Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_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	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q
Amp Peak  1(1q31.1)	0 (0%)	441	0.58357	1	0.30814	1	0.00020463	0.144	0.52809	1	0.47376	1	0.2894	1	0.089288	1	0.3201	1	0.76478	1	0.94434	1	0.22826	1	0.21316	1
Amp Peak  2(2q33.1)	0 (0%)	452	0.088273	1	0.00031948	0.22	1.5207e-06	0.00116	0.0097334	1	0.59604	1	0.90087	1	0.00017266	0.122	0.0001656	0.118	0.18061	1	0.0012944	0.844	0.40203	1	0.0017686	1
Amp Peak  3(5p12)	0 (0%)	468	0.097746	1	0.43491	1	6.5452e-06	0.00492	0.79444	1	0.074578	1	0.72076	1	0.10221	1	0.018933	1	0.88927	1	0.34721	1	0.01018	1	0.22853	1
Amp Peak  4(5q22.3)	0 (0%)	516	0.56517	1	0.88657	1	0.0037006	1	0.22632	1	0.67613	1	0.81532	1	0.24841	1	0.020002	1	0.46039	1	0.89428	1	0.1925	1	0.32589	1
Amp Peak  5(6p21.1)	0 (0%)	429	0.022387	1	0.0018435	1	3.9711e-14	3.36e-11	0.19965	1	0.69928	1	0.36883	1	0.00093145	0.618	0.015078	1	0.53094	1	0.0067783	1	0.021104	1	0.00013891	0.0993
Amp Peak  6(7p21.3)	0 (0%)	238	0.0022982	1	0.00093227	0.618	7.9137e-22	6.93e-19	1.043e-06	0.000803	0.30824	1	0.026569	1	6.8733e-10	5.59e-07	3.1463e-06	0.00238	0.022382	1	0.0025921	1	0.0046297	1	3.8046e-11	3.14e-08
Amp Peak  7(8p11.23)	0 (0%)	379	0.39583	1	0.048564	1	2.8317e-23	2.49e-20	0.26322	1	0.826	1	0.49971	1	0.2349	1	0.78078	1	0.015361	1	0.077226	1	0.13923	1	0.32731	1
Amp Peak  8(8p11.21)	0 (0%)	337	0.17312	1	0.0085408	1	3.3334e-31	2.95e-28	0.30066	1	0.3784	1	0.39445	1	0.41011	1	0.735	1	0.081506	1	0.20055	1	0.25233	1	0.26678	1
Amp Peak  9(8q12.1)	0 (0%)	266	0.14319	1	0.00074934	0.502	1.9068e-36	1.7e-33	0.020948	1	0.018292	1	0.054607	1	0.00051184	0.35	0.0072851	1	0.10208	1	0.1461	1	0.006211	1	0.0062419	1
Amp Peak 10(8q24.21)	0 (0%)	230	0.23902	1	0.00022654	0.159	3.1776e-35	2.82e-32	0.0024963	1	0.042735	1	0.28329	1	0.00029443	0.204	0.010935	1	0.25116	1	0.17643	1	0.0099467	1	0.0017483	1
Amp Peak 11(10q22.3)	0 (0%)	540	1	1	0.18228	1	0.65461	1	0.5614	1	0.26319	1	0.8502	1	0.57912	1	0.1871	1	0.58747	1	0.28086	1	0.39646	1	0.43329	1
Amp Peak 12(11p15.5)	0 (0%)	446	0.00020189	0.142	0.00068431	0.463	1.8397e-06	0.0014	0.007966	1	0.0056025	1	0.23771	1	4.7475e-05	0.0345	7.6788e-06	0.00576	0.35173	1	0.0090568	1	0.0019348	1	2.7747e-08	2.2e-05
Amp Peak 13(12p13.32)	0 (0%)	431	0.55635	1	0.78684	1	0.25212	1	0.10379	1	0.76788	1	0.81342	1	0.20541	1	0.3483	1	0.67615	1	0.88617	1	0.72672	1	0.58445	1
Amp Peak 14(13q12.13)	0 (0%)	204	1.9206e-07	0.00015	4.1221e-06	0.00311	6.4175e-44	5.75e-41	1.666e-10	1.36e-07	0.013058	1	0.063964	1	8.0009e-11	6.57e-08	4.9743e-07	0.000386	0.013611	1	0.23666	1	5.8918e-09	4.69e-06	1.2758e-12	1.07e-09
Amp Peak 15(13q12.2)	0 (0%)	209	4.6534e-06	0.00351	5.2465e-05	0.038	2.2045e-45	1.98e-42	3.9642e-11	3.26e-08	0.031887	1	0.16887	1	2.1277e-10	1.74e-07	1.0832e-06	0.000831	0.026046	1	0.28461	1	1.3295e-07	0.000104	3.9483e-12	3.28e-09
Amp Peak 16(13q22.1)	0 (0%)	204	9.7292e-06	0.00727	0.00019346	0.137	7.6851e-42	6.86e-39	4.9092e-09	3.92e-06	0.080803	1	0.17377	1	9.8228e-10	7.98e-07	5.3606e-07	0.000415	0.03008	1	0.04712	1	8.5365e-07	0.000658	1.2566e-09	1.02e-06
Amp Peak 17(15q26.1)	0 (0%)	532	0.52717	1	0.062925	1	0.24946	1	0.81352	1	0.10535	1	0.30767	1	0.19087	1	0.2414	1	0.92601	1	1	1	0.47298	1	0.29538	1
Amp Peak 18(16p11.2)	0 (0%)	414	0.017934	1	0.005738	1	1.3311e-20	1.16e-17	0.00018147	0.128	0.091544	1	0.015693	1	2.1703e-05	0.016	0.0036874	1	0.81077	1	0.11023	1	0.0049049	1	3.2496e-05	0.0237
Amp Peak 19(17q12)	0 (0%)	431	0.044286	1	0.027559	1	3.4581e-09	2.78e-06	0.012058	1	0.22957	1	0.059168	1	0.00042372	0.291	0.0021241	1	0.038998	1	0.23162	1	0.81203	1	0.071714	1
Amp Peak 20(17q24.1)	0 (0%)	447	0.025694	1	0.0012574	0.824	1.5413e-08	1.23e-05	0.00067812	0.459	0.12434	1	0.005577	1	0.0002006	0.141	0.0030881	1	0.0012716	0.832	0.041926	1	0.95349	1	0.0040284	1
Amp Peak 21(19p13.2)	0 (0%)	478	0.10769	1	0.43683	1	8.872e-08	6.96e-05	0.016928	1	0.93193	1	0.39022	1	0.32934	1	0.41774	1	0.27415	1	0.13138	1	0.35705	1	0.00026697	0.185
Amp Peak 22(19q12)	0 (0%)	453	0.028073	1	0.038973	1	6.2256e-08	4.9e-05	0.16619	1	0.258	1	0.32613	1	0.074742	1	0.078878	1	0.70958	1	0.49006	1	0.40718	1	0.01255	1
Amp Peak 23(20p11.23)	0 (0%)	274	0.0054725	1	0.0042234	1	5.5572e-17	4.8e-14	0.016883	1	0.0014249	0.928	0.17784	1	1.065e-05	0.00793	2.2906e-05	0.0168	0.35274	1	0.42547	1	0.00072478	0.487	2.0659e-05	0.0152
Amp Peak 24(20p11.21)	0 (0%)	236	0.00023143	0.162	1.806e-05	0.0133	8.5661e-23	7.51e-20	3.0086e-05	0.022	0.0071331	1	0.15844	1	4.8331e-09	3.87e-06	3.8008e-09	3.05e-06	0.10712	1	0.18811	1	0.00016133	0.115	2.14e-09	1.73e-06
Amp Peak 25(20q11.21)	0 (0%)	136	1.1905e-13	1e-10	9.5932e-13	8.04e-10	1.5402e-42	1.38e-39	3.3857e-16	2.92e-13	0.012869	1	0.010343	1	1.5937e-19	1.39e-16	5.246e-18	4.55e-15	0.12378	1	0.018878	1	5.5775e-10	4.55e-07	6.0181e-23	5.28e-20
Amp Peak 26(20q12)	0 (0%)	134	1.0598e-14	9e-12	4.1828e-14	3.53e-11	5.8367e-43	5.22e-40	5.8962e-15	5.03e-12	0.0068663	1	0.005549	1	5.4214e-19	4.72e-16	1.8134e-17	1.57e-14	0.065014	1	0.0077889	1	2.4418e-11	2.02e-08	1.0251e-24	9.05e-22
Amp Peak 27(20q13.32)	0 (0%)	131	7.7972e-14	6.57e-11	2.0156e-12	1.68e-09	5.6648e-43	5.07e-40	6.3224e-14	5.34e-11	0.012975	1	0.0044002	1	5.4214e-19	4.72e-16	1.8134e-17	1.57e-14	0.11691	1	0.032951	1	2.3341e-10	1.91e-07	3.5151e-23	3.09e-20
Amp Peak 28(Xq28)	0 (0%)	454	0.43576	1	0.88431	1	1.7197e-06	0.00131	0.16122	1	0.0033525	1	0.0093042	1	0.17084	1	0.024028	1	0.98952	1	0.78345	1	0.38092	1	0.16808	1
Del Peak  1(1p36.11)	0 (0%)	353	0.00011447	0.0822	0.0037923	1	2.207e-13	1.85e-10	9.0119e-05	0.0649	0.046797	1	0.14778	1	1.0504e-05	0.00784	6.5371e-05	0.0472	0.15838	1	0.018302	1	0.039236	1	0.0017647	1
Del Peak  2(1p33)	0 (0%)	419	0.030575	1	0.091327	1	8.9471e-13	7.51e-10	0.00081136	0.542	0.80118	1	0.57447	1	0.0015984	1	0.0020772	1	0.53241	1	0.015895	1	0.11685	1	0.0014259	0.928
Del Peak  3(1p13.2)	0 (0%)	418	0.28805	1	0.12889	1	3.379e-09	2.72e-06	0.026371	1	0.93711	1	0.7023	1	0.013159	1	0.00062049	0.422	0.75564	1	0.3515	1	0.13426	1	0.040174	1
Del Peak  4(2p12)	0 (0%)	555	1	1	0.81015	1	0.0019382	1	0.010971	1	0.18705	1	1	1	0.173	1	0.73813	1	0.016497	1	0.021531	1	0.38522	1	0.32068	1
Del Peak  5(2q22.1)	0 (0%)	542	0.92642	1	0.31059	1	0.14635	1	0.83244	1	0.09979	1	0.90131	1	0.97396	1	0.79732	1	0.31564	1	0.27226	1	0.936	1	0.48676	1
Del Peak  6(2q37.2)	0 (0%)	545	0.91149	1	0.86255	1	0.28501	1	0.83244	1	0.27828	1	0.16188	1	0.56014	1	0.09482	1	0.24408	1	0.36359	1	0.58235	1	0.90264	1
Del Peak  7(3p26.3)	0 (0%)	491	0.35771	1	0.75263	1	0.16257	1	0.36456	1	0.85594	1	0.82449	1	0.28049	1	0.0366	1	0.27674	1	0.72808	1	0.027438	1	0.12786	1
Del Peak  8(3p14.2)	0 (0%)	471	0.61954	1	0.9908	1	0.93155	1	0.46128	1	0.56538	1	0.67377	1	0.55342	1	0.66263	1	0.059527	1	0.91843	1	0.069608	1	0.43417	1
Del Peak  9(3q26.31)	0 (0%)	519	0.54351	1	0.78763	1	0.4484	1	0.36303	1	0.14521	1	0.51007	1	0.30763	1	0.05159	1	0.093407	1	0.12285	1	0.22428	1	0.047593	1
Del Peak 10(4p16.1)	0 (0%)	393	0.065426	1	0.43666	1	1.6474e-12	1.38e-09	0.0011364	0.748	0.41627	1	0.92296	1	1.322e-06	0.00101	0.00014327	0.102	0.62193	1	0.11684	1	0.00036129	0.248	0.00071185	0.48
Del Peak 11(4q22.1)	0 (0%)	377	0.021594	1	0.030995	1	1.2505e-14	1.06e-11	6.9942e-05	0.0504	0.76659	1	0.77009	1	7.0961e-06	0.00533	0.00018004	0.127	0.14791	1	0.4088	1	0.00050728	0.347	0.00071236	0.48
Del Peak 12(4q35.1)	0 (0%)	364	0.021025	1	0.1701	1	1.2462e-13	1.05e-10	0.00059525	0.406	0.46423	1	0.81052	1	5.0681e-05	0.0367	3.7357e-05	0.0272	0.52329	1	0.74296	1	3.702e-05	0.027	0.00098792	0.653
Del Peak 13(5q11.2)	0 (0%)	435	0.00059982	0.408	0.0046582	1	2.1328e-12	1.78e-09	0.0060295	1	0.10314	1	0.54742	1	0.0003174	0.22	0.0020471	1	1	1	0.75785	1	0.00012752	0.0913	3.1656e-05	0.0231
Del Peak 14(5q22.2)	0 (0%)	403	0.0010635	0.701	0.031384	1	2.2261e-09	1.79e-06	0.15829	1	0.38844	1	0.92197	1	0.0016795	1	0.1687	1	0.77075	1	0.85443	1	0.025749	1	0.0030059	1
Del Peak 15(6p25.3)	0 (0%)	497	0.90663	1	0.55332	1	0.08489	1	0.25687	1	0.17635	1	0.94018	1	0.96051	1	0.38499	1	0.60986	1	0.95718	1	0.035093	1	0.61429	1
Del Peak 16(6q26)	0 (0%)	485	0.77681	1	0.33063	1	0.04006	1	0.77867	1	0.05416	1	0.45135	1	0.9192	1	0.94771	1	0.22283	1	0.50721	1	0.47795	1	0.6278	1
Del Peak 17(7q31.1)	0 (0%)	560	0.29223	1	0.93264	1	1	1	1	1	0.58895	1	0.27267	1	0.66022	1	0.71365	1	0.23486	1	0.49815	1	0.36112	1	0.57151	1
Del Peak 18(8p23.2)	0 (0%)	303	0.00025797	0.179	0.00014587	0.104	2.1272e-34	1.88e-31	1.0636e-06	0.000817	0.096377	1	0.0031593	1	1.5158e-05	0.0112	0.00056078	0.383	0.80158	1	0.39873	1	3.4887e-08	2.76e-05	2.5952e-06	0.00197
Del Peak 19(8p22)	0 (0%)	290	0.0011796	0.774	0.00085665	0.569	1.581e-37	1.41e-34	6.7016e-07	0.000518	0.10002	1	0.0022544	1	1.0532e-06	0.00081	0.00022349	0.157	0.76329	1	0.64202	1	2.3398e-06	0.00178	2.0368e-06	0.00155
Del Peak 20(8p11.21)	0 (0%)	451	0.035375	1	0.12229	1	4.8516e-07	0.000377	0.17095	1	0.085255	1	0.090311	1	0.062079	1	0.049746	1	0.1625	1	0.40038	1	0.085128	1	0.018168	1
Del Peak 21(8q11.1)	0 (0%)	531	0.5801	1	0.55725	1	0.0026632	1	0.6323	1	0.39563	1	0.56794	1	0.31533	1	0.32022	1	0.081906	1	0.019346	1	0.25339	1	0.47166	1
Del Peak 22(9p24.2)	0 (0%)	497	0.45163	1	0.29858	1	0.0017841	1	0.112	1	0.53215	1	0.59166	1	0.029546	1	0.0024061	1	0.29637	1	0.2426	1	0.065082	1	0.048645	1
Del Peak 23(10p15.3)	0 (0%)	473	0.23157	1	0.16851	1	1.3776e-07	0.000108	0.024385	1	0.022956	1	0.15821	1	0.012185	1	0.057586	1	0.71014	1	0.30188	1	0.085128	1	0.063048	1
Del Peak 24(10q21.1)	0 (0%)	457	0.17122	1	0.11962	1	3.1348e-11	2.59e-08	0.13885	1	0.087092	1	0.13262	1	0.072765	1	0.043804	1	0.69109	1	0.57652	1	0.13834	1	0.61701	1
Del Peak 25(10q23.31)	0 (0%)	430	0.13642	1	0.5197	1	9.0881e-08	7.13e-05	0.21635	1	0.03301	1	0.24197	1	0.0026248	1	0.068467	1	0.76199	1	0.36526	1	0.0074648	1	0.023655	1
Del Peak 26(10q25.2)	0 (0%)	435	0.318	1	0.16237	1	3.0619e-12	2.55e-09	0.16645	1	0.0092232	1	0.24513	1	0.0002385	0.166	0.00032441	0.224	0.97166	1	0.77949	1	0.0041097	1	0.0092267	1
Del Peak 27(11q22.3)	0 (0%)	471	0.47835	1	0.065843	1	0.03853	1	0.11685	1	0.43699	1	0.14737	1	0.03654	1	0.52358	1	0.65677	1	0.36295	1	0.091419	1	0.10992	1
Del Peak 28(12p13.1)	0 (0%)	498	0.0059934	1	0.014154	1	3.8948e-08	3.08e-05	0.58938	1	0.9771	1	0.73193	1	0.057107	1	0.42333	1	0.44647	1	0.91879	1	0.0078824	1	0.12062	1
Del Peak 29(12q21.2)	0 (0%)	495	0.13733	1	0.02938	1	5.5178e-07	0.000427	0.32706	1	0.90127	1	0.54623	1	0.035123	1	0.2942	1	0.52063	1	0.97871	1	0.073602	1	0.034823	1
Del Peak 30(14q22.1)	0 (0%)	390	0.00074741	0.502	0.00011745	0.0842	1.9531e-28	1.73e-25	2.5421e-06	0.00193	0.00031769	0.22	0.12083	1	4.0917e-08	3.23e-05	3.0832e-05	0.0225	0.12679	1	0.43856	1	3.914e-07	0.000305	7.6826e-07	0.000593
Del Peak 31(15q11.2)	0 (0%)	342	0.0008209	0.548	0.0048717	1	1.2039e-23	1.06e-20	0.0063689	1	0.3501	1	0.35894	1	1.4108e-06	0.00108	1.375e-05	0.0102	0.47751	1	0.11089	1	0.00023284	0.163	1.6944e-05	0.0125
Del Peak 32(15q21.1)	0 (0%)	348	0.0008361	0.556	0.02392	1	2.4292e-21	2.13e-18	0.004424	1	0.12951	1	0.13029	1	2.2022e-07	0.000172	2.2976e-05	0.0168	0.74178	1	0.45864	1	0.00024913	0.173	6.46e-05	0.0467
Del Peak 33(15q22.33)	0 (0%)	358	0.00019922	0.14	0.0011582	0.761	4.4907e-23	3.95e-20	0.0010354	0.683	0.66051	1	0.46255	1	5.8136e-09	4.64e-06	5.4971e-06	0.00414	0.86536	1	0.1165	1	0.00068828	0.465	1.1367e-05	0.00846
Del Peak 34(16p13.3)	0 (0%)	517	0.13856	1	0.11894	1	0.21481	1	0.67618	1	0.66923	1	0.78854	1	0.92693	1	0.17584	1	0.63651	1	0.59521	1	0.90141	1	0.52771	1
Del Peak 35(16q23.1)	0 (0%)	503	0.04389	1	0.0072891	1	0.17918	1	0.36799	1	0.18011	1	0.92463	1	0.27086	1	0.22958	1	0.80518	1	0.63247	1	0.71456	1	0.30115	1
Del Peak 36(17p12)	0 (0%)	232	8.379e-08	6.59e-05	2.2016e-05	0.0162	2.0063e-34	1.78e-31	4.4089e-08	3.47e-05	0.10279	1	0.024703	1	1.5954e-08	1.27e-05	3.3152e-06	0.00251	0.051965	1	0.67329	1	1.8775e-05	0.0139	4.6838e-11	3.85e-08
Del Peak 37(17q24.3)	0 (0%)	491	1	1	0.22422	1	0.029627	1	0.52835	1	1	1	0.52344	1	0.18383	1	0.078066	1	0.91947	1	0.42487	1	0.22692	1	0.38361	1
Del Peak 38(18p11.31)	0 (0%)	234	5.7977e-12	4.81e-09	6.2426e-10	5.08e-07	1.1905e-41	1.06e-38	1.0792e-15	9.29e-13	0.10117	1	0.03053	1	1.4029e-20	1.22e-17	5.0845e-15	4.35e-12	0.018344	1	0.38647	1	5.6663e-12	4.7e-09	1.7462e-14	1.48e-11
Del Peak 39(18q12.2)	0 (0%)	189	1.0102e-09	8.19e-07	4.5892e-09	3.68e-06	1.2945e-49	1.16e-46	1.6711e-17	1.45e-14	0.043089	1	0.028019	1	2.8352e-19	2.47e-16	1.22e-10	1e-07	0.0057877	1	0.059024	1	9.4323e-12	7.81e-09	1.2733e-18	1.11e-15
Del Peak 40(18q21.2)	0 (0%)	172	3.7165e-10	3.03e-07	1.643e-08	1.3e-05	1.2388e-50	1.11e-47	5.2515e-15	4.48e-12	0.013386	1	0.024656	1	2.8314e-15	2.43e-12	1.4217e-09	1.15e-06	0.00065728	0.446	0.12629	1	2.3217e-11	1.92e-08	2.8319e-15	2.43e-12
Del Peak 41(18q22.1)	0 (0%)	177	2.012e-09	1.63e-06	1.232e-07	9.65e-05	9.5463e-53	8.59e-50	2.2045e-15	1.9e-12	0.033443	1	0.019973	1	2.8314e-15	2.43e-12	5.8399e-09	4.65e-06	0.0012813	0.837	0.17094	1	4.1248e-12	3.43e-09	4.2436e-15	3.63e-12
Del Peak 42(19p13.3)	0 (0%)	483	0.11712	1	0.15089	1	1.3518e-05	0.01	0.9441	1	0.63643	1	0.66556	1	0.032861	1	0.0086858	1	0.57921	1	0.91111	1	0.013378	1	0.00034243	0.236
Del Peak 43(19q13.43)	0 (0%)	507	0.72014	1	0.21925	1	0.0001104	0.0794	0.74946	1	0.085945	1	0.93678	1	0.0093455	1	0.0091629	1	0.25511	1	0.50243	1	0.1394	1	0.1057	1
Del Peak 44(20p12.1)	0 (0%)	396	0.019713	1	0.020259	1	6.5033e-15	5.54e-12	8.8947e-06	0.00666	0.32817	1	0.0071167	1	0.023187	1	0.015089	1	0.22326	1	0.97624	1	0.047016	1	0.024058	1
Del Peak 45(20p12.1)	0 (0%)	396	0.019713	1	0.020259	1	6.5033e-15	5.54e-12	8.8947e-06	0.00666	0.32817	1	0.0071167	1	0.023187	1	0.015089	1	0.22326	1	0.97624	1	0.047016	1	0.024058	1
Del Peak 46(21q11.2)	0 (0%)	380	0.022381	1	0.021634	1	4.0688e-09	3.26e-06	0.014236	1	0.58363	1	0.21291	1	0.00064744	0.44	0.0052738	1	0.23351	1	0.049362	1	0.00014276	0.102	0.022635	1
Del Peak 47(22q13.32)	0 (0%)	371	0.0047599	1	0.005782	1	9.8306e-15	8.36e-12	0.047023	1	0.47259	1	0.61741	1	0.00082402	0.549	0.034892	1	0.69579	1	0.011544	1	0.00075115	0.503	0.0068327	1