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(1p34.2)	58 (16%)	300	0.027997	1	0.48064	1	0.00027276	0.193	0.70971	1	0.4193	1	0.66819	1	0.04845	1	0.24108	1	0.29888	1	0.49421	1
Amp Peak  2(1q21.2)	186 (52%)	172	0.041886	1	0.0061823	1	7.3203e-07	0.000561	0.0012847	0.865	0.15526	1	0.057554	1	0.00068518	0.472	0.00048787	0.34	0.30475	1	0.056204	1
Amp Peak  3(2p16.1)	194 (54%)	164	0.00030485	0.215	0.0016452	1	2.412e-09	1.88e-06	7.0048e-05	0.0513	0.96653	1	0.74078	1	0.00033312	0.235	0.0011329	0.764	0.87945	1	0.031189	1
Amp Peak  4(2q31.2)	121 (34%)	237	0.020695	1	0.00094798	0.643	6.7367e-05	0.0494	4.9417e-06	0.00375	0.73767	1	0.91188	1	0.00080111	0.548	0.00093222	0.633	0.46534	1	0.25204	1
Amp Peak  5(3p11.1)	73 (20%)	285	0.074773	1	0.84409	1	0.67333	1	0.82621	1	0.20236	1	0.00083089	0.567	0.05549	1	0.44422	1	0.41045	1	0.94669	1
Amp Peak  6(3q26.33)	330 (92%)	28	0.00042663	0.299	1.7146e-05	0.0129	1.6279e-09	1.27e-06	0.00011311	0.0818	0.21321	1	0.094447	1	3.8139e-05	0.0283	0.00016431	0.118	0.2054	1	9.108e-05	0.0662
Amp Peak  7(4q12)	85 (24%)	273	0.67906	1	0.75873	1	0.0054816	1	0.2835	1	0.31214	1	0.088313	1	0.55476	1	0.74982	1	0.18505	1	0.57687	1
Amp Peak  8(5p15.33)	281 (78%)	77	0.85286	1	0.86716	1	8.3753e-06	0.00632	0.0036028	1	0.49766	1	0.42237	1	0.38708	1	0.32784	1	0.84118	1	0.26253	1
Amp Peak  9(5p12)	236 (66%)	122	0.91917	1	0.51401	1	1.3826e-09	1.08e-06	0.0066607	1	0.6689	1	1	1	0.063491	1	0.58557	1	0.041292	1	0.2193	1
Amp Peak 10(6q12)	107 (30%)	251	1	1	0.87303	1	0.069033	1	0.25977	1	0.34877	1	0.49551	1	0.39467	1	0.23611	1	0.5946	1	0.15472	1
Amp Peak 11(7p11.2)	174 (49%)	184	0.18606	1	0.09391	1	0.0016773	1	0.0025384	1	0.64222	1	0.85005	1	0.075977	1	0.014833	1	0.70005	1	0.1233	1
Amp Peak 12(7q21.2)	188 (53%)	170	0.10132	1	0.24997	1	3.3631e-10	2.64e-07	8.3452e-06	0.00631	0.040829	1	0.21491	1	0.016544	1	0.022055	1	0.2468	1	0.037662	1
Amp Peak 13(8p11.23)	168 (47%)	190	0.0081177	1	0.16822	1	0.11314	1	0.10015	1	0.21654	1	0.087117	1	0.0063053	1	0.71976	1	0.13452	1	0.62015	1
Amp Peak 14(8q24.21)	248 (69%)	110	0.8715	1	0.64417	1	0.33855	1	0.5892	1	0.9575	1	0.76758	1	0.7345	1	0.42772	1	0.4907	1	0.93231	1
Amp Peak 15(9p24.1)	67 (19%)	291	0.37518	1	0.029533	1	0.00058577	0.405	0.22826	1	0.0017579	1	0.0057256	1	0.041333	1	0.0029351	1	0.56116	1	0.38974	1
Amp Peak 16(9p13.3)	98 (27%)	260	0.16996	1	0.37287	1	0.010746	1	0.3878	1	0.077857	1	0.009373	1	0.021999	1	0.18844	1	0.40751	1	0.88918	1
Amp Peak 17(11q13.3)	131 (37%)	227	0.06969	1	0.030551	1	0.025564	1	0.0014782	0.992	0.18394	1	0.064128	1	0.012508	1	0.13883	1	0.15003	1	0.33037	1
Amp Peak 18(12p13.33)	177 (49%)	181	0.010156	1	0.057062	1	0.00025451	0.18	0.011248	1	0.35259	1	0.71121	1	0.00057533	0.399	0.0051835	1	0.67408	1	0.42873	1
Amp Peak 19(12q15)	132 (37%)	226	0.31238	1	0.5273	1	0.0087421	1	0.010511	1	0.80579	1	0.40853	1	0.10546	1	0.049145	1	0.56467	1	0.92632	1
Amp Peak 20(13q34)	64 (18%)	294	0.96435	1	0.048907	1	0.39591	1	0.16602	1	0.82393	1	0.19554	1	0.80276	1	0.40688	1	0.072351	1	0.2508	1
Amp Peak 21(14q13.3)	110 (31%)	248	0.34486	1	0.24581	1	0.52831	1	0.4696	1	0.50914	1	0.020208	1	0.61652	1	0.084716	1	0.016709	1	0.080992	1
Amp Peak 22(15q26.3)	128 (36%)	230	0.15118	1	0.02098	1	5.6345e-07	0.000433	1.784e-05	0.0134	0.3118	1	0.01616	1	0.00062217	0.429	0.0042628	1	0.017505	1	7.1387e-05	0.0521
Amp Peak 23(17q25.1)	171 (48%)	187	0.017661	1	0.060794	1	1.8694e-06	0.00143	0.00014806	0.107	0.29661	1	0.32262	1	0.027422	1	0.0080673	1	0.75564	1	0.74216	1
Amp Peak 24(18p11.32)	122 (34%)	236	0.060239	1	0.0062845	1	0.00014769	0.106	0.032789	1	0.22631	1	0.8444	1	0.60707	1	0.1765	1	0.52637	1	0.16253	1
Amp Peak 25(18q11.2)	115 (32%)	243	0.00045553	0.318	0.0022679	1	0.00023059	0.164	0.0041485	1	0.25187	1	0.77128	1	0.0043758	1	0.00057779	0.4	0.36947	1	0.0092619	1
Amp Peak 26(19q12)	149 (42%)	209	0.45483	1	0.24902	1	0.00011105	0.0804	0.44499	1	0.27364	1	0.024412	1	0.19265	1	0.081975	1	0.94942	1	0.68582	1
Amp Peak 27(19q13.2)	157 (44%)	201	0.47272	1	0.90909	1	0.00044692	0.313	0.25029	1	0.31842	1	0.13123	1	0.45374	1	0.033569	1	0.9747	1	0.28552	1
Amp Peak 28(20p12.2)	193 (54%)	165	0.00098685	0.668	0.0042983	1	4.62e-08	3.58e-05	0.0014115	0.949	0.95039	1	0.29284	1	0.1497	1	0.013404	1	0.48835	1	0.24628	1
Amp Peak 29(20q11.21)	206 (58%)	152	0.99122	1	0.84394	1	0.002749	1	0.038807	1	0.74317	1	0.69747	1	0.59324	1	0.54885	1	0.93707	1	0.61494	1
Amp Peak 30(22q11.21)	177 (49%)	181	0.11066	1	0.12309	1	0.014625	1	0.0029124	1	0.87358	1	0.33909	1	0.067121	1	0.067683	1	0.81595	1	0.13245	1
Amp Peak 31(Xq28)	92 (26%)	266	0.64364	1	0.51458	1	0.23994	1	0.098096	1	0.054611	1	0.072204	1	0.14256	1	0.22516	1	0.75361	1	0.80444	1
Del Peak  1(1p36.32)	155 (43%)	203	1.2758e-06	0.000976	1.2929e-08	1e-05	3.3385e-28	2.64e-25	4.7761e-16	3.77e-13	0.41877	1	0.0042054	1	1.0225e-10	8.04e-08	6.7545e-09	5.26e-06	0.023689	1	0.0010335	0.699
Del Peak  2(1p13.2)	156 (44%)	202	0.00023715	0.169	0.0005497	0.382	6.4672e-14	5.1e-11	6.5198e-09	5.09e-06	0.10687	1	0.1149	1	2.352e-05	0.0175	7.0749e-05	0.0517	0.19647	1	0.0096663	1
Del Peak  3(2p25.3)	34 (9%)	324	0.046105	1	0.17884	1	0.089917	1	0.36742	1	0.10989	1	0.7888	1	0.31965	1	0.22609	1	0.10548	1	0.064084	1
Del Peak  4(2q22.1)	96 (27%)	262	0.25483	1	0.31825	1	0.00021665	0.155	0.021581	1	0.65269	1	0.2097	1	0.18815	1	0.23144	1	0.68255	1	0.46017	1
Del Peak  5(2q36.2)	116 (32%)	242	0.00023576	0.168	4.7565e-05	0.0352	5.3215e-12	4.19e-09	0.00035165	0.248	0.13844	1	0.11332	1	8.4879e-05	0.0619	6.1471e-06	0.00466	0.94402	1	0.62414	1
Del Peak  6(3p25.3)	285 (80%)	73	0.54042	1	0.17616	1	0.029151	1	0.0040693	1	0.62364	1	0.2119	1	0.32711	1	0.008757	1	0.65508	1	0.013733	1
Del Peak  7(3p13)	310 (87%)	48	0.41881	1	0.54863	1	9.6788e-05	0.0703	0.0021125	1	0.9102	1	0.012673	1	0.36874	1	0.013408	1	0.87166	1	0.0082614	1
Del Peak  8(3p12.1)	280 (78%)	78	0.32181	1	0.041333	1	1.4599e-07	0.000113	2.7885e-05	0.0207	0.68789	1	0.10871	1	0.15465	1	0.0023519	1	0.17413	1	0.10066	1
Del Peak  9(4p15.31)	219 (61%)	139	0.00080707	0.551	0.001708	1	1.2105e-05	0.00912	0.0040584	1	0.67503	1	0.045415	1	0.088333	1	0.0514	1	0.40326	1	1	1
Del Peak 10(4q22.1)	199 (56%)	159	0.0068481	1	0.057857	1	0.00047348	0.33	0.040538	1	0.14712	1	0.34581	1	0.025247	1	0.0063574	1	0.36978	1	0.13363	1
Del Peak 11(4q32.3)	226 (63%)	132	0.0096682	1	0.025274	1	2.972e-07	0.000229	0.01118	1	0.10165	1	0.58456	1	0.005697	1	0.036026	1	0.4381	1	0.14446	1
Del Peak 12(4q35.2)	229 (64%)	129	0.10047	1	0.20573	1	1.0708e-06	0.00082	0.0025875	1	0.455	1	0.56096	1	0.0053154	1	0.10683	1	0.67091	1	0.33818	1
Del Peak 13(5q11.2)	265 (74%)	93	0.84151	1	0.30269	1	5.706e-10	4.47e-07	0.00026557	0.188	1	1	0.23658	1	0.24758	1	0.56007	1	0.88754	1	0.00016172	0.116
Del Peak 14(5q31.1)	277 (77%)	81	0.33159	1	0.2283	1	6.2132e-07	0.000477	3.2542e-05	0.0241	0.3522	1	0.20864	1	0.25406	1	0.40095	1	0.59267	1	0.0083154	1
Del Peak 15(6p25.3)	90 (25%)	268	0.21975	1	0.10989	1	0.016912	1	0.0006916	0.475	0.54156	1	0.0096737	1	0.010038	1	0.020398	1	0.23807	1	0.17921	1
Del Peak 16(6q26)	93 (26%)	265	0.065853	1	0.0029759	1	0.0090105	1	0.0016764	1	0.88496	1	0.86624	1	0.068692	1	0.14099	1	0.22561	1	0.10826	1
Del Peak 17(7q11.22)	35 (10%)	323	0.90823	1	0.40489	1	0.00038523	0.271	0.39377	1	0.95817	1	0.80009	1	0.046282	1	0.064437	1	0.80375	1	0.526	1
Del Peak 18(7q36.1)	73 (20%)	285	0.39297	1	0.56933	1	0.01427	1	0.38122	1	1	1	0.28601	1	0.11462	1	0.38834	1	0.36058	1	0.82792	1
Del Peak 19(8p23.2)	243 (68%)	115	0.86415	1	0.45866	1	0.00493	1	0.29491	1	0.38219	1	0.19557	1	0.15724	1	0.071999	1	0.45134	1	0.16658	1
Del Peak 20(9p23)	234 (65%)	124	0.005614	1	0.0029131	1	1.2081e-07	9.35e-05	0.10899	1	0.1339	1	0.18469	1	0.026141	1	0.087611	1	1	1	0.090096	1
Del Peak 21(9p21.3)	272 (76%)	86	0.37246	1	0.17169	1	3.2303e-06	0.00246	0.51738	1	0.67917	1	0.37927	1	0.16414	1	0.84599	1	0.86514	1	0.33662	1
Del Peak 22(9q21.11)	174 (49%)	184	0.00017721	0.127	4.9247e-05	0.0363	2.034e-07	0.000157	1.4151e-06	0.00108	0.57062	1	0.2396	1	4.4373e-06	0.00337	2.3951e-07	0.000185	0.044487	1	3.1585e-05	0.0235
Del Peak 23(10p15.3)	160 (45%)	198	0.37287	1	0.44184	1	0.0015018	1	0.00093137	0.633	0.40724	1	0.3908	1	0.0038329	1	0.016525	1	0.10443	1	0.0018531	1
Del Peak 24(10q23.31)	184 (51%)	174	0.039232	1	0.0038632	1	0.00019018	0.136	6.4182e-05	0.0472	0.28335	1	0.30267	1	0.0001037	0.0752	2.6262e-05	0.0196	0.46028	1	0.027698	1
Del Peak 25(11p15.5)	173 (48%)	185	0.00068877	0.474	0.052775	1	6.0397e-05	0.0445	0.011711	1	0.00044866	0.314	2.3365e-05	0.0175	0.019994	1	0.036223	1	0.025269	1	0.029138	1
Del Peak 26(11q22.1)	108 (30%)	250	0.49319	1	0.28778	1	0.0028054	1	0.077483	1	0.086811	1	0.97458	1	0.24499	1	0.42281	1	0.2778	1	0.052627	1
Del Peak 27(11q25)	131 (37%)	227	0.7979	1	0.42926	1	0.022871	1	0.38088	1	0.10894	1	0.86738	1	0.44743	1	0.40585	1	0.1848	1	0.17063	1
Del Peak 28(12q24.31)	57 (16%)	301	0.96498	1	0.33211	1	0.59815	1	0.30319	1	0.35883	1	0.20317	1	0.90035	1	0.68912	1	0.11839	1	0.30228	1
Del Peak 29(13q12.11)	240 (67%)	118	0.054743	1	0.61102	1	0.033756	1	0.15618	1	1	1	0.19261	1	0.69982	1	0.21445	1	0.95768	1	0.98657	1
Del Peak 30(13q14.2)	251 (70%)	107	0.051249	1	0.096235	1	0.0007298	0.501	0.12904	1	0.84956	1	0.54703	1	0.028092	1	0.14722	1	0.65383	1	0.54299	1
Del Peak 31(14q11.2)	130 (36%)	228	0.054625	1	0.29339	1	0.038313	1	0.32128	1	0.24278	1	0.15205	1	0.0026496	1	0.0021291	1	0.33337	1	0.17156	1
Del Peak 32(15q12)	122 (34%)	236	0.72495	1	0.22782	1	0.33369	1	0.31682	1	0.06973	1	0.0067351	1	0.13225	1	0.35649	1	0.099644	1	0.73786	1
Del Peak 33(16p13.3)	129 (36%)	229	0.23929	1	0.24492	1	0.0031756	1	0.36161	1	0.13524	1	0.49585	1	0.53052	1	0.24668	1	0.64255	1	0.16405	1
Del Peak 34(16q23.1)	144 (40%)	214	0.94193	1	0.65907	1	0.050565	1	0.31246	1	0.33635	1	0.86078	1	0.20485	1	0.026365	1	0.44087	1	0.58066	1
Del Peak 35(17p11.2)	185 (52%)	173	0.19384	1	0.4015	1	0.0039969	1	0.13557	1	0.13543	1	0.010067	1	0.36815	1	0.86032	1	0.069741	1	0.022024	1
Del Peak 36(17q11.2)	89 (25%)	269	1.2614e-05	0.00949	6.4433e-05	0.0473	9.3487e-09	7.27e-06	0.057932	1	0.45035	1	0.57718	1	0.00012202	0.0881	7.1613e-06	0.00542	0.40625	1	0.015373	1
Del Peak 37(17q25.3)	68 (19%)	290	0.004927	1	0.022034	1	0.00046787	0.327	0.079649	1	0.78241	1	0.97196	1	0.042335	1	0.00055337	0.384	0.58099	1	0.010792	1
Del Peak 38(18q23)	164 (46%)	194	0.50803	1	0.78802	1	0.51711	1	0.97048	1	0.85764	1	0.32501	1	0.2296	1	0.11539	1	0.80441	1	0.53628	1
Del Peak 39(19p13.3)	163 (46%)	195	0.33425	1	0.023076	1	0.00022732	0.162	0.1402	1	0.092838	1	0.40379	1	0.16017	1	0.012363	1	0.017892	1	0.047846	1
Del Peak 40(19q13.33)	96 (27%)	262	0.61681	1	0.06944	1	4.7591e-05	0.0352	0.0002493	0.177	0.27239	1	0.63492	1	0.43647	1	0.2122	1	0.33997	1	0.11881	1
Del Peak 41(19q13.43)	96 (27%)	262	0.64362	1	0.20683	1	9.0848e-05	0.0661	0.0007966	0.546	0.46604	1	0.46966	1	0.46535	1	0.15388	1	0.21643	1	0.30814	1
Del Peak 42(21q11.2)	176 (49%)	182	0.55805	1	0.22347	1	0.0058036	1	0.064673	1	0.96621	1	0.9036	1	0.90836	1	0.48476	1	0.20301	1	0.23308	1
Del Peak 43(21q22.3)	205 (57%)	153	0.95746	1	0.1932	1	2.2127e-08	1.72e-05	0.0010919	0.737	0.47843	1	0.1399	1	0.5636	1	0.30219	1	0.0087121	1	0.47399	1
Del Peak 44(22q11.21)	62 (17%)	296	0.09039	1	0.0093024	1	0.17242	1	0.34185	1	0.12526	1	0.11442	1	0.59809	1	0.7479	1	0.14887	1	0.10087	1
Del Peak 45(Xp22.2)	114 (32%)	244	0.59895	1	0.3507	1	1.573e-05	0.0118	0.016352	1	0.34318	1	0.66417	1	0.13988	1	0.12171	1	0.19485	1	0.26702	1
Del Peak 46(Xp21.1)	118 (33%)	240	0.35378	1	0.14801	1	2.0008e-05	0.015	0.0018051	1	0.38089	1	0.57002	1	0.077879	1	0.0071601	1	0.40668	1	0.10924	1
Del Peak 47(Xp11.3)	116 (32%)	242	0.06204	1	0.17505	1	2.8184e-06	0.00215	5.1573e-05	0.038	0.082309	1	0.077418	1	0.014157	1	0.017529	1	0.13253	1	0.19908	1
Del Peak 48(Xq22.3)	91 (25%)	267	0.0085301	1	0.10522	1	1.0311e-05	0.00777	0.00086092	0.586	0.74472	1	0.93472	1	0.051315	1	0.48519	1	0.71622	1	0.95432	1