Fig. 5

Integrating binding data (ChIP-seq) with expression data (RNA-seq) to identify high confidence Gro targets. A score corresponding to the extent of Gro occupancy within genes and adjacent areas was calculated for each gene using a previously published algorithm [35]. The algorithm was adjusted to allow for increased score contribution from regions binding more distantly from the target gene (see Methods). Plotted for each time point are the number of genes either down-regulated (top) or up-regulated (bottom) upon overexpression of Gro (vertical axis) out of the total number of genes meeting a score cutoff of decreasing stringency (horizontal axis). As the threshold Gro occupancy score decreases from left to right the number of genes that exceed this threshold (indicated by the horizontal axis labels) increases from left to right. Where a change in slope is clearly evident, the score cutoff selected for the high-confidence set of Groucho targets is indicated (circles). These are the data obtained using Gro overexpression line A. The “Experimental” curves show the data obtained using the experimentally determined up and down-regulated genes. The “Randomized” curves were obtained by generating random gene sets of the same size as the gene set used for the corresponding “Experimental” curve. Each “Randomized” curve is the average of the results obtained with 100 such random gene sets