Figure 1

Scores of different FoxA BS recognition models for TFBSs derived from ChIP-Seq data [[24]]. Six panels from A to F denote all possible pairwise combination of ChIPMunk, diChIPMunk, SiteGA and oPWM models. Black dots denote the sample of 466 potential BSs: (A) sites mapped in promoter regions located in 1000 bp upstream regions of RefSeq genes; (B) binding sites lying in peak regions with peak height of 15 or higher. The 64 BSs selected for experimental verification are shown as grey crossed squares, brown triangles and red circles, corresponding to the EMSA scores below 0.25 (non-sites), in the range from 0.25 to 0.75 (weak sites) and above 0.75 (strong sites). Solid lines mark the model thresholds selected to discard non-sites.