Analysis of differential gene expression in the hfq and rsmA mutants. Hfq is an activator while RsmA is a repressor of prodigiosin production as indicated by the level of pigment of the mutant strains. Generation of the hfq::cat, rsmA::Tn double mutant resulted in repression of pigment production indicating that the hfq mutant is epistatic over the rsmA mutant. A -B. The R package, DESeq, was used to analyze differential gene expression of the RNA-seq data. A scatter plot of the fold change (log2 ratio) versus mean expression is shown for the hfq (A) and rsmA (B) mutants. The red circles indicate genes identified as differentially expressed with a 1% false discovery rate according to the method of the Benjamini-Hochberg multiple testing adjustment. C- D. The RNA-seq and iTRAQ-proteomic datasets for the hfq (C) and rsmA (B) mutants were compared by plotting the fold change (log2 ratio) of differentially expressed genes. 13 and 73 genes had fold changes in the same direction in the hfq and rsmA datasets, respectively, which gave a Pearson correlation coefficient > 0.90 and >0.85. E- F. The Venn diagrams illustrate the overlap between the RNA-seq and protein iTRAQ datasets for the hfq and rsmA mutants to identify co-regulated genes (E). The uniquely regulated genes in the RNA and protein datasets for each mutant was combined to produce a list of all the genes that were significantly differentially expressed. The combined datasets for each mutant was also compared to identify the overlap between them (F).