Random forest-based modelling to detect biomarkers for prostate cancer progression

Toth, Reka; Schiffmann, Heiko; Hube-Magg, Claudia; Büscheck, Franziska; Höflmayer, Doris; Weidemann, Sören; Lebok, Patrick; Fraune, Christoph; Minner, Sarah; Schlomm, Thorsten; Sauter, Guido; Plass, Christoph; Assenov, Yassen; Simon, Ronald; Meiners, Jan; Gerhäuser, Clarissa

doi:10.1186/s13148-019-0736-8

Clinical Epigenetics

Table 3 Top 20 ranked candidate CpG probes and associated genes

From: Random forest-based modelling to detect biomarkers for prostate cancer progression

CG probe names	Chr.	Location	Mean decrease in accuracy	Mean decrease in Gini	ChromHMM PC3	ChromHMM PrEC	ChromHMM LNCaP	Gene symbol	Distance from TSS (bp)	Mean meth. good progn.	Mean meth. poor progn.
cg07443748	chr22	17073594	0.002194	0.221948	Heterochromatin	Heterochromatin	Heterochromatin	CCT8L2	105	0.585	0.434
cg18146506	chr20	2633340	0.002382	0.193534	Promoter	Promoter	Promoter	NOP56	550	0.430	0.327
cg05766896	chr1	157789933	0.001993	0.192736	Heterochromatin	Heterochromatin	Heterochromatin	FCRL1	− 39	0.657	0.508
cg16734913	chr11	55681277	0.001621	0.167347	Heterochromatin	Heterochromatin	Heterochromatin	OR5W2	780	0.688	0.567
cg16876647	chr2	43451842	0.002281	0.15899	Promoter	Promoter	Heterochromatin	ZFP36L2	1905	0.703	0.401
cg24100636	chr12	3600087	0.001015	0.145156	Heterochromatin	Promoter	Heterochromatin	PRMT8	− 314	0.280	0.446
cg16377872	chr19	15084823	0.00141	0.143848	Heterochromatin	Heterochromatin	Heterochromatin	SLC1A6	− 1094	0.747	0.641
cg27212232	chr20	53091600	0.001276	0.143601	Heterochromatin	Heterochromatin	Heterochromatin	DOK5	− 535	0.407	0.301
cg02601618	chr22	17075046	0.002015	0.134821	Heterochromatin	Heterochromatin	Heterochromatin	CCT8L2	− 1347	0.696	0.565
cg12092201	chr2	43451775	0.001586	0.122542	Promoter	Promoter	Heterochromatin	ZFP36L2	1972	0.473	0.285
cg12818557	chr8	89340139	0.00084	0.122408	Heterochromatin	Promoter	Promoter	MMP16	− 423	0.329	0.503
cg04211581	chr6	152011656	0.000859	0.117083	CTCF	Heterochromatin	Transcribed	ESR1	26	0.458	0.317
cg24690071	chr13	100635352	0.001171	0.116259	Poised promoter	Repressed	Promoter	ZIC2	1327	0.483	0.322
cg00874055	chr1	236306673	0.001063	0.115871	Promoter	Promoter	Poised promoter	GPR137B	842	0.487	0.342
cg10562114	chr10	120790501	0.000745	0.112334	Promoter	Promoter	Promoter	NANOS1	1274	0.353	0.230
cg26135325	chr1	152595322	0.000427	0.104978	Heterochromatin	Heterochromatin	Heterochromatin	LCE3A	256	0.540	0.431
cg00343414	chr11	109292465	0.000626	0.10478	Heterochromatin	Heterochromatin	Heterochromatin	C11orf87	− 380	0.795	0.691
cg25458871	chr19	57352584	0.000731	0.104688	Heterochromatin	Heterochromatin	Heterochromatin	PEG3	− 521	0.532	0.428
cg25458871	chr19	57352584	0.000731	0.104688	Heterochromatin	Heterochromatin	Heterochromatin	ZIM2	− 488	0.532	0.428
cg16118839	chr11	88069169	0.000997	0.103679	Promoter	Enhancer	Heterochromatin	CTSC	1785	0.526	0.408
cg16776350	chr1	160549158	0.000666	0.102419	Heterochromatin	Heterochromatin	Heterochromatin	CD84	135	0.590	0.459
cg00636390	chr8	57027352	0.000914	0.101489	Heterochromatin	Repressed	Repressed	MOS	− 812	0.616	0.485
cg17225407	chr17	41176954	0.000767	0.101076	Poised promoter	Poised promoter	Heterochromatin	RND2	− 303	0.388	0.287

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ISSN: 1868-7083

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