Extended Data Fig. 4: MultiDAP benchmarking with 92 E. coli TFs.

Triplicate multiDAP experiment with 92 E. coli TFs show that most TFs have strong affinity to a few genomic sites, and some also reproducibly bind weakly to many additional sites. Scatterplots depict the top 10 peaks ranked by fold-enrichment, as compared to merged negative control samples. Boxes represent median and quartiles with whiskers each extending to 1.5x interquartile range and outliers shown as individual points. (a) LacI is known to bind at and repress the promoter upstream of lacZ, along with a weaker accessory binding site just inside the lacZ coding sequence. Both of these binding sites were detected as strong peaks, while the additional weaker detected peaks do not have known biological functions. (b) LexA is known to have multiple binding sites at various promoters. The strongest detected peak corresponds to the known target recN, however in this case even the weakest detected peak in the ruvA promoter is a known functional regulatory site of LexA. (c) and (d) Top 10 peaks detected in triplicate experiments with 92 E. coli TFs.