Comparison of transcriptional and phenotypic differences between WT and <i>rho</i>* cells.

<p>(A) Key pathways showing significant patterns of over- or under-expression in <i>rho</i>* cells, assessed using iPAGE <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002744#pgen.1002744-Goodarzi3" target="_blank">[16]</a>. The log ratios of <i>rho</i>* to WT RNA at each probe were discretized as shown at the head of each chart (breaks correspond to 3, 2, and 1.5-fold differences in either direction). For each pathway, coloring at each cluster corresponds to the degree of over- or under-representation of that cluster in the relative expression level of genes in that pathway (with magnitude equal to the negative log₁₀ p-value for significance of the representation; positive and negative scores represent over- and under-representation, respectively). (B) Ratios of <i>rho</i>* to WT growth rates under a variety of conditions showing significant fitness differences; dashed lines indicate the ratio under the reference condition (black) or for equal growth rates (green). Error bars show a 95% confidence interval based on 10,000 samples from the posterior parameter distribution (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002744#pgen.1002744.s021" target="_blank">Text S1</a>, Section 1.3). Abbreviations are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002744#pgen.1002744.s019" target="_blank">Table S10</a>. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002744#pgen-1002744-t001" target="_blank">Table 1</a> for concentrations of antibiotics used. Ratios of <i>rho*</i> to WT growth rates differ significantly from that in the reference condition M9t/glucose (non-overlapping 95% confidence intervals) for all cases except LB, which is included simply as a second useful reference.