Statistically significant cytosine methylation differences in chronic kidney disease. (A) Volcano plot analysis of cytosine methylation differences. The x-axis represents the relative cytosine methylation difference of control (CTL) versus CKD samples, the y-axis represents the negative log2 of the P-value of that locus. The mean P-value and mean difference of 1.3 million loci present on the chips are plotted on the graph. The green and red lines represent the statistical criteria used for further analysis (P-value and fold change, respectively). (B) Hierarchical cluster analysis of the differentially methylated regions. Each column represents changes from one individual kidney sample; blue indicates hypermethylation in CKD, while red represents hypomethylation in CKD. The chart below shows the clinical parameters of the samples: glomerular filtration rate, diabetes status (DM, diabetes mellitus), sex, and age (aged >65 years or <65 years). (C) Gene Ontology analysis of the 1,535 DMRs mapped to unique genes using DAVID gene ontology annotation groups (biological process level 1 annotation).
Ko et al. Genome Biology 2013 14:R108 doi:10.1186/gb-2013-14-10-r108