Illustration of the results obtained by CSDeconv for DosR binding upstream of Rv2031c. (a) The forward and reverse enrichment profiles obtained after kernel density estimation of the read distributions are shown in black and shaded in gray. Colored lines display various fits arising from estimated binding. Note that no distinct peaks are evident in the enrichment profiles and, in particular, there are no dips. (b) Both forward and reverse reads are associated with fits: the forward fit 3 is the sum of the forward enrichment peaks 1 and 2, whereas the reverse fit 3' is the sum of the reverse enrichment peaks 1' and 2'. (c) The combined forward and reverse enrichment peaks arise from two binding sites, which are peaks 15 and 16 in Table 1. Motif logos overlay the actual sequence of the intergenic region truncated for brevity, showing the two binding sites, which are separated by a scant 57 bp. Enrichment is plotted as the fold magnitude of the ChIP read density over the control read density.
Lun et al. Genome Biology 2009 10:R142 doi:10.1186/gb-2009-10-12-r142