Figure 3

Identification and characterization of enriched motifs within PU.1 binding regions. (A) Sequence logos were shown for significant PU.1 motifs. The logo on the left was generated with V$PU.1_Q6 PSFM from TRANSFAC database, where the logo on the right was obtained by de novo motif finding using AMD. (B) Percentages of the PU.1 binding regions with the long motif (green) or the short motif only (orange). These two colors were consistently used to indicate the two specific sub regions in the following figure parts, respectively. (C) Histogram representing the distribution of the long PU.1 motif and only the short one within the PU.1 binding regions relative to the summit of the binding regions (represented as 0). (D) Comparison of tag density between the PU.1 binding regions with the long motif and only the short one. (E) Comparison of percentage of PU.1 binding sites between the long motif-containing and only the short motif-containing along the mean of peak fold enrichment. (F) Conservation analysis of PU.1 binding regions with the long motif or the short one used multiple alignments of 27 vertebrate genomes with Human. All of the regions are aligned at peak summits in a 5^′-to-3^′ manner. (G) Proportions of the long and only short motif-containing PU.1 binding sites from the promoter (inner circle) or non-promoter (outer circle) regions showed with annular charts. The proportion of neither the long nor short motif-containing PU.1 binding regions was indicated with the gray color.