Microarray and ChIP-chip analyses of murine AE9a leukemia cells. (A) Microarray and ChIP-chip analyses of AE9a leukemia cells. The LK cells of AE9a leukemia spleen and wild-type bone marrow from 3 independent sets of mice were sorted by FACS for microarray analysis. The leukemia splenocytes were also subjected to ChIP-chip analysis (HA, AML1, and IgG). The microarray and ChIP-chip (HA and/or AML1) target genes were compared. The numbers in circles indicate the number of microarray-only targets (831), ChIP-chip-only targets (3733), and their common targets (214), from which the 60 HA and AML1 ChIP-chip common targets are considered as top candidates for AE9a direct target genes. (B) AML1 motif (V$AML_Q6 from TRANSFAC database) density curves for the top 1000 HA only peaks (green), top 1000 AML1 only peaks (blue), top 1000 IgG only peaks (purple), and the 781 HA and AML1 overlapped peaks (red; see supplemental Figure 2A). The x-axis shows the distance (in bp) from center of peaks, which is indicated as zero. The y-axis represents the number of motifs per kbp. (C) Top biologic functions of the 214 microarray and ChIP-chip common targets. The numbers to the right represent the number of genes involved in various biologic functions. The −log(P value) axis means the significance of the functions to the dataset.