		Clinical Features	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	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	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q
amp_1q32.1	38 (8%)	425	NA	NA	NA	NA	3.8234e-10	1.88e-07	7.4627e-09	3.57e-06	0.16681	1	0.89336	1	4.0393e-08	1.91e-05	0.01151	1	0.0034238	1	0.39907	1	0.00094934	0.35	0.34378	1
amp_1q43	28 (6%)	435	NA	NA	NA	NA	6.275e-05	0.0263	0.00018468	0.0746	0.05073	1	1	1	6.587e-10	3.24e-07	0.074775	1	0.0083334	1	0.54086	1	0.0011324	0.412	0.046016	1
amp_2p24.3	20 (4%)	443	0.61538	1	0.046838	1	0.00081477	0.303	0.11876	1	0.49035	1	0.32069	1	7.251e-06	0.00321	0.12152	1	0.24265	1	0.34665	1	0.36695	1	0.24376	1
amp_3q26.32	18 (4%)	445	NA	NA	NA	NA	0.029468	1	0.0033984	1	0.014718	1	0.60489	1	6.1648e-05	0.0259	0.023847	1	0.0030748	1	0.090415	1	0.0011502	0.416	0.069895	1
amp_4q12	26 (6%)	437	1	1	0.087863	1	7.5689e-05	0.0316	0.0011202	0.409	0.0088307	1	0.59395	1	1.3661e-15	7.06e-13	0.0011543	0.417	0.00036845	0.143	0.42157	1	0.0099162	1	0.020931	1
amp_7p11.2	121 (26%)	342	0.7639	1	0.49526	1	3.1532e-54	1.74e-51	3.2465e-29	1.75e-26	4.731e-05	0.0201	0.0040541	1	1.0694e-20	5.66e-18	2.8985e-08	1.37e-05	2.0035e-11	1.01e-08	7.9097e-05	0.0328	1.3406e-13	6.85e-11	0.083465	1
amp_7q31.2	164 (35%)	299	1	1	0.76073	1	6.2839e-47	3.43e-44	4.2715e-16	2.21e-13	0.0043505	1	0.020516	1	1.8427e-09	8.94e-07	5.1408e-07	0.000236	3.4592e-05	0.0148	0.0017196	0.612	4.6798e-05	0.0199	0.56297	1
amp_7q32.3	173 (37%)	290	0.69472	1	0.94773	1	2.5301e-48	1.39e-45	2.1777e-16	1.13e-13	0.0065115	1	0.01551	1	6.9207e-09	3.33e-06	6.4597e-07	0.000296	2.8624e-05	0.0124	0.0012517	0.449	0.00010558	0.0435	0.40739	1
amp_8q24.13	92 (20%)	371	0.36962	1	0.16356	1	5.5175e-19	2.9e-16	5.221e-15	2.69e-12	0.043016	1	0.91726	1	1.292e-09	6.3e-07	0.00027129	0.109	0.0028624	0.99	0.77028	1	0.00010381	0.0429	0.087577	1
amp_10p15.3	62 (13%)	401	0.52569	1	0.20653	1	2.3171e-19	1.22e-16	3.0454e-16	1.58e-13	0.029862	1	0.18363	1	1.1134e-11	5.61e-09	1.9932e-08	9.45e-06	0.00034726	0.135	0.16972	1	0.00028088	0.112	0.42062	1
amp_11q23.3	76 (16%)	387	0.22462	1	0.025014	1	0.28414	1	0.043707	1	0.10565	1	0.14287	1	0.59957	1	0.72997	1	0.70058	1	0.93794	1	0.3061	1	0.79764	1
amp_12p13.32	66 (14%)	397	0.86379	1	0.048602	1	5.5936e-14	2.87e-11	8.1236e-08	3.81e-05	0.11688	1	0.21078	1	0.00027576	0.11	2.6603e-05	0.0115	4.8046e-05	0.0204	0.014535	1	0.0030483	1	0.0048267	1
amp_12q14.1	34 (7%)	429	NA	NA	NA	NA	1.1853e-05	0.0052	6.5323e-06	0.0029	0.016128	1	0.70781	1	7.8205e-09	3.74e-06	0.0036198	1	4.3737e-06	0.00196	0.0030052	1	1.1126e-07	5.2e-05	0.016981	1
amp_13q34	19 (4%)	444	NA	NA	NA	NA	1.3782e-05	0.00602	0.00041895	0.161	0.18774	1	0.26989	1	0.039122	1	0.012731	1	0.84654	1	0.34665	1	0.85425	1	0.24376	1
amp_15q26.3	18 (4%)	445	1	1	0.087863	1	5.874e-06	0.00261	0.00073766	0.277	0.22217	1	0.62827	1	9.209e-07	0.000421	0.0074287	1	0.013166	1	0.76098	1	0.26904	1	0.64837	1
amp_17q25.1	35 (8%)	428	NA	NA	NA	NA	0.01991	1	0.35948	1	0.33056	1	0.78212	1	2.6447e-07	0.000123	0.22525	1	0.090394	1	0.17329	1	0.25292	1	0.00045816	0.175
amp_19p13.3	115 (25%)	348	0.075249	1	0.12156	1	6.9532e-10	3.41e-07	1.3737e-17	7.18e-15	0.8789	1	0.61535	1	3.1075e-11	1.56e-08	1.7359e-06	0.00079	0.00017705	0.0717	0.95182	1	1.3557e-06	0.000618	0.58545	1
amp_19p13.2	109 (24%)	354	0.075249	1	0.12156	1	8.8948e-13	4.53e-10	7.3402e-21	3.89e-18	0.27624	1	0.26476	1	1.184e-12	6e-10	4.8617e-06	0.00217	4.8183e-06	0.00215	0.38848	1	8.2732e-08	3.87e-05	0.35843	1
amp_xp11.22	47 (10%)	416	0.65128	1	0.89231	1	1.9988e-10	9.91e-08	4.7123e-09	2.28e-06	0.095635	1	0.20191	1	0.0027679	0.966	0.0003864	0.149	0.19742	1	0.18473	1	0.11567	1	0.066881	1
del_1p36.23	194 (42%)	269	0.0060822	1	0.00066997	0.252	7.2276e-37	3.92e-34	7.0061e-82	3.87e-79	0.00082998	0.308	0.56847	1	6.9469e-43	3.79e-40	1.0411e-50	5.72e-48	3.352e-21	1.78e-18	5.8372e-05	0.0246	3.3612e-25	1.8e-22	0.00031192	0.123
del_1p32.3	179 (39%)	284	0.028572	1	0.00017271	0.0703	1.1865e-42	6.45e-40	2.8254e-92	1.57e-89	0.00048994	0.187	0.22005	1	1.6859e-47	9.22e-45	4.8902e-56	2.7e-53	3.5555e-21	1.89e-18	1.8033e-05	0.00784	6.5495e-25	3.5e-22	0.00013387	0.0549
del_1q43	29 (6%)	434	NA	NA	NA	NA	0.093519	1	0.016434	1	0.10036	1	0.54013	1	0.16014	1	0.034179	1	0.14452	1	0.59965	1	0.33365	1	0.53977	1
del_2q37.3	69 (15%)	394	0.36962	1	0.16356	1	9.9185e-10	4.86e-07	3.3925e-11	1.7e-08	0.005117	1	0.012573	1	1.2192e-07	5.68e-05	2.0282e-06	0.000917	0.091259	1	0.036718	1	0.026235	1	0.0022082	0.777
del_3p21.1	45 (10%)	418	1	1	0.0081481	1	3.2371e-06	0.00146	0.00094298	0.349	0.00060784	0.23	0.12898	1	5.0641e-11	2.53e-08	0.00014693	0.0599	0.0042913	1	0.044643	1	0.051072	1	0.00033102	0.129
del_3q29	41 (9%)	422	0.17504	1	0.56068	1	7.4217e-09	3.56e-06	0.0031547	1	0.40457	1	0.66841	1	5.0233e-09	2.42e-06	0.0029626	1	0.1969	1	0.049271	1	0.33527	1	0.015484	1
del_4q34.3	127 (27%)	336	1	1	0.60239	1	9.1574e-05	0.0379	5.6715e-08	2.67e-05	0.16273	1	0.051536	1	5.6716e-05	0.0239	0.09658	1	0.027861	1	0.19261	1	0.065197	1	0.78996	1
del_5p15.33	47 (10%)	416	1	1	0.042206	1	8.9503e-09	4.27e-06	3.1345e-05	0.0135	0.86046	1	0.61369	1	0.016209	1	0.0017936	0.637	0.0015278	0.547	0.68585	1	0.0030698	1	0.28939	1
del_5q34	56 (12%)	407	0.44623	1	0.018246	1	6.8693e-12	3.48e-09	7.6653e-08	3.6e-05	0.17074	1	1	1	2.1941e-07	0.000102	0.00039577	0.152	2.0254e-06	0.000917	0.31301	1	9.7278e-06	0.00429	0.0058672	1
del_6p25.3	48 (10%)	415	NA	NA	NA	NA	0.0001353	0.0553	0.14842	1	0.23781	1	0.65191	1	0.024898	1	0.064365	1	0.33064	1	0.18302	1	0.25056	1	0.63368	1
del_6q24.3	74 (16%)	389	0.16991	1	0.23966	1	0.00037273	0.145	3.2806e-05	0.0141	0.10129	1	0.3389	1	0.0087949	1	0.0010939	0.4	0.0048586	1	0.043394	1	0.0028198	0.978	0.028824	1
del_7p22.3	20 (4%)	443	NA	NA	NA	NA	0.01932	1	0.054863	1	0.31972	1	0.38286	1	0.13653	1	0.57772	1	0.81333	1	0.76098	1	0.69533	1	0.2569	1
del_8q24.3	26 (6%)	437	NA	NA	NA	NA	2.8337e-06	0.00128	7.6896e-06	0.0034	0.92799	1	0.6395	1	0.012197	1	0.0011543	0.417	0.0031137	1	0.034863	1	0.088299	1	0.057717	1
del_9p23	134 (29%)	329	0.44623	1	0.60733	1	1.6569e-08	7.87e-06	1.2953e-05	0.00567	0.039439	1	0.02796	1	0.0010496	0.385	0.088757	1	0.040478	1	0.7049	1	0.20721	1	0.28547	1
del_9p21.3	158 (34%)	305	0.33256	1	0.015262	1	6.1586e-18	3.23e-15	4.2141e-16	2.19e-13	1.7489e-05	0.00763	4.9421e-05	0.0209	1.0863e-09	5.31e-07	3.5212e-05	0.0151	1.0494e-05	0.00462	0.0515	1	1.9638e-06	0.000892	0.17255	1
del_10q26.3	139 (30%)	324	0.083761	1	0.16444	1	6.841e-36	3.71e-33	4.2924e-35	2.32e-32	8.977e-07	0.000411	0.00022767	0.0913	5.825e-26	3.13e-23	9.085e-18	4.76e-15	1.176e-12	5.97e-10	4.5047e-06	0.00202	8.5706e-17	4.47e-14	0.00030745	0.121
del_11p15.5	95 (21%)	368	0.64244	1	0.00074097	0.277	1.1587e-19	6.12e-17	8.2938e-22	4.42e-19	0.10112	1	0.89674	1	3.6223e-09	1.75e-06	3.5826e-11	1.79e-08	0.22491	1	0.44906	1	0.15482	1	0.090312	1
del_12p13.1	37 (8%)	426	NA	NA	NA	NA	0.016446	1	0.0022736	0.798	0.19723	1	0.87476	1	0.0064087	1	0.0011404	0.414	0.015004	1	0.39907	1	0.099248	1	0.84622	1
del_12q12	64 (14%)	399	1	1	0.0081481	1	1.4999e-10	7.45e-08	9.8111e-09	4.67e-06	0.90018	1	0.86112	1	0.00813	1	6.9961e-05	0.0292	0.0018399	0.651	0.43401	1	0.00076023	0.284	0.25382	1
del_13q14.2	129 (28%)	334	0.1801	1	0.00061812	0.234	2.1563e-13	1.1e-10	0.00048397	0.185	0.034041	1	0.80653	1	0.0006048	0.23	0.00028229	0.112	0.021663	1	0.17307	1	0.045646	1	0.10128	1
del_13q14.2	131 (28%)	332	0.1801	1	0.00061812	0.234	8.5088e-14	4.36e-11	0.00027249	0.109	0.033643	1	0.74884	1	0.00037656	0.146	0.00013092	0.0538	0.020314	1	0.1089	1	0.032475	1	0.0749	1
del_13q34	98 (21%)	365	0.50769	1	0.10604	1	4.6975e-07	0.000217	0.062764	1	0.086983	1	0.52616	1	0.017999	1	0.0088112	1	0.018469	1	0.12612	1	0.051341	1	0.050798	1
del_14q24.3	107 (23%)	356	0.30286	1	0.1709	1	0.008981	1	0.017322	1	0.0015963	0.57	0.012528	1	0.00032159	0.126	0.0024066	0.842	4.0744e-05	0.0174	0.003579	1	0.00017494	0.071	0.00028769	0.114
del_18q23	71 (15%)	392	0.32144	1	0.31568	1	0.43942	1	0.011223	1	0.45403	1	0.11004	1	0.41697	1	0.60964	1	0.87635	1	0.14248	1	0.8952	1	0.79602	1
del_19q13.42	250 (54%)	213	0.03533	1	0.12707	1	3.9858e-30	2.15e-27	2.6811e-52	1.47e-49	0.002152	0.76	0.60791	1	8.2072e-25	4.38e-22	1.2821e-32	6.92e-30	1.2975e-10	6.46e-08	0.00099225	0.365	1.0027e-11	5.06e-09	0.097595	1
del_22q13.31	68 (15%)	395	0.25043	1	0.058829	1	2.0066e-14	1.03e-11	1.6087e-09	7.83e-07	0.0002152	0.0867	0.010362	1	3.5866e-10	1.78e-07	3.3816e-07	0.000157	0.031007	1	0.060046	1	0.0052939	1	0.017723	1
del_22q13.31	68 (15%)	395	0.25043	1	0.058829	1	2.0066e-14	1.03e-11	1.6087e-09	7.83e-07	0.0002152	0.0867	0.010362	1	3.5866e-10	1.78e-07	3.3816e-07	0.000157	0.031007	1	0.060046	1	0.0052939	1	0.017723	1
del_xp21.1	93 (20%)	370	0.83946	1	0.13068	1	7.6508e-05	0.0318	0.010199	1	0.014394	1	0.089445	1	0.041258	1	0.017779	1	0.10141	1	1	1	0.086746	1	0.021019	1
del_xq21.1	67 (14%)	396	0.83946	1	0.022012	1	0.25234	1	0.024005	1	0.054417	1	0.031662	1	2.0968e-05	0.0091	0.0080193	1	0.0032635	1	0.922	1	0.0027836	0.969	0.44669	1
