MDS displays marked aberrant promoter DNA methylation. (A-C) Unsupervised clustering analysis of 14 MDS samples and 8 CD34+ normal controls with the use of 3 different algorithms: COA, PCA, and hierarchical clustering. (D) A plot of methylation difference between MDS cases and normal CD34+ controls (x-axis) versus statistical significance (y-axis) shows the marked asymmetry of the 2 branches, illustrating the overall tendency to higher methylation levels in the MDS cases. Red points mark probe sets that reached both criteria for differential methylation on our analysis [P < .0005 and absolute fold change in log(HpaII/MspI) > 1.5), whereas blue points mark probe sets that reached statistical significance but did not have an absolute change in log(HpaII/MspI) greater than 1.5. (E) Two-dimensional hierarchical clustering of genes differentially methylated between MDS and normal CD34+ controls, illustrated by a heatmap. Cases are represented in the columns and probe sets in the rows.