Figure 4.
Human and mouse E2F4 target promoters have similar characteristics. (A) ChIP-chip assays for E2F4 mouse 3T3 cells were performed and peaks were called for each of the ∼24,000 1.5-kb mouse promoter regions. E2F4 ChIP-chip data from MCF7 cells (Xu et al. 2007) was also analyzed for comparison. We ranked the promoters by the enrichment values (E2F4 IP vs. Input) of the peaks and then binned the promoters into ranked sets of 100 (x-axis). The ratio of promoters in each bin that contain a consensus E2F motif is indicated on the y-axis. (B). Functional annotations were performed using the program Database for Annotation, Visualization, and Integrated Discovery (DAVID) 2007 (Dennis et al. 2003; see also http://niaid.abcc.ncifcrf.gov/). The categories used were InterPro name and SP PIR Keywords. The top categories are shown for the sets human and mouse E2F4 target promoters, derived from the promoters that were in the top 2000 list in duplicate mouse or human ChIP-chip experiments. The x-axis indicates the percentage of each set represented by the different categories; see Supplemental Table S3A for the P-values for each category.