Extended Data Fig. 6: Core sets of TFBSs are conserved across flowering plants.

Scatterplot showing enrichment of each TF’s core regulon (defined as target orthogroups conserved in both grasses and all four brassica), for TFs assayed in the 10 species multiDAP experiment. The enrichment scores (y-axis) indicate the extent to which the number of TF target genes shared by both grasses and brassica species was more than expected by chance, given the number of TF target genes conserved within each lineage alone. The vast majority of TFs showed significant enrichment scores (blue dots), indicating that persistent core regulons are a common feature of TF regulatory networks. To ensure meaningful statistics, only the 70 TFs targeting at least 150 total brassica-c4 or grass-c2 target orthogroups were tested. Each point represents a single TF, and x-axis shows the total number of brassica-c4 orthogroups, dot size shows the total number of grass c2-orthogroups, and the y-axis shows the enrichment of orthogroups shared between these two sets. To calculate enrichments, true counts of core regulon target orthogroups for each TF (shown in parentheses after TF name for top examples) were compared to background distributions generated by shuffling orthogroup labels for c2-grass TFBSs 1,000 times. Significance (dot color) was calculated as the number of times the shuffled core regulon count met or exceeded the actual count, followed by FDR correction. Significance was assessed at FDR < 0.05. Enrichment score (y-axis) was calculated as the fold change between the actual count and the average shuffled count.