Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	nWild-Type	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	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(1p34.2)	45 (30%)	105	0.00019969	0.0943	4.0864e-05	0.0199	0.89402	1	0.70601	1	0.014691	1	0.51983	1	0.075073	1	0.61609	1
Amp Peak  2(1q21.3)	76 (51%)	74	6.85e-06	0.00337	0.00039988	0.186	0.011755	1	0.051123	1	0.0037395	1	0.36547	1	0.061565	1	0.15524	1
Amp Peak  3(1q23.3)	82 (55%)	68	2.5929e-05	0.0127	0.012382	1	0.9254	1	0.58916	1	0.063352	1	0.71896	1	0.00017659	0.0837	0.0001443	0.0687
Amp Peak  4(3p25.2)	72 (48%)	78	3.3553e-05	0.0163	0.0016134	0.718	0.27822	1	0.03928	1	0.00084835	0.386	0.0003715	0.173	0.0018182	0.8	0.00024699	0.116
Amp Peak  5(3q26.32)	84 (56%)	66	0.0044027	1	0.66438	1	0.16067	1	0.81172	1	0.60054	1	0.87483	1	0.62375	1	0.26996	1
Amp Peak  6(4p16.3)	31 (21%)	119	0.017605	1	0.1717	1	0.16214	1	0.18857	1	0.10257	1	0.11838	1	0.03785	1	0.28619	1
Amp Peak  7(4q13.3)	23 (15%)	127	8.4547e-05	0.0406	0.15965	1	0.51704	1	0.86705	1	0.57148	1	0.39991	1	0.28835	1	0.27856	1
Amp Peak  8(5p15.1)	69 (46%)	81	4.4953e-05	0.0218	0.20229	1	0.013987	1	0.45966	1	0.094042	1	0.45769	1	0.076767	1	0.095368	1
Amp Peak  9(6p22.3)	61 (41%)	89	0.00018288	0.0865	0.0023585	1	0.83415	1	0.87182	1	0.55965	1	0.58141	1	0.094761	1	0.44878	1
Amp Peak 10(6q12)	25 (17%)	125	0.0060126	1	0.62748	1	1	1	1	1	1	1	0.66707	1	0.17865	1	0.0050674	1
Amp Peak 11(6q21)	18 (12%)	132	0.24512	1	0.05116	1	0.62114	1	0.58438	1	0.19838	1	0.15454	1	0.89801	1	1	1
Amp Peak 12(7p11.2)	78 (52%)	72	4.4909e-07	0.000224	0.0020026	0.875	0.48139	1	0.24295	1	0.82484	1	0.67802	1	0.75701	1	0.874	1
Amp Peak 13(8p11.23)	48 (32%)	102	0.00049153	0.227	0.048781	1	0.073189	1	0.016951	1	0.42305	1	0.27108	1	0.1589	1	0.51611	1
Amp Peak 14(8p11.21)	48 (32%)	102	1.6173e-05	0.00794	0.014559	1	0.59619	1	0.63731	1	0.26825	1	0.44823	1	0.032444	1	0.29751	1
Amp Peak 15(8q22.3)	92 (61%)	58	0.0040913	1	0.0020564	0.897	0.16764	1	0.20779	1	0.10839	1	0.43684	1	0.014568	1	0.19162	1
Amp Peak 16(8q24.21)	88 (59%)	62	0.0013776	0.616	0.021955	1	0.22617	1	0.35378	1	0.12541	1	0.19638	1	0.031083	1	0.37538	1
Amp Peak 17(10p15.1)	61 (41%)	89	6.729e-09	3.38e-06	5.2508e-06	0.00259	0.89314	1	0.21526	1	0.22073	1	0.058297	1	0.33645	1	0.10868	1
Amp Peak 18(11q13.3)	59 (39%)	91	0.0016929	0.748	0.23702	1	0.5536	1	0.5971	1	0.22237	1	0.31929	1	0.0013641	0.611	0.12359	1
Amp Peak 19(12q15)	48 (32%)	102	0.050913	1	0.10718	1	0.76019	1	0.43903	1	0.0081952	1	0.0021946	0.955	0.20237	1	0.28068	1
Amp Peak 20(13q22.1)	49 (33%)	101	0.58019	1	0.65884	1	0.64121	1	0.097132	1	0.88569	1	0.89845	1	0.45457	1	0.52144	1
Amp Peak 21(16p12.1)	39 (26%)	111	0.010368	1	0.11247	1	0.078326	1	0.4535	1	0.90043	1	0.84647	1	0.52636	1	0.79019	1
Amp Peak 22(17q11.2)	68 (45%)	82	4.6173e-08	2.31e-05	0.0012197	0.549	0.76019	1	0.43903	1	0.0001339	0.064	0.0031839	1	0.015216	1	0.018398	1
Amp Peak 23(17q12)	63 (42%)	87	0.0018998	0.834	0.15321	1	0.9394	1	0.43903	1	0.05045	1	0.25997	1	0.011225	1	0.068986	1
Amp Peak 24(19q12)	65 (43%)	85	6.3489e-06	0.00313	0.0027118	1	0.37007	1	0.93577	1	0.4558	1	0.43786	1	0.51759	1	0.28244	1
Amp Peak 25(19q13.43)	63 (42%)	87	9.0782e-05	0.0435	0.025791	1	0.77788	1	0.76681	1	0.081185	1	0.81907	1	0.20163	1	0.053695	1
Amp Peak 26(20q11.21)	104 (69%)	46	0.00069982	0.32	0.42783	1	0.34208	1	0.86458	1	0.20399	1	0.22575	1	0.27061	1	0.21809	1
Amp Peak 27(22q11.23)	35 (23%)	115	0.0013077	0.587	0.38329	1	0.83664	1	0.091558	1	0.14625	1	0.23153	1	0.27493	1	0.60143	1
Del Peak  1(1p36.11)	27 (18%)	123	0.96736	1	0.0049925	1	0.069891	1	0.011411	1	0.21564	1	0.18112	1	0.76383	1	0.032255	1
Del Peak  2(1q32.1)	28 (19%)	122	0.07233	1	0.11463	1	0.73836	1	0.37988	1	0.28241	1	0.11132	1	0.92799	1	0.68733	1
Del Peak  3(2q22.1)	43 (29%)	107	0.0031733	1	0.29465	1	0.3152	1	0.27846	1	0.57724	1	0.10238	1	0.17685	1	0.76026	1
Del Peak  4(2q34)	60 (40%)	90	3.5259e-06	0.00175	0.13729	1	0.3093	1	0.47215	1	0.15195	1	0.11116	1	0.11742	1	0.13694	1
Del Peak  5(2q37.1)	73 (49%)	77	3.2969e-05	0.0161	0.012785	1	0.90782	1	0.87528	1	0.06586	1	0.018377	1	0.06649	1	0.01643	1
Del Peak  6(3p21.31)	47 (31%)	103	0.00039436	0.184	0.12029	1	0.0064897	1	0.0023042	1	0.00055753	0.255	0.020288	1	0.082678	1	0.051222	1
Del Peak  7(3p14.2)	48 (32%)	102	0.000507	0.233	0.56029	1	0.075854	1	0.00029355	0.138	0.00042488	0.197	0.0075294	1	0.49804	1	0.15432	1
Del Peak  8(3p12.3)	41 (27%)	109	0.012731	1	0.45467	1	0.018856	1	0.00049489	0.228	0.0016441	0.728	0.052339	1	0.50778	1	0.18402	1
Del Peak  9(4q22.1)	59 (39%)	91	0.53909	1	0.62787	1	0.3577	1	1	1	0.2965	1	0.14893	1	0.95309	1	0.48926	1
Del Peak 10(4q34.2)	65 (43%)	85	0.065426	1	0.37403	1	0.42198	1	0.87528	1	0.52653	1	0.033339	1	0.073202	1	0.0083151	1
Del Peak 11(5q11.2)	75 (50%)	75	0.001051	0.475	0.051099	1	0.8138	1	0.47385	1	0.73893	1	0.090612	1	0.24765	1	0.028922	1
Del Peak 12(5q35.1)	72 (48%)	78	0.022817	1	0.0060952	1	0.56722	1	0.56809	1	0.60958	1	0.21445	1	0.10058	1	0.082631	1
Del Peak 13(6p25.3)	40 (27%)	110	0.020667	1	0.26872	1	0.13456	1	0.66031	1	0.51234	1	0.82396	1	0.38894	1	0.75609	1
Del Peak 14(6q21)	63 (42%)	87	7.2861e-07	0.000363	0.012898	1	0.079914	1	0.27212	1	0.31418	1	0.015304	1	0.47936	1	0.10109	1
Del Peak 15(6q27)	62 (41%)	88	2.0443e-06	0.00102	0.0023544	1	0.1565	1	0.34607	1	0.22073	1	0.0062481	1	0.18314	1	0.29174	1
Del Peak 16(8p23.3)	80 (53%)	70	2.103e-08	1.06e-05	5.2414e-05	0.0253	0.14489	1	0.38887	1	0.16869	1	0.96879	1	0.0058957	1	0.0093054	1
Del Peak 17(8p21.1)	84 (56%)	66	1.5307e-09	7.71e-07	5.1974e-05	0.0251	0.14489	1	0.38887	1	0.71307	1	0.49814	1	0.0018043	0.796	0.00074721	0.341
Del Peak 18(9p23)	65 (43%)	85	0.0019894	0.871	0.87362	1	0.27398	1	0.71654	1	0.46018	1	0.06327	1	0.4169	1	0.91457	1
Del Peak 19(9p21.3)	86 (57%)	64	0.0004823	0.223	0.56608	1	0.071796	1	0.93048	1	0.25138	1	0.12762	1	0.75182	1	0.52534	1
Del Peak 20(10p12.1)	29 (19%)	121	0.90997	1	0.76928	1	0.45485	1	0.90556	1	0.068631	1	0.02926	1	0.2333	1	0.045086	1
Del Peak 21(10q23.31)	60 (40%)	90	0.010543	1	0.0025019	1	0.2284	1	0.92873	1	0.27708	1	0.045653	1	0.45274	1	0.10868	1
Del Peak 22(11p15.5)	73 (49%)	77	5.1247e-06	0.00254	0.037959	1	0.19518	1	0.6729	1	0.12502	1	0.00015223	0.0723	0.00164	0.728	0.01643	1
Del Peak 23(11q25)	47 (31%)	103	4.2645e-05	0.0207	0.33748	1	0.37822	1	1	1	0.19997	1	0.54929	1	0.11236	1	0.058781	1
Del Peak 24(13q14.2)	58 (39%)	92	0.00013481	0.0643	0.98586	1	0.00022903	0.108	0.0087455	1	0.092842	1	0.23523	1	0.9062	1	0.68684	1
Del Peak 25(14q12)	43 (29%)	107	0.0008936	0.406	0.00094091	0.426	0.8053	1	0.59817	1	0.14201	1	0.034159	1	0.12475	1	0.097877	1
Del Peak 26(14q32.31)	41 (27%)	109	5.9484e-05	0.0286	0.027201	1	0.8053	1	0.84344	1	0.21839	1	0.24745	1	0.00050295	0.231	0.0013936	0.622
Del Peak 27(15q13.1)	54 (36%)	96	0.00030099	0.141	0.0031238	1	0.082907	1	0.45966	1	0.5797	1	0.78021	1	0.084223	1	0.028272	1
Del Peak 28(16p13.3)	54 (36%)	96	0.0033236	1	0.0065187	1	0.19141	1	0.22993	1	1	1	0.49891	1	0.5912	1	0.37685	1
Del Peak 29(16q23.1)	38 (25%)	112	1.9895e-05	0.00975	0.043382	1	0.23182	1	0.7533	1	0.61133	1	0.95968	1	0.077252	1	0.080066	1
Del Peak 30(17p12)	77 (51%)	73	2.9136e-08	1.46e-05	0.017517	1	0.55568	1	0.40504	1	0.021805	1	0.02453	1	0.22497	1	0.52818	1
Del Peak 31(18q23)	63 (42%)	87	0.0037721	1	0.48466	1	0.97864	1	0.76299	1	0.84611	1	0.37044	1	0.019365	1	0.0027826	1
Del Peak 32(19p13.3)	60 (40%)	90	0.022727	1	0.026551	1	1	1	0.75741	1	0.9439	1	0.083106	1	0.42794	1	0.21547	1
Del Peak 33(22q13.32)	60 (40%)	90	0.0011155	0.503	0.25987	1	0.12831	1	0.067522	1	0.106	1	0.11469	1	0.6789	1	0.21547	1
Del Peak 34(Xp11.3)	39 (26%)	111	0.19953	1	0.0029406	1	0.77519	1	0.92232	1	0.076659	1	0.23561	1	0.40702	1	0.94284	1
Del Peak 35(Xq21.33)	35 (23%)	115	0.33434	1	0.078904	1	0.17296	1	0.17311	1	0.0091947	1	0.73532	1	0.1974	1	0.24851	1
Del Peak 36(Xq22.3)	32 (21%)	118	0.13645	1	0.017277	1	0.14922	1	0.52004	1	0.017407	1	0.79604	1	0.091401	1	0.27669	1