Figure 3.

ChIP, ChAP, and TChAP E2Fa majority peaks/genes. A, Venn diagrams showing overlap among all, the E2Fa-regulated, and the E2F motif majority genes identified through ChIP, ChAP, and TChAP-seq. B, Examples of known E2Fa-binding sites identified in the ChIP, ChAP, and TChAP-seq data. Visual representation is organized in four tracks. Gene structure is indicated with cyan rectangles. The normalized coverage for each of the methods is displayed as a bar chart around a central axis with coverage on the forward and reverse shown in green (up) and blue (down), respectively. Total coverage is indicated in yellow. The coverage scale is the same for all three protocols, and each track has been normalized for total coverage in that protocol, allowing direct comparison. C, Frequency of E2Fa-regulated or E2F motif genes among the ChIP-, ChAP-, and TChAP-identified majority peaks. Peaks are sorted based on descending MACS confidence peak scores. The gray lines depict the random occurrence of an E2Fa-regulated gene in the Arabidopsis genome (left) and the expected frequency of E2F motif genes based on randomized peak sequences (right).