (2%)	871	3.9005e-05	0.0212	0.00088887	0.387	7.0047e-05	0.0371	0.013918	1	0.08052	1	0.0084987	1	0.00050777	0.232	7.9708e-05	0.042	9.2541e-06	0.00543	9.9262e-05	0.0518
1p loss	123 (14%)	768	0.00047163	0.216	3.778e-10	2.68e-07	6.7727e-22	5.32e-19	2.3463e-06	0.00144	0.53055	1	0.28159	1	1.5402e-11	1.13e-08	2.2688e-07	0.000148	0.00016687	0.0833	0.00025942	0.127
1q loss	21 (2%)	870	0.25688	1	0.066969	1	0.042083	1	0.16188	1	0.40635	1	0.85225	1	0.018849	1	0.4614	1	0.022517	1	0.47953	1
2p loss	71 (8%)	820	0.0022224	0.891	0.00030953	0.149	5.1585e-12	3.83e-09	2.1984e-05	0.0124	0.060025	1	0.017223	1	1.2284e-06	0.000773	1.3695e-06	0.000856	2.219e-05	0.0124	0.0057124	1
2q loss	87 (10%)	804	0.076111	1	0.0032556	1	3.9277e-11	2.86e-08	1.9986e-05	0.0113	0.13675	1	0.084499	1	0.0016202	0.682	0.0021509	0.865	3.6148e-05	0.0197	0.4861	1
3p loss	90 (10%)	801	1.6334e-07	0.000107	0.0003375	0.16	1.1944e-08	8.22e-06	0.00013214	0.0675	0.0027497	1	6.6174e-05	0.0352	1.8309e-05	0.0105	0.0016684	0.696	1.8166e-07	0.000119	0.00013113	0.0671
3q loss	45 (5%)	846	2.8925e-05	0.0161	0.0041248	1	2.7099e-05	0.0151	0.032729	1	0.20628	1	0.079775	1	0.011985	1	0.12597	1	0.0011418	0.492	0.086565	1
4p loss	184 (21%)	707	2.6935e-08	1.83e-05	6.3619e-13	4.76e-10	8.6324e-26	6.84e-23	2e-14	1.52e-11	0.00018127	0.0901	1.3378e-05	0.00771	5.0797e-15	3.9e-12	6.3815e-15	4.89e-12	1.9904e-14	1.51e-11	1.7114e-10	1.23e-07
4q loss	154 (17%)	737	4.267e-05	0.0231	5.7122e-09	3.97e-06	6.3166e-22	4.97e-19	7.7831e-12	5.75e-09	0.015738	1	0.0019284	0.787	5.2511e-11	3.8e-08	4.6961e-11	3.41e-08	3.5513e-08	2.4e-05	7.552e-08	5.02e-05
5p loss	72 (8%)	819	4.4935e-05	0.0242	5.9757e-07	0.000382	7.5943e-21	5.95e-18	7.3006e-10	5.16e-07	0.00014137	0.0715	4.1934e-06	0.00253	9.1169e-09	6.3e-06	2.391e-08	1.64e-05	3.7384e-15	2.88e-12	1.7752e-12	1.32e-09
5q loss	123 (14%)	768	1.8211e-14	1.39e-11	4.8426e-15	3.72e-12	5.8457e-49	4.68e-46	1.0186e-31	8.13e-29	2.7511e-08	1.87e-05	1.4481e-10	1.04e-07	3.3066e-22	2.61e-19	7.8339e-24	6.2e-21	1.3106e-27	1.04e-24	1.2911e-30	1.03e-27
6p loss	105 (12%)	786	0.0083883	1	0.00024201	0.119	2.1878e-08	1.5e-05	3.0819e-05	0.017	0.016806	1	0.0050614	1	1.3604e-06	0.000853	6.9791e-06	0.00415	0.00014679	0.074	0.0030418	1
6q loss	164 (18%)	727	0.0016151	0.682	3.0393e-06	0.00186	1.5812e-13	1.19e-10	2.9037e-07	0.000188	0.00071134	0.317	0.0076028	1	7.5095e-09	5.2e-06	7.6592e-08	5.09e-05	0.00023601	0.116	3.0636e-06	0.00187
7p loss	47 (5%)	844	0.092594	1	0.031007	1	4.0682e-06	0.00246	0.004151	1	0.42364	1	0.44254	1	0.0017441	0.724	0.0095521	1	0.0084835	1	0.0080766	1
7q loss	63 (7%)	828	0.038155	1	0.15841	1	0.0058446	1	0.12502	1	0.23418	1	0.42096	1	0.043399	1	0.33309	1	0.019963	1	0.27639	1
8p loss	274 (31%)	617	0.009888	1	0.14156	1	1.9759e-16	1.53e-13	1.9266e-06	0.0012	0.61977	1	0.93589	1	0.00080907	0.357	0.14221	1	0.00046411	0.213	0.040201	1
8q loss	45 (5%)	846	0.57334	1	0.54889	1	0.16332	1	0.14802	1	0.82266	1	0.85639	1	0.025508	1	0.6523	1	0.073137	1	1	1
9p loss	184 (21%)	707	0.0086559	1	0.00043694	0.203	3.9931e-21	3.13e-18	3.3653e-11	2.45e-08	0.032834	1	0.74696	1	1.7595e-06	0.00109	0.088433	1	8.4319e-07	0.000535	0.0066855	1
9q loss	142 (16%)	749	0.0048587	1	0.00013816	0.0702	6.5689e-17	5.1e-14	1.103e-08	7.61e-06	0.010475	1	0.17035	1	1.3607e-08	9.35e-06	0.00038939	0.183	7.8388e-11	5.66e-08	0.00016199	0.0812
10p loss	71 (8%)	820	0.054651	1	0.032543	1	1.5214e-05	0.00871	0.010764	1	0.60506	1	0.39885	1	0.00029049	0.141	0.17247	1	0.0020105	0.814	0.20014	1
10q loss	110 (12%)	781	0.0055815	1	0.0024429	0.97	3.6907e-11	2.69e-08	3.7221e-06	0.00225	0.0034536	1	0.055923	1	7.5687e-06	0.0045	0.029949	1	0.0019991	0.812	0.013761	1
11p loss	148 (17%)	743	0.87393	1	0.21839	1	6.7038e-12	4.97e-09	2.7799e-08	1.88e-05	0.13274	1	0.022531	1	0.0035007	1	0.031121	1	9.8973e-05	0.0518	0.31888	1
11q loss	228 (26%)	663	3.8505e-05	0.021	0.0018533	0.76	6.2555e-26	4.96e-23	2.1216e-10	1.51e-07	0.17293	1	0.19832	1	3.0021e-06	0.00184	0.00034561	0.164	0.0024034	0.958	0.0047212	1
12p loss	67 (8%)	824	0.05201	1	0.19384	1	0.0018207	0.752	9.2139e-06	0.00542	0.15692	1	0.33272	1	0.00011246	0.0583	0.0037088	1	0.0074869	1	0.02552	1
12q loss	52 (6%)	839	0.003138	1	0.00018697	0.0927	4.0772e-07	0.000262	3.1711e-08	2.15e-05	0.0060035	1	0.003455	1	5.4024e-08	3.61e-05	1.3068e-07	8.61e-05	1.0816e-05	0.00629	1.9813e-05	0.0112
13q loss	264 (30%)	627	0.022469	1	0.00033248	0.159	2.4513e-26	1.95e-23	9.0633e-08	6e-05	0.83767	1	0.56749	1	0.00024182	0.119	0.003709	1	3.0853e-09	2.16e-06	0.15832	1
14q loss	131 (15%)	760	2.489e-07	0.000162	4.2258e-08	2.84e-05	1.0211e-21	8.02e-19	2.8904e-15	2.23e-12	0.00010274	0.0534	4.0634e-05	0.0221	1.2121e-10	8.71e-08	5.5902e-12	4.15e-09	6.4463e-13	4.82e-10	8.2486e-14	6.23e-11
15q loss	159 (18%)	732	0.0089415	1	0.00012602	0.0646	2.7288e-18	2.12e-15	2.0309e-06	0.00126	0.13423	1	0.0076182	1	3.1259e-05	0.0172	0.000971	0.421	1.9228e-07	0.000125	6.5848e-07	0.00042
16p loss	56 (6%)	835	0.069949	1	0.022374	1	6.4543e-05	0.0344	0.00010895	0.0565	0.088008	1	0.18584	1	0.001664	0.696	0.0039432	1	0.00086377	0.378	0.0018842	0.771
16q loss	392 (44%)	499	2.0648e-11	1.51e-08	1.5978e-13	1.2e-10	1.4062e-11	1.03e-08	2.7888e-14	2.11e-11	7.0305e-07	0.000447	5.2411e-11	3.8e-08	7.208e-19	5.62e-16	2.1146e-20	1.65e-17	1.9558e-19	1.53e-16	5.8682e-20	4.58e-17
17p loss	367 (41%)	524	0.037618	1	0.67782	1	2.0398e-12	1.52e-09	1.3967e-07	9.19e-05	0.0012091	0.519	0.15162	1	0.20966	1	0.91401	1	2.9401e-05	0.0163	0.027558	1
17q loss	141 (16%)	750	4.0151e-08	2.7e-05	1.0339e-06	0.000654	9.2734e-14	6.98e-11	1.1184e-06	0.000705	3.3791e-10	2.4e-07	5.8436e-07	0.000374	1.731e-10	1.24e-07	1.0572e-05	0.00617	3.6698e-09	2.57e-06	1.0935e-06	0.000691
18p loss	172 (19%)	719	0.062464	1	0.077894	1	3.2002e-08	2.16e-05	4.3221e-06	0.0026	0.98719	1	0.97434	1	0.036883	1	0.55878	1	0.045219	1	0.027529	1
18q loss	175 (20%)	716	0.0092465	1	0.12151	1	9.7614e-11	7.04e-08	4.0439e-08	2.72e-05	0.54752	1	0.79453	1	0.0035725	1	0.13641	1	0.055409	1	0.18796	1
19p loss	65 (7%)	826	0.14285	1	0.00027333	0.133	8.8289e-14	6.66e-11	1.8961e-09	1.33e-06	0.53801	1	0.11757	1	0.00084491	0.371	0.0021035	0.848	0.00080779	0.357	0.16504	1
19q loss	51 (6%)	840	0.11641	1	3.1205e-05	0.0172	1.4268e-11	1.05e-08	1.1502e-05	0.00667	0.14976	1	0.12495	1	0.0001328	0.0677	0.00088018	0.384	0.013739	1	0.25838	1
20p loss	54 (6%)	837	0.55448	1	0.015671	1	9.3784e-08	6.2e-05	0.00043131	0.201	0.36197	1	0.49766	1	0.0036639	1	0.00047878	0.219	5.0868e-05	0.0273	0.0032533	1
20q loss	29 (3%)	862	0.84842	1	0.10221	1	4.7509e-06	0.00285	8.4293e-06	0.00499	0.52909	1	0.16217	1	0.0041759	1	0.00021663	0.107	5.0627e-05	0.0272	2.7609e-05	0.0154
21q loss	87 (10%)	804	0.23477	1	0.29842	1	1.3137e-06	0.000825	0.35383	1	0.97797	1	0.87361	1	0.32439	1	0.401	1	0.034605	1	0.14465	1
22q loss	298 (33%)	593	3.0778e-05	0.017	5.4191e-07	0.000347	4.9693e-08	3.32e-05	9.121e-06	0.00537	0.00035787	0.169	1.0169e-05	0.00595	1.5413e-11	1.13e-08	8.2786e-10	5.84e-07	1.6457e-08	1.13e-05	6.5805e-07	0.00042
Xq loss	30 (3%)	861	0.0041487	1	0.12236	1	0.00011878	0.0612	0.0014259	0.607	0.035578	1	0.31662	1	0.0096351	1	0.069236	1	7.2127e-05	0.0382	0.027751	1
