		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	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
Amp Peak  1(1q31.1)	134 (23%)	441	0.46848	1	0.55953	1	0.00020463	0.125	0.72236	1	0.31062	1	0.82655	1	0.035772	1	0.59765	1	0.76478	1	0.94434	1
Amp Peak  2(2q33.1)	123 (21%)	452	0.042299	1	0.018839	1	1.5207e-06	0.000982	0.0050196	1	0.5325	1	0.29825	1	0.083012	1	0.0051763	1	0.18061	1	0.0012944	0.753
Amp Peak  3(5p12)	107 (19%)	468	0.10927	1	0.97471	1	6.5452e-06	0.00417	0.7939	1	0.042324	1	0.70151	1	0.10839	1	0.057672	1	0.88927	1	0.34721	1
Amp Peak  4(5q22.3)	59 (10%)	516	0.9046	1	0.41019	1	0.0037006	1	0.3195	1	0.35083	1	0.59065	1	0.18869	1	0.030709	1	0.46039	1	0.89428	1
Amp Peak  5(6p21.1)	146 (25%)	429	0.024692	1	0.0014495	0.842	3.9711e-14	2.79e-11	0.16938	1	0.48212	1	0.6576	1	0.00094035	0.555	0.00030314	0.183	0.53094	1	0.0067783	1
Amp Peak  6(7p21.3)	337 (59%)	238	0.00043479	0.26	0.0049714	1	7.9137e-22	5.75e-19	7.1064e-06	0.00451	0.022271	1	0.0020641	1	4.4469e-06	0.00285	6.0679e-06	0.00387	0.022382	1	0.0025921	1
Amp Peak  7(8p11.23)	196 (34%)	379	0.49951	1	0.33946	1	2.8317e-23	2.07e-20	0.30365	1	0.98119	1	0.64668	1	0.13548	1	0.3605	1	0.015361	1	0.077226	1
Amp Peak  8(8p11.21)	238 (41%)	337	0.25487	1	0.19058	1	3.3334e-31	2.45e-28	0.23711	1	0.49748	1	0.68152	1	0.015657	1	0.19942	1	0.081506	1	0.20055	1
Amp Peak  9(8q12.1)	309 (54%)	266	0.065106	1	0.084239	1	1.9068e-36	1.41e-33	0.015312	1	0.025169	1	0.14723	1	0.0011485	0.674	0.01408	1	0.10208	1	0.1461	1
Amp Peak 10(8q24.21)	345 (60%)	230	0.21136	1	0.089174	1	3.1776e-35	2.35e-32	0.0042881	1	0.034874	1	0.29211	1	0.0037086	1	0.041636	1	0.25116	1	0.17643	1
Amp Peak 11(10q22.3)	35 (6%)	540	0.90278	1	0.22385	1	0.65461	1	0.56037	1	0.63426	1	0.50643	1	0.79803	1	0.17974	1	0.58747	1	0.28086	1
Amp Peak 12(11p15.5)	129 (22%)	446	3.6048e-05	0.0224	0.0010011	0.59	1.8397e-06	0.00118	0.0034433	1	0.38932	1	0.36891	1	2.0728e-05	0.013	8.5631e-06	0.00541	0.35173	1	0.0090568	1
Amp Peak 13(12p13.32)	144 (25%)	431	0.17402	1	0.91102	1	0.25212	1	0.13658	1	0.42615	1	0.99748	1	0.23306	1	0.46864	1	0.67615	1	0.88617	1
Amp Peak 14(13q12.13)	371 (65%)	204	2.0857e-08	1.39e-05	5.8826e-07	0.000383	6.4175e-44	4.79e-41	8.9135e-11	6.1e-08	0.010542	1	0.19854	1	8.725e-11	5.98e-08	2.2476e-11	1.55e-08	0.013611	1	0.23666	1
Amp Peak 15(13q12.2)	366 (64%)	209	6.5088e-07	0.000423	3.3665e-06	0.00216	2.2045e-45	1.65e-42	2.3112e-11	1.59e-08	0.025639	1	0.36311	1	6.4939e-10	4.41e-07	7.1054e-11	4.87e-08	0.026046	1	0.28461	1
Amp Peak 16(13q22.1)	371 (65%)	204	5.1363e-06	0.00328	2.278e-05	0.0143	7.6851e-42	5.7e-39	2.9909e-09	2.02e-06	0.052981	1	0.16208	1	4.3351e-09	2.91e-06	6.6708e-11	4.58e-08	0.03008	1	0.04712	1
Amp Peak 17(15q26.1)	43 (7%)	532	0.85836	1	0.47865	1	0.24946	1	0.84162	1	0.1731	1	0.62275	1	0.8488	1	0.71952	1	0.92601	1	1	1
Amp Peak 18(16p11.2)	161 (28%)	414	0.016608	1	0.0095853	1	1.3311e-20	9.64e-18	0.0015397	0.891	0.023521	1	0.016375	1	0.010231	1	0.0002203	0.134	0.81077	1	0.11023	1
Amp Peak 19(17q12)	144 (25%)	431	0.010941	1	0.02859	1	3.4581e-09	2.33e-06	0.0072631	1	0.24984	1	0.10322	1	6.1523e-05	0.038	0.00036729	0.221	0.038998	1	0.23162	1
Amp Peak 20(17q24.1)	128 (22%)	447	0.011564	1	0.0010668	0.627	1.5413e-08	1.03e-05	0.00034993	0.211	0.093794	1	0.0076274	1	7.9837e-05	0.0492	0.0023711	1	0.0012716	0.743	0.041926	1
Amp Peak 21(19p13.2)	97 (17%)	478	0.048769	1	0.61167	1	8.872e-08	5.85e-05	0.031724	1	0.58719	1	0.64762	1	0.0315	1	0.010154	1	0.27415	1	0.13138	1
Amp Peak 22(19q12)	122 (21%)	453	0.019148	1	0.021801	1	6.2256e-08	4.11e-05	0.25113	1	0.072262	1	0.51708	1	0.010787	1	0.00028544	0.173	0.70958	1	0.49006	1
Amp Peak 23(20p11.23)	301 (52%)	274	0.0086402	1	0.0007773	0.461	5.5572e-17	4e-14	0.014078	1	0.017095	1	0.72049	1	0.010624	1	1.5041e-06	0.000973	0.35274	1	0.42547	1
Amp Peak 24(20p11.21)	339 (59%)	236	0.00016679	0.102	5.1112e-06	0.00327	8.5661e-23	6.24e-20	6.9846e-06	0.00444	0.015376	1	0.43129	1	3.2316e-05	0.0201	7.752e-10	5.25e-07	0.10712	1	0.18811	1
Amp Peak 25(20q11.21)	439 (76%)	136	2.5654e-15	1.83e-12	5.2538e-13	3.67e-10	1.5402e-42	1.14e-39	2.1295e-16	1.53e-13	0.0052758	1	0.028382	1	4.7734e-17	3.44e-14	4.3776e-22	3.19e-19	0.12378	1	0.018878	1
Amp Peak 26(20q12)	441 (77%)	134	2.0388e-16	1.46e-13	2.7776e-14	1.96e-11	5.8367e-43	4.34e-40	3.5601e-15	2.53e-12	0.0027205	1	0.013857	1	2.3358e-17	1.68e-14	5.058e-23	3.69e-20	0.065014	1	0.0077889	1
Amp Peak 27(20q13.32)	444 (77%)	131	1.7529e-15	1.25e-12	9.9082e-13	6.91e-10	5.6648e-43	4.22e-40	3.2142e-14	2.27e-11	0.0046907	1	0.013158	1	7.6055e-18	5.5e-15	4.9259e-22	3.58e-19	0.11691	1	0.032951	1
Amp Peak 28(Xq28)	121 (21%)	454	0.52638	1	0.36301	1	1.7197e-06	0.00111	0.10043	1	0.0033673	1	0.038687	1	0.24145	1	0.59193	1	0.98952	1	0.78345	1
Del Peak  1(1p36.11)	222 (39%)	353	3.2244e-05	0.0201	0.0025597	1	2.207e-13	1.54e-10	2.1039e-05	0.0132	0.025938	1	0.22537	1	7.3103e-06	0.00463	5.8883e-05	0.0364	0.15838	1	0.018302	1
Del Peak  2(1p33)	156 (27%)	419	0.0053664	1	0.064623	1	8.9471e-13	6.25e-10	0.00037065	0.223	0.16104	1	0.53027	1	0.030862	1	0.093483	1	0.53241	1	0.015895	1
Del Peak  3(1p13.2)	157 (27%)	418	0.13297	1	0.090829	1	3.379e-09	2.28e-06	0.015335	1	0.29926	1	0.78194	1	0.051289	1	0.092962	1	0.75564	1	0.3515	1
Del Peak  4(2p12)	20 (3%)	555	1	1	0.5615	1	0.0019382	1	0.011104	1	0.035896	1	0.97464	1	0.32466	1	0.22776	1	0.016497	1	0.021531	1
Del Peak  5(2q22.1)	33 (6%)	542	0.92667	1	0.6263	1	0.14635	1	0.83265	1	0.016431	1	0.82587	1	0.16658	1	0.16701	1	0.31564	1	0.27226	1
Del Peak  6(2q37.2)	30 (5%)	545	0.92364	1	0.57641	1	0.28501	1	0.83265	1	0.2341	1	0.59965	1	0.66595	1	0.2859	1	0.24408	1	0.36359	1
Del Peak  7(3p26.3)	84 (15%)	491	0.10553	1	0.77216	1	0.16257	1	0.35748	1	0.85894	1	0.5179	1	0.10099	1	0.28329	1	0.27674	1	0.72808	1
Del Peak  8(3p14.2)	104 (18%)	471	0.45951	1	0.88027	1	0.93155	1	0.59731	1	0.34078	1	0.89544	1	0.24711	1	0.071253	1	0.059527	1	0.91843	1
Del Peak  9(3q26.31)	56 (10%)	519	0.30358	1	0.83681	1	0.4484	1	0.37333	1	0.16321	1	0.26042	1	0.30589	1	0.87998	1	0.093407	1	0.12285	1
Del Peak 10(4p16.1)	182 (32%)	393	0.032415	1	0.27379	1	1.6474e-12	1.15e-09	0.0020286	1	0.34614	1	0.72213	1	0.045893	1	0.013706	1	0.62193	1	0.11684	1
Del Peak 11(4q22.1)	198 (34%)	377	0.018593	1	0.046098	1	1.2505e-14	8.84e-12	7.6585e-05	0.0473	0.35384	1	0.69721	1	0.17572	1	0.0035491	1	0.14791	1	0.4088	1
Del Peak 12(4q35.1)	211 (37%)	364	0.0089243	1	0.17749	1	1.2462e-13	8.75e-11	0.00064166	0.382	0.41054	1	0.47685	1	0.062888	1	0.014218	1	0.52329	1	0.74296	1
Del Peak 13(5q11.2)	140 (24%)	435	0.0015088	0.875	0.15356	1	2.1328e-12	1.48e-09	0.0028212	1	0.11051	1	0.30588	1	0.002261	1	0.0047844	1	1	1	0.75785	1
Del Peak 14(5q22.2)	172 (30%)	403	0.0007635	0.454	0.033253	1	2.2261e-09	1.5e-06	0.11369	1	0.39517	1	0.93398	1	0.00053973	0.322	0.00023768	0.145	0.77075	1	0.85443	1
Del Peak 15(6p25.3)	78 (14%)	497	0.82929	1	0.47471	1	0.08489	1	0.26246	1	0.18406	1	0.45478	1	0.66572	1	0.19589	1	0.60986	1	0.95718	1
Del Peak 16(6q26)	90 (16%)	485	0.89418	1	0.64768	1	0.04006	1	0.76234	1	0.051367	1	0.47981	1	0.31239	1	0.10362	1	0.22283	1	0.50721	1
Del Peak 17(7q31.1)	15 (3%)	560	0.091873	1	0.50151	1	1	1	1	1	0.59232	1	0.41129	1	0.14063	1	0.86915	1	0.23486	1	0.49815	1
Del Peak 18(8p23.2)	272 (47%)	303	0.0008907	0.526	0.029967	1	2.1272e-34	1.57e-31	1.9574e-06	0.00126	0.019188	1	0.014044	1	3.9437e-05	0.0245	0.001242	0.727	0.80158	1	0.39873	1
Del Peak 19(8p22)	285 (50%)	290	0.00173	0.998	0.027541	1	1.581e-37	1.17e-34	1.3157e-06	0.000854	0.012248	1	0.0070586	1	5.2503e-05	0.0326	0.00024313	0.148	0.76329	1	0.64202	1
Del Peak 20(8p11.21)	124 (22%)	451	0.012961	1	0.12546	1	4.8516e-07	0.000317	0.34128	1	0.0055675	1	0.30486	1	0.025063	1	0.10499	1	0.1625	1	0.40038	1
Del Peak 21(8q11.1)	44 (8%)	531	0.2885	1	0.92255	1	0.0026632	1	0.66125	1	0.05145	1	0.49439	1	0.56598	1	0.87863	1	0.081906	1	0.019346	1
Del Peak 22(9p24.2)	78 (14%)	497	0.266	1	0.265	1	0.0017841	1	0.050595	1	0.56196	1	0.51483	1	0.14724	1	0.017437	1	0.29637	1	0.2426	1
Del Peak 23(10p15.3)	102 (18%)	473	0.32308	1	0.39496	1	1.3776e-07	9.05e-05	0.028831	1	0.07997	1	0.27358	1	0.075746	1	0.18852	1	0.71014	1	0.30188	1
Del Peak 24(10q21.1)	118 (21%)	457	0.25872	1	0.070251	1	3.1348e-11	2.16e-08	0.14957	1	0.030401	1	0.055891	1	0.18118	1	0.01098	1	0.69109	1	0.57652	1
Del Peak 25(10q23.31)	145 (25%)	430	0.27414	1	0.24499	1	9.0881e-08	5.98e-05	0.15474	1	0.12712	1	0.51877	1	0.93582	1	0.033009	1	0.76199	1	0.36526	1
Del Peak 26(10q25.2)	140 (24%)	435	0.38224	1	0.066234	1	3.0619e-12	2.12e-09	0.10548	1	0.010775	1	0.50727	1	0.98443	1	0.0082783	1	0.97166	1	0.77949	1
Del Peak 27(11q22.3)	104 (18%)	471	0.58711	1	0.89518	1	0.03853	1	0.12502	1	0.11015	1	0.12343	1	0.14367	1	0.055971	1	0.65677	1	0.36295	1
Del Peak 28(12p13.1)	77 (13%)	498	0.0077768	1	0.018975	1	3.8948e-08	2.58e-05	0.42864	1	0.92075	1	0.85449	1	0.62374	1	0.0057525	1	0.44647	1	0.91879	1
Del Peak 29(12q21.2)	80 (14%)	495	0.12557	1	0.020082	1	5.5178e-07	0.00036	0.34774	1	0.83297	1	0.92388	1	0.68939	1	0.009644	1	0.52063	1	0.97871	1
Del Peak 30(14q22.1)	185 (32%)	390	9.4564e-05	0.0581	0.00011107	0.068	1.9531e-28	1.43e-25	8.1404e-06	0.00515	9.0789e-05	0.0558	0.078663	1	0.00051186	0.306	2.4861e-07	0.000163	0.12679	1	0.43856	1
Del Peak 31(15q11.2)	233 (41%)	342	0.00040277	0.242	0.0028174	1	1.2039e-23	8.82e-21	0.0057215	1	0.02598	1	0.46925	1	0.040473	1	0.0098446	1	0.47751	1	0.11089	1
Del Peak 32(15q21.1)	227 (39%)	348	0.0016117	0.932	0.031236	1	2.4292e-21	1.76e-18	0.0035788	1	0.011785	1	0.33141	1	0.11629	1	0.029654	1	0.74178	1	0.45864	1
Del Peak 33(15q22.33)	217 (38%)	358	0.00040405	0.242	0.0017515	1	4.4907e-23	3.28e-20	0.00084041	0.498	0.092059	1	0.49711	1	0.02199	1	0.0018439	1	0.86536	1	0.1165	1
Del Peak 34(16p13.3)	58 (10%)	517	0.14134	1	0.24152	1	0.21481	1	0.67595	1	0.065371	1	0.76625	1	0.31792	1	0.36867	1	0.63651	1	0.59521	1
Del Peak 35(16q23.1)	72 (13%)	503	0.05863	1	0.002199	1	0.17918	1	0.32666	1	0.28716	1	0.80712	1	0.0073968	1	0.021331	1	0.80518	1	0.63247	1
Del Peak 36(17p12)	343 (60%)	232	2.7601e-08	1.84e-05	2.2999e-05	0.0144	2.0063e-34	1.48e-31	6.04e-09	4.05e-06	0.0055355	1	0.0044117	1	1.4187e-06	0.000919	1.4557e-07	9.55e-05	0.051965	1	0.67329	1
Del Peak 37(17q24.3)	84 (15%)	491	0.91034	1	0.72248	1	0.029627	1	0.52806	1	0.74521	1	0.19596	1	0.66272	1	0.58654	1	0.91947	1	0.42487	1
Del Peak 38(18p11.31)	341 (59%)	234	1.6969e-13	1.19e-10	4.5705e-10	3.11e-07	1.1905e-41	8.82e-39	2.3143e-15	1.65e-12	0.14162	1	0.017301	1	2.2539e-12	1.56e-09	3.6811e-14	2.59e-11	0.018344	1	0.38647	1
Del Peak 39(18q12.2)	386 (67%)	189	3.4078e-10	2.32e-07	1.7113e-08	1.14e-05	1.2945e-49	9.68e-47	8.059e-18	5.82e-15	0.12764	1	0.028572	1	4.8797e-08	3.23e-05	3.4181e-12	2.37e-09	0.0057877	1	0.059024	1
Del Peak 40(18q21.2)	403 (70%)	172	1.3918e-10	9.49e-08	2.4012e-08	1.6e-05	1.2388e-50	9.28e-48	3.4304e-15	2.44e-12	0.028239	1	0.016591	1	2.9693e-08	1.97e-05	1.0354e-11	7.15e-09	0.00065728	0.391	0.12629	1
Del Peak 41(18q22.1)	398 (69%)	177	7.5002e-10	5.09e-07	5.1034e-07	0.000333	9.5463e-53	7.16e-50	1.3687e-15	9.8e-13	0.025896	1	0.020428	1	2.9693e-08	1.97e-05	1.015e-10	6.93e-08	0.0012813	0.747	0.17094	1
Del Peak 42(19p13.3)	92 (16%)	483	0.092294	1	0.7323	1	1.3518e-05	0.0085	0.82504	1	0.77606	1	0.46131	1	0.2538	1	0.3783	1	0.57921	1	0.91111	1
Del Peak 43(19q13.43)	68 (12%)	507	0.9509	1	0.41421	1	0.0001104	0.0677	0.59989	1	0.78233	1	0.91453	1	0.345	1	0.37836	1	0.25511	1	0.50243	1
Del Peak 44(20p12.1)	179 (31%)	396	0.016349	1	0.017955	1	6.5033e-15	4.62e-12	1.0094e-05	0.00637	0.87036	1	0.10544	1	0.0045376	1	0.0059842	1	0.22326	1	0.97624	1
Del Peak 45(20p12.1)	179 (31%)	396	0.016349	1	0.017955	1	6.5033e-15	4.62e-12	1.0094e-05	0.00637	0.87036	1	0.10544	1	0.0045376	1	0.0059842	1	0.22326	1	0.97624	1
Del Peak 46(21q11.2)	195 (34%)	380	0.0012074	0.708	0.11638	1	4.0688e-09	2.73e-06	0.010909	1	0.44016	1	0.3645	1	0.090612	1	0.062626	1	0.23351	1	0.049362	1
Del Peak 47(22q13.32)	204 (35%)	371	0.021477	1	0.0028973	1	9.8306e-15	6.96e-12	0.029932	1	0.39666	1	0.90788	1	0.08272	1	0.001792	1	0.69579	1	0.011544	1
