Figure 2

Concordance between promoter occupancy predictions, and evidence for functional regulation and ChIP-chip predictions. (A) The count of predicted promoters bound by NOTCH1, NANOG and SOX2 from ChIP-Seq data is given as data labels, while the proportion of associated genes with evidence for functional regulation from RNAi studies is given on the y-axis. (B) The number of predicted targets for FOXA1 is given as data labels, y-axis reports on the proportion of target predictions lost after TF silencing. (C) Common target gene predictions from ChIP-chip and ChIP-Seq, where data labels give the absolute count of targets predicted from ChIP-Seq data, and the y axis gives the frequency that these predictions were verified by ChIP-chip. We plot data for promoters that are predicted by dIP and not MACS, MACS but not dIP, and both dIP and MACS. dIP predicted more target genes and its predictions agree better with ChIP-chip predictions. (D) Common gene target predictions from ChIP-chip and ChIP-Seq as a function of decreasing ChIP-Seq binding scores. (E) Jaccard's similarity coefficient was used to compare predicted ETS1-target promoters using 3 replicate IPs and 4 replicate IgG control assays, comparing the average similarity between predictions across IgG controls using the same IP (replicate IgG) or across IP assays with the same IgG control (replicate IP); error bars are given as S.E.M.