Aberrant hypermethylation is a feature of CEBPA^sil leukemia. (A) Two-dimensional hierarchical clustering of genes differentially methylated between the CEBPA^sil cases and normal CD34⁺ hematopoietic progenitors, illustrated by a heatmap. Supervised analysis identified 1035 HpaII-amplifiable fragments (P < .001 and absolute difference in methylation > 2). Cases are represented in the columns; probe sets are represented in the rows. CEBPA^sil cases are clustered in the left node and display marked hypermethylation compared with the normals, as illustrated by the predominance of probe sets with low log2 (HpaII/MspI) ratios. (B) Methylation difference between CEBPA^sil and normal CD34⁺ cells (x-axis) versus statistical significance (y-axis) plot with marked asymmetry of the 2 branches, reflecting the tendency to higher methylation levels in this subgroup. Red points represent probe sets that reached both criteria for differential methylation in our analysis. (C) Two-dimensional hierarchical clustering of genes differentially methylated between the CEBPA^mut AML and normal CD34⁺ hematopoietic progenitors, illustrated by a heatmap. Supervised analysis identified 322 probe sets (286 genes). CEBPA^mut cases are clustered in the left node and display equal components of hypermethylation and hypomethylation compared with CD34⁺ normal cells. (D) A plot of methylation difference between mutant CEBPA and normal CD34⁺ cells (x-axis) versus statistical significance (y-axis) shows symmetric branches and less pronounced differences in methylation than in the case of the silenced CEBPA subgroup. Red points represent probe sets that reached both criteria for differential methylation on our analysis.