Pathway Enrichment Analysis of Differentially Methylated Regions

Pathway enrichment analyses were performed using the missMethyl package (v.1.22.0) [43 (link)] on the gene sets from the Molecular Signatures Database (MSigDB) [44 (link)] accessed via the msigdbr package (v.7.2.1). The gsameth function was used to interrogate the functionality of the DMPs identified, while the gsaregion function was used to analyse DMRs. Both take into account the number of probes mapping to each gene as a bias factor for the enrichment analyses. To visualise pathway enrichment results, several networks of gene-set similarity were built using the EnrichmentMap application [45 (link)] in Cytoscape (v.3.9.1) [46 (link)] using the RCy3 package (v.2.8.1) [47 (link)] with the default combined similarity cutoff.