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. Author manuscript; available in PMC: 2009 Oct 1.
Published in final edited form as: Nat Methods. 2009 Mar 22;6(4):283–289. doi: 10.1038/nmeth.1313

Fig. 2. Detection of footprints and corresponding sequence motifs.

Fig. 2

(a) Visualization of DNase I protection (footprinting) around 907 computationally-predicted Reb1 sites in a heat map. Rows show levels of DNase I cleavage 25 bp up- and downstream of each motif instance and are sorted by the ratio of mean cleavage over flanking regions to that within the motif itself. Red ticks (at left) indicate motif instances (n = 580) that coincide with footprints (FDR = 0.05) containing de novo-derived Reb1 motifs. Blue ticks (right) indicate motif instances (n = 151) coinciding with those identified by ChIP10. All motif instances are uniquely mappable within the yeast genome. (b) Mean per nucleotide DNase I cleavage (red) and evolutionary conservation (Phastcons?; blue) calculated for footprints that match the Reb1, Abf1, Rap1 and Hsf1 motifs (subpanel vertical axes). Significance of observed conservation patterns (blue text) (Supplementary Methods), extent of consensus motifs derived from the footprinted region (green shading), motifs derived from ChIP and footprinting below. Venn diagrams depict the overlap of motifs derived from and mapping to footprints (red) vs. ChIP (blue).