Differentially methylated regions correlate with transcript changes. (A) The 4,751 DMRs mapped to 1,092 unique genes that were present in the Affymetrix arrays. There were 415 transcripts that showed differences both in their methylation status and their expression in CKD samples. The RefSeq-based locations of the DMRs are also shown. While most differentially methylated regions localize to gene body regions, they also show correlation with the expression of many of those genes. Not only are the 415 transcripts differentially expressed, they also show differences in their cytosine methylation profiles as well. (B) DAVID-based gene ontology annotation of the 415 transcripts. (C) Network chart of the genes that are both differentially expressed and methylated). (D) Methylation and gene expression level of key molecules (RUNX3, RARB, SMAD6) identified by the network analysis in control (CTL) and CKD samples.