Extended Data Fig. 5: Conservation of P. simiae TF targets.
From: Persistence and plasticity in bacterial gene regulation
Quantification of TF target gene conservation across species reveals global patterns of conservation and evolution. Gray-shaded vertical bars mark phylogenetic clades (top to bottom): Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Bacteroidetes, Gram-positive. For each P. simiae TF (rows), the set of target genes in P. simiae was compared to the set of target genes in each of the other 47 species (columns, labeled 1-48). The two species used in this study as a source of TFs (E. coli and P. simiae) are indicated in the phylogenetic tree as colored dots (blue and green, respectively). Target gene similarity was quantified as the number of matching orthologs appearing in pairs of target gene sets. P-values were determined by comparing to a mock set of target genes randomly selected from each genome for 10,000 iterations (see Methods for details). Blue-to-red shades correspond to significance, with darkest red representing the most significant degree of conservation (p-value < = 1e-4).
