		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	Chi-square test_P	Chi-square 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	22 (4%)	482	1	1	1	1	9.4737e-07	0.000737	0.001635	1	0.0018281	1	0.010553	1	0.03158	1	0.0054073	1	0.00056009	0.38	0.63182	1	0.11698	1	0.0072822	1
1q gain	50 (10%)	454	0.41028	1	0.41105	1	1.2074e-14	1.05e-11	0.036895	1	0.087509	1	0.031246	1	5.6952e-05	0.0411	0.00076077	0.502	2.4588e-05	0.0182	0.65925	1	0.094511	1	0.025775	1
2p gain	75 (15%)	429	0.56067	1	0.40029	1	2.1666e-09	1.79e-06	0.20097	1	0.011792	1	0.87127	1	0.216	1	0.053703	1	0.74224	1	0.39804	1	0.034232	1	0.52066	1
2q gain	76 (15%)	428	0.56067	1	0.40029	1	1.7583e-07	0.00014	0.29955	1	0.011511	1	0.93353	1	0.1906	1	0.048823	1	0.82231	1	0.39804	1	0.087124	1	0.33448	1
3p gain	18 (4%)	486	0.053628	1	0.062305	1	0.0015512	0.982	0.58508	1	0.0073443	1	0.0033196	1	0.016282	1	0.0026705	1	3.7386e-05	0.0273	1.0753e-05	0.00808	0.0025021	1	0.15481	1
3q gain	57 (11%)	447	0.012193	1	0.018801	1	3.7039e-09	3.04e-06	0.012511	1	0.00087165	0.571	1.0317e-06	0.000801	9.9699e-05	0.071	4.4608e-05	0.0325	3.4813e-08	2.82e-05	6.1385e-07	0.000481	0.0014843	0.943	0.15984	1
4p gain	13 (3%)	491	NA	NA	NA	NA	0.067043	1	0.377	1	0.25321	1	0.0017483	1	0.00041752	0.286	0.0007913	0.521	0.0001451	0.103	0.019513	1	0.016245	1	0.19884	1
4q gain	13 (3%)	491	NA	NA	NA	NA	0.26741	1	0.4491	1	0.25321	1	0.020053	1	0.00041752	0.286	0.0076877	1	0.0001451	0.103	0.031207	1	0.016245	1	0.19884	1
5p gain	185 (37%)	319	0.83527	1	0.77796	1	0.0001611	0.114	0.23021	1	0.11822	1	0.096432	1	0.03616	1	0.0049547	1	0.16029	1	0.83645	1	0.19808	1	0.95117	1
5q gain	199 (39%)	305	0.29223	1	0.21196	1	0.012316	1	0.38892	1	0.40404	1	0.074721	1	0.16307	1	0.021387	1	0.7	1	0.40788	1	0.53983	1	0.79897	1
6p gain	10 (2%)	494	NA	NA	NA	NA	0.32172	1	0.34049	1	0.050507	1	0.25206	1	0.49408	1	0.68685	1	0.71617	1	0.45696	1	0.21995	1	0.037414	1
6q gain	8 (2%)	496	NA	NA	NA	NA	0.10135	1	0.56926	1	0.0051485	1	0.42668	1	0.72709	1	1	1	0.90431	1	0.53259	1	0.17799	1	0.11161	1
7p gain	167 (33%)	337	0.41594	1	0.57703	1	3.9934e-13	3.41e-10	0.006273	1	1.608e-05	0.012	0.001785	1	0.00057211	0.387	0.0028602	1	0.0087671	1	0.1528	1	0.038154	1	0.39329	1
7q gain	168 (33%)	336	0.41594	1	0.57703	1	2.1739e-12	1.85e-09	0.015616	1	2.7813e-05	0.0205	0.00069173	0.459	0.00065342	0.436	0.0028032	1	0.0058758	1	0.074202	1	0.1081	1	0.30774	1
8p gain	30 (6%)	474	NA	NA	NA	NA	1.1574e-08	9.46e-06	0.00096443	0.627	0.0045312	1	0.27136	1	7.8953e-06	0.00597	2.7348e-05	0.0202	3.3127e-06	0.00253	0.0059521	1	0.0027212	1	0.0014448	0.92
8q gain	59 (12%)	445	0.22618	1	0.32459	1	7.5562e-18	6.62e-15	2.9352e-06	0.00225	6.9975e-05	0.0502	0.015471	1	3.8039e-11	3.2e-08	5.4213e-10	4.51e-07	1.9582e-09	1.62e-06	0.0047915	1	3.7376e-06	0.00285	5.2663e-06	0.004
9p gain	14 (3%)	490	NA	NA	NA	NA	0.10782	1	1	1	0.80136	1	0.86106	1	0.43705	1	0.57875	1	1	1	0.017538	1	0.83205	1	0.91504	1
9q gain	12 (2%)	492	NA	NA	NA	NA	0.0046797	1	0.8353	1	0.56846	1	0.29075	1	0.24693	1	0.55899	1	0.75941	1	0.022721	1	0.69897	1	0.89032	1
10p gain	16 (3%)	488	NA	NA	NA	NA	0.00082307	0.54	0.11259	1	0.15913	1	0.36647	1	0.0024316	1	0.0005814	0.392	0.094246	1	0.47112	1	0.47137	1	0.27646	1
10q gain	12 (2%)	492	NA	NA	NA	NA	0.00028704	0.199	0.082229	1	0.067334	1	0.54603	1	0.016396	1	0.0091918	1	0.05843	1	0.37822	1	0.43913	1	0.097142	1
11p gain	30 (6%)	474	0.23165	1	0.25217	1	3.3032e-06	0.00253	0.30823	1	0.19528	1	0.24639	1	0.21729	1	0.27947	1	0.28244	1	0.041962	1	0.26844	1	0.55514	1
11q gain	28 (6%)	476	0.34099	1	0.53903	1	0.00012478	0.0886	0.18751	1	0.4232	1	0.51319	1	0.46321	1	0.54229	1	0.61197	1	0.030823	1	0.60284	1	0.91876	1
12p gain	118 (23%)	386	0.012874	1	0.014228	1	6.2131e-14	5.36e-11	0.00017395	0.122	1.3367e-12	1.14e-09	0.0010333	0.669	6.5293e-12	5.55e-09	1.759e-11	1.49e-08	1.0048e-09	8.33e-07	0.023981	1	4.884e-07	0.000383	0.00057518	0.388
12q gain	119 (24%)	385	0.012874	1	0.014228	1	5.4687e-14	4.72e-11	0.00011834	0.0841	3.7799e-14	3.27e-11	0.00028836	0.2	8.8975e-12	7.54e-09	7.9098e-12	6.71e-09	1.4276e-10	1.19e-07	0.030785	1	1.8077e-07	0.000144	0.00027986	0.195
13q gain	22 (4%)	482	NA	NA	NA	NA	0.30942	1	0.010383	1	0.64797	1	0.56881	1	0.072388	1	0.3016	1	0.34968	1	1	1	0.64474	1	0.18906	1
14q gain	16 (3%)	488	0.76851	1	0.78254	1	0.0005687	0.385	0.32823	1	0.012121	1	0.0069981	1	0.0083662	1	0.059607	1	0.0019572	1	5.453e-05	0.0396	0.43913	1	0.28998	1
15q gain	26 (5%)	478	1	1	1	1	0.001238	0.792	0.59897	1	0.45203	1	0.15002	1	0.66145	1	0.90187	1	0.77311	1	0.23706	1	0.65491	1	0.78759	1
16p gain	106 (21%)	398	0.28203	1	0.33712	1	0.00060105	0.404	0.39878	1	0.0014674	0.933	0.04981	1	0.030398	1	0.0010953	0.705	0.030014	1	0.095698	1	0.2116	1	0.22119	1
16q gain	98 (19%)	406	0.23296	1	0.21777	1	0.00027499	0.191	0.22724	1	0.0023038	1	0.063492	1	0.027589	1	0.0033498	1	0.0084671	1	0.12916	1	0.049185	1	0.30549	1
17p gain	24 (5%)	480	0.018559	1	0.034912	1	3.5237e-06	0.00269	0.72735	1	0.32918	1	0.073361	1	0.2434	1	0.081727	1	0.27223	1	0.0033119	1	0.25888	1	0.066561	1
17q gain	30 (6%)	474	0.069157	1	0.098773	1	2.5777e-05	0.0191	0.39423	1	0.49259	1	0.076145	1	0.18356	1	0.025393	1	0.11124	1	0.00094701	0.617	0.13149	1	0.021235	1
18p gain	25 (5%)	479	0.31209	1	0.25229	1	0.085635	1	0.40519	1	0.83155	1	0.19135	1	0.18402	1	0.82237	1	0.83002	1	0.60463	1	0.33105	1	0.13991	1
18q gain	25 (5%)	479	0.31209	1	0.25229	1	0.1245	1	0.41315	1	0.73299	1	0.51027	1	0.18402	1	0.82237	1	0.87382	1	0.60463	1	0.33105	1	0.13991	1
19p gain	50 (10%)	454	0.22618	1	0.32459	1	5.7314e-10	4.76e-07	0.0049435	1	0.0092424	1	0.079396	1	0.003764	1	0.011472	1	0.00016722	0.118	0.0040931	1	0.0064803	1	0.77908	1
19q gain	56 (11%)	448	0.10193	1	0.14864	1	7.3318e-12	6.22e-09	0.0006543	0.436	0.001838	1	0.010066	1	0.0017255	1	0.0051516	1	6.4294e-05	0.0463	0.00049104	0.335	0.001763	1	0.618	1
20p gain	110 (22%)	394	0.11564	1	0.16346	1	1.0909e-21	9.61e-19	5.6154e-05	0.0407	1.0713e-07	8.59e-05	0.0017354	1	3.9631e-13	3.39e-10	2.0056e-11	1.69e-08	2.0269e-10	1.69e-07	0.00025336	0.177	7.7965e-07	0.00061	0.0032897	1
20q gain	113 (22%)	391	0.045714	1	0.06749	1	4.6378e-23	4.1e-20	5.6154e-05	0.0407	6.7616e-09	5.54e-06	0.00089632	0.586	7.9661e-15	6.91e-12	2.0812e-12	1.77e-09	1.9619e-11	1.66e-08	0.00014455	0.102	3.2346e-07	0.000255	0.0019667	1
21q gain	50 (10%)	454	0.26897	1	0.27964	1	3.086e-07	0.000243	0.0086674	1	0.0011012	0.707	0.50897	1	0.00048323	0.33	9.7807e-05	0.0697	0.014447	1	1	1	0.029006	1	0.0321	1
22q gain	40 (8%)	464	0.32729	1	0.028901	1	1.732e-05	0.0129	0.67931	1	0.37794	1	0.5812	1	0.068023	1	0.18565	1	0.03258	1	0.23003	1	0.018795	1	0.27393	1
xq gain	27 (5%)	477	0.41403	1	0.42477	1	0.14654	1	0.7232	1	0.0047758	1	0.0044641	1	0.22879	1	0.34228	1	0.26368	1	1	1	0.18499	1	0.23348	1
1p loss	58 (12%)	446	0.0017522	1	0.00063021	0.421	1.3057e-09	1.08e-06	0.46941	1	0.00060551	0.406	0.18666	1	0.13792	1	0.00096605	0.627	0.18896	1	8.6312e-11	7.22e-08	0.091131	1	0.008453	1
1q loss	37 (7%)	467	0.021718	1	0.029804	1	1.0543e-09	8.72e-07	0.28899	1	0.012964	1	0.078698	1	0.0048811	1	0.00049978	0.34	0.20793	1	1.2314e-10	1.03e-07	0.085553	1	0.050892	1
2p loss	14 (3%)	490	3.5787e-05	0.0262	6.2984e-05	0.0454	8.8449e-07	0.000691	0.66785	1	4.5828e-05	0.0333	2.3548e-06	0.00181	2.107e-07	0.000167	4.802e-09	3.94e-06	5.5411e-05	0.0402	2.123e-14	1.84e-11	0.059273	1	0.039903	1
2q loss	14 (3%)	490	0.00024867	0.174	0.00038936	0.267	8.8449e-07	0.000691	1	1	0.00031624	0.219	2.3548e-06	0.00181	2.107e-07	0.000167	6.6769e-08	5.38e-05	8.1589e-06	0.00616	1.2328e-12	1.05e-09	0.059273	1	0.039903	1
3p loss	364 (72%)	140	0.0034866	1	0.00066344	0.441	4.7233e-22	4.17e-19	0.020668	1	0.028395	1	0.013867	1	9.0855e-07	0.000708	1.8404e-11	1.56e-08	0.12734	1	1.8069e-05	0.0134	0.13119	1	0.00071281	0.473
3q loss	101 (20%)	403	0.92264	1	0.85231	1	0.0010128	0.656	0.47319	1	0.3475	1	0.084712	1	0.048093	1	0.073637	1	0.60608	1	0.38802	1	0.075916	1	0.13867	1
4p loss	71 (14%)	433	0.53135	1	0.38886	1	1.0242e-09	8.48e-07	0.0013598	0.869	0.084529	1	0.33647	1	0.0020292	1	0.053551	1	0.86197	1	0.3232	1	0.1536	1	0.29872	1
4q loss	65 (13%)	439	0.38705	1	0.34568	1	3.3825e-13	2.9e-10	0.00052903	0.36	0.051013	1	0.19873	1	0.00081048	0.532	0.0021123	1	0.41785	1	0.16476	1	0.065362	1	0.12427	1
5p loss	7 (1%)	497	NA	NA	NA	NA	0.019476	1	0.29091	1	0.65716	1	0.2869	1	0.027023	1	0.030768	1	0.030136	1	0.0087386	1	NA	NA	NA	NA
5q loss	6 (1%)	498	NA	NA	NA	NA	0.041524	1	0.53395	1	0.47139	1	0.62591	1	0.046108	1	0.049578	1	0.065045	1	0.0010782	0.695	NA	NA	NA	NA
6p loss	100 (20%)	404	0.011254	1	0.0028151	1	1.1436e-17	9.99e-15	0.00072253	0.478	1.012e-06	0.000786	0.00023397	0.164	7.6223e-08	6.14e-05	1.66e-07	0.000133	2.3288e-11	1.96e-08	4.6115e-06	0.00351	3.0366e-08	2.47e-05	3.0782e-05	0.0226
6q loss	127 (25%)	377	0.047526	1	0.021165	1	3.5312e-17	3.08e-14	0.043405	1	9.8169e-06	0.00739	0.0027724	1	0.00033239	0.229	0.0017339	1	1.0834e-07	8.68e-05	0.00033608	0.231	1.7504e-05	0.013	0.0050607	1
7p loss	3 (1%)	501	NA	NA	NA	NA	0.34001	1	NA	NA	NA	NA	NA	NA	0.16616	1	0.13396	1	0.052701	1	0.27955	1	0.052414	1	0.19935	1
7q loss	4 (1%)	500	NA	NA	NA	NA	0.12575	1	0.36257	1	0.097958	1	1	1	0.050491	1	0.092462	1	0.29411	1	0.39697	1	0.052414	1	0.19935	1
8p loss	135 (27%)	369	0.35372	1	0.42649	1	2.6983e-05	0.0199	0.21585	1	0.23296	1	0.2765	1	0.11704	1	0.24344	1	0.072607	1	0.39388	1	0.05935	1	0.24304	1
8q loss	65 (13%)	439	0.64737	1	0.74664	1	0.044623	1	0.14364	1	0.29923	1	0.63009	1	0.78193	1	0.67291	1	0.54365	1	0.88293	1	0.076773	1	0.17146	1
9p loss	144 (29%)	360	0.004171	1	0.00053301	0.362	8.2256e-44	7.3e-41	5.7458e-19	5.05e-16	1.496e-05	0.0112	0.001095	0.705	1.3966e-22	1.23e-19	2.7006e-23	2.39e-20	2.1312e-13	1.83e-10	7.6453e-05	0.0548	2.0737e-08	1.69e-05	2.9621e-05	0.0218
9q loss	147 (29%)	357	0.010069	1	0.0014349	0.915	5.7102e-44	5.08e-41	1.8014e-18	1.58e-15	1.0599e-06	0.00082	0.0015911	1	4.9797e-24	4.42e-21	9.2988e-24	8.24e-21	1.6406e-15	1.42e-12	0.00016536	0.116	2.6318e-08	2.14e-05	3.107e-06	0.00238
10p loss	66 (13%)	438	0.17348	1	0.23862	1	2.2756e-09	1.87e-06	0.055321	1	0.76399	1	0.3493	1	0.082696	1	0.21532	1	0.030115	1	0.0011487	0.736	0.032442	1	0.47058	1
10q loss	86 (17%)	418	0.31524	1	0.36049	1	5.2031e-09	4.27e-06	0.0071475	1	0.99022	1	0.14926	1	0.069817	1	0.21315	1	0.072232	1	0.01746	1	0.052421	1	0.28741	1
11p loss	18 (4%)	486	NA	NA	NA	NA	7.7932e-05	0.0558	0.047325	1	0.13967	1	0.55314	1	0.19771	1	0.15659	1	0.17512	1	0.04552	1	0.1058	1	0.015088	1
11q loss	23 (5%)	481	0.18897	1	0.20731	1	1.8141e-06	0.0014	0.014251	1	0.10125	1	0.41768	1	0.019271	1	0.014138	1	0.037276	1	0.10897	1	0.028428	1	0.052863	1
12p loss	3 (1%)	501	NA	NA	NA	NA	0.18328	1	NA	NA	NA	NA	NA	NA	0.43191	1	0.37983	1	0.46976	1	0.43901	1	NA	NA	NA	NA
12q loss	4 (1%)	500	NA	NA	NA	NA	0.46231	1	NA	NA	0.52479	1	0.18488	1	1	1	0.80815	1	0.22911	1	0.75095	1	NA	NA	NA	NA
13q loss	69 (14%)	435	0.0030403	1	0.0045545	1	3.8062e-10	3.17e-07	0.00073734	0.487	7.6632e-06	0.0058	0.0030671	1	1.2109e-05	0.00907	2.1731e-07	0.000172	1.0415e-06	0.000807	1.6647e-05	0.0124	0.016281	1	0.00029428	0.204
14q loss	211 (42%)	293	3.1171e-05	0.0228	4.3065e-05	0.0314	1.4553e-18	1.28e-15	6.2116e-08	5.02e-05	1.0117e-13	8.71e-11	1.2787e-07	0.000102	1.0241e-19	9.01e-17	1.4895e-15	1.29e-12	6.2732e-11	5.26e-08	0.91072	1	0.0010654	0.688	0.00031657	0.219
15q loss	35 (7%)	469	0.11774	1	0.12687	1	4.0811e-11	3.43e-08	0.0078729	1	0.041965	1	0.4139	1	7.5108e-06	0.00569	1.0817e-05	0.00811	0.0014998	0.951	0.035895	1	0.00091268	0.595	0.1403	1
16p loss	9 (2%)	495	NA	NA	NA	NA	0.12607	1	0.63136	1	0.036005	1	0.83662	1	0.11489	1	0.021851	1	0.10211	1	0.061784	1	0.45276	1	0.073506	1
16q loss	14 (3%)	490	NA	NA	NA	NA	0.0048311	1	0.34392	1	0.05764	1	0.59467	1	0.1486	1	0.0037119	1	0.11522	1	0.014415	1	0.50361	1	0.15481	1
17p loss	46 (9%)	458	0.00013537	0.096	0.00027063	0.189	8.3574e-09	6.84e-06	0.13987	1	0.0051073	1	0.0016327	1	2.0815e-07	0.000165	1.0012e-07	8.05e-05	1.5457e-08	1.26e-05	6.2246e-08	5.02e-05	0.056609	1	0.30662	1
17q loss	28 (6%)	476	0.00061803	0.413	0.00091193	0.595	2.9509e-06	0.00226	0.58508	1	0.15674	1	0.023748	1	8.5827e-05	0.0613	3.1124e-05	0.0228	6.3419e-06	0.00481	4.6254e-07	0.000364	0.11698	1	0.33473	1
18p loss	91 (18%)	413	0.057359	1	0.13502	1	2.15e-13	1.85e-10	2.6816e-07	0.000212	3.0725e-08	2.49e-05	0.0018299	1	8.1767e-18	7.15e-15	4.86e-16	4.23e-13	7.1182e-11	5.97e-08	6.24e-07	0.000489	1.0109e-07	8.12e-05	7.9631e-05	0.0569
18q loss	93 (18%)	411	0.046805	1	0.064915	1	3.8083e-13	3.26e-10	1.9663e-06	0.00152	1.9858e-07	0.000158	0.0067011	1	7.3368e-17	6.4e-14	7.8624e-16	6.84e-13	2.104e-10	1.75e-07	3.5106e-07	0.000276	3.0366e-08	2.47e-05	9.2777e-06	0.007
19p loss	11 (2%)	493	NA	NA	NA	NA	0.00061479	0.412	0.060367	1	0.00058958	0.397	0.00078757	0.519	0.18842	1	0.02217	1	0.23727	1	0.43644	1	0.16181	1	0.10982	1
19q loss	4 (1%)	500	NA	NA	NA	NA	0.016143	1	NA	NA	0.88973	1	0.16833	1	0.43575	1	0.39309	1	0.82613	1	1	1	NA	NA	NA	NA
20p loss	8 (2%)	496	NA	NA	NA	NA	0.34247	1	1	1	0.058197	1	1	1	0.10635	1	0.10503	1	0.011089	1	0.075981	1	NA	NA	NA	NA
20q loss	3 (1%)	501	NA	NA	NA	NA	0.34001	1	NA	NA	NA	NA	NA	NA	0.16616	1	0.13396	1	0.052701	1	0.053466	1	NA	NA	NA	NA
21q loss	55 (11%)	449	0.026008	1	0.030636	1	2.1484e-07	0.00017	0.024137	1	0.027744	1	0.0078775	1	0.0063275	1	0.00041566	0.285	0.024907	1	3.264e-05	0.0239	0.15553	1	0.05749	1
22q loss	39 (8%)	465	0.010053	1	0.015526	1	1.4934e-08	1.22e-05	0.0069517	1	0.0042271	1	0.035821	1	2.1663e-06	0.00167	1.057e-05	0.00795	1.9109e-05	0.0142	0.045024	1	0.030723	1	0.18494	1
xq loss	48 (10%)	456	0.071856	1	0.033098	1	0.000204	0.143	0.026585	1	0.19482	1	0.0076257	1	0.065449	1	0.0047694	1	0.086249	1	6.5192e-05	0.0469	0.018898	1	0.01425	1
