Figure 3

Human ChIP-seq motif predictions. Motif predictions of cERMIT on six human ChIP-seq datasets: STAT1 [35], the insulator binding protein CTCF [36], SRF, GABP [37], FoxA1 [38], and NRSF [39]. The 'ensemble' column includes results from using the ensemble of all six datasets to define the space of regulatory regions (see text). The 'DNaseI' column includes cERMIT predictions when using open chromatin regions, as defined by DNaseI peaks, to be the set of putative regulatory regions. Literature position-specific scoring matrices (PSSMs) were extracted from TRANSFAC 2009.1. Asterisks indicate the optimal alignment of motif prediction to literature. CTCF, due to its ubiquitous binding, was recovered using the top 25,000 DNase peaks as input to cERMIT. All other datasets consider the top 5,000 peaks from each factor (in the two different scenarios).