Graphical summary of differential sense and antisense expression (DE) in Rho⁺ and Δ<i>rho</i> across strands and growth phases.

DE compared to WT (q-value≤0.05 and |log2FC|≥1) is shown for the antisense (A) and sense (B) strands of the 4,292 AL009126.3-annotated genes. Up: Barplot representation of the numbers of DE genes: numbers reported above each bar correspond to the total of DE genes and, in parentheses, to the subset exhibiting a minimal expression of log2(fpkm+5) ≥5 in one of the two compared genetic backgrounds. Below: Cluster heatmaps highlighting overlaps between these sets of DE genes: up-regulated genes in yellow, down-regulated genes in blue; all other genes, for which there is no statistical evidence for DE, are in gray. Left-side of each heatmap: average-link hierarchical clustering tree based on pairwise distance between genes (L1-norm after encoding down-regulation and up-regulation as -1 and 1, 0 otherwise). (C) Barplot representation of the numbers of DE S-segments, which were defined regarding to their locations as described in [15]: 5’- and 3’-UTR (for all 5’- and 3’-untranslated regions, respectively), inter and intra (for regions situated between genes), and indep (for independently transcribed segments). The up-regulated S-segments are in yellow, down-regulated are in blue. The number on the left side indicates the total number of S-segments of each defined category. The numbers reported above each bar correspond to the total of DE S-segments and, in parentheses, to the subset exhibiting a minimal expression of log2(fpkm+5) ≥5 in one of the two compared genetic backgrounds.