Gene ontology and gene set enrichment analysis of differentially methylated genes

GR Gesa M. Richter
JK Jochen Kruppa
HK H. Gencay Keceli
EA Emel Tuğba Ataman-Duruel
CG Christian Graetz
NP Nicole Pischon
GW Gunar Wagner
CR Carsten Rendenbach
YJ Yvonne Jockel-Schneider
OM Orlando Martins
CB Corinna Bruckmann
IS Ingmar Staufenbiel
AF Andre Franke
RN Rahime M. Nohutcu
SJ Søren Jepsen
HD Henrik Dommisch
AS Arne S. Schaefer
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For gene set and gene ontology enrichment analysis, we used the r packages missMethl and gometh [19]. The R package IlluminaHumanMethylationEPICanno.ilm10b4.hg19 (Version 3.13) was used for annotation. 344 KEGG terms were gathered using limma’s internal function getGeneKEGGLinks with default options for gene set enrichment analysis. 22,746 GO terms were derived fromorg.Hs.eg.db after cleaning. Gene ontology terms and gene sets with q < 0.05 were considered as being significantly enriched.

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