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	33 (7%)	417	0.81181	1	0.63447	1	0.02765	1	0.76352	1	0.01159	1	0.075489	1	0.14056	1	0.16061	1	0.6761	1	0.10186	1	0.30857	1	0.16235	1
1q gain	79 (18%)	371	0.54342	1	0.82825	1	0.01429	1	0.15447	1	0.24154	1	0.0074499	1	0.19122	1	0.50711	1	0.93878	1	0.1134	1	0.073139	1	0.48465	1
2p gain	82 (18%)	368	0.070399	1	0.02272	1	0.00048	0.377	0.0067999	1	0.10961	1	0.13188	1	0.0055799	1	0.00315	1	0.40661	1	0.01594	1	0.90082	1	0.80966	1
2q gain	78 (17%)	372	0.070389	1	0.02219	1	9.9999e-05	0.0817	0.00406	1	0.28766	1	0.14674	1	0.03663	1	0.00082999	0.641	0.49247	1	0.074719	1	1	1	0.56051	1
3p gain	46 (10%)	404	0.13682	1	0.0066199	1	3e-05	0.0248	0.25292	1	0.14659	1	0.12287	1	0.054299	1	0.12568	1	0.69023	1	0.84894	1	0.72277	1	0.39135	1
3q gain	66 (15%)	384	0.095699	1	0.00014	0.113	9.9999e-06	0.00914	0.050319	1	0.094949	1	0.28333	1	0.00069999	0.543	0.0061799	1	0.66997	1	0.63732	1	0.78851	1	0.057759	1
4p gain	12 (3%)	438	NA	NA	NA	NA	0.055949	1	0.1276	1	0.31463	1	0.92195	1	0.12543	1	0.2406	1	0.61069	1	0.57778	1	NA	NA	NA	NA
4q gain	17 (4%)	433	0.12702	1	0.12046	1	0.096049	1	0.79038	1	0.0067199	1	0.1193	1	0.24662	1	0.45096	1	0.14933	1	0.13581	1	NA	NA	NA	NA
5p gain	70 (16%)	380	0.41746	1	0.18116	1	0.065309	1	0.41256	1	0.46554	1	0.99725	1	0.87627	1	0.03512	1	0.8206	1	0.35729	1	0.72529	1	0.55755	1
5q gain	44 (10%)	406	0.87469	1	0.77576	1	0.01474	1	0.49303	1	0.47774	1	0.64538	1	0.21389	1	0.064699	1	0.50546	1	0.094089	1	1	1	0.85362	1
6p gain	84 (19%)	366	0.21255	1	2e-05	0.0167	9.9999e-06	0.00914	0.22753	1	0.56312	1	0.98926	1	0.01965	1	0.0059899	1	0.58947	1	0.97483	1	0.2656	1	0.16301	1
6q gain	76 (17%)	374	0.18406	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.32921	1	0.95641	1	0.51912	1	0.13283	1	0.16331	1	0.52674	1	0.95414	1	0.61104	1	0.1661	1
7p gain	246 (55%)	204	0.0055999	1	9.9999e-06	0.00914	9.9999e-06	0.00914	4e-04	0.316	0.00033	0.263	0.00213	1	2e-05	0.0167	9.9999e-06	0.00914	0.5364	1	0.47741	1	0.96009	1	0.01776	1
7q gain	224 (50%)	226	0.0038	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.0082699	1	0.0057999	1	0.0096999	1	2e-04	0.161	9.9999e-06	0.00914	0.41385	1	0.63952	1	0.8184	1	0.0096099	1
8p gain	132 (29%)	318	0.97433	1	0.96473	1	0.0069299	1	1	1	0.30329	1	0.38789	1	0.0094699	1	0.068849	1	0.57183	1	0.18305	1	0.8802	1	0.91776	1
8q gain	227 (50%)	223	0.88129	1	0.01962	1	9.9999e-06	0.00914	0.04315	1	0.074149	1	0.03556	1	0.00463	1	0.00065999	0.513	0.65472	1	0.01441	1	0.40684	1	0.074069	1
9p gain	81 (18%)	369	0.19285	1	0.13494	1	0.00080999	0.626	0.82236	1	0.00179	1	0.3823	1	0.55836	1	0.31573	1	0.87426	1	0.92382	1	0.071619	1	0.14441	1
9q gain	70 (16%)	380	0.16624	1	0.20401	1	0.02396	1	0.49688	1	0.00046	0.362	0.56947	1	0.87422	1	0.78411	1	0.42284	1	0.26398	1	0.30937	1	0.5358	1
10p gain	37 (8%)	413	0.59629	1	1	1	0.0062999	1	0.86476	1	0.02161	1	0.071639	1	0.50345	1	0.49025	1	0.4221	1	0.72158	1	0.93248	1	0.35423	1
10q gain	23 (5%)	427	0.16959	1	0.44147	1	0.051879	1	0.10583	1	0.36562	1	0.59063	1	1	1	0.99534	1	0.75278	1	0.86232	1	0.88852	1	0.24668	1
11p gain	54 (12%)	396	0.00077999	0.604	9.9999e-05	0.0817	9.9999e-06	0.00914	0.00031	0.247	0.093819	1	0.43251	1	0.00333	1	0.00014	0.113	0.81876	1	0.00425	1	0.92535	1	0.090569	1
11q gain	51 (11%)	399	2e-04	0.161	9.9999e-06	0.00914	9.9999e-06	0.00914	0.00211	1	0.02797	1	0.60487	1	3e-05	0.0248	2e-05	0.0167	0.62832	1	0.0061699	1	1	1	0.03477	1
12p gain	92 (20%)	358	0.17737	1	1	1	0.0058699	1	0.0067699	1	0.72436	1	0.76722	1	0.20514	1	0.29131	1	0.28043	1	0.41544	1	0.53327	1	0.93526	1
12q gain	86 (19%)	364	0.19712	1	0.89631	1	0.0052799	1	0.0051399	1	0.5456	1	0.79298	1	0.059159	1	0.36481	1	0.11236	1	0.10542	1	0.53148	1	0.65814	1
13q gain	256 (57%)	194	0.00012	0.0973	3e-05	0.0248	9.9999e-06	0.00914	0.00057999	0.452	0.03688	1	0.11859	1	2e-05	0.0167	9.9999e-06	0.00914	0.43975	1	0.79275	1	0.13779	1	0.16585	1
14q gain	35 (8%)	415	0.3428	1	0.63766	1	0.29112	1	0.9238	1	0.40374	1	0.75633	1	0.23805	1	0.37128	1	0.67007	1	0.18251	1	0.23798	1	0.33984	1
15q gain	12 (3%)	438	1	1	0.81212	1	0.34768	1	0.81386	1	0.081389	1	0.079059	1	0.87743	1	0.96343	1	0.92398	1	0.76917	1	NA	NA	NA	NA
16p gain	107 (24%)	343	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	0.16632	1	0.16045	1	0.10382	1	0.00258	1	9.9999e-06	0.00914	0.57279	1	0.18744	1	0.90428	1	0.139	1
16q gain	105 (23%)	345	4e-05	0.0329	9.9999e-06	0.00914	9.9999e-06	0.00914	0.25491	1	0.18309	1	0.1553	1	0.00268	1	9.9999e-06	0.00914	0.80179	1	0.1787	1	1	1	0.17664	1
17p gain	28 (6%)	422	0.84116	1	0.56315	1	0.80455	1	0.4483	1	0.21141	1	0.431	1	0.075329	1	0.059609	1	0.51791	1	0.82558	1	0.54791	1	0.46083	1
17q gain	82 (18%)	368	0.16574	1	0.04086	1	9.9999e-06	0.00914	0.00034	0.27	0.463	1	0.03018	1	9.9999e-06	0.00914	0.00048	0.377	0.0075299	1	0.096669	1	0.52083	1	0.69979	1
18p gain	22 (5%)	428	0.091999	1	0.67427	1	3e-05	0.0248	0.00095999	0.739	0.82828	1	0.8929	1	0.01605	1	9.9999e-06	0.00914	0.27049	1	0.17351	1	0.91114	1	0.48119	1
18q gain	13 (3%)	437	0.14483	1	1	1	0.00223	1	0.0077099	1	0.67622	1	0.47829	1	0.0055899	1	9.9999e-06	0.00914	0.55956	1	0.18402	1	0.44721	1	0.19479	1
19p gain	73 (16%)	377	0.14518	1	0.076679	1	5.9999e-05	0.0491	0.064149	1	0.25838	1	0.22572	1	0.10025	1	0.00099999	0.769	0.066599	1	0.32333	1	0.17914	1	0.01879	1
19q gain	82 (18%)	368	0.11136	1	0.055459	1	0.0069899	1	0.22002	1	0.04342	1	0.0406	1	0.14322	1	9.9999e-05	0.0817	0.14534	1	0.64475	1	0.04004	1	0.00056999	0.445
20p gain	243 (54%)	207	0.00309	1	2e-05	0.0167	9.9999e-06	0.00914	5e-04	0.391	0.04408	1	0.23559	1	3e-05	0.0248	9.9999e-06	0.00914	0.70218	1	0.069759	1	0.14966	1	0.2445	1
20q gain	321 (71%)	129	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	0.00034	0.27	0.00058999	0.459	9.9999e-06	0.00914	9.9999e-06	0.00914	0.79521	1	0.00125	0.955	0.8936	1	0.0065999	1
21q gain	24 (5%)	426	0.03512	1	0.29803	1	0.0079099	1	0.81202	1	0.73132	1	0.972	1	0.39103	1	0.24345	1	0.22045	1	0.26716	1	NA	NA	NA	NA
22q gain	12 (3%)	438	1	1	0.78819	1	0.050459	1	0.12814	1	0.60412	1	0.3219	1	0.28286	1	0.32941	1	1	1	0.68906	1	0.8285	1	0.48303	1
xq gain	74 (16%)	376	0.01408	1	0.26369	1	0.00205	1	0.16561	1	0.12985	1	0.50752	1	0.20767	1	0.83204	1	0.47703	1	0.94981	1	0.32462	1	0.26971	1
1p loss	98 (22%)	352	0.02622	1	0.17716	1	9.9999e-06	0.00914	0.00157	1	0.57942	1	0.77486	1	0.00122	0.933	2e-05	0.0167	0.77947	1	0.02201	1	0.9485	1	0.53669	1
1q loss	57 (13%)	393	0.27414	1	0.55971	1	0.00016	0.129	0.081709	1	0.44085	1	0.5615	1	0.02279	1	0.00297	1	0.662	1	0.00356	1	0.18756	1	0.84711	1
2p loss	6 (1%)	444	0.89752	1	0.8118	1	0.31137	1	NA	NA	0.70418	1	0.78687	1	0.086889	1	0.13144	1	0.6378	1	0.47783	1	NA	NA	NA	NA
2q loss	7 (2%)	443	1	1	0.50768	1	0.58972	1	NA	NA	0.31085	1	0.43738	1	0.03586	1	0.066469	1	0.38954	1	0.24391	1	NA	NA	NA	NA
3p loss	55 (12%)	395	0.78151	1	0.48654	1	0.03793	1	0.34934	1	0.60043	1	0.62587	1	0.25779	1	0.20627	1	0.61364	1	0.60484	1	0.30313	1	0.65444	1
3q loss	34 (8%)	416	0.82511	1	1	1	0.52482	1	0.75826	1	0.40928	1	0.87308	1	0.94862	1	0.14631	1	0.26259	1	0.93308	1	0.89659	1	0.12584	1
4p loss	138 (31%)	312	5e-05	0.0411	0.00142	1	9.9999e-06	0.00914	0.00015	0.121	0.10281	1	0.36167	1	9.9999e-05	0.0817	9.9999e-06	0.00914	0.46401	1	0.37901	1	0.060099	1	0.02405	1
4q loss	126 (28%)	324	0.00026	0.208	0.0091699	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.10538	1	0.25253	1	0.0027	1	9.9999e-06	0.00914	0.25861	1	0.24734	1	0.2508	1	0.20514	1
5p loss	56 (12%)	394	0.82302	1	0.94455	1	0.00038	0.301	0.00488	1	0.36466	1	0.74008	1	0.12788	1	0.01825	1	0.83376	1	0.73452	1	0.30375	1	0.39606	1
5q loss	77 (17%)	373	0.16489	1	0.30489	1	9.9999e-06	0.00914	0.01258	1	0.0233	1	0.14276	1	0.0056999	1	0.00144	1	0.90288	1	0.70113	1	0.75663	1	0.35129	1
6p loss	34 (8%)	416	1	1	0.4554	1	0.55694	1	0.36755	1	0.17426	1	0.14005	1	1	1	0.98331	1	0.61676	1	0.78644	1	0.02609	1	0.083269	1
6q loss	46 (10%)	404	0.8221	1	1	1	0.68626	1	0.42325	1	0.20092	1	0.097949	1	0.66457	1	0.62	1	0.60732	1	0.96342	1	0.059369	1	0.065909	1
7q loss	3 (1%)	447	NA	NA	NA	NA	0.12215	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
8p loss	142 (32%)	308	0.01489	1	0.00076999	0.597	9.9999e-06	0.00914	0.00042	0.331	0.01477	1	0.01165	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.6241	1	0.13322	1	0.81111	1	0.0209	1
8q loss	25 (6%)	425	0.80959	1	0.40064	1	0.005	1	0.19961	1	0.42766	1	0.6619	1	0.74394	1	0.073059	1	0.38783	1	0.74526	1	0.40508	1	0.00224	1
9p loss	54 (12%)	396	0.57345	1	0.065109	1	7.9999e-05	0.0654	0.0012	0.92	0.90673	1	0.36024	1	0.01188	1	0.00194	1	0.37259	1	0.27621	1	0.41243	1	0.31926	1
9q loss	54 (12%)	396	0.11924	1	0.061199	1	0.00011	0.0894	0.00013	0.105	0.97581	1	0.66329	1	0.00183	1	0.00421	1	0.44487	1	0.16326	1	0.22483	1	0.3702	1
10p loss	69 (15%)	381	0.02053	1	0.02433	1	9.9999e-06	0.00914	0.00126	0.961	0.01315	1	0.35095	1	0.0014	1	0.00011	0.0894	0.49917	1	0.23327	1	0.50237	1	0.093479	1
10q loss	73 (16%)	377	0.02477	1	0.04241	1	9.9999e-06	0.00914	0.00038	0.301	0.01174	1	0.17382	1	0.00151	1	9.9999e-06	0.00914	0.60981	1	0.3945	1	0.072119	1	0.45072	1
11p loss	51 (11%)	399	0.22314	1	0.19323	1	0.0033	1	0.0071799	1	0.80701	1	0.86913	1	0.21507	1	0.02163	1	0.9114	1	0.24191	1	0.63762	1	0.76895	1
11q loss	63 (14%)	387	0.04119	1	0.01556	1	0.00305	1	0.00119	0.914	0.60171	1	0.93005	1	0.29168	1	0.0057699	1	0.84135	1	0.68119	1	0.77731	1	0.83582	1
12p loss	47 (10%)	403	0.060749	1	0.0079399	1	9.9999e-06	0.00914	0.0062499	1	0.40996	1	0.8003	1	0.00093999	0.725	5e-05	0.0411	0.88018	1	0.41184	1	0.44173	1	0.02116	1
12q loss	49 (11%)	401	0.10892	1	0.0077599	1	9.9999e-06	0.00914	0.0069199	1	0.51931	1	0.6862	1	0.00021	0.168	0.00022	0.176	0.95437	1	0.68304	1	0.91557	1	0.02102	1
13q loss	12 (3%)	438	0.87355	1	0.43832	1	0.34543	1	0.04085	1	0.00155	1	0.091709	1	0.66507	1	0.59807	1	0.59543	1	0.10612	1	0.03555	1	0.80446	1
14q loss	139 (31%)	311	2e-05	0.0167	5e-05	0.0411	9.9999e-06	0.00914	9.9999e-06	0.00914	0.00192	1	0.02415	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.29569	1	0.02136	1	0.082479	1	0.0053299	1
15q loss	157 (35%)	293	0.00177	1	0.00154	1	9.9999e-06	0.00914	0.00038	0.301	0.0137	1	0.050149	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.90107	1	0.84058	1	0.14248	1	0.066739	1
16p loss	31 (7%)	419	0.40886	1	0.69017	1	0.5835	1	0.38622	1	0.38612	1	0.0126	1	0.02246	1	0.13906	1	0.50523	1	0.47916	1	0.62401	1	1	1
16q loss	29 (6%)	421	0.4064	1	0.68618	1	0.11275	1	0.57648	1	0.21776	1	0.03309	1	0.17697	1	0.29268	1	0.52425	1	0.7543	1	0.62371	1	1	1
17p loss	237 (53%)	213	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	0.01954	1	0.00395	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.79645	1	0.03759	1	0.60687	1	0.0012	0.92
17q loss	66 (15%)	384	0.076759	1	0.3778	1	2e-05	0.0167	0.0081299	1	0.45768	1	0.50946	1	0.057159	1	0.02928	1	0.36081	1	0.30377	1	0.70201	1	0.16405	1
18p loss	254 (56%)	196	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	0.0014	1	0.00374	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.99059	1	0.01902	1	0.46382	1	0.00043	0.338
18q loss	271 (60%)	179	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	9.9999e-06	0.00914	0.0058799	1	0.00324	1	9.9999e-06	0.00914	9.9999e-06	0.00914	0.74655	1	0.01256	1	0.25815	1	0.00048	0.377
19p loss	40 (9%)	410	1	1	0.34269	1	0.0075299	1	0.32275	1	0.57089	1	0.35437	1	0.04588	1	0.01315	1	0.04217	1	0.0050899	1	0.65066	1	0.62957	1
19q loss	36 (8%)	414	0.73423	1	0.70446	1	0.0098199	1	0.36868	1	0.23059	1	0.13153	1	0.10852	1	0.0064699	1	0.28661	1	0.065659	1	0.32124	1	0.4662	1
20p loss	44 (10%)	406	0.088929	1	0.0025	1	0.00022	0.176	0.092729	1	0.9084	1	0.25962	1	0.00254	1	0.01969	1	0.82823	1	0.04602	1	0.48378	1	0.62633	1
20q loss	4 (1%)	446	NA	NA	NA	NA	0.65005	1	NA	NA	NA	NA	NA	NA	0.55024	1	0.52539	1	0.38869	1	0.30388	1	NA	NA	NA	NA
21q loss	124 (28%)	326	0.01015	1	0.083579	1	9.9999e-06	0.00914	0.052759	1	0.22628	1	0.60007	1	0.0088599	1	0.0099699	1	0.4586	1	0.051219	1	0.81374	1	0.37912	1
22q loss	146 (32%)	304	0.00050999	0.398	0.00033	0.263	9.9999e-06	0.00914	0.00133	1	0.17495	1	0.30671	1	0.00031	0.247	9.9999e-06	0.00914	0.18549	1	0.40194	1	0.61371	1	0.44861	1
xq loss	54 (12%)	396	0.01623	1	0.2506	1	0.00017	0.137	0.16201	1	0.24568	1	0.37377	1	0.1371	1	0.23987	1	0.069979	1	0.6607	1	0.48379	1	0.068169	1