		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	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	133 (27%)	360	0.38828	1	1	1	1.2579e-08	1.16e-05	0.31235	1	0.072931	1	0.0045887	1	0.11665	1	0.0025921	1	0.07297	1	0.98713	1	0.31268	1	0.65376	1
1q gain	297 (60%)	196	0.12081	1	1	1	0.0016886	1	0.0012471	0.897	0.00075568	0.56	0.020816	1	0.1276	1	0.91788	1	0.51805	1	0.14539	1	0.014861	1	0.12551	1
2p gain	148 (30%)	345	0.30129	1	0.11932	1	3.8613e-08	3.53e-05	0.00061413	0.46	0.44423	1	0.35765	1	8.9162e-05	0.0709	5.1814e-06	0.0045	1.1006e-06	0.000974	7.3597e-06	0.00634	0.0020359	1	6.1237e-05	0.0493
2q gain	135 (27%)	358	0.12584	1	0.30226	1	7.8906e-06	0.00678	0.0012956	0.926	0.6937	1	0.74854	1	0.076497	1	0.00098685	0.72	0.0017828	1	0.0014724	1	0.028117	1	0.00059742	0.448
3p gain	40 (8%)	453	NA	NA	NA	NA	0.0035995	1	0.013725	1	0.10825	1	0.13748	1	0.00040292	0.307	0.0011224	0.813	0.063049	1	0.18115	1	0.16326	1	0.056428	1
3q gain	86 (17%)	407	0.079672	1	0.14032	1	0.0014221	1	0.14585	1	0.026508	1	0.10576	1	3.113e-05	0.0254	1.5186e-05	0.0128	0.015583	1	0.032266	1	0.0094912	1	0.023323	1
4p gain	80 (16%)	413	0.87647	1	0.86914	1	1.2353e-05	0.0105	0.035007	1	0.3008	1	0.090841	1	0.044606	1	0.014789	1	0.087957	1	0.17303	1	0.43443	1	0.28376	1
4q gain	46 (9%)	447	0.32875	1	0.50473	1	0.010757	1	0.901	1	0.39863	1	0.39211	1	0.004419	1	0.028401	1	0.01658	1	0.23748	1	0.15973	1	0.28871	1
5p gain	267 (54%)	226	0.79801	1	0.58978	1	6.7508e-11	6.31e-08	0.77708	1	0.16035	1	0.57063	1	0.02361	1	0.032184	1	0.044599	1	0.11591	1	0.091127	1	0.037499	1
5q gain	124 (25%)	369	0.19462	1	0.45314	1	0.005579	1	0.54938	1	0.028253	1	0.36491	1	0.0058512	1	0.07743	1	0.14585	1	0.013453	1	0.036217	1	0.059195	1
6p gain	141 (29%)	352	0.35354	1	0.064478	1	1.595e-05	0.0134	1.9411e-06	0.00171	0.029593	1	0.74151	1	0.096529	1	0.57799	1	0.026705	1	0.0080089	1	0.066679	1	0.0023723	1
6q gain	60 (12%)	433	1	1	1	1	0.0131	1	0.0067896	1	0.16448	1	0.94356	1	0.20116	1	0.13668	1	0.0020307	1	0.00010518	0.0831	0.28196	1	0.0019122	1
7p gain	251 (51%)	242	0.85612	1	0.53529	1	1.3376e-20	1.27e-17	0.0027245	1	0.00044276	0.336	0.00054246	0.408	2.7835e-11	2.61e-08	1.0065e-11	9.45e-09	4.2318e-06	0.00369	0.00090763	0.666	0.00031979	0.247	1.6595e-05	0.0139
7q gain	207 (42%)	286	0.48233	1	0.38782	1	9.7223e-11	9.07e-08	0.034878	1	0.13273	1	0.22115	1	5.6994e-09	5.27e-06	1.213e-08	1.12e-05	0.0026025	1	0.0037147	1	0.011738	1	0.001582	1
8p gain	123 (25%)	370	0.15102	1	0.17643	1	2.147e-10	2e-07	0.053278	1	0.43602	1	0.37614	1	0.0012639	0.906	0.0067352	1	0.45508	1	0.34982	1	0.84189	1	0.7841	1
8q gain	235 (48%)	258	0.02399	1	0.024375	1	2.345e-20	2.22e-17	1.3444e-05	0.0114	0.28673	1	0.039596	1	9.1815e-08	8.35e-05	1.9298e-05	0.016	4.2379e-06	0.00369	2.4055e-05	0.0199	0.00019919	0.155	1.1273e-05	0.00962
9p gain	42 (9%)	451	NA	NA	NA	NA	0.014333	1	0.10356	1	0.44902	1	0.45008	1	0.00099809	0.727	0.61919	1	0.2048	1	0.64811	1	0.20368	1	0.21081	1
9q gain	30 (6%)	463	NA	NA	NA	NA	0.25167	1	0.29705	1	0.57222	1	0.56582	1	0.078286	1	0.78197	1	0.49389	1	0.72392	1	0.44245	1	0.25491	1
10p gain	105 (21%)	388	0.23589	1	0.30806	1	0.00064123	0.478	1.2604e-05	0.0107	0.018019	1	0.0040528	1	7.6406e-05	0.0611	1.5164e-05	0.0128	0.0091341	1	0.0012984	0.927	0.038411	1	0.0043897	1
10q gain	76 (15%)	417	NA	NA	NA	NA	0.0378	1	0.0014852	1	0.2861	1	0.090161	1	0.00033408	0.257	0.016906	1	0.37155	1	0.082705	1	0.21351	1	0.67941	1
11p gain	92 (19%)	401	0.0095212	1	0.0090621	1	1.6156e-05	0.0136	0.60694	1	0.54505	1	0.46763	1	0.1883	1	0.01606	1	0.00044079	0.335	0.00053334	0.403	0.00052283	0.395	0.0010865	0.789
11q gain	112 (23%)	381	0.010002	1	0.019998	1	2.8012e-08	2.57e-05	0.074216	1	0.2609	1	0.34316	1	0.0041166	1	0.00019397	0.151	5.1516e-05	0.0416	8.6648e-05	0.0691	0.00031716	0.245	0.0036997	1
12p gain	131 (27%)	362	0.2214	1	0.050147	1	1.0561e-06	0.000936	0.050933	1	0.016594	1	0.020457	1	4.4628e-09	4.13e-06	4.3027e-11	4.02e-08	1.4617e-05	0.0124	1.8075e-05	0.0151	6.6171e-08	6.03e-05	4.9046e-08	4.48e-05
12q gain	126 (26%)	367	0.2214	1	0.10317	1	3.785e-08	3.47e-05	0.016832	1	0.17028	1	0.039899	1	1.1421e-11	1.07e-08	5.738e-12	5.39e-09	1.1859e-05	0.0101	3.1257e-06	0.00273	2.2222e-07	0.000201	6.1889e-07	0.000554
13q gain	43 (9%)	450	0.41448	1	0.46587	1	0.7361	1	0.0025772	1	0.048625	1	0.057722	1	0.051311	1	0.085429	1	0.97757	1	0.86592	1	0.81049	1	0.80546	1
14q gain	120 (24%)	373	0.80335	1	0.72164	1	9.1143e-09	8.4e-06	0.015628	1	0.22937	1	0.12677	1	7.4264e-05	0.0595	0.0035596	1	3.1973e-05	0.0261	2.6652e-05	0.0219	0.00078041	0.577	0.01473	1
15q gain	35 (7%)	458	0.19234	1	0.15726	1	0.38441	1	0.34265	1	0.56058	1	0.32554	1	6.8412e-09	6.31e-06	0.00051264	0.388	0.7727	1	0.80572	1	0.19401	1	0.69094	1
16p gain	127 (26%)	366	0.5324	1	0.23461	1	0.0031238	1	1	1	0.29765	1	0.14996	1	0.178	1	0.18925	1	0.0099595	1	0.0086846	1	0.048869	1	0.44354	1
16q gain	94 (19%)	399	0.43694	1	0.27001	1	0.0025571	1	0.93901	1	0.069268	1	0.072901	1	0.42644	1	0.7834	1	0.0019804	1	0.002143	1	0.020928	1	0.77492	1
17p gain	83 (17%)	410	0.45264	1	0.41099	1	6.1676e-05	0.0496	0.091083	1	0.83068	1	0.081675	1	0.0099556	1	0.0028684	1	1.0453e-05	0.00893	0.0011128	0.807	0.22742	1	0.058805	1
17q gain	186 (38%)	307	0.30533	1	0.31155	1	1.725e-08	1.58e-05	0.00090892	0.666	0.62385	1	0.17191	1	4.2949e-05	0.0348	6.2002e-06	0.00536	8.9114e-06	0.00765	0.00036678	0.28	0.060584	1	0.00063731	0.475
18p gain	91 (18%)	402	0.87647	1	0.75137	1	3.3542e-05	0.0273	2.4025e-05	0.0199	0.2564	1	0.64993	1	0.020332	1	0.0046644	1	0.01514	1	0.00091953	0.673	0.0057136	1	2.6651e-05	0.0219
18q gain	66 (13%)	427	0.59513	1	0.14027	1	0.00013857	0.109	1.6119e-06	0.00142	0.021706	1	0.017199	1	1.8137e-05	0.0151	2.6035e-05	0.0214	0.010915	1	0.00079018	0.583	0.0026987	1	0.0017427	1
19p gain	32 (6%)	461	0.19234	1	0.051411	1	0.18757	1	0.31812	1	1	1	0.79069	1	0.98744	1	0.61657	1	0.4403	1	0.63046	1	0.021932	1	0.26552	1
19q gain	71 (14%)	422	0.050202	1	0.051411	1	0.0029619	1	0.0065941	1	0.94613	1	0.69482	1	0.16823	1	0.013761	1	0.38163	1	0.041014	1	0.072116	1	0.049883	1
20p gain	164 (33%)	329	0.081506	1	0.19076	1	6.6586e-05	0.0535	0.0064355	1	0.42121	1	0.26487	1	0.0002136	0.166	6.5561e-06	0.00566	2.8245e-05	0.0231	5.4035e-06	0.00468	0.00018899	0.148	2.7744e-05	0.0227
20q gain	189 (38%)	304	0.010002	1	0.023852	1	1.6435e-07	0.000149	0.0011383	0.822	0.22791	1	0.031396	1	4.4717e-06	0.00389	3.338e-07	3e-04	2.0395e-06	0.00179	6.8503e-07	0.000612	1.774e-05	0.0148	1.6931e-05	0.0141
21q gain	94 (19%)	399	0.53812	1	0.46587	1	5.7793e-05	0.0466	0.98376	1	0.33142	1	0.063761	1	0.027585	1	0.12962	1	0.33538	1	0.65706	1	0.63948	1	0.73441	1
22q gain	61 (12%)	432	0.1081	1	0.13192	1	0.003481	1	0.78453	1	0.21538	1	0.19105	1	0.16304	1	0.054617	1	0.60015	1	0.75774	1	0.46237	1	0.50862	1
xq gain	68 (14%)	425	0.65837	1	0.50473	1	0.00070957	0.526	0.26001	1	0.27352	1	0.1163	1	0.034592	1	0.33634	1	0.11352	1	0.31758	1	0.22139	1	0.47405	1
1p loss	79 (16%)	414	0.079672	1	0.14032	1	1.8837e-05	0.0157	0.00013787	0.109	0.90819	1	0.1083	1	9.6613e-05	0.0766	0.0010216	0.743	0.52071	1	0.049142	1	0.45555	1	0.2244	1
1q loss	28 (6%)	465	NA	NA	NA	NA	0.17933	1	0.0039475	1	0.17896	1	0.46293	1	0.069639	1	0.012124	1	0.6939	1	0.36266	1	0.29406	1	0.076264	1
2p loss	24 (5%)	469	0.7496	1	0.59113	1	0.12289	1	0.1903	1	0.61117	1	1	1	0.97778	1	0.77128	1	0.086451	1	0.1329	1	0.068615	1	0.49061	1
2q loss	23 (5%)	470	NA	NA	NA	NA	0.0016673	1	0.0038802	1	0.42571	1	1	1	0.26843	1	0.47517	1	0.31982	1	0.14439	1	0.45315	1	0.25988	1
3p loss	205 (42%)	288	0.34278	1	0.11718	1	2.0211e-05	0.0167	4.8123e-06	0.00418	0.2533	1	0.32289	1	0.031085	1	5.3118e-06	0.00461	0.021911	1	0.35048	1	0.12295	1	0.10953	1
3q loss	140 (28%)	353	0.55213	1	0.19076	1	0.014647	1	0.00054581	0.41	0.916	1	0.84465	1	0.064673	1	0.16789	1	0.67359	1	0.92287	1	0.84465	1	0.64735	1
4p loss	116 (24%)	377	0.18625	1	0.14514	1	4.4452e-05	0.036	0.2122	1	0.19513	1	0.21827	1	8.7611e-05	0.0697	8.2264e-08	7.49e-05	7.7068e-06	0.00663	3.5467e-06	0.0031	0.0059345	1	0.00035643	0.273
4q loss	132 (27%)	361	0.00042963	0.327	0.00081068	0.597	2.35e-06	0.00206	0.0033578	1	0.27835	1	0.047574	1	9.3867e-08	8.52e-05	7.5433e-13	7.1e-10	1.7738e-06	0.00156	2.3122e-07	0.000209	0.00028652	0.222	0.00028897	0.223
5p loss	40 (8%)	453	0.59513	1	0.45337	1	0.67557	1	0.018172	1	0.38815	1	0.28743	1	0.028894	1	2.9091e-05	0.0238	0.071112	1	0.064116	1	0.016922	1	0.0011244	0.813
5q loss	137 (28%)	356	0.064056	1	0.041059	1	2.4899e-09	2.31e-06	0.00064361	0.479	0.0011653	0.84	0.0055446	1	1.5522e-06	0.00137	1.4381e-08	1.32e-05	9.3854e-07	0.000832	2.6517e-06	0.00232	6.9646e-06	0.006	4.6042e-07	0.000413
6p loss	101 (20%)	392	0.012603	1	0.0083823	1	0.053831	1	0.3878	1	0.52836	1	0.57995	1	0.18686	1	0.29173	1	0.53787	1	0.25161	1	0.50602	1	0.40281	1
6q loss	208 (42%)	285	0.24676	1	0.3205	1	0.029877	1	8.9567e-05	0.0711	0.81299	1	0.53771	1	0.080879	1	0.089927	1	0.33754	1	0.042303	1	0.72592	1	0.1011	1
7p loss	33 (7%)	460	1	1	1	1	1.6088e-05	0.0135	0.03668	1	0.32995	1	0.71286	1	0.0052914	1	0.018353	1	0.27905	1	0.3657	1	0.86743	1	0.22977	1
7q loss	39 (8%)	454	0.80335	1	0.17643	1	0.0070837	1	0.29078	1	0.91036	1	0.46293	1	0.085857	1	0.29129	1	0.35536	1	0.34922	1	0.26922	1	0.4598	1
8p loss	191 (39%)	302	0.13237	1	0.028494	1	8.7346e-19	8.25e-16	0.24061	1	0.049567	1	0.0099482	1	0.00010063	0.0797	3.935e-05	0.0319	0.0025819	1	0.032556	1	0.0056586	1	0.0013984	0.994
8q loss	54 (11%)	439	NA	NA	NA	NA	0.00027764	0.215	0.53005	1	0.29344	1	0.375	1	0.15332	1	0.13289	1	0.21262	1	0.73896	1	0.41198	1	0.65109	1
9p loss	254 (52%)	239	0.051609	1	0.46519	1	0.0018175	1	0.041059	1	0.21517	1	0.063753	1	0.0012186	0.877	0.00015351	0.121	0.062769	1	0.063191	1	0.35211	1	0.088901	1
9q loss	238 (48%)	255	0.49923	1	1	1	2.4034e-05	0.0199	0.0036064	1	0.41765	1	0.029011	1	0.13892	1	9.2855e-06	0.00795	0.0064196	1	0.0025025	1	0.025852	1	0.00017277	0.135
10p loss	108 (22%)	385	0.81611	1	0.41625	1	7.1269e-07	0.000636	0.18443	1	0.039387	1	0.012315	1	7.2867e-05	0.0584	0.026863	1	0.0037635	1	0.050776	1	0.001876	1	0.035867	1
10q loss	128 (26%)	365	0.81611	1	0.41625	1	1.947e-05	0.0161	0.064231	1	0.054274	1	0.013063	1	0.0013508	0.962	0.066205	1	0.00521	1	0.0068298	1	0.0012901	0.924	0.00085233	0.626
11p loss	108 (22%)	385	0.14383	1	0.07995	1	7.9314e-05	0.0633	0.01472	1	0.035575	1	0.28276	1	0.0038343	1	1.6406e-05	0.0137	0.026522	1	0.015778	1	0.026955	1	0.019687	1
11q loss	88 (18%)	405	0.84072	1	0.41099	1	0.0069997	1	0.010757	1	0.0035906	1	0.51337	1	0.0014558	1	0.00037776	0.288	0.055931	1	0.026001	1	0.028509	1	0.027321	1
12p loss	106 (22%)	387	0.62977	1	0.76969	1	0.0057341	1	0.35686	1	0.047271	1	0.098243	1	0.0065035	1	0.057611	1	0.26444	1	0.32933	1	0.60679	1	0.52143	1
12q loss	93 (19%)	400	0.55363	1	0.41815	1	1.5165e-05	0.0128	0.081696	1	0.094653	1	0.017535	1	0.0012567	0.902	0.010518	1	0.20228	1	0.10736	1	0.55538	1	0.36132	1
13q loss	243 (49%)	250	0.10512	1	0.26812	1	2.6211e-17	2.47e-14	0.15654	1	0.00053754	0.405	2.7859e-06	0.00244	3.087e-07	0.000278	5.4292e-06	0.0047	0.013662	1	0.010265	1	0.04279	1	0.16224	1
14q loss	111 (23%)	382	0.92941	1	0.46587	1	0.060991	1	0.36255	1	0.17079	1	0.060193	1	0.021678	1	0.0016216	1	0.074004	1	0.034501	1	0.00075552	0.56	0.036069	1
15q loss	233 (47%)	260	0.10108	1	0.17632	1	7.262e-07	0.000646	0.020114	1	0.12744	1	0.073543	1	5.61e-13	5.28e-10	1.4917e-06	0.00132	1.59e-05	0.0134	0.0019864	1	0.017719	1	0.0029467	1
16p loss	108 (22%)	385	0.45264	1	0.41099	1	9.3253e-06	0.00797	0.00055809	0.419	0.23169	1	0.51745	1	4.7142e-05	0.0381	1.4236e-05	0.0121	0.008445	1	0.036404	1	0.0078309	1	0.0023967	1
16q loss	137 (28%)	356	0.55081	1	0.70728	1	9.1431e-06	0.00784	0.00032059	0.247	0.073755	1	0.21883	1	1.6908e-07	0.000153	3.5316e-07	0.000317	0.0066681	1	0.03131	1	0.0013291	0.948	3.359e-05	0.0273
17p loss	206 (42%)	287	0.54898	1	0.58978	1	2.1682e-11	2.03e-08	0.00012973	0.102	0.13187	1	0.0062744	1	0.00094178	0.688	0.00062505	0.468	0.50024	1	0.47772	1	0.6056	1	0.30282	1
17q loss	55 (11%)	438	0.29434	1	0.54617	1	0.00011393	0.0899	0.048648	1	0.010862	1	0.0076213	1	0.12856	1	0.12326	1	0.42172	1	0.16031	1	0.08217	1	0.78215	1
18p loss	169 (34%)	324	0.43788	1	0.63133	1	1.3149e-05	0.0112	0.75048	1	0.037091	1	0.0021054	1	0.022038	1	0.0046717	1	0.02878	1	0.69363	1	0.14442	1	0.78986	1
18q loss	207 (42%)	286	0.51884	1	0.66816	1	3.7566e-10	3.49e-07	0.81938	1	0.0035651	1	0.00026862	0.209	0.00027743	0.215	0.0059768	1	0.025314	1	1	1	0.68737	1	0.77157	1
19p loss	235 (48%)	258	0.81493	1	1	1	5.3393e-08	4.87e-05	1.1983e-10	1.12e-07	0.33549	1	0.52185	1	7.1457e-07	0.000637	2.3499e-07	0.000212	2.495e-05	0.0206	3.1832e-07	0.000286	0.006204	1	1.6259e-05	0.0136
19q loss	153 (31%)	340	0.34392	1	0.47514	1	1.4712e-07	0.000133	8.178e-07	0.000727	0.27163	1	0.22028	1	0.00010314	0.0816	0.00017676	0.138	0.00067685	0.503	7.7953e-05	0.0623	0.026017	1	0.00035903	0.275
20p loss	114 (23%)	379	0.33286	1	0.63133	1	0.00036005	0.275	0.0038422	1	0.0006309	0.471	0.0027194	1	0.015964	1	0.049365	1	0.96519	1	0.94962	1	0.12634	1	0.83895	1
20q loss	67 (14%)	426	0.51331	1	0.88223	1	0.40782	1	0.61378	1	0.2619	1	0.89363	1	0.62471	1	0.97944	1	0.59942	1	0.89639	1	0.13177	1	0.93289	1
21q loss	157 (32%)	336	0.18356	1	0.19076	1	7.21e-07	0.000642	0.041512	1	0.031546	1	0.0031638	1	2.2562e-10	2.1e-07	5.8582e-09	5.41e-06	0.00042468	0.323	1.3727e-06	0.00121	0.0069757	1	0.00099566	0.726
22q loss	212 (43%)	281	0.12589	1	0.11814	1	1.0621e-09	9.86e-07	2.7959e-05	0.0229	0.79781	1	0.068814	1	8.9791e-08	8.17e-05	5.3763e-07	0.000482	0.00020464	0.159	9.0383e-07	0.000803	0.00033726	0.259	3.3522e-05	0.0273
xq loss	64 (13%)	429	0.27619	1	0.039801	1	0.00082434	0.607	0.0029389	1	0.45527	1	0.36311	1	0.43996	1	0.22149	1	0.34593	1	0.25154	1	0.50623	1	0.33836	1
