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(2q33.1)	79 (19%)	334	0.073363	1	0.10484	1	3.054e-05	0.0174	0.25825	1	0.31656	1	0.01389	1	0.0005156	0.271	0.013678	1	0.27725	1	0.25803	1
Amp Peak  2(5p13.2)	81 (20%)	332	0.33423	1	0.46916	1	0.00020181	0.109	0.14972	1	0.39333	1	0.54293	1	0.086386	1	0.069637	1	0.9268	1	0.58108	1
Amp Peak  3(5q22.3)	40 (10%)	373	0.78032	1	0.629	1	0.029319	1	0.87467	1	0.031738	1	0.73476	1	0.16547	1	0.11152	1	0.69302	1	0.83892	1
Amp Peak  4(6p21.1)	89 (22%)	324	0.09021	1	0.00099634	0.503	3.3666e-09	2.06e-06	0.16999	1	0.60956	1	0.019508	1	0.0064373	1	0.033042	1	0.77582	1	0.25832	1
Amp Peak  5(8p11.23)	144 (35%)	269	0.44402	1	0.23056	1	2.9884e-13	1.94e-10	0.8676	1	0.53191	1	0.44625	1	0.21112	1	0.78274	1	0.17898	1	0.18914	1
Amp Peak  6(8p11.21)	173 (42%)	240	0.35459	1	0.12919	1	4.5091e-10	2.8e-07	0.88585	1	0.31387	1	0.033841	1	0.42103	1	0.60595	1	0.50206	1	0.21775	1
Amp Peak  7(8q12.1)	215 (52%)	198	0.15037	1	0.064623	1	9.3098e-12	5.92e-09	0.038349	1	0.15278	1	0.0033592	1	0.014129	1	0.22829	1	0.12567	1	0.29537	1
Amp Peak  8(8q24.21)	239 (58%)	174	0.20284	1	0.10723	1	7.8615e-14	5.13e-11	0.010196	1	0.2937	1	0.018859	1	0.0063634	1	0.44468	1	0.4037	1	0.21493	1
Amp Peak  9(11p15.5)	86 (21%)	327	1.3774e-05	0.00793	0.00020098	0.109	1.539e-09	9.48e-07	0.00061244	0.318	0.083593	1	0.0010927	0.549	0.001929	0.951	0.0084545	1	0.11742	1	0.20078	1
Amp Peak 10(12p13.33)	104 (25%)	309	0.46331	1	0.88218	1	0.06118	1	0.24692	1	0.52123	1	0.70169	1	0.33441	1	0.97693	1	0.30362	1	0.17308	1
Amp Peak 11(13q12.13)	250 (61%)	163	7.2138e-08	4.31e-05	5.2734e-06	0.00306	5.0359e-36	3.39e-33	0.00027008	0.145	0.23778	1	0.0067255	1	1.2693e-06	0.000745	0.00019564	0.106	0.45926	1	0.79848	1
Amp Peak 12(13q22.1)	254 (62%)	159	6.3426e-05	0.0356	5.4308e-05	0.0306	7.1998e-33	4.83e-30	0.00051007	0.269	0.34516	1	0.0089053	1	1.1465e-06	0.000674	7.6662e-05	0.0427	0.2718	1	0.97749	1
Amp Peak 13(16p11.2)	116 (28%)	297	0.00044664	0.236	0.00037543	0.2	8.5536e-19	5.67e-16	0.021155	1	0.097692	1	0.0013022	0.646	0.00042856	0.228	0.0083752	1	0.77077	1	0.80885	1
Amp Peak 14(16q12.1)	102 (25%)	311	3.0222e-05	0.0173	0.00012608	0.0692	1.6709e-20	1.11e-17	0.05111	1	0.41059	1	0.0081542	1	0.000642	0.333	0.0025448	1	0.90192	1	0.93019	1
Amp Peak 15(17q12)	101 (24%)	312	0.098898	1	0.085195	1	7.529e-07	0.000443	0.016408	1	0.70991	1	0.00025435	0.137	4.5905e-05	0.0259	0.014164	1	0.012101	1	0.98573	1
Amp Peak 16(17q24.1)	92 (22%)	321	0.051891	1	0.008206	1	1.6072e-08	9.69e-06	0.012293	1	0.50039	1	0.00091661	0.465	6.0366e-06	0.0035	0.0031161	1	0.0025416	1	0.78116	1
Amp Peak 17(19p13.2)	65 (16%)	348	0.053531	1	0.034546	1	4.8203e-05	0.0272	0.28305	1	0.90658	1	0.59622	1	0.50145	1	0.53917	1	0.20371	1	0.38494	1
Amp Peak 18(19q13.11)	83 (20%)	330	0.33237	1	0.017695	1	0.0019963	0.98	0.51687	1	0.26117	1	0.84144	1	0.073608	1	0.16703	1	0.41715	1	0.49068	1
Amp Peak 19(20p12.3)	184 (45%)	229	0.001879	0.928	0.00084421	0.43	1.8596e-12	1.2e-09	0.4343	1	0.042122	1	0.32421	1	0.030504	1	0.0097172	1	0.59687	1	0.19482	1
Amp Peak 20(20p11.23)	205 (50%)	208	0.026709	1	0.00079247	0.406	1.2622e-16	8.32e-14	0.10514	1	0.27181	1	0.23567	1	0.00051306	0.27	0.0010395	0.524	0.45496	1	0.2118	1
Amp Peak 21(20p11.21)	230 (56%)	183	0.00069189	0.357	4.2653e-05	0.0242	4.0003e-23	2.67e-20	0.0011341	0.568	0.24401	1	0.04663	1	2.4063e-07	0.000143	1.3852e-06	0.000812	0.17441	1	0.50927	1
Amp Peak 22(20q11.21)	296 (72%)	117	1.0709e-10	6.69e-08	2.8619e-11	1.8e-08	1.5358e-43	1.04e-40	2.1904e-09	1.34e-06	0.039267	1	0.00023238	0.126	1.4664e-14	9.62e-12	3.8499e-12	2.47e-09	0.44287	1	1	1
Amp Peak 23(20q12)	297 (72%)	116	9.2845e-12	5.91e-09	1.8183e-11	1.15e-08	6.2847e-43	4.24e-40	1.5835e-08	9.58e-06	0.008137	1	0.00016739	0.0912	5.477e-14	3.59e-11	1.3447e-11	8.53e-09	0.40581	1	0.94846	1
Amp Peak 24(20q13.32)	300 (73%)	113	2.8741e-10	1.79e-07	6.2668e-12	4e-09	3.1794e-43	2.15e-40	1.5835e-08	9.58e-06	0.010986	1	0.00011898	0.0654	5.477e-14	3.59e-11	1.3447e-11	8.53e-09	0.414	1	0.96035	1
Del Peak  1(1p36.11)	150 (36%)	263	6.8119e-05	0.0382	0.0057606	1	6.3163e-17	4.17e-14	0.00079247	0.406	0.028058	1	0.0020014	0.981	0.0003474	0.186	0.0012029	0.599	0.4086	1	0.06244	1
Del Peak  2(1p33)	107 (26%)	306	0.02462	1	0.53242	1	1.0878e-11	6.91e-09	0.0066849	1	0.10594	1	0.035644	1	0.0050982	1	0.014081	1	0.8934	1	0.051913	1
Del Peak  3(1p13.1)	103 (25%)	310	0.11505	1	0.37439	1	6.8461e-10	4.25e-07	0.18487	1	0.30835	1	0.15513	1	0.083567	1	0.00481	1	0.86754	1	0.37862	1
Del Peak  4(1q43)	44 (11%)	369	0.098319	1	0.45814	1	6.9784e-06	0.00404	0.10478	1	0.49989	1	0.68967	1	0.031175	1	0.011378	1	0.33504	1	0.30091	1
Del Peak  5(2q37.2)	21 (5%)	392	0.92768	1	0.059766	1	0.97728	1	0.70132	1	0.044596	1	0.76813	1	1	1	0.18364	1	0.44659	1	0.44658	1
Del Peak  6(3p26.1)	60 (15%)	353	0.099398	1	0.30369	1	0.00043027	0.228	0.26787	1	0.88619	1	0.46377	1	0.53918	1	0.088268	1	0.5406	1	0.9578	1
Del Peak  7(3p14.2)	75 (18%)	338	0.46592	1	0.74447	1	0.2053	1	0.73514	1	0.95891	1	0.48273	1	0.63238	1	0.48277	1	0.20335	1	0.53643	1
Del Peak  8(3q26.31)	39 (9%)	374	0.12215	1	0.60527	1	0.0081756	1	0.49692	1	0.089676	1	0.38482	1	0.45817	1	0.022264	1	0.14968	1	0.93943	1
Del Peak  9(4p16.2)	121 (29%)	292	0.0019405	0.955	0.010727	1	1.1565e-12	7.47e-10	0.011034	1	0.18206	1	0.063983	1	0.0002371	0.128	0.00010675	0.059	0.37622	1	0.20636	1
Del Peak 10(4q22.1)	126 (31%)	287	0.00058503	0.306	0.0086401	1	8.4971e-12	5.42e-09	0.0020663	1	0.34086	1	0.14663	1	9.2324e-05	0.0512	2.8143e-05	0.0161	0.20975	1	0.51791	1
Del Peak 11(4q35.1)	137 (33%)	276	0.00012764	0.0699	0.0092819	1	1.0461e-13	6.82e-11	7.6854e-05	0.0427	0.24211	1	0.18155	1	0.00023919	0.129	0.00052743	0.276	0.41578	1	0.23487	1
Del Peak 12(5q11.2)	91 (22%)	322	0.001293	0.643	0.0037754	1	4.9424e-09	3.01e-06	0.03386	1	0.52788	1	0.016896	1	0.0014217	0.704	0.0078063	1	0.83478	1	0.21521	1
Del Peak 13(5q21.3)	117 (28%)	296	0.11805	1	0.028088	1	1.1415e-09	7.04e-07	0.035903	1	0.19902	1	0.055601	1	0.0043777	1	0.01043	1	0.65358	1	0.36044	1
Del Peak 14(5q23.1)	107 (26%)	306	0.062839	1	0.035574	1	1.5714e-08	9.52e-06	0.087019	1	0.18276	1	0.081973	1	0.021902	1	0.012593	1	0.62161	1	0.24578	1
Del Peak 15(6p25.3)	54 (13%)	359	0.97109	1	0.79153	1	0.00010249	0.0568	0.052651	1	0.71434	1	0.46846	1	0.35329	1	0.788	1	0.40629	1	0.45348	1
Del Peak 16(6q26)	60 (15%)	353	0.38305	1	0.30369	1	0.15693	1	0.35648	1	0.14683	1	0.66744	1	0.87302	1	0.69718	1	0.79664	1	0.52977	1
Del Peak 17(7q31.1)	11 (3%)	402	1	1	0.50413	1	0.81645	1	0.79545	1	0.32235	1	0.43926	1	0.49001	1	1	1	1	1	0.56392	1
Del Peak 18(8p23.3)	171 (41%)	242	0.0027614	1	0.00060268	0.315	6.8386e-26	4.58e-23	3.6131e-06	0.0021	0.20677	1	0.00024328	0.131	0.00067246	0.348	0.0023104	1	0.1544	1	0.84763	1
Del Peak 19(8p22)	185 (45%)	228	0.0011512	0.576	0.00095796	0.485	2.4052e-30	1.61e-27	3.4605e-07	0.000205	0.13347	1	1.2813e-05	0.00739	2.1632e-05	0.0124	0.00065641	0.34	0.11474	1	0.83207	1
Del Peak 20(8p11.22)	80 (19%)	333	0.21341	1	0.11826	1	8.8799e-09	5.4e-06	0.061445	1	0.017787	1	0.039351	1	0.099284	1	0.080437	1	0.35945	1	0.8314	1
Del Peak 21(8p11.21)	43 (10%)	370	0.023081	1	0.3509	1	5.8112e-07	0.000343	0.36576	1	0.28608	1	0.067672	1	0.48334	1	0.30826	1	0.099704	1	0.54888	1
Del Peak 22(9p21.3)	56 (14%)	357	0.25087	1	0.26423	1	4.5111e-05	0.0256	0.20379	1	0.80802	1	0.14978	1	0.063689	1	0.12685	1	0.90376	1	0.66315	1
Del Peak 23(10p15.3)	68 (16%)	345	0.2615	1	0.14131	1	2.2472e-08	1.35e-05	0.029141	1	0.33083	1	0.051944	1	0.12642	1	0.033979	1	0.67983	1	0.56551	1
Del Peak 24(10q21.1)	82 (20%)	331	0.0092802	1	0.037387	1	2.2397e-11	1.41e-08	0.19404	1	0.6001	1	0.0047147	1	0.19132	1	0.043135	1	0.8868	1	0.8314	1
Del Peak 25(10q23.31)	94 (23%)	319	0.24899	1	0.082921	1	3.4604e-07	0.000205	0.08012	1	0.52789	1	0.21357	1	0.034832	1	0.16507	1	0.8849	1	0.98489	1
Del Peak 26(10q25.2)	93 (23%)	320	0.17166	1	0.010498	1	1.9136e-11	1.21e-08	0.013884	1	0.14806	1	0.20467	1	0.0031176	1	0.0025038	1	0.92109	1	0.5932	1
Del Peak 27(12p13.2)	44 (11%)	369	0.040366	1	0.0079614	1	9.8715e-08	5.89e-05	0.20712	1	0.45186	1	0.82607	1	0.026163	1	0.0036908	1	0.69486	1	0.97344	1
Del Peak 28(13q14.13)	18 (4%)	395	0.39468	1	0.87562	1	0.00012763	0.0699	0.15251	1	0.65407	1	0.12661	1	0.22843	1	0.45153	1	0.61393	1	0.83372	1
Del Peak 29(14q32.11)	133 (32%)	280	2.1229e-05	0.0122	0.00011007	0.0608	1.6095e-20	1.07e-17	0.00070714	0.364	0.00060777	0.317	0.0011958	0.597	7.3029e-05	0.0408	0.00084042	0.429	0.31936	1	0.061222	1
Del Peak 30(15q11.2)	160 (39%)	253	0.00042205	0.225	0.0068286	1	1.1969e-21	7.98e-19	0.0043207	1	0.036727	1	0.059791	1	2.0921e-06	0.00122	0.00011707	0.0645	0.87692	1	0.8927	1
Del Peak 31(15q21.1)	151 (37%)	262	0.012982	1	0.041108	1	8.1471e-18	5.39e-15	0.0074658	1	0.063854	1	0.039485	1	2.0274e-07	0.000121	2.0517e-05	0.0118	0.9795	1	0.62069	1
Del Peak 32(15q22.33)	145 (35%)	268	0.00075795	0.389	0.0032684	1	2.4843e-21	1.65e-18	0.00043461	0.23	0.15245	1	0.033043	1	3.0692e-08	1.84e-05	7.5506e-06	0.00436	0.94865	1	0.3645	1
Del Peak 33(16p13.3)	45 (11%)	368	0.33381	1	0.15535	1	0.20817	1	0.37632	1	0.17412	1	0.92247	1	0.61959	1	0.57186	1	0.84166	1	0.73884	1
Del Peak 34(16q23.1)	49 (12%)	364	0.25945	1	0.0078488	1	0.13094	1	0.33681	1	0.62963	1	0.72583	1	0.042079	1	0.070054	1	0.97682	1	0.50466	1
Del Peak 35(17p12)	229 (55%)	184	6.1168e-08	3.66e-05	1.5957e-06	0.000933	2.8124e-35	1.89e-32	1.803e-09	1.11e-06	0.032084	1	1.9e-06	0.00111	1.0566e-10	6.61e-08	3.2016e-08	1.92e-05	0.36262	1	0.7291	1
Del Peak 36(17q24.3)	59 (14%)	354	0.10177	1	0.67597	1	0.0034819	1	0.011753	1	0.50305	1	0.12138	1	0.0032861	1	0.032904	1	0.68104	1	0.97867	1
Del Peak 37(18p11.31)	220 (53%)	193	1.5056e-12	9.71e-10	3.6545e-09	2.23e-06	1.9303e-42	1.3e-39	3.1072e-13	2.02e-10	0.036885	1	7.236e-05	0.0404	3.1119e-17	2.06e-14	8.1919e-10	5.07e-07	0.48029	1	0.84148	1
Del Peak 38(18q12.2)	247 (60%)	166	8.3716e-11	5.25e-08	1.0824e-09	6.69e-07	1.8686e-45	1.27e-42	8.9817e-16	5.9e-13	0.091817	1	6.9882e-05	0.0391	7.6643e-16	5.04e-13	1.0742e-08	6.52e-06	0.44898	1	0.86493	1
Del Peak 39(18q21.2)	260 (63%)	153	3.0616e-10	1.91e-07	6.8492e-10	4.25e-07	1.5149e-45	1.03e-42	3.2902e-12	2.11e-09	0.024586	1	4.5081e-05	0.0256	8.7386e-13	5.66e-10	7.1392e-07	0.000421	0.051698	1	0.90124	1
Del Peak 40(18q22.1)	260 (63%)	153	6.923e-11	4.35e-08	3.6479e-09	2.23e-06	1.5789e-47	1.07e-44	2.0207e-12	1.3e-09	0.039653	1	3.1605e-05	0.018	4.0541e-12	2.59e-09	2.7626e-07	0.000164	0.074601	1	0.91179	1
Del Peak 41(19p13.3)	57 (14%)	356	0.26846	1	0.19814	1	0.0036238	1	0.56533	1	0.07645	1	0.11389	1	0.051162	1	0.024394	1	0.5818	1	0.016593	1
Del Peak 42(20p12.1)	79 (19%)	334	0.065611	1	0.17327	1	1.3778e-13	8.97e-11	0.0040359	1	0.50149	1	0.15111	1	0.00014971	0.0817	0.0067416	1	0.093065	1	0.10088	1
Del Peak 43(21q11.2)	125 (30%)	288	0.002984	1	0.093343	1	3.3671e-09	2.06e-06	0.030185	1	0.78777	1	0.31858	1	0.00089656	0.455	0.018699	1	0.92346	1	0.4701	1
Del Peak 44(22q13.32)	138 (33%)	275	0.00042836	0.228	0.00074726	0.384	9.7641e-13	6.32e-10	0.0049006	1	0.38196	1	0.052356	1	0.0022174	1	0.0010638	0.535	0.39369	1	0.069036	1