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	89 (18%)	412	0.13293	1	0.15415	1	0.74475	1	0.43736	1	0.48769	1	0.91612	1	0.79945	1	0.43456	1	0.3504	1	0.74649	1	0.3526	1	0.32427	1
1q gain	203 (41%)	298	0.68116	1	0.5503	1	9.9999e-06	0.0096	0.00017	0.146	0.4914	1	0.45614	1	0.00364	1	0.00067999	0.553	0.0011	0.879	0.00404	1	0.04244	1	0.03911	1
2p gain	223 (45%)	278	0.10297	1	0.0238	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.42188	1	0.75802	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.0074799	1	0.03032	1	0.00272	1	3e-05	0.0266
2q gain	140 (28%)	361	0.4735	1	0.36198	1	5e-04	0.415	0.03163	1	0.45106	1	0.64682	1	0.00142	1	0.02127	1	0.14692	1	0.26917	1	0.00217	1	0.01224	1
3p gain	109 (22%)	392	0.97725	1	0.85035	1	0.21997	1	0.083779	1	1	1	0.25168	1	0.31443	1	0.14943	1	0.92134	1	0.69204	1	0.97196	1	0.50084	1
3q gain	316 (63%)	185	0.60134	1	0.73689	1	0.01379	1	0.31528	1	1	1	0.11136	1	0.30753	1	0.3086	1	0.44749	1	0.02735	1	0.68956	1	0.18894	1
4p gain	32 (6%)	469	0.56021	1	0.20321	1	0.00016	0.137	0.091719	1	0.57601	1	0.40958	1	0.0287	1	0.0061999	1	0.0053899	1	0.31116	1	0.01243	1	0.01552	1
4q gain	23 (5%)	478	0.74163	1	0.73049	1	0.01034	1	0.078569	1	0.87466	1	0.17206	1	0.84208	1	0.88958	1	0.095039	1	0.35083	1	0.14611	1	0.18962	1
5p gain	309 (62%)	192	0.77592	1	0.8552	1	0.03007	1	0.70811	1	0.31166	1	0.22962	1	0.3189	1	0.47582	1	0.2324	1	0.053779	1	0.04167	1	0.12717	1
5q gain	93 (19%)	408	0.23744	1	0.21011	1	0.37688	1	0.32192	1	0.71263	1	0.14694	1	0.31739	1	0.01813	1	0.5207	1	0.28273	1	0.11294	1	0.03643	1
6p gain	109 (22%)	392	0.053179	1	0.18157	1	0.00067999	0.553	0.94388	1	0.93522	1	0.18975	1	0.00163	1	0.0061899	1	0.95121	1	0.3395	1	0.17169	1	0.1558	1
6q gain	94 (19%)	407	0.067809	1	0.121	1	0.00179	1	0.60956	1	0.87757	1	0.96289	1	0.01635	1	0.01688	1	0.80322	1	0.18028	1	0.4677	1	0.03944	1
7p gain	243 (49%)	258	0.060279	1	0.01269	1	3e-05	0.0266	0.00016	0.137	0.56927	1	0.65626	1	9.9999e-05	0.0867	9.9999e-06	0.0096	0.00060999	0.498	0.00039	0.327	0.0132	1	0.081729	1
7q gain	221 (44%)	280	0.00327	1	2e-04	0.17	9.9999e-06	0.0096	9.9999e-06	0.0096	0.90285	1	0.22887	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00057999	0.476	0.00018	0.154	0.00108	0.864	0.00070999	0.576
8p gain	129 (26%)	372	0.40504	1	0.55026	1	0.40256	1	0.14961	1	0.25652	1	0.95016	1	0.03717	1	0.02399	1	0.39105	1	0.01556	1	0.85413	1	0.86204	1
8q gain	257 (51%)	244	0.04811	1	0.03765	1	0.02169	1	0.0090699	1	0.26244	1	0.75634	1	0.0063699	1	0.00026	0.219	0.066179	1	0.00445	1	0.41844	1	0.45978	1
9p gain	62 (12%)	439	0.085689	1	0.02076	1	5.9999e-05	0.0525	0.00014	0.121	0.17749	1	0.04863	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.01366	1	0.04924	1	0.00087999	0.708	0.073199	1
9q gain	92 (18%)	409	0.00471	1	0.00052999	0.437	9.9999e-06	0.0096	9.9999e-06	0.0096	0.058709	1	0.02697	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00024	0.203	0.00014	0.121	0.00098999	0.795	0.00163	1
10p gain	79 (16%)	422	0.32145	1	0.70156	1	0.1099	1	0.16073	1	0.065069	1	0.084419	1	0.071019	1	0.054579	1	0.04561	1	0.00053999	0.444	0.90198	1	0.18206	1
10q gain	45 (9%)	456	0.11304	1	0.13884	1	0.051699	1	0.5726	1	0.02725	1	0.20831	1	0.060269	1	0.01098	1	0.41321	1	0.13239	1	0.76184	1	0.35232	1
11p gain	74 (15%)	427	0.67769	1	0.47783	1	0.060209	1	0.30633	1	0.24303	1	0.0097399	1	0.65635	1	0.92436	1	0.13092	1	0.075829	1	0.18573	1	0.03804	1
11q gain	91 (18%)	410	0.01782	1	0.20885	1	0.00103	0.826	0.43	1	0.39313	1	0.052509	1	0.25126	1	0.063979	1	0.14348	1	0.11094	1	0.64227	1	0.071679	1
12p gain	229 (46%)	272	0.01819	1	0.03439	1	9.9999e-06	0.0096	0.00249	1	0.22083	1	0.80175	1	5e-05	0.044	0.00226	1	0.03151	1	0.0095599	1	0.02262	1	0.00138	1
12q gain	153 (31%)	348	0.02348	1	0.31014	1	9.9999e-06	0.0096	0.0035	1	0.53749	1	0.61195	1	0.0032	1	0.00122	0.97	0.11654	1	0.12638	1	0.0093499	1	5e-05	0.044
13q gain	39 (8%)	462	0.70005	1	0.66288	1	0.79708	1	0.96697	1	0.41422	1	0.66363	1	0.50864	1	0.70943	1	0.22971	1	0.59014	1	0.8922	1	0.91314	1
14q gain	129 (26%)	372	0.14539	1	0.02314	1	0.03881	1	0.096869	1	0.2533	1	0.33172	1	0.18126	1	0.00441	1	0.072699	1	0.16771	1	0.57076	1	0.90619	1
15q gain	105 (21%)	396	0.83808	1	0.42672	1	0.00086999	0.7	0.00168	1	0.21973	1	0.65887	1	0.00166	1	0.01117	1	0.10882	1	0.03763	1	0.086119	1	0.00236	1
16p gain	86 (17%)	415	0.35278	1	0.5566	1	0.11706	1	0.50425	1	0.613	1	0.78468	1	0.68794	1	0.76846	1	0.48121	1	0.01999	1	0.47393	1	0.28871	1
16q gain	87 (17%)	414	0.91803	1	0.93649	1	0.02498	1	0.33085	1	0.68989	1	0.43738	1	0.15897	1	0.65002	1	0.21397	1	0.02675	1	0.41798	1	0.42017	1
17p gain	68 (14%)	433	0.00383	1	0.10071	1	9.9999e-06	0.0096	0.00316	1	0.84088	1	0.13847	1	0.00057999	0.476	0.00072999	0.591	0.01615	1	0.094009	1	0.050069	1	0.0074899	1
17q gain	158 (32%)	343	0.00147	1	0.00052999	0.437	9.9999e-06	0.0096	9.9999e-06	0.0096	0.42131	1	0.97792	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00059999	0.491	0.01155	1	0.00042	0.351	5e-05	0.044
18p gain	150 (30%)	351	0.0084299	1	0.00113	0.902	9.9999e-06	0.0096	9.9999e-06	0.0096	0.49218	1	0.71288	1	0.00116	0.925	9.9999e-06	0.0096	0.01753	1	0.28007	1	0.086779	1	0.00049	0.408
18q gain	104 (21%)	397	0.01583	1	0.01474	1	9.9999e-06	0.0096	0.00347	1	0.51863	1	0.33341	1	0.00059999	0.491	0.00018	0.154	0.058529	1	0.03291	1	0.26153	1	0.00249	1
19p gain	111 (22%)	390	0.04562	1	0.12311	1	9.9999e-06	0.0096	0.00023	0.195	0.02209	1	0.066859	1	0.00015	0.129	0.00203	1	0.13083	1	0.00143	1	0.068269	1	0.0055899	1
19q gain	159 (32%)	342	0.11459	1	0.17897	1	8.9999e-05	0.0782	0.0097999	1	0.23046	1	0.12008	1	0.02302	1	0.5087	1	0.94262	1	0.41814	1	0.3628	1	0.14684	1
20p gain	261 (52%)	240	0.01965	1	0.0221	1	9.9999e-06	0.0096	5e-04	0.415	0.88814	1	0.31346	1	0.22849	1	0.14426	1	0.076029	1	0.71699	1	0.63488	1	0.9276	1
20q gain	251 (50%)	250	0.675	1	0.31799	1	0.00045	0.375	0.23087	1	0.55964	1	0.58438	1	0.30858	1	0.11729	1	0.096209	1	0.02897	1	0.84633	1	0.35107	1
21q gain	57 (11%)	444	0.89428	1	0.81552	1	0.96827	1	0.061789	1	0.37785	1	1	1	0.40977	1	0.77703	1	0.51308	1	0.46749	1	0.21867	1	0.52477	1
22q gain	221 (44%)	280	0.0080199	1	0.02985	1	0.00391	1	0.03799	1	0.96663	1	0.067179	1	0.00051999	0.43	5.9999e-05	0.0525	0.79943	1	0.11096	1	0.98945	1	0.75559	1
xq gain	78 (16%)	423	0.36314	1	0.12431	1	3e-05	0.0266	0.00478	1	0.67897	1	0.6234	1	0.0097299	1	0.02828	1	0.058599	1	0.33124	1	0.41658	1	0.20858	1
1p loss	152 (30%)	349	7.9999e-05	0.0697	9.9999e-06	0.0096	9.9999e-06	0.0096	9.9999e-06	0.0096	0.88441	1	0.17186	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00149	1	9.9999e-06	0.0096	0.00071999	0.583	5e-04	0.415
1q loss	60 (12%)	441	0.55118	1	0.66818	1	0.00216	1	0.04352	1	0.95876	1	0.61452	1	0.0346	1	0.02777	1	0.24596	1	0.083179	1	0.2246	1	0.52862	1
2p loss	21 (4%)	480	0.12921	1	0.19105	1	0.37959	1	0.15323	1	0.14183	1	0.10111	1	0.44798	1	0.02843	1	0.0060899	1	0.52772	1	0.03739	1	0.00049	0.408
2q loss	42 (8%)	459	0.71003	1	1	1	0.2747	1	0.35797	1	0.88166	1	0.14234	1	0.064579	1	0.02479	1	8.9999e-05	0.0782	0.19594	1	0.12779	1	0.00133	1
3p loss	309 (62%)	192	0.36759	1	0.051609	1	0.12959	1	0.00194	1	0.9314	1	0.10396	1	0.3977	1	0.38272	1	0.27379	1	0.00017	0.146	0.03096	1	0.11022	1
3q loss	69 (14%)	432	0.94401	1	0.92842	1	0.4929	1	0.69312	1	0.63344	1	0.40925	1	0.90491	1	0.31747	1	0.60876	1	0.23828	1	0.1617	1	0.34301	1
4p loss	315 (63%)	186	0.00147	1	5.9999e-05	0.0525	9.9999e-06	0.0096	9.9999e-06	0.0096	0.2118	1	0.3736	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00060999	0.498	0.054209	1	9.9999e-06	0.0096	9.9999e-06	0.0096
4q loss	298 (59%)	203	0.00226	1	0.0012	0.955	9.9999e-06	0.0096	3e-05	0.0266	0.29451	1	0.54609	1	2e-05	0.0179	0.00032	0.269	0.00329	1	0.03079	1	0.00060999	0.498	5e-05	0.044
5p loss	78 (16%)	423	0.82661	1	0.93489	1	0.0043	1	0.00289	1	0.43215	1	0.03474	1	0.22771	1	0.28479	1	0.04035	1	0.37164	1	0.01575	1	0.093959	1
5q loss	291 (58%)	210	0.13341	1	0.053669	1	0.00031	0.261	0.0086799	1	0.26786	1	0.12383	1	0.0057399	1	0.00028	0.236	0.13307	1	0.01908	1	0.0141	1	0.093859	1
6p loss	112 (22%)	389	0.03512	1	0.01457	1	0.00428	1	0.00024	0.203	0.14838	1	0.14412	1	2e-05	0.0179	2e-05	0.0179	0.19597	1	0.16263	1	0.17854	1	0.40464	1
6q loss	113 (23%)	388	0.0050499	1	0.00081999	0.661	0.02603	1	0.00178	1	0.70084	1	0.39675	1	0.00154	1	0.02332	1	0.55271	1	0.75854	1	0.11482	1	0.345	1
7p loss	58 (12%)	443	0.39688	1	1	1	9.9999e-05	0.0867	0.27436	1	0.4817	1	0.12372	1	0.40238	1	0.092779	1	0.090659	1	0.0054499	1	0.92698	1	0.29575	1
7q loss	51 (10%)	450	0.16221	1	0.090539	1	0.00317	1	0.33068	1	0.83042	1	0.063069	1	2e-05	0.0179	2e-05	0.0179	0.10689	1	0.03356	1	0.80933	1	0.40438	1
8p loss	244 (49%)	257	0.92268	1	0.95941	1	0.0051699	1	0.00206	1	0.10028	1	0.44342	1	0.11301	1	0.086119	1	0.38968	1	0.01501	1	0.18679	1	0.62168	1
8q loss	48 (10%)	453	0.34684	1	0.35721	1	0.39275	1	0.0059799	1	0.071299	1	0.8774	1	0.26686	1	0.04137	1	0.099879	1	0.12535	1	0.25935	1	0.90915	1
9p loss	310 (62%)	191	0.0074999	1	0.00122	0.97	9.9999e-06	0.0096	0.01884	1	0.2071	1	0.076959	1	9.9999e-06	0.0096	4e-05	0.0353	0.04432	1	0.00042	0.351	0.43416	1	0.02643	1
9q loss	245 (49%)	256	2e-05	0.0179	2e-05	0.0179	9.9999e-06	0.0096	9.9999e-06	0.0096	0.1717	1	0.01412	1	9.9999e-06	0.0096	9.9999e-06	0.0096	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00426	1	9.9999e-05	0.0867
10p loss	214 (43%)	287	0.20455	1	0.21948	1	7.9999e-05	0.0697	9.9999e-06	0.0096	0.39521	1	0.15952	1	2e-05	0.0179	6.9999e-05	0.061	0.00035	0.294	9.9999e-06	0.0096	0.04791	1	0.00392	1
10q loss	229 (46%)	272	0.00106	0.849	0.00015	0.129	9.9999e-06	0.0096	9.9999e-06	0.0096	0.095749	1	0.079349	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00041	0.343	9.9999e-06	0.0096	0.0146	1	0.0072899	1
11p loss	171 (34%)	330	0.25349	1	0.24883	1	0.0055699	1	0.00214	1	0.14097	1	0.00319	1	0.12084	1	0.62655	1	0.055439	1	0.58299	1	0.47447	1	0.064779	1
11q loss	141 (28%)	360	0.9872	1	0.75744	1	0.0061299	1	0.00139	1	0.54181	1	0.86764	1	0.12516	1	0.70484	1	0.066809	1	0.23235	1	0.42091	1	0.094659	1
12p loss	39 (8%)	462	0.02374	1	0.0051699	1	0.26469	1	0.88193	1	0.099929	1	0.88638	1	0.98118	1	0.11195	1	0.18704	1	0.083349	1	0.067009	1	0.19204	1
12q loss	48 (10%)	453	0.36612	1	0.14272	1	0.81102	1	0.67329	1	0.02724	1	0.75225	1	0.70314	1	0.79067	1	0.80561	1	0.11557	1	0.54264	1	0.14961	1
13q loss	311 (62%)	190	0.61956	1	0.7097	1	0.077239	1	0.04534	1	0.70418	1	0.36959	1	0.27763	1	0.70219	1	0.074479	1	0.1079	1	0.00076999	0.621	0.02497	1
14q loss	166 (33%)	335	0.00013	0.112	0.00036	0.302	0.01783	1	0.1521	1	0.054299	1	0.15291	1	9.9999e-06	0.0096	9.9999e-06	0.0096	0.00017	0.146	9.9999e-06	0.0096	0.00286	1	0.00196	1
15q loss	142 (28%)	359	0.71942	1	0.7434	1	0.1226	1	0.050949	1	0.32788	1	0.00182	1	0.090509	1	0.28916	1	0.0296	1	0.15639	1	0.53217	1	0.41236	1
16p loss	163 (33%)	338	0.97831	1	0.70198	1	0.0036	1	0.11553	1	0.11955	1	0.26797	1	0.32754	1	0.44326	1	0.1994	1	0.83219	1	0.02762	1	0.084819	1
16q loss	182 (36%)	319	0.77579	1	0.12428	1	0.01734	1	0.16004	1	0.13145	1	0.84951	1	0.052479	1	0.053319	1	0.00019	0.162	0.393	1	0.00253	1	0.00152	1
17p loss	291 (58%)	210	0.00473	1	0.17086	1	4e-05	0.0353	0.01023	1	0.43547	1	0.0063799	1	0.00155	1	0.00147	1	0.095989	1	0.00072999	0.591	0.13425	1	0.093429	1
17q loss	94 (19%)	407	0.01035	1	0.0048	1	0.00056999	0.468	4e-04	0.335	0.66237	1	0.96855	1	0.00023	0.195	9.9999e-06	0.0096	0.076029	1	0.0099999	1	0.69675	1	0.04239	1
18p loss	140 (28%)	361	0.85652	1	0.65311	1	0.092009	1	0.085919	1	0.62765	1	0.91787	1	0.19563	1	0.073069	1	0.41856	1	0.077609	1	0.068269	1	0.6183	1
18q loss	189 (38%)	312	0.22427	1	0.33146	1	0.053099	1	0.2732	1	0.70379	1	0.38914	1	0.48744	1	0.14708	1	0.073629	1	0.12352	1	0.080669	1	0.62125	1
19p loss	167 (33%)	334	0.03878	1	0.053279	1	5e-05	0.044	0.60004	1	0.8914	1	0.31727	1	0.04459	1	0.0193	1	0.10054	1	0.00019	0.162	0.83701	1	0.16202	1
19q loss	112 (22%)	389	0.61309	1	0.51071	1	0.04133	1	0.048	1	0.34084	1	0.69256	1	0.82127	1	0.34183	1	0.47832	1	0.1209	1	0.45911	1	0.56859	1
20p loss	42 (8%)	459	0.1437	1	0.14069	1	0.02523	1	0.0073199	1	0.11246	1	0.14394	1	0.20014	1	0.03031	1	0.44113	1	0.064099	1	0.96202	1	0.33846	1
20q loss	46 (9%)	455	0.057869	1	0.076459	1	0.00201	1	0.01939	1	0.43498	1	0.42492	1	5e-05	0.044	0.00161	1	0.01052	1	0.097409	1	0.46354	1	0.26843	1
21q loss	265 (53%)	236	0.90151	1	0.31839	1	2e-05	0.0179	0.03628	1	0.5225	1	0.44863	1	0.059879	1	0.03928	1	0.01624	1	0.00051999	0.43	0.02392	1	0.01229	1
22q loss	98 (20%)	403	0.0083399	1	0.10097	1	0.17254	1	0.0393	1	0.25311	1	0.057189	1	0.00013	0.112	9.9999e-06	0.0096	0.79031	1	0.0090099	1	0.19338	1	0.20125	1
xq loss	115 (23%)	386	0.20057	1	0.55972	1	9.9999e-06	0.0096	0.00051999	0.43	0.77375	1	0.82309	1	0.01605	1	0.98158	1	0.01126	1	0.01183	1	0.0060199	1	9.9999e-06	0.0096