σB-dependent genes identified by RNA-Seq and microarray analyses. Venn diagram of σB-dependent genes identified in stationary phase cells in this study and in previous microarray studies of stationary phase L. monocytogenes [10,12]. Numbers in bold are the number of up-regulated annotated CDS identified as σB-dependent in each study; numbers followed by down arrows are down-regulated σB-dependent genes. No down-regulated σB-dependent genes were identified by RNA-Seq. The 13 genes identified as σB-dependent in stationary phase only by RNA-Seq, but not by previous microarray studies of L. monocytogenes 10403S, include 5 genes that had been found to be σB-dependent, by microarray studies  in salt stressed cells (see Table 5). In a number of instances, (e.g. opuCB, rsbX; See Additional file 8: Comparison of genes found to be σB-dependent by microarray analysis and not by RNA-Seq) genes with significantly different transcript levels in both microarrays [10,12] had significant binomial probabilities (q < 0.05) and a fold change ≥ 2.0 for most of the possible combinations (i.e. 10403S replicate 1 vs ΔsigB replicate 1; 10403S replicate 1 vs ΔsigB replicate 2; 10403S replicate 2 vs ΔsigB replicate 1; 10403S replicate 2 vs ΔsigB replicate 2), but not for all four comparisons and these genes were, therefore, not identified as showing significant differences in normalized RNA-Seq coverage (based on our conservative definition of genes with significant differences in normalized RNA-Seq coverage); see Additional file 8: Comparison of genes found to be σB-dependent by microarray analysis and not by RNA-Seq for detailed RNA-Seq data for genes identified as σB-dependent by microarrays, but not by RNA-Seq.
Oliver et al. BMC Genomics 2009 10:641 doi:10.1186/1471-2164-10-641