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	1	1	0.014691	1	0.51983	1	0.4596	1	0.051214	1
Amp Peak  2(1q21.3)	76 (51%)	74	6.85e-06	0.00337	0.00039988	0.187	0.011755	1	0.00635	1	0.0037395	1	0.36547	1	0.27025	1	0.0020646	0.906
Amp Peak  3(1q23.3)	82 (55%)	68	2.5929e-05	0.0127	0.012382	1	0.9254	1	0.68055	1	0.063352	1	0.71896	1	0.001037	0.471	0.0011876	0.534
Amp Peak  4(3p25.2)	72 (48%)	78	3.3553e-05	0.0163	0.0016134	0.72	0.27822	1	0.2373	1	0.00084835	0.388	0.0003715	0.174	0.0028882	1	0.00042236	0.197
Amp Peak  5(3q26.32)	84 (56%)	66	0.0044027	1	0.66438	1	0.16067	1	0.20572	1	0.60054	1	0.87483	1	0.53477	1	0.52538	1
Amp Peak  6(4p16.3)	31 (21%)	119	0.017605	1	0.1717	1	0.16214	1	0.13656	1	0.10257	1	0.11838	1	0.053135	1	0.56582	1
Amp Peak  7(4q13.3)	23 (15%)	127	8.4547e-05	0.0406	0.15965	1	0.51704	1	1	1	0.57148	1	0.39991	1	0.37821	1	0.6822	1
Amp Peak  8(5p15.1)	69 (46%)	81	4.4953e-05	0.0218	0.20229	1	0.013987	1	0.33188	1	0.094042	1	0.45769	1	0.14338	1	0.25481	1
Amp Peak  9(6p22.3)	61 (41%)	89	0.00018288	0.0865	0.0023585	1	0.83415	1	0.76099	1	0.55965	1	0.58141	1	0.24072	1	0.32338	1
Amp Peak 10(6q12)	25 (17%)	125	0.0060126	1	0.62748	1	1	1	0.84195	1	1	1	0.66707	1	0.17286	1	1	1
Amp Peak 11(6q21)	18 (12%)	132	0.24512	1	0.05116	1	0.62114	1	0.44988	1	0.19838	1	0.15454	1	0.73488	1	0.76716	1
Amp Peak 12(7p11.2)	78 (52%)	72	4.4909e-07	0.000224	0.0020026	0.883	0.48139	1	0.18619	1	0.82484	1	0.67802	1	0.62169	1	0.88995	1
Amp Peak 13(8p11.23)	48 (32%)	102	0.00049153	0.228	0.048781	1	0.073189	1	0.022922	1	0.42305	1	0.27108	1	0.078607	1	0.10488	1
Amp Peak 14(8p11.21)	48 (32%)	102	1.6173e-05	0.00794	0.014559	1	0.59619	1	0.52776	1	0.26825	1	0.44823	1	0.27024	1	0.1358	1
Amp Peak 15(8q22.3)	92 (61%)	58	0.0040913	1	0.0020564	0.905	0.16764	1	0.4202	1	0.10839	1	0.43684	1	0.038071	1	0.27285	1
Amp Peak 16(8q24.21)	88 (59%)	62	0.0013776	0.616	0.021955	1	0.22617	1	0.62289	1	0.12541	1	0.19638	1	0.074887	1	0.20723	1
Amp Peak 17(10p15.1)	61 (41%)	89	6.729e-09	3.38e-06	5.2508e-06	0.00259	0.89314	1	0.72506	1	0.22073	1	0.058297	1	0.46805	1	0.13162	1
Amp Peak 18(11q13.3)	59 (39%)	91	0.0016929	0.752	0.23702	1	0.5536	1	0.64834	1	0.22237	1	0.31929	1	0.017553	1	0.88738	1
Amp Peak 19(12q15)	48 (32%)	102	0.050913	1	0.10718	1	0.76019	1	0.71714	1	0.0081952	1	0.0021946	0.961	0.027458	1	0.1312	1
Amp Peak 20(13q22.1)	49 (33%)	101	0.58019	1	0.65884	1	0.64121	1	0.091166	1	0.88569	1	0.89845	1	0.44567	1	0.42454	1
Amp Peak 21(16p12.1)	39 (26%)	111	0.010368	1	0.11247	1	0.078326	1	0.15156	1	0.90043	1	0.84647	1	0.27062	1	0.32861	1
Amp Peak 22(17q11.2)	68 (45%)	82	4.6173e-08	2.31e-05	0.0012197	0.548	0.76019	1	0.67251	1	0.0001339	0.0639	0.0031839	1	0.015514	1	0.13343	1
Amp Peak 23(17q12)	63 (42%)	87	0.0018998	0.842	0.15321	1	0.9394	1	0.67251	1	0.05045	1	0.25997	1	0.0078267	1	0.00082054	0.376
Amp Peak 24(19q12)	65 (43%)	85	6.3489e-06	0.00313	0.0027118	1	0.37007	1	0.68055	1	0.4558	1	0.43786	1	0.29008	1	0.2111	1
Amp Peak 25(19q13.43)	63 (42%)	87	9.0782e-05	0.0435	0.025791	1	0.77788	1	0.77196	1	0.081185	1	0.81907	1	0.13705	1	0.095744	1
Amp Peak 26(20q11.21)	104 (69%)	46	0.00069982	0.321	0.42783	1	0.34208	1	0.52334	1	0.20399	1	0.22575	1	0.35237	1	0.093794	1
Amp Peak 27(22q11.23)	35 (23%)	115	0.0013077	0.586	0.38329	1	0.83664	1	0.17219	1	0.14625	1	0.23153	1	0.34	1	0.32269	1
Del Peak  1(1p36.11)	27 (18%)	123	0.96736	1	0.0049925	1	0.069891	1	0.082591	1	0.21564	1	0.18112	1	0.84224	1	0.88053	1
Del Peak  2(1q32.1)	28 (19%)	122	0.07233	1	0.11463	1	0.73836	1	0.22864	1	0.28241	1	0.11132	1	0.70227	1	0.55838	1
Del Peak  3(2q22.1)	43 (29%)	107	0.0031733	1	0.29465	1	0.3152	1	0.31458	1	0.57724	1	0.10238	1	0.37593	1	0.63079	1
Del Peak  4(2q34)	60 (40%)	90	3.5259e-06	0.00175	0.13729	1	0.3093	1	0.3197	1	0.15195	1	0.11116	1	0.09042	1	0.058568	1
Del Peak  5(2q37.1)	73 (49%)	77	3.2969e-05	0.0161	0.012785	1	0.90782	1	0.93591	1	0.06586	1	0.018377	1	0.040151	1	0.031428	1
Del Peak  6(3p21.31)	47 (31%)	103	0.00039436	0.185	0.12029	1	0.0064897	1	0.068072	1	0.00055753	0.257	0.020288	1	0.078896	1	0.16461	1
Del Peak  7(3p14.2)	48 (32%)	102	0.000507	0.234	0.56029	1	0.075854	1	0.015843	1	0.00042488	0.198	0.0075294	1	0.13203	1	0.64462	1
Del Peak  8(3p12.3)	41 (27%)	109	0.012731	1	0.45467	1	0.018856	1	0.018111	1	0.0016441	0.732	0.052339	1	0.22134	1	0.49553	1
Del Peak  9(4q22.1)	59 (39%)	91	0.53909	1	0.62787	1	0.3577	1	0.68037	1	0.2965	1	0.14893	1	0.74178	1	0.85158	1
Del Peak 10(4q34.2)	65 (43%)	85	0.065426	1	0.37403	1	0.42198	1	0.1513	1	0.52653	1	0.033339	1	0.24204	1	0.45493	1
Del Peak 11(5q11.2)	75 (50%)	75	0.001051	0.475	0.051099	1	0.8138	1	0.48698	1	0.73893	1	0.090612	1	0.19545	1	0.029113	1
Del Peak 12(5q35.1)	72 (48%)	78	0.022817	1	0.0060952	1	0.56722	1	0.81467	1	0.60958	1	0.21445	1	0.050701	1	0.1233	1
Del Peak 13(6p25.3)	40 (27%)	110	0.020667	1	0.26872	1	0.13456	1	0.49135	1	0.51234	1	0.82396	1	0.60162	1	1	1
Del Peak 14(6q21)	63 (42%)	87	7.2861e-07	0.000363	0.012898	1	0.079914	1	0.12261	1	0.31418	1	0.015304	1	0.41236	1	0.11707	1
Del Peak 15(6q27)	62 (41%)	88	2.0443e-06	0.00102	0.0023544	1	0.1565	1	0.16257	1	0.22073	1	0.0062481	1	0.22936	1	0.16828	1
Del Peak 16(8p23.3)	80 (53%)	70	2.103e-08	1.06e-05	5.2414e-05	0.0253	0.14489	1	0.32464	1	0.16869	1	0.96879	1	0.094501	1	0.017958	1
Del Peak 17(8p21.1)	84 (56%)	66	1.5307e-09	7.71e-07	5.1974e-05	0.0251	0.14489	1	0.32464	1	0.71307	1	0.49814	1	0.030864	1	0.051578	1
Del Peak 18(9p23)	65 (43%)	85	0.0019894	0.879	0.87362	1	0.27398	1	0.27535	1	0.46018	1	0.06327	1	0.50082	1	0.10853	1
Del Peak 19(9p21.3)	86 (57%)	64	0.0004823	0.224	0.56608	1	0.071796	1	0.57543	1	0.25138	1	0.12762	1	0.14987	1	0.20723	1
Del Peak 20(10p12.1)	29 (19%)	121	0.90997	1	0.76928	1	0.45485	1	0.73749	1	0.068631	1	0.02926	1	0.19434	1	1	1
Del Peak 21(10q23.31)	60 (40%)	90	0.010543	1	0.0025019	1	0.2284	1	0.74818	1	0.27708	1	0.045653	1	0.36629	1	0.50755	1
Del Peak 22(11p15.5)	73 (49%)	77	5.1247e-06	0.00254	0.037959	1	0.19518	1	0.72656	1	0.12502	1	0.00015223	0.0722	0.011267	1	0.0088849	1
Del Peak 23(11q25)	47 (31%)	103	4.2645e-05	0.0207	0.33748	1	0.37822	1	0.45365	1	0.19997	1	0.54929	1	0.14267	1	0.294	1
Del Peak 24(13q14.2)	58 (39%)	92	0.00013481	0.0642	0.98586	1	0.00022903	0.108	0.00011695	0.0559	0.092842	1	0.23523	1	0.97302	1	0.13026	1
Del Peak 25(14q12)	43 (29%)	107	0.0008936	0.407	0.00094091	0.428	0.8053	1	0.66312	1	0.14201	1	0.034159	1	0.017125	1	0.0006645	0.306
Del Peak 26(14q32.31)	41 (27%)	109	5.9484e-05	0.0286	0.027201	1	0.8053	1	0.92244	1	0.21839	1	0.24745	1	0.00013579	0.0645	0.0010443	0.473
Del Peak 27(15q13.1)	54 (36%)	96	0.00030099	0.141	0.0031238	1	0.082907	1	0.33188	1	0.5797	1	0.78021	1	0.13461	1	0.11304	1
Del Peak 28(16p13.3)	54 (36%)	96	0.0033236	1	0.0065187	1	0.19141	1	0.6135	1	1	1	0.49891	1	0.79796	1	0.77932	1
Del Peak 29(16q23.1)	38 (25%)	112	1.9895e-05	0.00975	0.043382	1	0.23182	1	0.52044	1	0.61133	1	0.95968	1	0.093165	1	0.083969	1
Del Peak 30(17p12)	77 (51%)	73	2.9136e-08	1.46e-05	0.017517	1	0.55568	1	0.1687	1	0.021805	1	0.02453	1	0.34655	1	0.36323	1
Del Peak 31(18q23)	63 (42%)	87	0.0037721	1	0.48466	1	0.97864	1	0.82167	1	0.84611	1	0.37044	1	0.13218	1	0.24926	1
Del Peak 32(19p13.3)	60 (40%)	90	0.022727	1	0.026551	1	1	1	0.71543	1	0.9439	1	0.083106	1	0.54762	1	0.15946	1
Del Peak 33(22q13.32)	60 (40%)	90	0.0011155	0.503	0.25987	1	0.12831	1	0.0028294	1	0.106	1	0.11469	1	0.50209	1	0.12933	1
Del Peak 34(Xp11.3)	39 (26%)	111	0.19953	1	0.0029406	1	0.77519	1	0.57846	1	0.076659	1	0.23561	1	0.63075	1	0.43876	1
Del Peak 35(Xq21.33)	35 (23%)	115	0.33434	1	0.078904	1	0.17296	1	0.47084	1	0.0091947	1	0.73532	1	0.053632	1	0.433	1
Del Peak 36(Xq22.3)	32 (21%)	118	0.13645	1	0.017277	1	0.14922	1	1	1	0.017407	1	0.79604	1	0.12722	1	0.60638	1