TABLE 1 .
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) |
Genes were classified with upstream σB-dependent promoters by in silico analysis using a hidden Markov model as described by Oliver et al. (17).
Genes were classified as positively regulated by σB 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).
Genes were classified as negatively regulated by σB 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).
Genes reported as differentially regulated in previous microarray or RNA-Seq studies (5–8, 16, 17), including genes reported as negatively regulated by σB in one study and positively regulated by σB in another study and genes that were found to be negatively and positively regulated by σB under different conditions in the same study (see Table S2).