Figure 3

The proportional representation of functional genomic elements by different DNA methylation assays. Using annotations of human embryonic stem cells by Segway (a) and ChromHMM (b), we calculated how four types of genome-wide DNA methylation assays represent each type of functional element. When the proportion of functional genomic elements tested by each assay is calculated, all of the assays work best to represent the candidate promoters annotated by Segway (a) or ChromHMM (b), but generally only represent a minority of candidate cis-regulatory elements. Even WGBS does not represent 100% of each functional genomic element, so no assay achieves complete comprehensiveness, and the penalty of the WGBS approach is that it sequences equally deeply a number of genomic contexts that are not as likely to be informative, an inefficient use of costly sequencing resources.