Levels of factor occupancy and genome accessibility correlate. The median DNase-seq tag density in non-overlapping cohorts of 200 1-kb ChIP-chip peaks is shown down the ChIP-chip rank list (continuous lines). The ChIP-chip data are from stage 5 embryos and the DNaseI accessibility data are from stages 5 (green) and 14 (purple). The 95% confidence limit for median DNaseI accessibility of each cohort is indicated. Shown also is the percent of ChIP-chip peaks that are overlapped by 5% FDR accessible regions in stage 5 embryos (dashed green line). The regions most highly bound by transcription factors are to the left along the x-axis and results are plotted as far as the 25% FDR cutoff. The location of the ChIP-chip 1% FDR threshold is indicated by the vertical black dotted line. Results for the regulatory transcription factors (a) Dichaete (D) and (b) Twist (TWI) are shown. Additional file 7 shows plots for all 21 regulators.
Li et al. Genome Biology 2011 12:R34 doi:10.1186/gb-2011-12-4-r34