Molecular subtypes	CN_CNMF		METHLYATION_CNMF		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
Amp Peak  1(1p36.22)	24 (10%)	213	7.552e-06	0.00276	0.06896	1	0.41206	1	0.55652	1	0.042094	1	0.1814	1
Amp Peak  2(1q21.3)	75 (32%)	162	1.2492e-14	5.22e-12	7.5349e-06	0.00276	0.21515	1	0.020274	1	0.00079959	0.257	0.0016418	0.514
Amp Peak  3(1q42.3)	73 (31%)	164	6.7066e-13	2.78e-10	0.00063918	0.208	0.75462	1	0.36101	1	9.6899e-05	0.033	0.005871	1
Amp Peak  4(3q26.31)	67 (28%)	170	1.4476e-05	0.00518	0.030695	1	0.11591	1	0.1419	1	0.15927	1	0.49012	1
Amp Peak  5(5p13.1)	58 (24%)	179	1.1736e-12	4.84e-10	0.020049	1	1	1	0.56103	1	0.031573	1	0.0052468	1
Amp Peak  6(6p21.1)	60 (25%)	177	6.7282e-13	2.78e-10	7.523e-05	0.0259	0.33189	1	0.67761	1	0.041978	1	0.0069018	1
Amp Peak  7(6q12)	42 (18%)	195	7.4818e-08	2.87e-05	0.043893	1	0.50979	1	0.89859	1	0.066925	1	0.017928	1
Amp Peak  8(7p11.2)	96 (41%)	141	3.2624e-11	1.32e-08	0.00052393	0.171	0.54669	1	0.65082	1	0.0043733	1	0.020756	1
Amp Peak  9(7q21.2)	97 (41%)	140	3.6667e-10	1.47e-07	0.013428	1	0.54669	1	0.43311	1	0.022891	1	0.072933	1
Amp Peak 10(8p23.1)	79 (33%)	158	2.2684e-16	9.64e-14	0.96038	1	0.36404	1	0.16522	1	0.55777	1	0.62345	1
Amp Peak 11(8q24.21)	139 (59%)	98	6.3886e-16	2.69e-13	0.00069647	0.226	0.28058	1	0.46435	1	0.083808	1	0.020196	1
Amp Peak 12(9p24.1)	30 (13%)	207	0.79332	1	0.63833	1	0.69808	1	0.15927	1	0.70147	1	0.35278	1
Amp Peak 13(9q34.3)	48 (20%)	189	4.0972e-06	0.00151	0.24095	1	0.74699	1	1	1	0.39448	1	0.3133	1
Amp Peak 14(10q26.13)	45 (19%)	192	5.8244e-05	0.0203	0.011637	1	1	1	1	1	0.44665	1	0.26962	1
Amp Peak 15(11p13)	38 (16%)	199	0.00031529	0.104	0.061998	1	0.69808	1	0.29321	1	0.29326	1	0.070048	1
Amp Peak 16(11q13.3)	47 (20%)	190	1.3461e-06	0.000509	0.053724	1	1	1	0.26386	1	0.010746	1	0.050021	1
Amp Peak 17(12p12.1)	54 (23%)	183	4.4691e-06	0.00164	0.023798	1	0.41206	1	0.55652	1	0.16	1	0.79878	1
Amp Peak 18(12q15)	49 (21%)	188	6.907e-05	0.0238	0.0021919	0.679	0.72051	1	1	1	0.47451	1	0.8036	1
Amp Peak 19(13q12.3)	81 (34%)	156	5.9436e-09	2.33e-06	0.0025724	0.79	0.22314	1	0.11529	1	0.40816	1	0.15094	1
Amp Peak 20(13q22.1)	88 (37%)	149	1.999e-08	7.76e-06	0.004822	1	0.13084	1	0.65181	1	0.32341	1	0.00077724	0.251
Amp Peak 21(15q26.1)	52 (22%)	185	1.956e-14	8.16e-12	0.00011765	0.0398	1	1	0.88507	1	0.024062	1	0.013245	1
Amp Peak 22(17q12)	61 (26%)	176	7.7395e-12	3.17e-09	0.039542	1	0.73604	1	0.16166	1	0.0088044	1	0.0036189	1
Amp Peak 23(18q11.2)	61 (26%)	176	8.7674e-07	0.000332	0.0096275	1	1	1	0.61561	1	0.33841	1	0.16432	1
Amp Peak 24(19q12)	61 (26%)	176	6.2628e-10	2.5e-07	0.00044888	0.147	0.50979	1	0.060358	1	0.013821	1	1.133e-05	0.00409
Amp Peak 25(20q13.2)	147 (62%)	90	9.2311e-20	3.95e-17	8.7274e-06	0.00318	0.75462	1	0.11648	1	0.031477	1	0.023879	1
Amp Peak 26(Xq27.3)	43 (18%)	194	1.8219e-06	0.000685	0.18136	1	0.45655	1	0.67439	1	0.039613	1	0.61701	1
Del Peak  1(1p36.11)	63 (27%)	174	2.707e-12	1.11e-09	0.0052846	1	0.35798	1	0.53759	1	0.069801	1	0.011841	1
Del Peak  2(1p31.1)	37 (16%)	200	7.7789e-10	3.1e-07	0.19137	1	0.69808	1	0.64102	1	0.24074	1	0.031088	1
Del Peak  3(1q44)	14 (6%)	223	0.24783	1	0.13672	1	0.41206	1	0.83965	1	0.20854	1	0.061731	1
Del Peak  4(2q32.1)	28 (12%)	209	0.0033272	1	0.47295	1	0.66403	1	0.72994	1	0.27886	1	0.061364	1
Del Peak  5(2q33.3)	23 (10%)	214	0.0012275	0.392	0.39039	1	0.48837	1	NA	NA	0.69571	1	0.23577	1
Del Peak  6(2q37.2)	33 (14%)	204	1.5892e-05	0.00567	0.049138	1	0.60692	1	0.64265	1	0.11383	1	0.008889	1
Del Peak  7(3p26.1)	56 (24%)	181	2.4911e-10	1e-07	0.0012517	0.398	0.31015	1	0.21026	1	0.03865	1	0.0027181	0.829
Del Peak  8(3p14.2)	71 (30%)	166	1.9038e-11	7.75e-09	0.0046755	1	0.48761	1	0.13786	1	0.20507	1	0.013841	1
Del Peak  9(3q26.31)	20 (8%)	217	1.4187e-05	0.00509	0.013519	1	0.34487	1	0.35593	1	0.059945	1	0.0065904	1
Del Peak 10(4p16.3)	76 (32%)	161	4.9795e-12	2.04e-09	2.7317e-05	0.00964	0.34747	1	0.36101	1	0.0010511	0.337	1.5044e-06	0.000567
Del Peak 11(4q22.1)	91 (38%)	146	2.0073e-20	8.61e-18	1.38e-05	0.00497	0.22314	1	0.54349	1	0.0033435	1	0.00020491	0.0682
Del Peak 12(4q35.1)	87 (37%)	150	8.7836e-18	3.74e-15	6.7789e-05	0.0235	0.066585	1	0.49828	1	0.015808	1	0.00018804	0.063
Del Peak 13(5q11.2)	70 (30%)	167	4.2658e-19	1.82e-16	4.6422e-09	1.83e-06	0.045209	1	0.14976	1	2.2719e-05	0.00804	4.0518e-06	0.0015
Del Peak 14(6p25.3)	48 (20%)	189	2.0465e-07	7.82e-05	0.052421	1	0.69808	1	0.42391	1	0.28028	1	0.00029289	0.0967
Del Peak 15(6q26)	47 (20%)	190	9.4377e-06	0.00342	0.015402	1	0.45655	1	0.60269	1	0.22263	1	0.16146	1
Del Peak 16(6q27)	47 (20%)	190	2.4391e-06	0.000912	0.012373	1	0.24044	1	0.29321	1	0.53184	1	0.039348	1
Del Peak 17(7q31.1)	26 (11%)	211	4.8424e-06	0.00178	0.016308	1	0.41206	1	0.55652	1	0.030548	1	0.083854	1
Del Peak 18(7q36.3)	42 (18%)	195	2.5395e-10	1.02e-07	0.0012972	0.411	0.69808	1	0.49912	1	0.17944	1	0.0016965	0.529
Del Peak 19(8p23.2)	56 (24%)	181	8.789e-14	3.65e-11	6.6478e-05	0.0231	0.50979	1	0.89859	1	0.047351	1	0.00017717	0.0595
Del Peak 20(9p23)	90 (38%)	147	5.7789e-16	2.44e-13	0.0026957	0.825	0.12426	1	0.44922	1	0.033106	1	0.026195	1
Del Peak 21(9p21.3)	88 (37%)	149	3.4625e-16	1.47e-13	1.6283e-08	6.33e-06	0.21515	1	0.83869	1	0.0066167	1	0.0024305	0.751
Del Peak 22(9q21.11)	52 (22%)	185	2.6546e-08	1.02e-05	0.0087911	1	0.69808	1	0.64102	1	0.081703	1	0.0024815	0.764
Del Peak 23(10p14)	34 (14%)	203	3.3972e-07	0.000129	0.0019864	0.618	0.72051	1	0.88507	1	0.016654	1	0.045935	1
Del Peak 24(10q22.3)	34 (14%)	203	2.2566e-08	8.73e-06	0.016519	1	0.13239	1	0.15048	1	0.019372	1	0.0015599	0.49
Del Peak 25(10q23.31)	54 (23%)	183	2.1655e-14	9.01e-12	0.0013305	0.42	0.0068449	1	0.089908	1	8.965e-05	0.0307	4.6912e-05	0.0165
Del Peak 26(11p15.5)	46 (19%)	191	2.2264e-09	8.79e-07	0.0040018	1	1	1	1	1	0.18041	1	0.0048163	1
Del Peak 27(11q23.2)	43 (18%)	194	0.00024456	0.081	0.0002021	0.0675	1	1	0.21463	1	0.060725	1	0.22129	1
Del Peak 28(12p13.2)	34 (14%)	203	5.3004e-09	2.08e-06	0.013688	1	1	1	1	1	0.033707	1	0.2217	1
Del Peak 29(14q21.1)	52 (22%)	185	3.9484e-06	0.00146	0.11801	1	0.13239	1	0.67439	1	0.034287	1	0.017706	1
Del Peak 30(14q32.33)	59 (25%)	178	1.8794e-06	0.000705	0.21932	1	0.088339	1	0.4576	1	0.25067	1	0.17404	1
Del Peak 31(15q11.2)	56 (24%)	181	1.014e-11	4.14e-09	0.00013804	0.0465	0.0093419	1	0.010985	1	0.010034	1	0.0001066	0.0362
Del Peak 32(15q15.1)	57 (24%)	180	2.6335e-10	1.06e-07	0.00066115	0.215	0.045209	1	0.089908	1	0.035369	1	5.9551e-05	0.0207
Del Peak 33(16p13.3)	34 (14%)	203	3.7573e-06	0.0014	0.25221	1	0.66403	1	0.72994	1	0.0071118	1	0.12717	1
Del Peak 34(16q23.1)	74 (31%)	163	1.7927e-05	0.00638	0.68803	1	0.54337	1	0.91536	1	0.66532	1	0.18215	1
Del Peak 35(17p12)	79 (33%)	158	6.7954e-23	2.92e-20	2.5105e-06	0.000936	0.20275	1	0.50906	1	0.0014182	0.447	2.0086e-05	0.00713
Del Peak 36(17q24.3)	36 (15%)	201	2.572e-08	9.93e-06	0.22725	1	0.088339	1	0.055065	1	0.014457	1	0.0011503	0.368
Del Peak 37(18q21.2)	95 (40%)	142	5.1019e-16	2.16e-13	0.014402	1	0.76349	1	0.19112	1	0.11159	1	0.014249	1
Del Peak 38(18q22.3)	92 (39%)	145	8.5106e-16	3.57e-13	0.013339	1	1	1	0.9173	1	0.087003	1	0.036344	1
Del Peak 39(19p13.3)	71 (30%)	166	2.4591e-25	1.06e-22	7.5666e-09	2.96e-06	0.34747	1	0.36101	1	8.9338e-05	0.0306	1.5457e-09	6.12e-07
Del Peak 40(19q13.11)	30 (13%)	207	8.5411e-10	3.39e-07	4.9934e-05	0.0175	0.094572	1	0.22978	1	0.0035446	1	5.2174e-05	0.0183
Del Peak 41(20p12.1)	33 (14%)	204	9.1827e-06	0.00333	0.0001125	0.0381	1	1	0.83965	1	0.024356	1	0.015975	1
Del Peak 42(21q11.2)	73 (31%)	164	2.8986e-11	1.18e-08	0.0034726	1	0.33189	1	0.67761	1	0.011543	1	0.27471	1
Del Peak 43(22q13.31)	70 (30%)	167	7.5253e-15	3.15e-12	1.1448e-08	4.46e-06	1	1	1	1	0.0030447	0.926	0.00020955	0.0696
Del Peak 44(Xp22.2)	38 (16%)	199	3.9622e-08	1.52e-05	0.014757	1	0.69808	1	0.73203	1	0.13075	1	0.0083929	1
Del Peak 45(Xp21.1)	33 (14%)	204	1.0936e-10	4.42e-08	0.085444	1	0.28058	1	0.28273	1	0.020849	1	0.076217	1
Del Peak 46(Xq21.33)	30 (13%)	207	3.6761e-07	0.00014	0.066334	1	0.45655	1	0.67439	1	0.049573	1	0.010772	1