Figure 1

EREs and ChIP sites. A. Number of hERα sites for 1 kbp sequences centered around the ChIP sites identified by SLM. The number of sites is computed from a Hidden Markov Model (cf. Methods) using posterior decoding. Results are stratified in function of the strength of the binding site (t-score). The density profile (red) shows bimodality for high t-scores. The median (dots) is calculated in bins of one unit in t-scores. A smoothed estimator (in grey) has been added as visual aid. The cut-offs used for defining highest (t < 16) and lower stringency sites (t > 10) are indicated with vertical lines. The monotonous trend can be approximated by a sigmoid (tanh) function with half-height at t~10 and saturating at t~16 (>90%). B. Left: Average occupation profile at each genomic position computed using posterior decoding for the hERα consensus (e.g. 0.01 means that 1% of sequences have an ERE at this precise position). The profile is centered on the mode of the ChIP-chip site (red dashed line). Right: Fraction of EREs within a given radius of the mode of the ChIP signal. The ChIP sites identified with SLM have a width of about 1 kbp (width of the peak) while the binding sites for the 80% sites with a consensus (one position with posterior probability >0.5) are found within 200-bp of the mode in the t-profile.