While in many ways this study used a logically similar approach as that used by Liu (2009), the incorporation of bisulfite treatment instead of immunoprecipitation for 5mC is likely to be more precise as a tool to identify DMRs. Unfortunately, the Affymetrix microarray designed to probe promoter sequences excluded about 25% of all CpG islands and likely most adjacent sequences, termed “shores.” It appears that one difficulty in analyzing combinations of methylation and expression datasets is that subtle methylation differences in subsets of sequence regions may be masked by applying uniform filtering to the entire dataset.
