De novo AML presents with a lesser extent of aberrant promoter DNA methylation and aberrant hypomethylation. (A-C) Unsupervised clustering analysis of 15 de novo AML samples and 8 CD34⁺ normal controls with COA, PCA, and hierarchical clustering. (D) Plot of DNA methylation difference between AML cases and normal CD34⁺ controls (x-axis) versus statistical significance (y-axis). As before, 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 de novo AML and normal CD34⁺ controls identified by a supervised analysis, illustrated using a heatmap. Cases are represented in the columns and probe sets in the rows.