TABLE 1 .

Relationships between genes identified as differentially expressed after treatment with FPSS and genes identified previously as σ^B dependent

Gene type	No. of genes (no. with an upstream σB-dependent promotera)
	Downregulated by FPSS	Upregulated by FPSS
Identified previously as positively regulated by σBb	152 (86)	2 (0)
Identified previously as negatively regulated by σBc	2 (0)	7 (0)
Reported previously to be positively or negatively regulated under different conditions or in different studiesd	4 (0)	0
Having no previous evidence of σB-dependent transcript levels	50 (0)	23 (0)
Total	208 (86)	32 (0)

^a Genes were classified with upstream σ^B-dependent promoters by in silico analysis using a hidden Markov model as described by Oliver et al. (17).

^b Genes were classified as positively regulated by σ^B based on evidence from at least one of six previous microarray or RNA-Seq studies (5–8, 16, 17) (see Tables S2 and S3 for details).

^c Genes were classified as negatively regulated by σ^B based on evidence from at least one of six previous microarray or RNA-Seq studies (5–8, 16, 17) (see Tables S2 and S4 for details).

^d Genes reported as differentially regulated in previous microarray or RNA-Seq studies (5–8, 16, 17), including genes reported as negatively regulated by σ^B in one study and positively regulated by σ^B in another study and genes that were found to be negatively and positively regulated by σ^B under different conditions in the same study (see Table S2).