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. 2014 Jul 10;10(7):e1004495. doi: 10.1371/journal.pgen.1004495

Figure 2. The presence of the extended PHO/PHOL motif does not correlate with efficient PhoRC binding to PREs.

Figure 2

A. The logo representation of the extended PHO/PHOL motif derived from the analysis of the top 100 strongest TSS-proximal PHOL sites. Note the central conserved GCCAT core between positions 6 and 10. B. The logo representation of the sequence motif enriched in the top 100 computationally defined PREs ranked by the strength of PHO ChIP-chip signal. 840 TSS-proximal PHOL binding sites (C, D) and 166 computationally defined PREs that show significant binding of PHO in ChIP-chip experiment (E, F) were divided in bins according to the strength of PHOL/PHO binding. Histograms show the mean score for the sequences best matching the extended PHO/PHOL motif (C, E) or the mean number of conserved GCCAT core sequences (D, F) within each bin. Whiskers indicate 95% confidence intervals. There is a clear statistically significant (Wilcoxon rank sum test) trend for the stronger TSS-proximal PHOL binding sites (C) to have extended PHO/PHOL motifs. This is in contrast to PREs (E) which show no correlation between the strength of PhoRC binding and the presence of extended motifs. We note a weak trend for the stronger binding PREs to have multiple GCCAT cores.