		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	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	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
Amp Peak  1(1q31.1)	134 (23%)	441	0.4442	1	0.81342	1	0.00020463	0.122	0.72236	1	0.4195	1	0.87385	1	0.089288	1	0.3201	1	0.76478	1	0.94434	1
Amp Peak  2(2q33.1)	123 (21%)	452	0.04804	1	0.060868	1	1.5207e-06	0.000978	0.0050196	1	0.31104	1	0.35953	1	0.00017266	0.103	0.0001656	0.0992	0.18061	1	0.0012944	0.725
Amp Peak  3(5p12)	107 (19%)	468	0.097844	1	0.97392	1	6.5452e-06	0.00414	0.7939	1	0.47066	1	0.39976	1	0.10221	1	0.018933	1	0.88927	1	0.34721	1
Amp Peak  4(5q22.3)	59 (10%)	516	0.89444	1	1	1	0.0037006	1	0.3195	1	0.68971	1	0.76879	1	0.24841	1	0.020002	1	0.46039	1	0.89428	1
Amp Peak  5(6p21.1)	146 (25%)	429	0.026325	1	0.0030838	1	3.9711e-14	2.78e-11	0.16938	1	0.18907	1	0.57828	1	0.00093145	0.529	0.015078	1	0.53094	1	0.0067783	1
Amp Peak  6(7p21.3)	337 (59%)	238	0.00063586	0.368	0.0068793	1	7.9137e-22	5.77e-19	7.1064e-06	0.00448	0.41594	1	0.0075144	1	6.8733e-10	4.69e-07	3.1463e-06	0.002	0.022382	1	0.0025921	1
Amp Peak  7(8p11.23)	196 (34%)	379	0.57345	1	0.40042	1	2.8317e-23	2.07e-20	0.30365	1	0.88421	1	0.65326	1	0.2349	1	0.78078	1	0.015361	1	0.077226	1
Amp Peak  8(8p11.21)	238 (41%)	337	0.30634	1	0.25613	1	3.3334e-31	2.45e-28	0.23711	1	0.49049	1	0.61284	1	0.41011	1	0.735	1	0.081506	1	0.20055	1
Amp Peak  9(8q12.1)	309 (54%)	266	0.079837	1	0.11835	1	1.9068e-36	1.41e-33	0.015312	1	0.10139	1	0.40856	1	0.00051184	0.298	0.0072851	1	0.10208	1	0.1461	1
Amp Peak 10(8q24.21)	345 (60%)	230	0.24015	1	0.19563	1	3.1776e-35	2.35e-32	0.0042881	1	0.34453	1	0.43979	1	0.00029443	0.174	0.010935	1	0.25116	1	0.17643	1
Amp Peak 11(10q22.3)	35 (6%)	540	0.90315	1	0.14493	1	0.65461	1	0.56037	1	0.37964	1	0.3414	1	0.57912	1	0.1871	1	0.58747	1	0.28086	1
Amp Peak 12(11p15.5)	129 (22%)	446	4.3117e-05	0.0263	0.0011533	0.649	1.8397e-06	0.00118	0.0034433	1	0.010806	1	0.10027	1	4.7475e-05	0.029	7.6788e-06	0.00482	0.35173	1	0.0090568	1
Amp Peak 13(12p13.32)	144 (25%)	431	0.18079	1	0.78626	1	0.25212	1	0.13658	1	1	1	0.87363	1	0.20541	1	0.3483	1	0.67615	1	0.88617	1
Amp Peak 14(13q12.13)	371 (65%)	204	3.2507e-08	2.16e-05	1.565e-06	0.001	6.4175e-44	4.79e-41	8.9135e-11	6.11e-08	0.077968	1	0.060103	1	8.0009e-11	5.5e-08	4.9743e-07	0.000324	0.013611	1	0.23666	1
Amp Peak 15(13q12.2)	366 (64%)	209	9.9561e-07	0.000646	1.9696e-05	0.0122	2.2045e-45	1.65e-42	2.3112e-11	1.59e-08	0.20878	1	0.13462	1	2.1277e-10	1.46e-07	1.0832e-06	0.000701	0.026046	1	0.28461	1
Amp Peak 16(13q22.1)	371 (65%)	204	7.5802e-06	0.00477	7.2369e-05	0.0439	7.6851e-42	5.7e-39	2.9909e-09	2.02e-06	0.16925	1	0.081763	1	9.8228e-10	6.68e-07	5.3606e-07	0.000349	0.03008	1	0.04712	1
Amp Peak 17(15q26.1)	43 (7%)	532	0.52584	1	0.39376	1	0.24946	1	0.84162	1	0.63974	1	0.59102	1	0.19087	1	0.2414	1	0.92601	1	1	1
Amp Peak 18(16p11.2)	161 (28%)	414	0.013406	1	0.0069521	1	1.3311e-20	9.68e-18	0.0015397	0.859	0.036894	1	0.0317	1	2.1703e-05	0.0134	0.0036874	1	0.81077	1	0.11023	1
Amp Peak 19(17q12)	144 (25%)	431	0.015027	1	0.1003	1	3.4581e-09	2.33e-06	0.0072631	1	0.50619	1	0.044214	1	0.00042372	0.248	0.0021241	1	0.038998	1	0.23162	1
Amp Peak 20(17q24.1)	128 (22%)	447	0.0096287	1	0.0080793	1	1.5413e-08	1.03e-05	0.00034993	0.206	0.088685	1	0.012439	1	0.0002006	0.12	0.0030881	1	0.0012716	0.715	0.041926	1
Amp Peak 21(19p13.2)	97 (17%)	478	0.043869	1	0.37731	1	8.872e-08	5.83e-05	0.031724	1	0.62231	1	0.74495	1	0.32934	1	0.41774	1	0.27415	1	0.13138	1
Amp Peak 22(19q12)	122 (21%)	453	0.030799	1	0.010651	1	6.2256e-08	4.12e-05	0.25113	1	0.29029	1	0.46249	1	0.074742	1	0.078878	1	0.70958	1	0.49006	1
Amp Peak 23(20p11.23)	301 (52%)	274	0.011702	1	0.00040084	0.235	5.5572e-17	3.98e-14	0.014078	1	0.068775	1	0.37584	1	1.065e-05	0.00663	2.2906e-05	0.0141	0.35274	1	0.42547	1
Amp Peak 24(20p11.21)	339 (59%)	236	0.00023856	0.141	1.5383e-06	0.000988	8.5661e-23	6.25e-20	6.9846e-06	0.00441	0.13479	1	0.26756	1	4.8331e-09	3.24e-06	3.8008e-09	2.55e-06	0.10712	1	0.18811	1
Amp Peak 25(20q11.21)	439 (76%)	136	4.1451e-15	2.93e-12	7.4821e-14	5.22e-11	1.5402e-42	1.14e-39	2.1295e-16	1.52e-13	0.12124	1	0.00091279	0.519	1.5937e-19	1.16e-16	5.246e-18	3.78e-15	0.12378	1	0.018878	1
Amp Peak 26(20q12)	441 (77%)	134	3.226e-16	2.31e-13	3.2727e-15	2.32e-12	5.8367e-43	4.34e-40	3.5601e-15	2.52e-12	0.054733	1	0.00089654	0.511	5.4214e-19	3.92e-16	1.8134e-17	1.3e-14	0.065014	1	0.0077889	1
Amp Peak 27(20q13.32)	444 (77%)	131	2.88e-15	2.04e-12	1.2514e-13	8.71e-11	5.6648e-43	4.22e-40	3.2142e-14	2.25e-11	0.076835	1	0.00045984	0.269	5.4214e-19	3.92e-16	1.8134e-17	1.3e-14	0.11691	1	0.032951	1
Amp Peak 28(Xq28)	121 (21%)	454	0.34508	1	0.58069	1	1.7197e-06	0.0011	0.10043	1	0.00068292	0.392	0.13281	1	0.17084	1	0.024028	1	0.98952	1	0.78345	1
Del Peak  1(1p36.11)	222 (39%)	353	7.4515e-05	0.0452	0.0021128	1	2.207e-13	1.53e-10	2.1039e-05	0.013	0.033102	1	0.058686	1	1.0504e-05	0.00655	6.5371e-05	0.0397	0.15838	1	0.018302	1
Del Peak  2(1p33)	156 (27%)	419	0.010261	1	0.071826	1	8.9471e-13	6.2e-10	0.00037065	0.218	0.21767	1	0.095474	1	0.0015984	0.89	0.0020772	1	0.53241	1	0.015895	1
Del Peak  3(1p13.2)	157 (27%)	418	0.18918	1	0.092345	1	3.379e-09	2.28e-06	0.015335	1	0.90798	1	0.069001	1	0.013159	1	0.00062049	0.36	0.75564	1	0.3515	1
Del Peak  4(2p12)	20 (3%)	555	1	1	0.43462	1	0.0019382	1	0.011104	1	0.47992	1	0.80739	1	0.173	1	0.73813	1	0.016497	1	0.021531	1
Del Peak  5(2q22.1)	33 (6%)	542	0.92685	1	0.85059	1	0.14635	1	0.83265	1	0.36323	1	0.61845	1	0.97396	1	0.79732	1	0.31564	1	0.27226	1
Del Peak  6(2q37.2)	30 (5%)	545	0.92384	1	0.69056	1	0.28501	1	0.83265	1	0.20452	1	0.44389	1	0.56014	1	0.09482	1	0.24408	1	0.36359	1
Del Peak  7(3p26.3)	84 (15%)	491	0.10463	1	0.81892	1	0.16257	1	0.35748	1	0.98369	1	0.34579	1	0.28049	1	0.0366	1	0.27674	1	0.72808	1
Del Peak  8(3p14.2)	104 (18%)	471	0.47522	1	0.89997	1	0.93155	1	0.59731	1	0.92799	1	0.784	1	0.55342	1	0.66263	1	0.059527	1	0.91843	1
Del Peak  9(3q26.31)	56 (10%)	519	0.29676	1	0.55419	1	0.4484	1	0.37333	1	0.13392	1	0.67614	1	0.30763	1	0.05159	1	0.093407	1	0.12285	1
Del Peak 10(4p16.1)	182 (32%)	393	0.052415	1	0.42363	1	1.6474e-12	1.14e-09	0.0020286	1	0.88241	1	0.4007	1	1.322e-06	0.000853	0.00014327	0.086	0.62193	1	0.11684	1
Del Peak 11(4q22.1)	198 (34%)	377	0.019286	1	0.05072	1	1.2505e-14	8.77e-12	7.6585e-05	0.0463	0.9259	1	0.36478	1	7.0961e-06	0.00448	0.00018004	0.107	0.14791	1	0.4088	1
Del Peak 12(4q35.1)	211 (37%)	364	0.016065	1	0.18529	1	1.2462e-13	8.69e-11	0.00064166	0.371	0.85993	1	0.66867	1	5.0681e-05	0.0309	3.7357e-05	0.0229	0.52329	1	0.74296	1
Del Peak 13(5q11.2)	140 (24%)	435	0.0019081	1	0.48007	1	2.1328e-12	1.47e-09	0.0028212	1	0.79264	1	0.1416	1	0.0003174	0.187	0.0020471	1	1	1	0.75785	1
Del Peak 14(5q22.2)	172 (30%)	403	0.0014099	0.788	0.058116	1	2.2261e-09	1.51e-06	0.11369	1	0.88423	1	0.71216	1	0.0016795	0.934	0.1687	1	0.77075	1	0.85443	1
Del Peak 15(6p25.3)	78 (14%)	497	0.83957	1	0.59942	1	0.08489	1	0.26246	1	1	1	0.31536	1	0.96051	1	0.38499	1	0.60986	1	0.95718	1
Del Peak 16(6q26)	90 (16%)	485	0.88608	1	0.69786	1	0.04006	1	0.76234	1	0.23479	1	0.58184	1	0.9192	1	0.94771	1	0.22283	1	0.50721	1
Del Peak 17(7q31.1)	15 (3%)	560	0.10252	1	1	1	1	1	1	1	0.43394	1	0.51037	1	0.66022	1	0.71365	1	0.23486	1	0.49815	1
Del Peak 18(8p23.2)	272 (47%)	303	0.00058553	0.34	0.032242	1	2.1272e-34	1.57e-31	1.9574e-06	0.00125	0.30663	1	0.014477	1	1.5158e-05	0.0094	0.00056078	0.326	0.80158	1	0.39873	1
Del Peak 19(8p22)	285 (50%)	290	0.0010879	0.617	0.033402	1	1.581e-37	1.17e-34	1.3157e-06	0.00085	0.27708	1	0.0011064	0.626	1.0532e-06	0.000682	0.00022349	0.133	0.76329	1	0.64202	1
Del Peak 20(8p11.21)	124 (22%)	451	0.011149	1	0.12636	1	4.8516e-07	0.000317	0.34128	1	0.3515	1	0.15854	1	0.062079	1	0.049746	1	0.1625	1	0.40038	1
Del Peak 21(8q11.1)	44 (8%)	531	0.27183	1	0.68653	1	0.0026632	1	0.66125	1	0.75678	1	0.096474	1	0.31533	1	0.32022	1	0.081906	1	0.019346	1
Del Peak 22(9p24.2)	78 (14%)	497	0.2561	1	0.14982	1	0.0017841	0.988	0.050595	1	0.29746	1	0.54105	1	0.029546	1	0.0024061	1	0.29637	1	0.2426	1
Del Peak 23(10p15.3)	102 (18%)	473	0.24648	1	0.41669	1	1.3776e-07	9.02e-05	0.028831	1	0.39481	1	0.038444	1	0.012185	1	0.057586	1	0.71014	1	0.30188	1
Del Peak 24(10q21.1)	118 (21%)	457	0.2001	1	0.1105	1	3.1348e-11	2.16e-08	0.14957	1	0.47561	1	0.0097587	1	0.072765	1	0.043804	1	0.69109	1	0.57652	1
Del Peak 25(10q23.31)	145 (25%)	430	0.13535	1	0.49569	1	9.0881e-08	5.96e-05	0.15474	1	0.35683	1	0.0035237	1	0.0026248	1	0.068467	1	0.76199	1	0.36526	1
Del Peak 26(10q25.2)	140 (24%)	435	0.31218	1	0.11639	1	3.0619e-12	2.11e-09	0.10548	1	0.80755	1	0.18913	1	0.0002385	0.141	0.00032441	0.191	0.97166	1	0.77949	1
Del Peak 27(11q22.3)	104 (18%)	471	0.58489	1	0.53036	1	0.03853	1	0.12502	1	0.45358	1	0.18433	1	0.03654	1	0.52358	1	0.65677	1	0.36295	1
Del Peak 28(12p13.1)	77 (13%)	498	0.0069737	1	0.017316	1	3.8948e-08	2.58e-05	0.42864	1	0.64276	1	0.66392	1	0.057107	1	0.42333	1	0.44647	1	0.91879	1
Del Peak 29(12q21.2)	80 (14%)	495	0.172	1	0.029424	1	5.5178e-07	0.000359	0.34774	1	0.9473	1	0.36008	1	0.035123	1	0.2942	1	0.52063	1	0.97871	1
Del Peak 30(14q22.1)	185 (32%)	390	0.00011737	0.0707	0.00012002	0.0721	1.9531e-28	1.43e-25	8.1404e-06	0.0051	0.00010769	0.065	0.036584	1	4.0917e-08	2.71e-05	3.0832e-05	0.0189	0.12679	1	0.43856	1
Del Peak 31(15q11.2)	233 (41%)	342	0.0006869	0.394	0.01779	1	1.2039e-23	8.82e-21	0.0057215	1	0.94729	1	0.11558	1	1.4108e-06	0.000909	1.375e-05	0.00854	0.47751	1	0.11089	1
Del Peak 32(15q21.1)	227 (39%)	348	0.0024331	1	0.076694	1	2.4292e-21	1.77e-18	0.0035788	1	0.72041	1	0.12209	1	2.2022e-07	0.000144	2.2976e-05	0.0141	0.74178	1	0.45864	1
Del Peak 33(15q22.33)	217 (38%)	358	0.00064515	0.372	0.0074628	1	4.4907e-23	3.28e-20	0.00084041	0.48	0.83873	1	0.18036	1	5.8136e-09	3.89e-06	5.4971e-06	0.00349	0.86536	1	0.1165	1
Del Peak 34(16p13.3)	58 (10%)	517	0.14152	1	0.38223	1	0.21481	1	0.67595	1	0.81089	1	0.78404	1	0.92693	1	0.17584	1	0.63651	1	0.59521	1
Del Peak 35(16q23.1)	72 (13%)	503	0.064553	1	0.0011468	0.648	0.17918	1	0.32666	1	0.86696	1	0.26129	1	0.27086	1	0.22958	1	0.80518	1	0.63247	1
Del Peak 36(17p12)	343 (60%)	232	6.9273e-08	4.57e-05	2.789e-05	0.0171	2.0063e-34	1.48e-31	6.04e-09	4.03e-06	0.41222	1	0.0048567	1	1.5954e-08	1.06e-05	3.3152e-06	0.00211	0.051965	1	0.67329	1
Del Peak 37(17q24.3)	84 (15%)	491	0.90508	1	0.87587	1	0.029627	1	0.52806	1	0.49804	1	0.25779	1	0.18383	1	0.078066	1	0.91947	1	0.42487	1
Del Peak 38(18p11.31)	341 (59%)	234	5.5331e-13	3.84e-10	2.3459e-09	1.59e-06	1.1905e-41	8.82e-39	2.3143e-15	1.65e-12	0.62657	1	0.0017883	0.989	1.4029e-20	1.02e-17	5.0845e-15	3.58e-12	0.018344	1	0.38647	1
Del Peak 39(18q12.2)	386 (67%)	189	9.6445e-10	6.57e-07	7.3142e-08	4.82e-05	1.2945e-49	9.68e-47	8.059e-18	5.8e-15	0.26821	1	0.0041222	1	2.8352e-19	2.05e-16	1.22e-10	8.36e-08	0.0057877	1	0.059024	1
Del Peak 40(18q21.2)	403 (70%)	172	3.9826e-10	2.72e-07	8.2446e-08	5.42e-05	1.2388e-50	9.28e-48	3.4304e-15	2.43e-12	0.089592	1	0.0011476	0.648	2.8314e-15	2.02e-12	1.4217e-09	9.65e-07	0.00065728	0.378	0.12629	1
Del Peak 41(18q22.1)	398 (69%)	177	2.428e-09	1.64e-06	2.0701e-06	0.00132	9.5463e-53	7.16e-50	1.3687e-15	9.77e-13	0.14897	1	0.0029053	1	2.8314e-15	2.02e-12	5.8399e-09	3.9e-06	0.0012813	0.719	0.17094	1
Del Peak 42(19p13.3)	92 (16%)	483	0.088724	1	0.68379	1	1.3518e-05	0.00841	0.82504	1	0.49303	1	0.45578	1	0.032861	1	0.0086858	1	0.57921	1	0.91111	1
Del Peak 43(19q13.43)	68 (12%)	507	0.95095	1	0.69771	1	0.0001104	0.0666	0.59989	1	1	1	0.32273	1	0.0093455	1	0.0091629	1	0.25511	1	0.50243	1
Del Peak 44(20p12.1)	179 (31%)	396	0.023368	1	0.023571	1	6.5033e-15	4.58e-12	1.0094e-05	0.00632	0.25333	1	0.0033053	1	0.023187	1	0.015089	1	0.22326	1	0.97624	1
Del Peak 45(20p12.1)	179 (31%)	396	0.023368	1	0.023571	1	6.5033e-15	4.58e-12	1.0094e-05	0.00632	0.25333	1	0.0033053	1	0.023187	1	0.015089	1	0.22326	1	0.97624	1
Del Peak 46(21q11.2)	195 (34%)	380	0.0017735	0.984	0.12577	1	4.0688e-09	2.73e-06	0.010909	1	0.50126	1	0.049319	1	0.00064744	0.373	0.0052738	1	0.23351	1	0.049362	1
Del Peak 47(22q13.32)	204 (35%)	371	0.022573	1	0.0046102	1	9.8306e-15	6.9e-12	0.029932	1	0.11758	1	0.53247	1	0.00082402	0.471	0.034892	1	0.69579	1	0.011544	1
