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	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
1p gain	24 (5%)	504	0.81857	1	0.92554	1	9.9999e-06	0.00875	0.00057999	0.378	0.00126	0.799	0.02638	1	0.00126	0.799	3e-04	0.202	0.00212	1	0.0065999	1	0.75086	1	0.03915	1
1q gain	51 (10%)	477	0.41047	1	0.90014	1	9.9999e-06	0.00875	0.01443	1	0.0271	1	0.01589	1	2e-05	0.0148	0.0064699	1	9.9999e-06	0.00875	0.0052599	1	0.4187	1	0.75512	1
2p gain	77 (15%)	451	0.70421	1	0.46098	1	9.9999e-06	0.00875	0.083229	1	0.052839	1	0.9409	1	0.30468	1	0.0090699	1	0.62021	1	0.14458	1	0.22874	1	0.47223	1
2q gain	79 (15%)	449	0.55764	1	0.26616	1	9.9999e-06	0.00875	0.16447	1	0.04351	1	1	1	0.32085	1	0.02471	1	0.70621	1	0.02612	1	0.31985	1	0.65478	1
3p gain	19 (4%)	509	0.053689	1	0.43015	1	0.00028	0.189	0.58302	1	0.02373	1	0.00242	1	0.0089199	1	0.00265	1	0.00016	0.11	0.12527	1	0.39133	1	0.73621	1
3q gain	61 (12%)	467	0.01176	1	0.03081	1	9.9999e-06	0.00875	0.00363	1	0.00076999	0.497	9.9999e-06	0.00875	2e-05	0.0148	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00039	0.257	0.00187	1	0.081239	1
4p gain	13 (2%)	515	NA	NA	NA	NA	0.072239	1	0.37428	1	0.070379	1	0.01018	1	0.00021	0.143	0.00102	0.653	0.00025	0.169	0.04399	1	NA	NA	NA	NA
4q gain	13 (2%)	515	NA	NA	NA	NA	0.21105	1	0.45632	1	0.070199	1	0.0497	1	0.00026	0.176	0.0121	1	3e-04	0.202	0.04438	1	NA	NA	NA	NA
5p gain	193 (37%)	335	0.88016	1	0.92331	1	0.00031	0.208	0.26058	1	0.30452	1	0.33704	1	0.02208	1	0.03435	1	0.069309	1	0.15319	1	0.083589	1	0.90731	1
5q gain	207 (39%)	321	0.33425	1	0.62491	1	0.02161	1	0.43403	1	0.6679	1	0.44649	1	0.12428	1	0.17447	1	0.44672	1	0.20404	1	0.12712	1	0.90746	1
6p gain	11 (2%)	517	NA	NA	NA	NA	0.15046	1	0.44484	1	0.074699	1	0.43081	1	0.68021	1	0.85865	1	0.85865	1	0.11258	1	0.60388	1	0.77897	1
6q gain	9 (2%)	519	NA	NA	NA	NA	0.080559	1	0.68202	1	0.01907	1	0.63118	1	1	1	1	1	1	1	0.18604	1	0.60582	1	0.77984	1
7p gain	171 (32%)	357	0.44919	1	0.85897	1	9.9999e-06	0.00875	0.00166	1	0.00025	0.169	0.0051099	1	0.00011	0.0761	0.00311	1	0.00411	1	0.03007	1	0.10321	1	0.76604	1
7q gain	172 (33%)	356	0.45351	1	0.85953	1	9.9999e-06	0.00875	0.00377	1	0.00024	0.163	0.00256	1	5.9999e-05	0.0423	0.00296	1	0.0052799	1	0.01797	1	0.17301	1	0.58878	1
8p gain	31 (6%)	497	NA	NA	NA	NA	9.9999e-06	0.00875	0.00036	0.239	0.0097099	1	0.064909	1	9.9999e-06	0.00875	6.9999e-05	0.049	9.9999e-06	0.00875	0.0052899	1	0.01104	1	0.107	1
8q gain	62 (12%)	466	0.22882	1	0.10645	1	9.9999e-06	0.00875	9.9999e-06	0.00875	4e-05	0.0286	0.00044	0.29	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	7.9999e-05	0.0558	4e-04	0.264	0.40672	1
9p gain	13 (2%)	515	NA	NA	NA	NA	0.01502	1	0.90319	1	0.86604	1	1	1	0.21858	1	0.82837	1	1	1	0.86165	1	1	1	1	1
9q gain	12 (2%)	516	NA	NA	NA	NA	0.00128	0.808	0.90745	1	0.68742	1	0.23137	1	0.21967	1	0.60591	1	0.5315	1	0.6714	1	1	1	1	1
10p gain	17 (3%)	511	NA	NA	NA	NA	0.00013	0.0898	0.25567	1	0.098829	1	0.17562	1	0.00092999	0.596	0.00044	0.29	0.01951	1	0.068919	1	NA	NA	NA	NA
10q gain	12 (2%)	516	NA	NA	NA	NA	0.00015	0.103	0.11639	1	0.057149	1	0.21762	1	0.01224	1	0.00123	0.782	0.01532	1	0.21413	1	NA	NA	NA	NA
11p gain	31 (6%)	497	0.23193	1	0.67119	1	2e-05	0.0148	0.2708	1	0.086609	1	0.095239	1	0.14339	1	0.085729	1	0.14645	1	0.28006	1	0.39347	1	0.85511	1
11q gain	29 (5%)	499	0.3407	1	0.90701	1	0.00016	0.11	0.52681	1	0.33567	1	0.51721	1	0.34587	1	0.43033	1	0.36011	1	0.18569	1	0.74924	1	0.68186	1
12p gain	121 (23%)	407	0.01302	1	0.03269	1	9.9999e-06	0.00875	4e-05	0.0286	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00153	0.958	0.10225	1
12q gain	122 (23%)	406	0.01306	1	0.03297	1	9.9999e-06	0.00875	5e-05	0.0354	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00319	1	0.12654	1
13q gain	22 (4%)	506	NA	NA	NA	NA	0.48497	1	0.03417	1	0.63666	1	0.79876	1	0.061469	1	0.92445	1	0.34766	1	0.2612	1	0.28775	1	0.32559	1
14q gain	16 (3%)	512	0.76763	1	0.57464	1	0.00141	0.885	0.35018	1	0.0061599	1	0.03938	1	0.0057299	1	0.01254	1	0.00377	1	0.112	1	NA	NA	NA	NA
15q gain	26 (5%)	502	1	1	0.11727	1	0.00078999	0.508	0.72371	1	0.49854	1	0.46448	1	0.58165	1	0.86704	1	0.70402	1	0.40768	1	0.6857	1	0.8261	1
16p gain	107 (20%)	421	0.2728	1	0.38237	1	5.9999e-05	0.0423	0.16553	1	0.03768	1	0.41333	1	0.0118	1	0.00273	1	0.060169	1	0.02648	1	0.12889	1	0.39627	1
16q gain	99 (19%)	429	0.23315	1	0.34883	1	5e-05	0.0354	0.087139	1	0.052009	1	0.30196	1	0.0096699	1	0.00124	0.787	0.0163	1	0.14741	1	0.18123	1	0.26798	1
17p gain	26 (5%)	502	0.01914	1	0.0057899	1	9.9999e-06	0.00875	0.81872	1	0.095459	1	0.144	1	0.11637	1	0.053189	1	0.14623	1	0.26782	1	0.0363	1	0.73734	1
17q gain	33 (6%)	495	0.068209	1	0.02555	1	3e-05	0.0217	0.23587	1	0.084089	1	0.12715	1	0.063639	1	0.01082	1	0.077399	1	0.22343	1	0.00198	1	0.29263	1
18p gain	25 (5%)	503	0.31096	1	0.076709	1	0.073039	1	0.44849	1	0.81351	1	0.080899	1	0.36811	1	0.93009	1	0.83469	1	0.45417	1	0.20092	1	0.04464	1
18q gain	25 (5%)	503	0.31348	1	0.077119	1	0.066919	1	0.55935	1	0.42724	1	0.21235	1	0.36653	1	0.92942	1	0.96589	1	0.45278	1	0.20064	1	0.04446	1
19p gain	51 (10%)	477	0.22731	1	0.48294	1	9.9999e-06	0.00875	7.9999e-05	0.0558	0.00419	1	0.12956	1	0.0014	0.881	0.00034	0.226	9.9999e-06	0.00875	0.35473	1	0.92003	1	0.62547	1
19q gain	57 (11%)	471	0.10189	1	0.22494	1	9.9999e-06	0.00875	2e-05	0.0148	0.00023	0.156	0.0138	1	0.00062999	0.409	4e-05	0.0286	9.9999e-06	0.00875	0.16986	1	0.57849	1	0.28736	1
20p gain	112 (21%)	416	0.11699	1	0.11458	1	9.9999e-06	0.00875	3e-05	0.0217	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	3e-05	0.0217	0.051729	1
20q gain	115 (22%)	413	0.04157	1	0.074289	1	9.9999e-06	0.00875	2e-05	0.0148	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.03159	1
21q gain	50 (9%)	478	0.26988	1	0.2095	1	9.9999e-06	0.00875	0.00127	0.803	0.00186	1	0.51742	1	0.00031	0.208	0.00028	0.189	0.00281	1	0.03231	1	0.34995	1	0.47563	1
22q gain	40 (8%)	488	0.32677	1	0.21745	1	2e-05	0.0148	0.20984	1	0.41951	1	0.97425	1	0.0434	1	0.03552	1	0.061709	1	0.41157	1	0.9086	1	0.3071	1
xq gain	31 (6%)	497	0.39016	1	0.70307	1	0.22339	1	0.29267	1	0.03058	1	0.0075299	1	0.13313	1	0.02626	1	0.32076	1	0.60359	1	0.91894	1	0.81272	1
1p loss	57 (11%)	471	0.00074999	0.484	0.00289	1	9.9999e-06	0.00875	0.6786	1	0.00146	0.915	0.15565	1	0.071799	1	0.03937	1	0.0081299	1	0.023	1	0.03593	1	0.82344	1
1q loss	36 (7%)	492	0.01085	1	0.01144	1	9.9999e-06	0.00875	0.3691	1	0.02811	1	0.10532	1	0.00245	1	0.0080099	1	0.0057699	1	0.0428	1	0.22447	1	0.7082	1
2p loss	14 (3%)	514	3e-05	0.0217	0.00076999	0.497	9.9999e-06	0.00875	0.66305	1	0.00021	0.143	2e-05	0.0148	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	5.9999e-05	0.0423	0.13166	1	0.096309	1
2q loss	14 (3%)	514	0.00035	0.232	0.00068999	0.448	3e-05	0.0217	1	1	0.00052999	0.347	2e-05	0.0148	9.9999e-06	0.00875	4e-05	0.0286	9.9999e-06	0.00875	9.9999e-06	0.00875	0.13092	1	0.097419	1
3p loss	380 (72%)	148	0.00326	1	0.01042	1	9.9999e-06	0.00875	0.00053999	0.352	0.03384	1	0.04546	1	9.9999e-06	0.00875	2e-05	0.0148	0.0214	1	0.0081999	1	0.091309	1	0.73155	1
3q loss	99 (19%)	429	0.92194	1	0.52002	1	0.00154	0.962	0.40451	1	0.25276	1	0.21268	1	0.12054	1	0.74438	1	0.65138	1	0.02633	1	0.79947	1	0.86106	1
4p loss	72 (14%)	456	0.53092	1	0.81701	1	9.9999e-06	0.00875	9.9999e-05	0.0693	0.20379	1	0.28829	1	0.00051999	0.341	9.9999e-06	0.00875	0.57312	1	0.073029	1	0.079069	1	0.0072099	1
4q loss	65 (12%)	463	0.38877	1	0.7831	1	9.9999e-06	0.00875	4e-05	0.0286	0.18195	1	0.092019	1	0.00036	0.239	9.9999e-06	0.00875	0.19796	1	0.064349	1	0.43287	1	0.056909	1
5p loss	7 (1%)	521	NA	NA	NA	NA	0.01607	1	0.28813	1	0.46575	1	0.12662	1	0.02442	1	0.00394	1	0.04122	1	0.066029	1	NA	NA	NA	NA
5q loss	6 (1%)	522	NA	NA	NA	NA	0.04414	1	0.54301	1	0.34931	1	0.39523	1	0.03354	1	0.00239	1	0.073129	1	0.092559	1	NA	NA	NA	NA
6p loss	100 (19%)	428	0.01101	1	0.0141	1	9.9999e-06	0.00875	5.9999e-05	0.0423	0.00013	0.0898	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.081349	1	0.02376	1
6q loss	128 (24%)	400	0.050259	1	0.051979	1	9.9999e-06	0.00875	0.0062799	1	5e-05	0.0354	6.9999e-05	0.049	0.00027	0.182	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.17041	1	0.02517	1
7p loss	3 (1%)	525	NA	NA	NA	NA	0.16478	1	NA	NA	NA	NA	NA	NA	0.10529	1	0.01289	1	0.058659	1	0.35588	1	NA	NA	NA	NA
7q loss	4 (1%)	524	NA	NA	NA	NA	0.11923	1	0.34811	1	0.084599	1	0.17726	1	0.04696	1	0.00308	1	0.01934	1	0.77179	1	NA	NA	NA	NA
8p loss	137 (26%)	391	0.37864	1	0.16748	1	9.9999e-06	0.00875	0.27748	1	0.12227	1	0.088549	1	0.098889	1	0.0016	0.998	0.04297	1	0.02238	1	0.27613	1	0.24248	1
8q loss	64 (12%)	464	0.64835	1	0.12543	1	0.12158	1	0.04452	1	0.15994	1	0.93448	1	0.70628	1	0.94109	1	0.58969	1	0.40715	1	0.68402	1	0.088509	1
9p loss	149 (28%)	379	0.00351	1	0.03689	1	9.9999e-06	0.00875	9.9999e-06	0.00875	2e-05	0.0148	5e-05	0.0354	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.01645	1	0.098779	1
9q loss	150 (28%)	378	0.01002	1	0.058809	1	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00019	0.13	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00373	1	0.03706	1
10p loss	67 (13%)	461	0.17295	1	0.40878	1	9.9999e-06	0.00875	0.081739	1	0.80746	1	0.068099	1	0.12478	1	0.062499	1	0.01729	1	0.10884	1	0.77585	1	0.29447	1
10q loss	89 (17%)	439	0.32752	1	0.40182	1	9.9999e-06	0.00875	0.00454	1	0.98512	1	0.01999	1	0.11548	1	0.03557	1	0.03861	1	0.00050999	0.335	0.80155	1	0.43718	1
11p loss	18 (3%)	510	NA	NA	NA	NA	9.9999e-06	0.00875	0.02274	1	0.29785	1	0.25921	1	0.1753	1	0.0091399	1	0.16925	1	0.15013	1	0.29932	1	0.30564	1
11q loss	23 (4%)	505	0.18838	1	0.37478	1	9.9999e-06	0.00875	0.0058799	1	0.18024	1	0.069649	1	0.01199	1	8.9999e-05	0.0625	0.02357	1	0.03629	1	0.2971	1	0.30714	1
12p loss	4 (1%)	524	NA	NA	NA	NA	0.085239	1	NA	NA	NA	NA	NA	NA	0.19938	1	0.69341	1	0.29634	1	0.14334	1	NA	NA	NA	NA
12q loss	4 (1%)	524	NA	NA	NA	NA	0.48235	1	NA	NA	0.37596	1	0.26134	1	1	1	1	1	0.23319	1	0.61126	1	NA	NA	NA	NA
13q loss	71 (13%)	457	0.00321	1	0.04704	1	9.9999e-06	0.00875	0.00031	0.208	2e-05	0.0148	3e-05	0.0217	2e-05	0.0148	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.10776	1	0.10481	1
14q loss	216 (41%)	312	3e-05	0.0217	3e-05	0.0217	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.04988	1	0.88012	1
15q loss	36 (7%)	492	0.11877	1	0.33334	1	9.9999e-06	0.00875	0.00072999	0.473	0.02955	1	0.10811	1	2e-05	0.0148	9.9999e-06	0.00875	0.00080999	0.52	0.0165	1	0.070219	1	0.13278	1
16p loss	10 (2%)	518	NA	NA	NA	NA	0.20122	1	0.87769	1	0.12936	1	0.02689	1	0.31924	1	0.0060299	1	0.090849	1	0.11369	1	0.11635	1	0.11391	1
16q loss	16 (3%)	512	NA	NA	NA	NA	0.0378	1	0.90952	1	0.18482	1	0.15782	1	0.115	1	0.01354	1	0.064289	1	0.0082999	1	0.071159	1	0.0289	1
17p loss	46 (9%)	482	0.00014	0.0965	0.00019	0.13	9.9999e-06	0.00875	0.087719	1	0.0093599	1	0.00052999	0.347	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00022	0.15	0.20647	1	0.086889	1
17q loss	28 (5%)	500	0.00072999	0.473	0.00034	0.226	9.9999e-06	0.00875	0.58162	1	0.27736	1	0.0078199	1	6.9999e-05	0.049	4e-05	0.0286	9.9999e-06	0.00875	0.00497	1	0.45764	1	0.15024	1
18p loss	93 (18%)	435	0.058959	1	0.45982	1	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00031	0.208	0.00422	1
18q loss	95 (18%)	433	0.04672	1	0.22171	1	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	7.9999e-05	0.0558	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	9.9999e-06	0.00875	0.00307	1	0.03158	1
19p loss	11 (2%)	517	NA	NA	NA	NA	3e-05	0.0217	0.03183	1	0.0051499	1	0.00036	0.239	0.16163	1	5.9999e-05	0.0423	0.24285	1	0.0093999	1	0.03408	1	0.03804	1
19q loss	4 (1%)	524	NA	NA	NA	NA	0.01129	1	NA	NA	0.91784	1	0.16984	1	0.42788	1	0.052269	1	0.83021	1	0.083969	1	NA	NA	NA	NA
20p loss	8 (2%)	520	NA	NA	NA	NA	0.17472	1	1	1	0.02986	1	1	1	0.076329	1	0.089209	1	0.01913	1	0.23152	1	NA	NA	NA	NA
20q loss	3 (1%)	525	NA	NA	NA	NA	0.16507	1	NA	NA	NA	NA	NA	NA	0.10413	1	0.16223	1	0.057809	1	0.02909	1	NA	NA	NA	NA
21q loss	55 (10%)	473	0.02626	1	0.090579	1	9.9999e-06	0.00875	0.01384	1	0.074109	1	0.00106	0.677	0.00366	1	0.01499	1	0.0064199	1	0.0088299	1	0.88421	1	1	1
22q loss	39 (7%)	489	0.0096499	1	0.00129	0.813	9.9999e-06	0.00875	0.00345	1	0.00122	0.778	0.068619	1	2e-05	0.0148	3e-05	0.0217	9.9999e-06	0.00875	0.00352	1	0.02614	1	0.26002	1
xq loss	47 (9%)	481	0.02363	1	0.063679	1	9.9999e-06	0.00875	0.01872	1	0.22824	1	0.00122	0.778	0.068789	1	0.17281	1	0.01146	1	0.0017	1	0.2299	1	0.17556	1