Figure 2

Comparison of the characteristics of ChIP-chip and ChIP-seq profiles. Figures (a) and (b) summarize the skewness of the signal distributions of all the ChIP-chip and ChIP-seq profiles. A ChIP profile with a good signal-to-noise ratio should have a signal distribution that is positively skewed (i.e., skewness >0). Higher skewness implies a better signal-to-noise ratio. In almost all cases, a ChIP-seq profile has higher signal skewness than its corresponding ChIP-chip profile. Figures (c) and (d) show the ratios of the number and mean width of the enrichment regions identified by ChIP-chip and ChIP-seq using our heuristic approach (see the Methods section of this paper). In almost all cases, we can identify larger number and narrower peaks in a ChIP-seq profile than its corresponding ChIP-chip profile.