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	12 (7%)	153	0.51082	1	0.9408	1	0.82815	1	0.52839	1	0.03175	1	0.01758	1	0.21946	1	0.76757	1	0.93975	1	0.45989	1	0.86788	1	0.65062	1
1q gain	34 (21%)	131	0.58587	1	0.65435	1	0.13781	1	0.31431	1	0.070449	1	0.21104	1	0.54124	1	0.946	1	0.54193	1	0.8814	1	0.87057	1	0.36833	1
2p gain	41 (25%)	124	0.50861	1	0.01938	1	0.2593	1	0.02553	1	0.6669	1	0.64224	1	0.04602	1	0.03941	1	0.18771	1	0.077319	1	0.72431	1	0.50271	1
2q gain	43 (26%)	122	0.091989	1	0.056999	1	0.1216	1	0.059869	1	0.71958	1	0.82777	1	0.082279	1	0.0093299	1	0.2148	1	0.30397	1	0.16151	1	0.19163	1
3p gain	27 (16%)	138	1	1	0.90216	1	0.00048	0.428	0.65449	1	0.087359	1	0.45359	1	0.4258	1	0.62115	1	0.37752	1	0.36124	1	0.65648	1	0.82541	1
3q gain	34 (21%)	131	0.60559	1	0.61394	1	0.00018	0.161	0.86824	1	0.25023	1	0.41974	1	0.41627	1	0.22443	1	0.21876	1	0.31668	1	0.65826	1	0.89588	1
4p gain	9 (5%)	156	1	1	0.79119	1	0.96545	1	0.76563	1	0.086619	1	0.17125	1	0.35549	1	0.43654	1	0.22093	1	0.37609	1	0.74242	1	0.95	1
4q gain	5 (3%)	160	0.29684	1	0.64939	1	0.67674	1	NA	NA	0.21808	1	0.48616	1	0.55441	1	1	1	0.89043	1	1	1	NA	NA	NA	NA
5p gain	36 (22%)	129	0.20066	1	0.099019	1	0.00164	1	0.099249	1	0.21628	1	0.68595	1	0.04501	1	0.00377	1	0.19244	1	0.92355	1	0.49324	1	0.62916	1
5q gain	24 (15%)	141	0.24346	1	0.086929	1	0.0067499	1	0.074169	1	0.18543	1	0.96075	1	0.51038	1	0.16397	1	0.24608	1	0.5217	1	1	1	0.65377	1
6p gain	41 (25%)	124	0.33639	1	0.56301	1	0.0088999	1	0.00351	1	0.77377	1	0.25391	1	0.61582	1	0.59353	1	0.23956	1	0.29972	1	0.279	1	0.81109	1
6q gain	36 (22%)	129	0.67086	1	0.22882	1	0.01664	1	0.0065499	1	0.84383	1	0.47159	1	0.66325	1	0.33008	1	0.34101	1	0.58143	1	0.20199	1	0.5625	1
7p gain	102 (62%)	63	0.00235	1	0.00294	1	9.9999e-06	0.00899	0.00335	1	0.48389	1	0.37731	1	0.0199	1	0.00022	0.196	0.04044	1	0.096609	1	0.59712	1	0.81232	1
7q gain	85 (52%)	80	0.04726	1	0.0076099	1	2e-05	0.0179	0.13641	1	0.6184	1	0.94815	1	0.04276	1	0.00285	1	0.49923	1	0.82901	1	0.85675	1	0.85392	1
8p gain	42 (25%)	123	0.41851	1	0.2352	1	0.00179	1	0.51602	1	0.45416	1	0.091199	1	0.15375	1	0.33326	1	0.81207	1	0.28699	1	0.91613	1	0.14192	1
8q gain	89 (54%)	76	0.03651	1	0.27464	1	2e-05	0.0179	0.20964	1	0.5462	1	0.78883	1	0.56985	1	0.13102	1	0.24273	1	0.065489	1	0.02059	1	0.37408	1
9p gain	42 (25%)	123	0.01669	1	0.19891	1	0.441	1	0.16615	1	0.65081	1	0.22949	1	0.02233	1	0.99444	1	0.27421	1	0.3282	1	0.86496	1	0.86827	1
9q gain	33 (20%)	132	0.01535	1	0.20999	1	0.28152	1	0.46788	1	0.56382	1	0.098739	1	0.2425	1	0.16175	1	0.7855	1	0.62185	1	0.83068	1	0.93127	1
10p gain	13 (8%)	152	1	1	0.91859	1	0.33924	1	0.71172	1	0.66612	1	0.7505	1	0.088019	1	0.04164	1	0.65366	1	0.91819	1	0.61277	1	0.7893	1
10q gain	7 (4%)	158	0.51866	1	0.081509	1	0.25615	1	1	1	1	1	0.87082	1	0.4109	1	0.083319	1	0.76962	1	0.86192	1	NA	NA	NA	NA
11p gain	32 (19%)	133	0.13484	1	0.39007	1	0.0089599	1	0.41951	1	0.72133	1	0.36072	1	0.24077	1	0.04063	1	0.02043	1	0.20637	1	0.65254	1	0.5375	1
11q gain	26 (16%)	139	0.23812	1	0.43095	1	0.00209	1	0.01905	1	0.57145	1	0.30237	1	0.050049	1	0.00115	1	0.02581	1	0.59069	1	0.11954	1	0.15706	1
12p gain	33 (20%)	132	0.69081	1	0.4815	1	0.23652	1	0.72796	1	0.17979	1	0.12344	1	0.2317	1	0.32489	1	0.37232	1	0.55232	1	0.28282	1	0.87165	1
12q gain	24 (15%)	141	0.77537	1	0.52301	1	0.74258	1	0.30652	1	0.26298	1	0.21319	1	0.19569	1	0.81514	1	0.22418	1	0.73865	1	0.054089	1	0.94903	1
13q gain	113 (68%)	52	0.28423	1	0.38124	1	9.9999e-06	0.00899	0.071019	1	0.83781	1	0.31971	1	0.0044	1	0.02649	1	0.00315	1	0.065129	1	0.71267	1	0.47327	1
14q gain	8 (5%)	157	0.83282	1	0.91447	1	0.1122	1	0.22629	1	0.52009	1	0.54741	1	0.4118	1	0.40294	1	0.13046	1	0.86165	1	NA	NA	NA	NA
15q gain	3 (2%)	162	NA	NA	NA	NA	0.41806	1	0.48445	1	NA	NA	NA	NA	0.34997	1	0.69496	1	NA	NA	NA	NA	NA	NA	NA	NA
16p gain	41 (25%)	124	0.14787	1	0.85337	1	0.00124	1	0.2717	1	0.92402	1	1	1	0.2514	1	0.32126	1	0.15218	1	0.67771	1	0.33824	1	0.98136	1
16q gain	41 (25%)	124	0.051089	1	0.59226	1	3e-05	0.0268	0.23315	1	1	1	0.66711	1	0.03016	1	0.04376	1	0.02114	1	0.24388	1	0.2301	1	0.91654	1
17p gain	8 (5%)	157	0.1096	1	0.37844	1	0.23343	1	0.46625	1	1	1	0.87263	1	0.1456	1	0.55764	1	0.48956	1	0.44033	1	NA	NA	NA	NA
17q gain	32 (19%)	133	0.19843	1	0.94268	1	0.0064999	1	0.41911	1	0.87997	1	0.94097	1	0.41759	1	0.37188	1	0.055159	1	0.46267	1	0.12046	1	0.63716	1
18p gain	8 (5%)	157	0.51459	1	0.38968	1	0.21816	1	0.72972	1	0.80605	1	0.73645	1	0.88476	1	0.9248	1	0.50682	1	0.55943	1	1	1	0.89086	1
18q gain	6 (4%)	159	NA	NA	NA	NA	0.79135	1	0.38192	1	0.49199	1	0.89236	1	0.45784	1	0.89136	1	0.65453	1	0.62973	1	1	1	0.89093	1
19p gain	33 (20%)	132	0.066109	1	0.4185	1	0.10497	1	0.76629	1	0.54398	1	0.46066	1	0.57229	1	0.63697	1	0.1399	1	0.95694	1	1	1	0.97367	1
19q gain	32 (19%)	133	0.082389	1	0.53218	1	0.073009	1	0.53038	1	0.95808	1	0.59537	1	0.078439	1	0.35343	1	0.35584	1	0.5794	1	1	1	0.97294	1
20p gain	109 (66%)	56	0.095919	1	0.72646	1	0.13931	1	0.25358	1	0.13321	1	0.83348	1	0.20759	1	0.12975	1	0.097169	1	0.047	1	0.30652	1	0.075749	1
20q gain	145 (88%)	20	0.0078499	1	0.16215	1	0.00057999	0.516	0.23364	1	0.16076	1	0.33857	1	0.1233	1	0.01991	1	0.04429	1	0.3639	1	0.3613	1	1	1
21q gain	10 (6%)	155	0.53726	1	0.65621	1	0.63547	1	1	1	0.61899	1	0.79249	1	0.88591	1	0.73689	1	0.29062	1	0.72475	1	NA	NA	NA	NA
22q gain	9 (5%)	156	0.72971	1	0.061389	1	0.072879	1	1	1	0.42642	1	0.23407	1	0.47995	1	0.082799	1	1	1	1	1	NA	NA	NA	NA
xq gain	34 (21%)	131	0.1562	1	0.38197	1	0.04559	1	0.2927	1	0.81912	1	0.30183	1	0.16026	1	0.54761	1	0.98024	1	1	1	0.45945	1	0.2102	1
1p loss	46 (28%)	119	0.68986	1	0.02634	1	0.051979	1	0.1853	1	0.93485	1	0.20603	1	0.80525	1	0.070969	1	0.44364	1	0.60894	1	0.55874	1	0.56835	1
1q loss	26 (16%)	139	0.91236	1	0.056279	1	0.26164	1	0.02843	1	0.84416	1	0.52773	1	0.89188	1	0.65133	1	0.56272	1	0.2277	1	0.50184	1	0.2739	1
2p loss	11 (7%)	154	0.64012	1	0.75123	1	0.00387	1	0.4845	1	0.90747	1	0.54207	1	0.1232	1	0.24054	1	0.43277	1	0.60432	1	NA	NA	NA	NA
2q loss	6 (4%)	159	1	1	0.56938	1	0.051859	1	NA	NA	0.10204	1	0.30701	1	0.20059	1	0.22495	1	0.20581	1	0.46829	1	NA	NA	NA	NA
3p loss	15 (9%)	150	1	1	0.36562	1	0.20597	1	0.77522	1	0.25877	1	0.89596	1	0.15851	1	0.53689	1	0.45356	1	0.13699	1	0.096869	1	0.04292	1
3q loss	10 (6%)	155	0.51646	1	0.79271	1	0.19645	1	0.41189	1	0.32512	1	0.6587	1	0.03805	1	0.28729	1	0.49328	1	0.0095599	1	0.4201	1	0.36797	1
4p loss	59 (36%)	106	0.66832	1	0.37334	1	0.00193	1	0.02755	1	0.96998	1	0.51326	1	0.5248	1	0.64669	1	0.97464	1	0.098649	1	0.22512	1	0.2074	1
4q loss	66 (40%)	99	0.78051	1	0.26934	1	0.00111	0.986	0.03965	1	0.81821	1	0.51806	1	0.7023	1	0.2665	1	0.81225	1	0.21716	1	0.56595	1	0.91939	1
5p loss	26 (16%)	139	0.23752	1	0.81627	1	0.13715	1	0.17798	1	0.52653	1	0.064749	1	0.69523	1	0.22767	1	0.72318	1	0.58014	1	0.16785	1	0.24561	1
5q loss	40 (24%)	125	0.090129	1	0.01132	1	0.21681	1	0.16655	1	1	1	0.54403	1	0.99326	1	0.20603	1	0.91201	1	0.21149	1	0.11193	1	0.22826	1
6p loss	13 (8%)	152	0.54271	1	0.92904	1	0.69905	1	0.12339	1	0.31241	1	0.36008	1	0.7246	1	0.24146	1	0.56132	1	0.25258	1	NA	NA	NA	NA
6q loss	22 (13%)	143	0.16942	1	0.64391	1	0.15305	1	0.41814	1	0.4507	1	0.60527	1	0.13432	1	0.0374	1	0.26335	1	0.4096	1	0.01217	1	0.55595	1
7q loss	3 (2%)	162	NA	NA	NA	NA	0.3567	1	NA	NA	0.78744	1	0.77291	1	0.599	1	1	1	0.85762	1	1	1	NA	NA	NA	NA
8p loss	73 (44%)	92	0.12209	1	0.24526	1	0.1337	1	0.96509	1	0.78596	1	0.25245	1	0.36792	1	0.29267	1	0.89314	1	0.97286	1	0.73438	1	0.2289	1
8q loss	11 (7%)	154	0.688	1	0.71454	1	0.40899	1	0.46493	1	0.79527	1	0.27939	1	0.18527	1	0.23731	1	0.86635	1	0.30169	1	0.16669	1	0.40672	1
9p loss	23 (14%)	142	0.63559	1	0.61749	1	0.32109	1	0.14049	1	0.74864	1	0.56695	1	0.82004	1	0.95538	1	0.31088	1	0.04618	1	0.70806	1	0.03844	1
9q loss	23 (14%)	142	0.20935	1	0.44719	1	0.28047	1	0.13782	1	0.94287	1	0.90387	1	0.98768	1	0.3817	1	0.069689	1	0.00165	1	0.46477	1	0.01417	1
10p loss	33 (20%)	132	0.14431	1	0.17289	1	0.1394	1	0.065829	1	0.14534	1	0.23928	1	0.87617	1	0.509	1	0.8384	1	0.11497	1	0.8168	1	0.74694	1
10q loss	38 (23%)	127	0.1766	1	0.15707	1	0.058369	1	0.091929	1	0.12929	1	0.03138	1	0.49512	1	0.16162	1	0.68319	1	0.087539	1	0.8986	1	0.53687	1
11p loss	23 (14%)	142	0.24129	1	0.37461	1	0.0062199	1	0.20579	1	0.22636	1	0.17499	1	0.46475	1	0.090649	1	0.97687	1	0.74236	1	0.60094	1	0.29038	1
11q loss	30 (18%)	135	0.054579	1	0.20514	1	0.0069399	1	0.02554	1	0.60477	1	0.38315	1	0.11018	1	0.0075899	1	0.20522	1	0.37545	1	0.41411	1	0.66526	1
12p loss	22 (13%)	143	0.42387	1	0.28471	1	0.65759	1	0.40111	1	0.69439	1	0.076989	1	0.92157	1	0.21705	1	0.45122	1	0.77803	1	0.067069	1	0.50854	1
12q loss	19 (12%)	146	0.50278	1	0.76937	1	0.23744	1	0.93196	1	0.55665	1	0.25963	1	0.82206	1	0.11209	1	0.37932	1	0.3194	1	0.27178	1	0.86664	1
13q loss	8 (5%)	157	0.51566	1	1	1	0.6536	1	0.10478	1	0.055119	1	0.43068	1	1	1	0.89019	1	0.17658	1	1	1	NA	NA	NA	NA
14q loss	67 (41%)	98	0.50176	1	0.24633	1	0.01978	1	0.57159	1	0.80508	1	0.49437	1	0.1073	1	0.16562	1	0.33244	1	0.20082	1	0.75178	1	0.78235	1
15q loss	73 (44%)	92	0.44691	1	0.11166	1	0.00068999	0.613	1	1	0.089759	1	0.24892	1	0.86626	1	0.50082	1	0.81779	1	0.63288	1	0.90687	1	0.74514	1
16p loss	9 (5%)	156	0.37696	1	0.7592	1	0.098149	1	0.061879	1	0.65335	1	0.63325	1	0.96455	1	0.96448	1	0.56046	1	1	1	0.25048	1	0.48908	1
16q loss	15 (9%)	150	0.27884	1	0.67695	1	0.04852	1	0.33396	1	0.72562	1	0.8991	1	0.8244	1	0.8995	1	0.86904	1	1	1	0.93916	1	0.96317	1
17p loss	107 (65%)	58	0.2066	1	0.37391	1	0.094149	1	0.19676	1	0.97078	1	0.32052	1	0.80049	1	0.96164	1	0.98102	1	0.39583	1	0.28973	1	0.66524	1
17q loss	26 (16%)	139	0.90437	1	0.73682	1	0.02837	1	0.089849	1	0.74853	1	0.97476	1	0.31547	1	0.62667	1	0.8703	1	0.94736	1	0.42421	1	0.47689	1
18p loss	128 (78%)	37	0.058649	1	0.70983	1	0.00135	1	0.02595	1	0.60083	1	0.15206	1	0.65664	1	0.23296	1	0.17024	1	0.16339	1	0.61489	1	0.59409	1
18q loss	138 (84%)	27	0.02041	1	0.17582	1	4e-05	0.0358	0.01237	1	0.79611	1	0.48588	1	0.88778	1	0.68037	1	0.42726	1	0.02732	1	0.51418	1	0.53542	1
19p loss	21 (13%)	144	0.7282	1	0.83475	1	0.13388	1	0.03055	1	0.64645	1	0.80559	1	0.38172	1	0.32993	1	0.37791	1	0.01877	1	0.9635	1	0.73991	1
19q loss	20 (12%)	145	0.8327	1	0.50331	1	0.069169	1	0.082569	1	0.82172	1	0.77656	1	0.43618	1	0.36562	1	0.067919	1	0.0086199	1	1	1	0.74534	1
20p loss	23 (14%)	142	1	1	0.95149	1	0.050759	1	0.28341	1	0.37775	1	0.98479	1	0.48491	1	0.29986	1	0.03207	1	0.02123	1	0.30567	1	0.01416	1
21q loss	68 (41%)	97	0.28788	1	0.24901	1	0.41655	1	1	1	0.97332	1	0.53031	1	0.58099	1	0.83344	1	0.0161	1	0.18341	1	0.22431	1	0.068599	1
22q loss	58 (35%)	107	0.85124	1	0.30862	1	0.064359	1	0.77635	1	0.75	1	0.29707	1	0.067709	1	0.093459	1	0.0063299	1	0.18104	1	0.125	1	0.01944	1
xq loss	25 (15%)	140	0.91128	1	0.58239	1	0.86652	1	0.31253	1	0.54795	1	0.87026	1	0.80726	1	0.97837	1	0.91666	1	0.49347	1	0.47441	1	0.80171	1