Figure 4.

Mouse ChIP-seq mouse. Motif predictions of cERMIT on mouse ChIP-seq data from [40]. The predictions of cERMIT use the 'ensemble' approach to define the set of putative regulatory regions (see text for details). Literature position-specific scoring matrices (PSSMs) were extracted from TRANSFAC 2009.1, except for CTCF [45], Klf4 [57], and Zfx (unknown). Asterisks are used to indicate the optimal alignment of motif prediction to literature. Each individual factor contributes (the top scoring) 5,000 peaks to the ensemble set of putative regulatory regions.