One can also inspect enriched regions of interest for discovery of putative TF binding events using two approaches. The first approach is straightforward and is based on comparing sequence data against a database of known TF motifs. The second type of analysis can be computationally intensive and involves the de novo discovery of novel TF binding sites. A number of available software (MEME [154, 155], DREME [156], Patser (http://stormo.wustl.edu/software.html), Matrix Scan [157], LASAGNA [158], CompleteMOTIFs [159], and MatInspector (Genomatix) [160]), and TF motif databases (MatBase Genomatix; http://www.genomatix.de/online_help/help_matbase/matbase_help.html), JASPAR [161], TRANSFAC [162] and UniPROBE [163]) can arrogate TF motif identification and de novo discovery within enriched regions.
