Fig. 6

Arbitrary, stringent thresholds can lead to an incomplete and biased view of DNA methylation remodeling during monocyte–macrophage differentiation. Enrichments for chromatin segments, DNAseI hypersensitive sites and top 10 binding sites of macrophage TFs were calculated for gain-DMCs and for loss-DMCs for all DMCs identified in this study with different thresholds. For effect size cutoffs and DMRs, we used DMCs sufficiently measured in WGBS data. For the DMCs with consistent direction, we used effect size cutoffs of > 5%, between 5 and 30% or > 30%. Enrichment analysis for different effect size cutoffs was plotted separately or in combination with DMR thresholds: ≤ 4 or > 4