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.
Do you have any questions about this protocol?
Post your question to gather feedback from the community. We will also invite the authors of this article to respond.