Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_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	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q
Amp Peak  1(1q22)	0 (0%)	242	NA	NA	NA	NA	0.00025409	0.114	0.13274	1	0.25071	1	0.40311	1	0.16922	1	0.31175	1	0.93697	1	0.30866	1	0.13449	1	0.49917	1
Amp Peak  2(1q32.1)	0 (0%)	242	NA	NA	NA	NA	2.1359e-07	0.000108	2.2792e-06	0.00113	0.10441	1	0.84578	1	0.0099616	1	0.24942	1	0.61808	1	8.9609e-05	0.0415	0.0219	1	2.7917e-05	0.0132
Amp Peak  3(3p24.3)	0 (0%)	255	NA	NA	NA	NA	0.031218	1	0.93334	1	0.9069	1	0.0322	1	0.081505	1	0.25243	1	0.73528	1	0.64324	1	0.62994	1	0.62063	1
Amp Peak  4(3q26.32)	0 (0%)	255	NA	NA	NA	NA	0.00065479	0.282	0.11768	1	0.014718	1	0.68023	1	0.54844	1	0.43376	1	0.17618	1	0.64324	1	0.11907	1	0.27586	1
Amp Peak  5(4q12)	0 (0%)	255	NA	NA	NA	NA	0.0014002	0.584	0.25777	1	0.020387	1	0.73748	1	0.69622	1	0.37246	1	0.099641	1	0.32996	1	0.19091	1	0.52919	1
Amp Peak  6(7p11.2)	0 (0%)	196	0.86379	1	0.72616	1	2.0561e-29	1.12e-26	4.4066e-16	2.36e-13	0.00011329	0.052	0.0062583	1	1.9556e-05	0.00933	0.00075645	0.322	0.0013329	0.558	6.4291e-06	0.00312	4.4978e-07	0.000226	3.1035e-12	1.65e-09
Amp Peak  7(7q32.3)	0 (0%)	169	0.7639	1	0.75539	1	5.1903e-23	2.81e-20	2.108e-08	1.08e-05	0.0081443	1	0.024236	1	0.00026739	0.119	0.0012009	0.507	0.068039	1	0.0042816	1	0.0028249	1	1.0218e-05	0.00489
Amp Peak  8(8q24.12)	0 (0%)	214	0.36962	1	0.16356	1	2.3191e-12	1.23e-09	5.516e-09	2.85e-06	0.028691	1	0.88353	1	0.22461	1	0.0071546	1	0.22076	1	0.18003	1	0.00025736	0.115	0.001777	0.736
Amp Peak  9(10p15.3)	0 (0%)	228	0.52569	1	0.20653	1	1.0019e-09	5.27e-07	2.9709e-09	1.54e-06	0.034318	1	0.24449	1	0.35179	1	0.00060479	0.262	0.099296	1	0.22533	1	0.00028404	0.126	0.046467	1
Amp Peak 10(11q23.3)	0 (0%)	224	0.22462	1	0.025014	1	0.18454	1	0.12153	1	0.10123	1	0.14072	1	0.60296	1	0.59857	1	0.57889	1	0.62748	1	0.05793	1	0.24607	1
Amp Peak 11(12p13.32)	0 (0%)	226	0.86379	1	0.048602	1	1.694e-10	8.94e-08	5.1627e-05	0.0243	0.11574	1	0.2181	1	0.021763	1	0.0021367	0.88	0.014171	1	0.037104	1	0.00080342	0.341	0.077648	1
Amp Peak 12(12p12.1)	0 (0%)	241	1	1	0.013836	1	4.7472e-06	0.00234	0.025597	1	0.16869	1	0.68799	1	0.00060099	0.261	0.00039238	0.173	0.004792	1	0.023026	1	6.8355e-05	0.0318	0.16097	1
Amp Peak 13(12q14.1)	0 (0%)	250	NA	NA	NA	NA	1.9722e-05	0.00939	0.10068	1	0.022757	1	0.8814	1	0.029073	1	0.42258	1	0.054276	1	0.19191	1	0.32463	1	0.010953	1
Amp Peak 14(13q33.3)	0 (0%)	254	NA	NA	NA	NA	0.00043112	0.189	0.005488	1	0.18705	1	0.29343	1	0.42559	1	0.08062	1	0.86063	1	0.6656	1	0.4078	1	0.263	1
Amp Peak 15(17q25.1)	0 (0%)	253	0.088889	1	0.046838	1	7.6383e-06	0.0037	0.27442	1	0.20811	1	1	1	0.46798	1	0.72466	1	0.016313	1	0.38855	1	0.0094399	1	0.82972	1
Amp Peak 16(18q23)	0 (0%)	257	NA	NA	NA	NA	0.0013348	0.558	0.02682	1	0.0001317	0.0601	1	1	0.0059438	1	0.0029558	1	0.054324	1	0.32206	1	0.00027031	0.12	0.083043	1
Amp Peak 17(19p13.3)	0 (0%)	209	0.18636	1	0.40979	1	9.0915e-05	0.042	1.0729e-08	5.5e-06	0.867	1	0.68379	1	0.65423	1	0.012087	1	0.44936	1	0.23838	1	0.039596	1	0.012475	1
Amp Peak 18(19q13.2)	0 (0%)	250	0.36923	1	0.1935	1	7.2856e-07	0.000365	1.0096e-05	0.00485	0.038086	1	0.34043	1	0.00012208	0.0558	0.0031551	1	0.0025075	1	0.0039726	1	5.2529e-06	0.00258	5.8894e-06	0.00288
Amp Peak 19(Xp22.33)	0 (0%)	251	NA	NA	NA	NA	0.00024115	0.109	0.0022519	0.923	0.34098	1	0.34043	1	0.15426	1	0.02247	1	0.77944	1	0.0088493	1	0.58967	1	0.30558	1
Amp Peak 20(Xp11.22)	0 (0%)	231	0.65128	1	0.89231	1	1.8448e-09	9.65e-07	1.5365e-06	0.000762	0.026767	1	0.1432	1	0.083493	1	0.00035472	0.156	0.13242	1	0.057547	1	0.29157	1	0.022579	1
Del Peak  1(1p36.31)	0 (0%)	173	0.0005487	0.239	5.8557e-05	0.0274	8.4902e-14	4.53e-11	4.9174e-43	2.7e-40	0.00073228	0.313	0.53988	1	7.9002e-06	0.00382	3.232e-23	1.75e-20	8.8576e-06	0.00426	0.00030349	0.134	1.1544e-08	5.91e-06	0.00010415	0.0479
Del Peak  2(1p32.3)	0 (0%)	181	0.028572	1	0.00017271	0.0782	2.2069e-17	1.19e-14	2.3028e-48	1.27e-45	0.00047666	0.209	0.23538	1	2.7298e-09	1.42e-06	3.0628e-27	1.67e-24	5.7784e-08	2.93e-05	3.2003e-05	0.0151	1.5448e-09	8.09e-07	1.0872e-06	0.00054
Del Peak  3(1q43)	0 (0%)	254	NA	NA	NA	NA	0.060364	1	0.22757	1	0.10089	1	0.56675	1	0.89399	1	0.18648	1	0.55897	1	0.6656	1	0.63828	1	0.55666	1
Del Peak  4(2p25.3)	0 (0%)	245	0.36923	1	0.40684	1	1.9651e-06	0.000973	0.0044694	1	0.19471	1	1	1	0.45531	1	0.072857	1	0.45343	1	0.81473	1	0.5604	1	0.14402	1
Del Peak  5(2q37.1)	0 (0%)	236	0.65128	1	0.16444	1	9.7046e-07	0.000483	1.9279e-05	0.00922	0.0022261	0.915	0.023973	1	0.024879	1	0.001271	0.534	0.13996	1	0.012229	1	0.082934	1	0.0022583	0.924
Del Peak  6(2q37.3)	0 (0%)	229	0.18013	1	0.11586	1	6.0679e-06	0.00296	1.8009e-07	9.09e-05	0.011927	1	0.021719	1	0.22702	1	0.004055	1	0.58898	1	0.15469	1	0.2315	1	0.00011388	0.0522
Del Peak  7(3p21.1)	0 (0%)	241	1	1	0.0081481	1	5.0367e-07	0.000253	0.012098	1	0.0004777	0.209	0.15162	1	0.015448	1	0.0038053	1	0.0059708	1	0.049134	1	0.07283	1	0.019653	1
Del Peak  8(4q35.2)	0 (0%)	193	1	1	0.60239	1	9.3367e-09	4.8e-06	9.6593e-07	0.000482	0.082611	1	0.068983	1	0.003709	1	0.008547	1	0.19459	1	0.34864	1	0.0050957	1	0.007366	1
Del Peak  9(5q35.2)	0 (0%)	235	0.44623	1	0.018246	1	4.0814e-09	2.11e-06	0.0016557	0.687	0.09938	1	0.94121	1	0.066282	1	0.0091265	1	0.39287	1	0.50205	1	0.0063719	1	0.26128	1
Del Peak 10(6p25.3)	0 (0%)	241	NA	NA	NA	NA	0.055128	1	0.3594	1	0.16064	1	0.80837	1	0.4286	1	0.23999	1	0.57378	1	0.70485	1	0.16352	1	0.10895	1
Del Peak 11(6q24.3)	0 (0%)	224	0.047863	1	0.1935	1	0.00013422	0.0611	0.0012529	0.527	0.16523	1	0.27342	1	0.67362	1	0.088196	1	0.00017129	0.0778	0.53161	1	0.50707	1	0.10242	1
Del Peak 12(9p21.3)	0 (0%)	170	0.33256	1	0.015262	1	3.0423e-11	1.61e-08	2.6624e-08	1.36e-05	8.6667e-06	0.00418	9.222e-05	0.0425	0.023741	1	0.0093475	1	0.17715	1	0.2064	1	0.057353	1	0.0001988	0.0899
Del Peak 13(10q26.3)	0 (0%)	188	0.17949	1	0.022012	1	6.2115e-19	3.35e-16	1.3025e-20	7.03e-18	1.561e-07	7.9e-05	0.00021438	0.0967	2.1266e-08	1.08e-05	2.9205e-09	1.52e-06	0.0046146	1	5.9782e-06	0.00292	4.4955e-09	2.32e-06	1.263e-11	6.69e-09
Del Peak 14(11p15.5)	0 (0%)	212	0.64244	1	0.00074097	0.316	1.8779e-09	9.8e-07	2.1114e-10	1.11e-07	0.14648	1	0.84889	1	0.0026739	1	2.6195e-05	0.0124	0.2289	1	0.36417	1	0.14737	1	0.3783	1
Del Peak 15(11q25)	0 (0%)	248	NA	NA	NA	NA	0.00024318	0.109	0.0060907	1	0.40599	1	0.42362	1	0.11016	1	0.040979	1	0.44217	1	0.17392	1	0.72497	1	0.20686	1
Del Peak 16(12q12)	0 (0%)	234	1	1	0.087863	1	5.2808e-06	0.00259	0.000714	0.306	0.50523	1	0.88189	1	0.11497	1	0.014793	1	0.92227	1	0.95559	1	0.47056	1	0.60735	1
Del Peak 17(13q14.2)	0 (0%)	192	0.1801	1	0.00061812	0.267	3.935e-30	2.16e-27	0.0077958	1	0.034269	1	0.81314	1	0.33884	1	0.13031	1	0.20259	1	0.28913	1	0.30841	1	0.28288	1
Del Peak 18(13q21.2)	0 (0%)	189	0.1801	1	0.00061812	0.267	1.5191e-29	8.31e-27	0.0027824	1	0.018509	1	0.713	1	0.14521	1	0.061065	1	0.075413	1	0.22935	1	0.33988	1	0.2904	1
Del Peak 19(13q22.1)	0 (0%)	192	0.43813	1	0.00077385	0.329	2.7479e-25	1.49e-22	0.016294	1	0.0089914	1	0.78838	1	0.45712	1	0.13031	1	0.1382	1	0.45176	1	0.61054	1	0.42089	1
Del Peak 20(13q34)	0 (0%)	212	0.50769	1	0.10604	1	5.3741e-17	2.89e-14	0.26309	1	0.085567	1	0.52441	1	0.45404	1	0.16053	1	0.093471	1	0.23875	1	0.60484	1	0.69945	1
Del Peak 21(14q24.3)	0 (0%)	208	0.30286	1	0.1709	1	5.5433e-05	0.026	0.04903	1	0.0029918	1	0.019319	1	0.0063754	1	0.071021	1	0.00051366	0.224	0.0034467	1	0.07472	1	0.0025874	1
Del Peak 22(17q25.3)	0 (0%)	252	NA	NA	NA	NA	0.0015508	0.645	0.21583	1	0.24748	1	0.16087	1	0.77848	1	0.16111	1	0.20448	1	0.1532	1	0.71622	1	0.34112	1
Del Peak 23(18p11.32)	0 (0%)	227	0.32144	1	0.31568	1	0.060438	1	0.12543	1	0.43019	1	0.060905	1	1	1	1	1	0.6091	1	0.78509	1	0.68156	1	0.68899	1
Del Peak 24(18q23)	0 (0%)	226	0.32144	1	0.31568	1	0.13363	1	0.065076	1	0.46041	1	0.11497	1	0.38343	1	0.82155	1	0.67235	1	0.42135	1	0.51638	1	0.24697	1
Del Peak 25(19q13.42)	0 (0%)	133	0.03533	1	0.12707	1	1.5459e-15	8.27e-13	9.4945e-28	5.17e-25	0.0021242	0.877	0.59991	1	7.9893e-07	0.000399	9.0612e-15	4.84e-12	8.2429e-05	0.0382	0.0002984	0.132	2.2822e-05	0.0108	5.1886e-08	2.64e-05
Del Peak 26(22q13.31)	0 (0%)	229	0.25043	1	0.058829	1	1.4111e-09	7.41e-07	2.8505e-06	0.00141	6.7535e-05	0.0315	0.018731	1	6.9188e-06	0.00336	3.7738e-05	0.0178	0.010987	1	0.026851	1	0.016071	1	0.0077946	1
Del Peak 27(Xp22.2)	0 (0%)	211	0.83946	1	0.13068	1	6.728e-09	3.46e-06	0.12783	1	0.043945	1	0.029381	1	0.96461	1	0.067559	1	0.49071	1	0.11858	1	0.81028	1	0.0436	1
Del Peak 28(Xq21.1)	0 (0%)	234	0.73001	1	0.0010709	0.453	5.9204e-05	0.0276	0.11805	1	0.028868	1	0.049544	1	0.52265	1	0.014254	1	0.11945	1	0.17646	1	0.041647	1	0.88393	1