Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		MIR_CNMF		MIR_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_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	Chi-square test_P	Chi-square test_Q	Chi-square test_P	Chi-square test_Q
Amp Peak  1(1p36.21)	89 (16%)	474	0.94102	1	0.23569	1	0.17861	1	0.007401	1	1.6333e-08	1.08e-05	0.44794	1	0.082138	1	0.052243	1	0.14244	1	0.4183	1
Amp Peak  2(1q32.1)	153 (27%)	410	0.72684	1	0.63768	1	0.23933	1	0.097026	1	1.7641e-08	1.17e-05	0.34979	1	0.87778	1	0.56297	1	0.18298	1	0.052376	1
Amp Peak  3(1q44)	96 (17%)	467	0.88331	1	0.5007	1	0.40262	1	0.44141	1	8.3221e-09	5.56e-06	0.59013	1	0.4044	1	0.12729	1	0.25279	1	0.00483	1
Amp Peak  4(2p24.3)	46 (8%)	517	0.004038	1	0.08243	1	0.74778	1	0.38452	1	0.00023794	0.138	0.028898	1	0.20809	1	0.43194	1	0.80074	1	4.3567e-06	0.00274
Amp Peak  5(3q26.33)	108 (19%)	455	0.051105	1	0.5584	1	0.90035	1	0.7237	1	3.5604e-06	0.00225	0.00029114	0.168	0.03943	1	0.0061397	1	0.10308	1	0.59484	1
Amp Peak  6(4p16.3)	46 (8%)	517	0.87634	1	0.60261	1	0.82766	1	0.4027	1	0.46549	1	0.16153	1	0.66204	1	0.13402	1	0.70426	1	0.46679	1
Amp Peak  7(4q12)	104 (18%)	459	0.00012711	0.0756	5.2378e-05	0.032	0.47905	1	0.052749	1	4.309e-07	0.000281	0.15652	1	0.29895	1	0.43662	1	0.012791	1	0.056936	1
Amp Peak  8(7p11.2)	494 (88%)	69	7.0174e-13	4.78e-10	1.6222e-10	1.1e-07	3.4793e-07	0.000228	2.3446e-13	1.6e-10	1.23e-20	8.56e-18	1.0352e-06	0.000664	9.2976e-06	0.00579	4.5228e-05	0.0277	5.3418e-05	0.0325	6.5753e-07	0.000424
Amp Peak  9(7q11.21)	452 (80%)	111	5.6825e-07	0.000368	1.8181e-05	0.0113	4.6898e-06	0.00295	7.422e-09	4.97e-06	1.7172e-09	1.15e-06	0.0032282	1	0.0045815	1	0.39561	1	0.0068015	1	0.0048377	1
Amp Peak 10(7q21.2)	468 (83%)	95	3.3403e-05	0.0205	0.00032133	0.185	0.010678	1	1.9215e-06	0.00122	1.06e-10	7.2e-08	0.0071632	1	0.019423	1	0.3314	1	0.080251	1	0.0033636	1
Amp Peak 11(7q31.2)	460 (82%)	103	0.00012865	0.0764	0.00049722	0.283	0.0020723	1	0.00014384	0.0852	2.2065e-07	0.000145	0.037816	1	0.11234	1	1	1	0.072202	1	0.0097972	1
Amp Peak 12(7q36.1)	465 (83%)	98	0.0010301	0.57	0.0033942	1	0.058961	1	4.5897e-05	0.028	1.4149e-05	0.00877	0.0071632	1	0.24197	1	0.65246	1	0.019286	1	0.00088796	0.494
Amp Peak 13(8q24.21)	64 (11%)	499	2.0093e-07	0.000132	0.00015657	0.0922	0.039655	1	8.3446e-05	0.0502	3.5071e-06	0.00222	0.062687	1	0.10018	1	0.083032	1	0.22692	1	5.5197e-05	0.0336
Amp Peak 14(11p13)	26 (5%)	537	0.41116	1	0.82691	1	0.32356	1	0.76882	1	0.45166	1	0.28509	1	0.24594	1	0.082222	1	0.52337	1	0.075739	1
Amp Peak 15(12p13.32)	81 (14%)	482	0.86726	1	0.64121	1	0.71588	1	0.8116	1	1.9604e-05	0.0121	0.23403	1	0.38059	1	0.59745	1	0.034324	1	0.75309	1
Amp Peak 16(12q14.1)	131 (23%)	432	0.084009	1	0.28276	1	0.30885	1	0.12133	1	1.7047e-09	1.15e-06	0.34721	1	0.042836	1	0.92784	1	0.023282	1	0.0062197	1
Amp Peak 17(12q15)	92 (16%)	471	0.74863	1	0.37677	1	0.75118	1	0.51534	1	2.8312e-07	0.000185	0.40426	1	0.24609	1	0.17813	1	0.11124	1	0.10563	1
Amp Peak 18(13q34)	30 (5%)	533	0.53564	1	0.75792	1	0.17	1	0.11474	1	0.013951	1	NA	NA	0.056909	1	0.16355	1	0.9322	1	0.55113	1
Amp Peak 19(14q32.33)	34 (6%)	529	0.35039	1	0.47327	1	0.021052	1	0.94256	1	0.7935	1	1	1	0.037293	1	0.29994	1	0.26238	1	0.014016	1
Amp Peak 20(17p13.2)	45 (8%)	518	0.0023145	1	0.032718	1	0.075141	1	0.22116	1	0.0069571	1	0.52729	1	0.056836	1	0.19389	1	0.72649	1	0.10537	1
Amp Peak 21(17q25.1)	78 (14%)	485	0.060519	1	0.64557	1	0.40211	1	0.70871	1	5.9807e-05	0.0362	0.64297	1	0.14227	1	0.24371	1	0.4901	1	0.5604	1
Amp Peak 22(19p13.2)	240 (43%)	323	9.1223e-14	6.25e-11	8.1227e-09	5.43e-06	0.24827	1	0.0082518	1	1.8589e-20	1.29e-17	0.013413	1	0.0065172	1	0.00032659	0.187	0.0027437	1	0.010325	1
Amp Peak 23(19q12)	203 (36%)	360	1.2362e-09	8.32e-07	2.0983e-07	0.000138	0.21792	1	0.0044907	1	1.5008e-15	1.03e-12	0.10657	1	0.011702	1	0.005225	1	0.010145	1	0.00044483	0.254
Amp Peak 24(21q21.1)	67 (12%)	496	0.00044606	0.254	0.0077101	1	0.10796	1	0.079617	1	0.00077057	0.433	0.74817	1	0.69438	1	0.52078	1	0.025259	1	0.088891	1
Del Peak  1(1p36.32)	99 (18%)	464	0.21853	1	0.029283	1	0.5031	1	0.23348	1	0.61356	1	0.57683	1	0.49896	1	0.59989	1	0.23329	1	0.17194	1
Del Peak  2(1p36.23)	135 (24%)	428	0.040546	1	0.063934	1	0.36941	1	0.33027	1	0.0011817	0.648	0.49345	1	0.23955	1	0.9546	1	0.24246	1	0.1688	1
Del Peak  3(1p32.3)	60 (11%)	503	0.35939	1	0.43897	1	0.96958	1	0.87072	1	0.097256	1	0.68643	1	0.29465	1	0.68969	1	0.1545	1	0.31796	1
Del Peak  4(1p22.1)	47 (8%)	516	0.793	1	0.83917	1	0.76148	1	0.22798	1	0.17561	1	0.27123	1	0.7624	1	0.90441	1	0.095898	1	0.06371	1
Del Peak  5(1q42.11)	47 (8%)	516	0.77108	1	0.83569	1	0.40243	1	0.67875	1	0.6191	1	0.5282	1	0.18215	1	0.048686	1	0.6405	1	0.15337	1
Del Peak  6(1q44)	32 (6%)	531	0.60147	1	0.2904	1	0.68467	1	0.31498	1	0.61181	1	0.2919	1	0.79802	1	0.5141	1	0.60615	1	0.55212	1
Del Peak  7(2q22.1)	44 (8%)	519	0.028065	1	0.098038	1	0.43667	1	0.065113	1	1.6039e-06	0.00102	0.002189	1	0.47033	1	0.86922	1	0.27385	1	0.083153	1
Del Peak  8(2q37.1)	56 (10%)	507	0.015366	1	0.014728	1	0.23888	1	0.00096981	0.538	0.0068428	1	0.012237	1	0.67727	1	0.70128	1	0.16254	1	0.083153	1
Del Peak  9(3p21.1)	52 (9%)	511	0.066478	1	0.47017	1	0.91116	1	0.1043	1	0.00018654	0.109	0.27084	1	0.13015	1	0.82378	1	0.085343	1	0.022307	1
Del Peak 10(3q13.31)	55 (10%)	508	0.3672	1	0.77554	1	0.98007	1	0.70784	1	5.6848e-06	0.00356	0.20298	1	0.90192	1	0.85033	1	0.039999	1	0.0001803	0.105
Del Peak 11(3q22.1)	55 (10%)	508	0.45956	1	0.63909	1	0.61682	1	0.3777	1	0.00023454	0.136	0.37209	1	0.85836	1	0.76597	1	0.10843	1	0.0002559	0.148
Del Peak 12(3q29)	64 (11%)	499	0.11527	1	0.13685	1	0.61162	1	0.98373	1	0.0068314	1	0.13911	1	0.34482	1	0.55706	1	0.36795	1	0.57767	1
Del Peak 13(4p16.3)	78 (14%)	485	0.015761	1	0.035948	1	0.34963	1	0.17784	1	0.058245	1	1	1	0.82099	1	0.70057	1	0.90316	1	0.91556	1
Del Peak 14(4q34.3)	90 (16%)	473	0.00010123	0.0608	0.011968	1	0.088006	1	0.051942	1	0.00015259	0.0902	0.060983	1	0.085848	1	0.038486	1	0.63465	1	0.35355	1
Del Peak 15(5q35.3)	54 (10%)	509	1.9784e-05	0.0122	0.0021811	1	0.0015578	0.847	2.2734e-05	0.014	5.6874e-05	0.0345	0.011651	1	0.82904	1	0.28004	1	0.43601	1	0.1866	1
Del Peak 16(6q22.31)	153 (27%)	410	0.87323	1	0.63949	1	0.55412	1	0.029047	1	9.8261e-11	6.68e-08	0.1129	1	0.21048	1	0.12279	1	0.92696	1	0.41399	1
Del Peak 17(6q26)	173 (31%)	390	0.77495	1	0.24397	1	0.86611	1	0.12458	1	1.0804e-06	0.000691	0.7579	1	0.016615	1	0.017925	1	0.6332	1	0.28233	1
Del Peak 18(8p23.2)	67 (12%)	496	0.58115	1	0.13298	1	0.25599	1	0.35505	1	0.038237	1	0.89809	1	0.92889	1	0.8148	1	0.56947	1	0.57816	1
Del Peak 19(9p21.3)	408 (72%)	155	4.1856e-06	0.00264	7.9755e-07	0.000513	0.55421	1	0.0015261	0.832	3.77e-10	2.55e-07	0.011835	1	0.091677	1	0.040337	1	0.0077208	1	0.0023699	1
Del Peak 20(9q34.2)	71 (13%)	492	0.29155	1	0.061655	1	0.83957	1	0.40063	1	0.29163	1	0.8232	1	0.12275	1	0.083876	1	0.76246	1	0.24605	1
Del Peak 21(10p15.3)	457 (81%)	106	0.00012096	0.0722	2.847e-05	0.0175	0.013341	1	1.8478e-07	0.000122	1.4534e-14	9.97e-12	0.027238	1	0.0054922	1	0.025286	1	0.043724	1	0.0001028	0.0617
Del Peak 22(10p13)	459 (82%)	104	7.9461e-06	0.00496	2.1703e-06	0.00137	0.0028195	1	1.28e-07	8.46e-05	1.1124e-15	7.68e-13	0.027238	1	0.00013348	0.0792	0.0058353	1	0.16772	1	0.00079548	0.446
Del Peak 23(10p11.23)	463 (82%)	100	5.7848e-07	0.000374	1.97e-07	0.00013	0.0005396	0.306	1.2577e-08	8.38e-06	9.8539e-17	6.84e-14	0.03582	1	0.00080678	0.451	0.0016185	0.879	0.17048	1	0.00055652	0.315
Del Peak 24(10q23.31)	499 (89%)	64	6.5364e-05	0.0395	1.3387e-05	0.00831	0.007814	1	7.2286e-05	0.0437	1.1895e-16	8.24e-14	0.14247	1	0.010361	1	0.06089	1	0.38122	1	0.00063938	0.361
Del Peak 25(10q26.3)	500 (89%)	63	0.0001226	0.0731	6.4756e-06	0.00405	0.077666	1	0.00043043	0.246	1.8918e-13	1.29e-10	0.013491	1	0.12762	1	0.044861	1	0.64987	1	7.9912e-07	0.000513
Del Peak 26(11p15.5)	127 (23%)	436	7.7138e-10	5.2e-07	7.4077e-06	0.00463	0.22993	1	1.5029e-06	0.000959	2.0981e-15	1.44e-12	0.00011638	0.0696	0.28239	1	0.55424	1	0.0011032	0.608	0.0035396	1
Del Peak 27(11p11.2)	101 (18%)	462	4.4938e-07	0.000293	0.00099251	0.55	0.92055	1	2.4387e-05	0.015	2.1813e-13	1.49e-10	0.00087431	0.488	0.85673	1	0.67925	1	0.035635	1	0.11496	1
Del Peak 28(11q14.1)	95 (17%)	468	0.00030827	0.178	0.014871	1	0.93635	1	0.0078286	1	1.3012e-16	9e-14	0.23559	1	0.57052	1	0.58959	1	0.04517	1	0.13187	1
Del Peak 29(12p13.1)	75 (13%)	488	0.00015352	0.0906	0.0011282	0.619	0.12914	1	0.055956	1	0.077048	1	0.5945	1	0.84153	1	0.2712	1	0.83557	1	0.31829	1
Del Peak 30(12q12)	76 (13%)	487	0.00017816	0.104	0.0024229	1	0.18792	1	0.0064012	1	0.00017466	0.102	0.088888	1	0.13055	1	0.7477	1	0.16244	1	0.52908	1
Del Peak 31(12q15)	77 (14%)	486	0.00030733	0.177	0.00016274	0.0955	0.24664	1	0.046702	1	5.3978e-07	0.00035	0.2295	1	0.54885	1	0.84098	1	0.14705	1	0.39485	1
Del Peak 32(13q14.2)	236 (42%)	327	4.7635e-07	0.00031	1.6022e-06	0.00102	0.10858	1	0.080008	1	1.1047e-15	7.63e-13	0.030543	1	0.88338	1	0.028717	1	0.013066	1	0.00052326	0.297
Del Peak 33(14q13.1)	175 (31%)	388	7.1699e-07	0.000462	0.032877	1	0.618	1	0.42115	1	3.3563e-30	2.34e-27	0.10564	1	0.41863	1	0.29727	1	0.15361	1	0.35658	1
Del Peak 34(14q24.2)	170 (30%)	393	9.6566e-08	6.39e-05	0.0034891	1	0.065571	1	0.87103	1	7.6795e-39	5.36e-36	0.032748	1	0.45495	1	0.47092	1	0.012112	1	0.07808	1
Del Peak 35(14q31.3)	156 (28%)	407	1.3123e-08	8.73e-06	0.0019078	1	0.42159	1	0.8353	1	8.4204e-41	5.89e-38	0.0082937	1	0.53224	1	0.28867	1	0.058427	1	0.11349	1
Del Peak 36(15q14)	151 (27%)	412	8.6238e-09	5.75e-06	9.2921e-06	0.00579	0.0097737	1	1.3143e-06	0.00084	4.0889e-07	0.000267	0.00015874	0.0933	0.074824	1	0.0082756	1	0.0011053	0.608	0.00071179	0.401
Del Peak 37(16p12.2)	89 (16%)	474	0.30161	1	0.55774	1	0.06167	1	0.57751	1	0.094213	1	0.31033	1	0.45636	1	0.63966	1	0.26959	1	0.23163	1
Del Peak 38(16q23.3)	95 (17%)	468	0.15307	1	0.31328	1	0.75171	1	1	1	0.0044967	1	0.65087	1	0.046518	1	0.081594	1	0.26746	1	0.32243	1
Del Peak 39(17p13.2)	85 (15%)	478	0.20742	1	0.62887	1	0.9262	1	0.79959	1	2e-10	1.35e-07	0.27667	1	0.67324	1	0.41525	1	0.3558	1	0.048196	1
Del Peak 40(17p13.1)	95 (17%)	468	0.037084	1	0.1794	1	0.87993	1	0.60542	1	1.4187e-15	9.77e-13	0.1037	1	0.758	1	0.27253	1	0.1799	1	0.10182	1
Del Peak 41(17q11.2)	71 (13%)	492	7.3902e-05	0.0446	0.00072375	0.407	0.0019169	1	0.0095928	1	5.3222e-07	0.000345	0.6443	1	0.0071615	1	0.046703	1	0.033413	1	0.00087653	0.488
Del Peak 42(18q22.3)	79 (14%)	484	0.057195	1	0.32303	1	0.49848	1	0.4205	1	0.0020303	1	0.016903	1	0.030424	1	0.11546	1	0.058245	1	0.06093	1
Del Peak 43(19q13.41)	99 (18%)	464	1.9911e-06	0.00126	0.00019098	0.111	0.0017986	0.975	0.0010812	0.597	0.0012043	0.659	0.61857	1	0.033398	1	0.16674	1	0.015078	1	0.084941	1
Del Peak 44(21q22.3)	59 (10%)	504	0.0014835	0.81	0.018353	1	0.00010776	0.0646	0.0023862	1	0.14038	1	0.14459	1	0.36026	1	0.1438	1	0.10335	1	0.48091	1
Del Peak 45(22q13.32)	208 (37%)	355	0.70537	1	0.4324	1	0.019396	1	0.087987	1	0.00080426	0.45	0.75192	1	0.86427	1	0.37337	1	0.13442	1	0.027044	1
Del Peak 46(Xp22.2)	123 (22%)	440	0.00034646	0.199	0.022386	1	0.15546	1	0.20925	1	6.6031e-10	4.46e-07	0.0075275	1	0.57521	1	0.55209	1	0.73691	1	0.82906	1