ChIP-Chip profiling identifies leukemia-specific loci with altered H3K9me3 loci in leukemia. (A) The Venn diagrams depict the number of genomic loci that were significantly altered in the indicated analyses. Genomic loci included here had a Benjamini-Hochberg corrected P < .05 and were at least 2-fold altered between 2 analyzed groups. The numbers in the overlaps indicate genomic loci that were altered in the same direction in at least 2 analyses. A detailed list of all genomic loci altered in H3K9me3 levels is provided in the supplemental data. (B) PCA identifies distinct patterns of H3K9me3 distribution in AML compared with ALL samples. PC1 is the first principal component, and PC2 and PC3 are the second and third principle components, respectively. (C) Gene Ontology analysis of promoter regions with altered H3K9me3 levels. Among others, regulation of DNA binding and myeloid leukocyte differentiation was overrepresented, indicating that functionally relevant genes were altered in H3K9me3 levels between AML and ALL specimens. (D) Genomic regions differing in H3K9me3 patterns were hierarchically clustered and are indicated in this heatmap. Green represents higher H3K9me3 levels; and red, decreased H3K9me3 levels.