Figure 4

The fraction of ChIP-Seq peaks [[25]] with recognized sites as a function of the peak height cut-off value. Six panels from A to F denote predictions computed for all possible pairwise combinations of ChIPMunk, diChIPMunk, SiteGA and oPWM models. The X and Y axes show the fraction of peaks having at least one FoxA binding site recognized by the respective model and the peak height cut-off value. The panels from A to F show the comparisons between SiteGA and oPWM, ChIPMunk and diChIPMunk, SiteGA and ChIPMunk, SiteGA and diChIPMunk models, respectively. The following grouping of recognized TFBSs is used: loci with TFBSs recognized by both the first and second models (e.g. D – SiteGA & ChIPMunk, respectively) that either overlap or not, are marked by RED and ORANGE, respectively; loci with at least one FoxA binding site recognized by the first but not by the second model, or vice versa, are marked by GREEN and BLUE, respectively. Black vertical lines denote the coverage threshold (peak height of 10).