Differentially Methylated CpGs from each pairwise comparison

Differentially methylated cytosines between groups were identified using the Chi-squared test in methylKit and annotated using the genomation package (Akalin et al., 2012; Akalin et al., 2015 [77, 78]). Results were filtered for ‘in gene/promoter’ to remove intergenic regions, and for a minimum difference of >20% methylation (Du et al., 2010; Slieker et al., 2015) [79, 80].