Fig. 1

Overlap of TF and interactions between data sets. a The coverage of S. cerevisiae TFs (rows) in GRNs derived from the four data sets (columns); ChIP: Chromatin Immuno-Precipitation. Deletion: knockout mutant expression data. PBM: Protein-Binding Microarray. PWM: Position Weight Matrix. The numbers of TFs shared between datasets or that dataset-specific are indicated on the right. b Percentage of target genes of each S. cerevisiae TF (row) belonging to each GRN. Darker red indicates a higher percentage of interactions found within a data set, while darker blue indicates a lower percentage of interactions. TFs are ordered as in (a) to illustrate that, despite the overlap seen in (a), there is bias in the distribution of interactions across data sets. c Venn-diagram of the number of overlapping TF-target interactions from different data sets: ChIP (blue), Deletion (red), PWM1 (orange), PWM2 (purple), PBM (green). The outermost leaves indicate the number of TF-target interactions unique to each data set while the central value indicates the overlap amongst all data sets. d Expected and observed numbers of overlaps between TF-target interaction data sets. Boxplots of the expected number of overlapping TF-target interactions between each pair of GRNs based on randomly drawing TF-target interactions from the total pool of interactions across all data sets (see Methods). Blue filled circles indicate the observed number of overlaps between each pair of GRNs. Of these, ChIP, Deletion, and PWM1 have significantly fewer TF-target interactions with each other than expected