Core promoter elements are associated with initiation pattern. PATSER was used to evaluate the presence of the eight core promoter elements at any location in the 100-bp sequences surrounding 3,788 TSSs, 876 TSS cluster groups, and three sets of 1,299 random intergenic sites. All counts were rounded to the nearest whole number after normalization. (a) Individual motif occurrences. The number of motif matches were counted and normalized to the number of occurrences per 100 kb. For the random intergenic sites, the mean numbers of motif occurrences across all three sets are shown. (b) Module occurrences. The number of pairs of motif matches present in the designated order, with respect to the orientation of transcription, were counted and normalized to the number of occurrences per 100 kb.
Rach et al. Genome Biology 2009 10:R73 doi:10.1186/gb-2009-10-7-r73