Figure 2.

Density of regulatory and repetitive DNA sequences in human core promoters. The plot displays results for 7914 human core promoters. Its X-axis runs from −1000 bp to +1000 bp, relative to the TSS for each promoter at 0 bp. The Y-axis represents the normalized count of: (A) TE-derived sequences; (B) TFBSs predicted with our positional methods and (C) TFBSs predicted with phylogenetic footprinting. In each case, the raw counts were normalized to make the area under each graph 1. The boundaries of the three curves indicate the density of predicted sequences in the different regions. Our methods tend to predict TFBSs in the [−200, +100] region of core promoters.