Figure 6.

An evaluation of the performance of MM-ChIP on ChIP-seq data. (a) The fraction of CTCF binding sites containing a canonical CTCF binding motif is plotted as a function of the number of top-ranked binding sites for both the individual and combined datasets. The results of integrative analysis using the region intersection method are also shown. Binding sites were ranked in ascending order by P-value. Broad, Broad Institute; UT-Austin, University of Texas at Austin. (b) A comparison between MM-ChIP and the Merge MACS method on one real dataset and two synthetic datasets. The fraction of CTCF binding sites containing a canonical CTCF binding motif is plotted as a function of the number of top-ranked binding sites for different datasets when the inter-library size difference (Δd) is 0, 100 or 200. MACS, Model-based Analysis of ChIP-Seq data.