		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	0.060664	1	0.070305	1	3.054e-05	0.0173	0.25825	1	0.36713	1	0.036586	1	0.28767	1	0.019619	1	0.27725	1	0.25803	1
Amp Peak  2(5p13.2)	81 (20%)	332	0.34026	1	0.49288	1	0.00020181	0.111	0.14972	1	0.43755	1	0.63757	1	0.54528	1	0.31285	1	0.9268	1	0.58108	1
Amp Peak  3(5q22.3)	40 (10%)	373	0.77925	1	0.55824	1	0.029319	1	0.87467	1	0.19172	1	0.45923	1	0.1854	1	0.072243	1	0.69302	1	0.83892	1
Amp Peak  4(6p21.1)	89 (22%)	324	0.2682	1	0.00032756	0.178	3.3666e-09	2.06e-06	0.16999	1	0.6005	1	0.0999	1	0.016459	1	0.0037293	1	0.77582	1	0.25832	1
Amp Peak  5(8p11.23)	144 (35%)	269	0.26998	1	0.10461	1	2.9884e-13	1.93e-10	0.8676	1	0.78411	1	0.3675	1	0.11026	1	0.14102	1	0.17898	1	0.18914	1
Amp Peak  6(8p11.21)	173 (42%)	240	0.24477	1	0.091398	1	4.5091e-10	2.8e-07	0.88585	1	0.24064	1	0.021267	1	0.021732	1	0.05654	1	0.50206	1	0.21775	1
Amp Peak  7(8q12.1)	215 (52%)	198	0.20906	1	0.039423	1	9.3098e-12	5.87e-09	0.038349	1	0.055189	1	0.0011065	0.574	0.039755	1	0.0020429	1	0.12567	1	0.29537	1
Amp Peak  8(8q24.21)	239 (58%)	174	0.2789	1	0.11999	1	7.8615e-14	5.12e-11	0.010196	1	0.17733	1	0.0061843	1	0.033385	1	0.0070387	1	0.4037	1	0.21493	1
Amp Peak  9(11p15.5)	86 (21%)	327	9.3916e-06	0.0054	0.0010544	0.549	1.539e-09	9.5e-07	0.00061244	0.328	0.028419	1	0.00078181	0.416	5.544e-07	0.000327	9.8512e-07	0.000575	0.11742	1	0.20078	1
Amp Peak 10(12p13.33)	104 (25%)	309	0.61009	1	0.22298	1	0.06118	1	0.24692	1	0.33217	1	0.5994	1	0.44851	1	0.55781	1	0.30362	1	0.17308	1
Amp Peak 11(13q12.13)	250 (61%)	163	1.5566e-07	9.25e-05	3.332e-07	0.000197	5.0359e-36	3.39e-33	0.00027008	0.148	0.12378	1	0.017848	1	8.1929e-09	4.97e-06	3.1727e-07	0.000188	0.45926	1	0.79848	1
Amp Peak 12(13q22.1)	254 (62%)	159	0.00010564	0.0587	1.2224e-05	0.007	7.1998e-33	4.83e-30	0.00051007	0.274	0.20341	1	0.023309	1	8.125e-07	0.000475	3.8488e-06	0.00222	0.2718	1	0.97749	1
Amp Peak 13(16p11.2)	116 (28%)	297	0.00040219	0.218	0.00075302	0.401	8.5536e-19	5.67e-16	0.021155	1	0.22851	1	0.011929	1	0.0017742	0.903	1.1424e-06	0.000666	0.77077	1	0.80885	1
Amp Peak 14(16q12.1)	102 (25%)	311	2.7946e-05	0.0159	0.00093969	0.495	1.6709e-20	1.11e-17	0.05111	1	0.47138	1	0.050979	1	0.001095	0.569	1.4478e-06	0.000841	0.90192	1	0.93019	1
Amp Peak 15(17q12)	101 (24%)	312	0.06705	1	0.15286	1	7.529e-07	0.000441	0.016408	1	0.59585	1	0.00103	0.539	0.0001871	0.103	0.013614	1	0.012101	1	0.98573	1
Amp Peak 16(17q24.1)	92 (22%)	321	0.091862	1	0.049797	1	1.6072e-08	9.61e-06	0.012293	1	0.162	1	0.0031803	1	0.0022117	1	0.002068	1	0.0025416	1	0.78116	1
Amp Peak 17(19p13.2)	65 (16%)	348	0.094151	1	0.066953	1	4.8203e-05	0.0271	0.28305	1	0.94829	1	0.75349	1	0.46278	1	0.093504	1	0.20371	1	0.38494	1
Amp Peak 18(19q13.11)	83 (20%)	330	0.24921	1	0.0069702	1	0.0019963	1	0.51687	1	0.23399	1	0.95809	1	0.024916	1	0.0088802	1	0.41715	1	0.49068	1
Amp Peak 19(20p12.3)	184 (45%)	229	0.0026263	1	0.0021266	1	1.8596e-12	1.19e-09	0.4343	1	0.01385	1	0.54814	1	0.00018089	0.0999	1.5283e-06	0.000886	0.59687	1	0.19482	1
Amp Peak 20(20p11.23)	205 (50%)	208	0.028468	1	0.0020305	1	1.2622e-16	8.32e-14	0.10514	1	0.19932	1	0.51345	1	0.0017969	0.913	5.8669e-07	0.000344	0.45496	1	0.2118	1
Amp Peak 21(20p11.21)	230 (56%)	183	0.00078287	0.416	7.2499e-05	0.0406	4.0003e-23	2.67e-20	0.0011341	0.586	0.20536	1	0.19224	1	2.4721e-06	0.00143	7.8283e-10	4.85e-07	0.17441	1	0.50927	1
Amp Peak 22(20q11.21)	296 (72%)	117	1.0016e-10	6.25e-08	6.725e-13	4.32e-10	1.5358e-43	1.04e-40	2.1904e-09	1.34e-06	0.012756	1	0.0017974	0.913	1.0017e-15	6.55e-13	1.8177e-16	1.2e-13	0.44287	1	1	1
Amp Peak 23(20q12)	297 (72%)	116	8.4564e-12	5.35e-09	6.3607e-13	4.1e-10	6.2847e-43	4.24e-40	1.5835e-08	9.5e-06	0.0020855	1	0.00028925	0.158	2.295e-16	1.51e-13	2.4463e-17	1.62e-14	0.40581	1	0.94846	1
Amp Peak 24(20q13.32)	300 (73%)	113	2.3107e-10	1.44e-07	8.1633e-14	5.31e-11	3.1794e-43	2.15e-40	1.5835e-08	9.5e-06	0.0030026	1	0.00021277	0.117	1.3727e-15	8.96e-13	5.9316e-16	3.89e-13	0.414	1	0.96035	1
Del Peak  1(1p36.11)	150 (36%)	263	2.0587e-05	0.0118	0.0087915	1	6.3163e-17	4.17e-14	0.00079247	0.42	0.012428	1	0.0049486	1	6.2327e-05	0.035	3.6354e-05	0.0206	0.4086	1	0.06244	1
Del Peak  2(1p33)	107 (26%)	306	0.015076	1	0.54217	1	1.0878e-11	6.85e-09	0.0066849	1	0.38186	1	0.036296	1	0.29264	1	0.15311	1	0.8934	1	0.051913	1
Del Peak  3(1p13.1)	103 (25%)	310	0.067977	1	0.296	1	6.8461e-10	4.25e-07	0.18487	1	0.38424	1	0.19201	1	0.21567	1	0.053048	1	0.86754	1	0.37862	1
Del Peak  4(1q43)	44 (11%)	369	0.072143	1	0.17599	1	6.9784e-06	0.00402	0.10478	1	0.71884	1	0.66639	1	0.52957	1	0.2841	1	0.33504	1	0.30091	1
Del Peak  5(2q37.2)	21 (5%)	392	0.92682	1	0.013768	1	0.97728	1	0.70132	1	0.037326	1	0.27131	1	0.44244	1	1	1	0.44659	1	0.44658	1
Del Peak  6(3p26.1)	60 (15%)	353	0.37187	1	0.3572	1	0.00043027	0.232	0.26787	1	0.77406	1	0.68519	1	0.6633	1	0.48853	1	0.5406	1	0.9578	1
Del Peak  7(3p14.2)	75 (18%)	338	0.71746	1	0.81917	1	0.2053	1	0.73514	1	0.93391	1	0.73401	1	0.60648	1	0.602	1	0.20335	1	0.53643	1
Del Peak  8(3q26.31)	39 (9%)	374	0.4099	1	0.6758	1	0.0081756	1	0.49692	1	0.1114	1	0.10871	1	0.15709	1	0.70291	1	0.14968	1	0.93943	1
Del Peak  9(4p16.2)	121 (29%)	292	0.00074003	0.395	0.016198	1	1.1565e-12	7.4e-10	0.011034	1	0.14262	1	0.21897	1	0.0056097	1	0.0028796	1	0.37622	1	0.20636	1
Del Peak 10(4q22.1)	126 (31%)	287	0.00045277	0.244	0.0085629	1	8.4971e-12	5.37e-09	0.0020663	1	0.11834	1	0.37098	1	0.033809	1	0.0037212	1	0.20975	1	0.51791	1
Del Peak 11(4q35.1)	137 (33%)	276	4.7615e-05	0.0269	0.0040626	1	1.0461e-13	6.79e-11	7.6854e-05	0.0429	0.056963	1	0.37548	1	0.01576	1	0.019717	1	0.41578	1	0.23487	1
Del Peak 12(5q11.2)	91 (22%)	322	0.00099096	0.52	0.0034616	1	4.9424e-09	3.01e-06	0.03386	1	0.39208	1	0.041163	1	0.010307	1	0.022368	1	0.83478	1	0.21521	1
Del Peak 13(5q21.3)	117 (28%)	296	0.06062	1	0.033912	1	1.1415e-09	7.05e-07	0.035903	1	0.20334	1	0.23161	1	0.0029624	1	0.00097163	0.511	0.65358	1	0.36044	1
Del Peak 14(5q23.1)	107 (26%)	306	0.03612	1	0.040301	1	1.5714e-08	9.44e-06	0.087019	1	0.19566	1	0.28015	1	0.0017055	0.87	0.0054696	1	0.62161	1	0.24578	1
Del Peak 15(6p25.3)	54 (13%)	359	0.6972	1	0.4805	1	0.00010249	0.0571	0.052651	1	0.29197	1	0.39726	1	0.41796	1	0.77433	1	0.40629	1	0.45348	1
Del Peak 16(6q26)	60 (15%)	353	0.35618	1	0.19262	1	0.15693	1	0.35648	1	0.035913	1	0.88855	1	0.57057	1	0.69606	1	0.79664	1	0.52977	1
Del Peak 17(7q31.1)	11 (3%)	402	1	1	0.55731	1	0.81645	1	0.79545	1	0.24897	1	0.33053	1	0.49075	1	0.79196	1	1	1	0.56392	1
Del Peak 18(8p23.3)	171 (41%)	242	0.0029721	1	0.0064792	1	6.8386e-26	4.58e-23	3.6131e-06	0.00209	0.074238	1	0.0014121	0.726	0.0012656	0.653	0.0019807	1	0.1544	1	0.84763	1
Del Peak 19(8p22)	185 (45%)	228	0.0011134	0.577	0.0063227	1	2.4052e-30	1.61e-27	3.4605e-07	0.000205	0.071478	1	0.00013933	0.077	0.00038687	0.21	0.00032272	0.176	0.11474	1	0.83207	1
Del Peak 20(8p11.22)	80 (19%)	333	0.21715	1	0.085636	1	8.8799e-09	5.38e-06	0.061445	1	0.0086673	1	0.066856	1	0.27028	1	0.091525	1	0.35945	1	0.8314	1
Del Peak 21(8p11.21)	43 (10%)	370	0.025787	1	0.34774	1	5.8112e-07	0.000342	0.36576	1	0.12193	1	0.11155	1	0.17354	1	0.43273	1	0.099704	1	0.54888	1
Del Peak 22(9p21.3)	56 (14%)	357	0.62695	1	0.34138	1	4.5111e-05	0.0255	0.20379	1	0.47402	1	0.24493	1	0.073284	1	0.34763	1	0.90376	1	0.66315	1
Del Peak 23(10p15.3)	68 (16%)	345	0.2045	1	0.13614	1	2.2472e-08	1.34e-05	0.029141	1	0.11325	1	0.14553	1	0.17359	1	0.33612	1	0.67983	1	0.56551	1
Del Peak 24(10q21.1)	82 (20%)	331	0.0031381	1	0.019125	1	2.2397e-11	1.4e-08	0.19404	1	0.16663	1	0.017947	1	0.01164	1	0.0037293	1	0.8868	1	0.8314	1
Del Peak 25(10q23.31)	94 (23%)	319	0.13811	1	0.17818	1	3.4604e-07	0.000205	0.08012	1	0.2693	1	0.59884	1	0.043202	1	0.003508	1	0.8849	1	0.98489	1
Del Peak 26(10q25.2)	93 (23%)	320	0.11614	1	0.0019122	0.968	1.9136e-11	1.2e-08	0.013884	1	0.010667	1	0.39509	1	0.22644	1	0.0010081	0.528	0.92109	1	0.5932	1
Del Peak 27(12p13.2)	44 (11%)	369	0.042882	1	0.0055376	1	9.8715e-08	5.88e-05	0.20712	1	0.4149	1	0.81514	1	0.30827	1	0.41898	1	0.69486	1	0.97344	1
Del Peak 28(13q14.13)	18 (4%)	395	0.39244	1	0.4776	1	0.00012763	0.0708	0.15251	1	0.59963	1	0.17006	1	0.12199	1	1	1	0.61393	1	0.83372	1
Del Peak 29(14q32.11)	133 (32%)	280	1.1415e-05	0.00655	0.00024187	0.133	1.6095e-20	1.07e-17	0.00070714	0.378	0.00083549	0.442	0.0050055	1	7.2501e-05	0.0406	4.3463e-05	0.0246	0.31936	1	0.061222	1
Del Peak 30(15q11.2)	160 (39%)	253	0.00012901	0.0715	0.0075292	1	1.1969e-21	7.98e-19	0.0043207	1	0.038063	1	0.34262	1	0.01062	1	0.0037785	1	0.87692	1	0.8927	1
Del Peak 31(15q21.1)	151 (37%)	262	0.0070028	1	0.052283	1	8.1471e-18	5.39e-15	0.0074658	1	0.06759	1	0.17242	1	0.14769	1	0.0069032	1	0.9795	1	0.62069	1
Del Peak 32(15q22.33)	145 (35%)	268	0.00028025	0.153	0.0027866	1	2.4843e-21	1.65e-18	0.00043461	0.234	0.05743	1	0.22592	1	0.01419	1	3.0013e-05	0.0171	0.94865	1	0.3645	1
Del Peak 33(16p13.3)	45 (11%)	368	0.34502	1	0.12481	1	0.20817	1	0.37632	1	0.029788	1	0.88583	1	0.42799	1	0.47329	1	0.84166	1	0.73884	1
Del Peak 34(16q23.1)	49 (12%)	364	0.28256	1	0.023267	1	0.13094	1	0.33681	1	0.44463	1	0.88542	1	0.009194	1	0.0035851	1	0.97682	1	0.50466	1
Del Peak 35(17p12)	229 (55%)	184	9.315e-09	5.64e-06	1.2219e-06	0.000711	2.8124e-35	1.89e-32	1.803e-09	1.11e-06	0.013863	1	4.8892e-05	0.0275	1.0424e-07	6.2e-05	1.3545e-08	8.17e-06	0.36262	1	0.7291	1
Del Peak 36(17q24.3)	59 (14%)	354	0.10997	1	0.57888	1	0.0034819	1	0.011753	1	0.52377	1	0.32944	1	0.58635	1	0.39531	1	0.68104	1	0.97867	1
Del Peak 37(18p11.31)	220 (53%)	193	2.862e-12	1.82e-09	7.255e-09	4.41e-06	1.9303e-42	1.3e-39	3.1072e-13	2.01e-10	0.010143	1	0.00093252	0.492	1.8188e-11	1.14e-08	7.9741e-13	5.12e-10	0.48029	1	0.84148	1
Del Peak 38(18q12.2)	247 (60%)	166	6.795e-12	4.31e-09	3.9508e-09	2.41e-06	1.8686e-45	1.27e-42	8.9817e-16	5.88e-13	0.048739	1	0.00156	0.799	1.0718e-09	6.63e-07	2.6299e-14	1.71e-11	0.44898	1	0.86493	1
Del Peak 39(18q21.2)	260 (63%)	153	2.4618e-11	1.54e-08	2.0891e-09	1.28e-06	1.5149e-45	1.03e-42	3.2902e-12	2.09e-09	0.011116	1	0.0014052	0.724	5.066e-09	3.09e-06	6.1154e-13	3.94e-10	0.051698	1	0.90124	1
Del Peak 40(18q22.1)	260 (63%)	153	8.4075e-11	5.25e-08	1.1175e-08	6.75e-06	1.5789e-47	1.07e-44	2.0207e-12	1.29e-09	0.018693	1	0.0010331	0.539	1.5206e-08	9.15e-06	6.772e-12	4.3e-09	0.074601	1	0.91179	1
Del Peak 41(19p13.3)	57 (14%)	356	0.27513	1	0.19611	1	0.0036238	1	0.56533	1	0.38728	1	0.14937	1	0.030125	1	0.14936	1	0.5818	1	0.016593	1
Del Peak 42(20p12.1)	79 (19%)	334	0.039347	1	0.034695	1	1.3778e-13	8.93e-11	0.0040359	1	0.35176	1	0.16745	1	0.015774	1	0.18804	1	0.093065	1	0.10088	1
Del Peak 43(21q11.2)	125 (30%)	288	0.008218	1	0.057575	1	3.3671e-09	2.06e-06	0.030185	1	0.58663	1	0.55359	1	0.03387	1	0.049064	1	0.92346	1	0.4701	1
Del Peak 44(22q13.32)	138 (33%)	275	0.0015249	0.782	0.0016016	0.818	9.7641e-13	6.26e-10	0.0049006	1	0.36376	1	0.20989	1	0.068393	1	1.9902e-05	0.0114	0.39369	1	0.069036	1
