Fig. 4
The FruA regulon is extensive, but does not include all developmentally regulated genes. RNA from a ΔfruA strain was isolated and sequenced. The reads per gene for WT and ΔfruA cells were averaged over the two biological replicates and normalized to library size, and these normalized, average read counts are compared in scatter plots (A). The read counts for WT and ΔfruA for each time point were also compared using HTseq and DEseq, and are presented as bar graphs showing the log2 fold change of genes statistically significantly up-regulated in WT (yellow) and in ΔfruA (blue) (B). HTseq and DEseq were used to generate all pairwise time comparisons for WT and ΔfruA separately, and the log2 fold changes were extracted from the DEseq outputs. Scatter plots (C) represent a comparison between the log2 fold changes for WT on the x-axis, and ΔfruA on the y-axis. Genes that are more highly expressed in WT cells are represented by points below or to the right of the trend line, while genes that are expressed at higher levels in ΔfruA cells are above or to the left the trend line