Fig. 4

ICA provides answers to unasked questions. a Schematic illustration of appending four new datasets^42,43,44,45 to PRECISE. b Comparison of ICA results on three nested subsets of the PRECISE compendium. Each node represents an i-modulon and is colored by type (e.g. regulatory or genomic). Components are linked by an arrow if their gene coefficients are correlated (Pearson R > 0.5). Arrow widths and color represent correlation strength. c Compendium-wide activities for selected i-modulons. Each bar represents the activity of the denoted i-modulon in a single expression profile. Starred i-modulons were discovered after addition of the four new datasets. I-modulons in red font propose regulons for previously uncharacterized TFs. I-modulons are grouped based on the genetic perturbation (e.g. TF KO, mutation in regulator) that activated the specific i-modulon. The dataset responsible for the i-modulon activation is highlighted in gray for each i-modulon. d Venn diagram comparing genes in the YiaJ i-modulon and genes with ChIP-exo determined binding sites for YiaJ. e Venn diagram comparing genes in the YieP i-modulon and genes with ChIP-exo determined binding sites for YieP. f Predicted regulatory roles based on i-modulons for YneJ, YgbI, and KdgR. g Scatterplot of gene expression in strain with 39-gene deletion against the Deletion-1 i-modulon gene coefficients. The Deletion-1 i-modulon has a negative activity for the strain with the deletion, indicating that genes with positive i-modulon coefficients are not expressed in this strain, whereas genes with negative i-modulon coefficients are over-expressed in this strain.