Motifs in 12 mouse ES Cell ChIP-seq data sets.

FMotif was tested using mouse ChIP-seq data sets for 12 DNA-binding TFs (CTCF, cMyc, Esrrb, Klf4, Nanog, nMyc, Oct4, Smad1, Sox2, STAT3, Tcfcp2I1, and Zfx) involved in mouse embryonic stem cell pluripotency and self-renewal [40]. Results from CisFinder and published motifs in literature are shown for comparison. ‘Nb’ indicates the number of peak-enriched regions predicted by the peak-calling program MACS with an FDR threshold of 0.2 or a -value threshold of , ‘FMotif’ and ‘CisFinder’ indicate the closest matching motif logos found by these programs (all motif logos were generated using the web-based tool Weblogo [45]), ‘Literature’ indicates the corresponding motif logos published in literature, ‘’ indicates the number of binding sites found by either FMotif or CisFinder, and ‘Rank’ after ‘’ is the ranking number of a reported motif found by either FMotif or CisFinder.