Fig. 3

ICA reveals independent modules within the PurR regulon. a Histograms of gene coefficients in the PurR-1 and PurR-2 i-modulons. b Comparison of genes in the reported PurR regulon (blue), PurR-1 i-modulon (red) and PurR-2 i-modulon (green). Gene names for co-transcribed genes were combined (e.g. codAB represents codA and codB). c Motif identified upstream of genes in the PurR-1 i-modulon compared to the reported PurR motif from RegulonDB⁴. This motif was identified upstream of the guanine/hypoxanthine transporter encoding gene ghxP, although regulator binding was not previously reported. d The two PurR-associated i-modulons exhibited distinct responses to environmental perturbations. Asterisks denote significant i-modulon activities as compared to the reference condition (see the “Methods” section). Each bar represents a single biological replicate. e The PurR-1 i-modulon activity level is highly correlated with purR expression level across all conditions (excluding the PurR knock-out), whereas the PurR-2 i-modulon activity exhibits poor correlation (see Supplementary Fig. 4d). Similar information on all 92 i-modulons is available in Supplementary Data 2. Abbreviations: log-TPM log-transformed transcripts per million.