Reclassification of TF occupancy at ChIP-chip “bound” (P < 0.001) intergenic regions as likely being due to direct DNA-binding sites versus indirect association of the TF with the DNA. Blue bars above the horizontal axis for each TF indicate the number of ChIP-chip bound intergenic regions that were previously called “indirect” (i.e., the regions do not contain a good match to the ChIP-chip motif as determined by MacIsaac et al. (2006) that are reclassified as potential “direct” TF targets by PBM data (i.e., the regions contain a PBM k-mer with an E-score > 0.45). Red bars below the axis indicate the number of intergenic regions previously annotated as “direct” targets by MacIsaac et al. (2006) that are reclassified as potential sites of indirect TF association according to the PBM data (i.e., the regions do not contain any k-mers with E-score > 0.45).
