Figure 5

TFBS-bi-motif view for visualization of motif spatial arrangements. The left plot of a TFBS-bi-motif view presents the distance of the primary motif to the peakMax of each sequence on the y-axis, and the distance of a second motif relative to the primary motif on the x-axis. A band of enrichment at y = 0 indicates enrichment near the peakMax for the primary motif, while a diagonal band of enrichment (with a negative slope) indicates enrichment near the peakMax for the second motif. The diagonal limits of the plot arise from the uniform length of the sequences (here 1001 bp). The right plot is a histogram of the distances between the two motifs. The gap in both plots results from the exclusion of overlapping motifs. (a) ESRRB motifs in an ESRRB ChIP-Seq data set. The top-scoring ESRRB motif is the primary motif, and the second-best motif is the second motif. (b) NFYB motifs in a NFYB ChIP-Seq data set. The top-scoring NFYB motif is the primary motif, and the second-best motif is the second motif. (c) SRF ChIP-Seq dataset. The SRF top-scoring motif is the primary motif, and the ELK4 top-scoring motif is the second motif.