Table 3.
Functional Evaluation of the S. Typhimurium Expression Classes.
| S. Typhimurium expression class | Scl1 | Scl2 | Scl3 | Scl4 | Scl5 |
|---|---|---|---|---|---|
| No. genes | 833 genes | 545 genes | 741 genes | 445 genes | 321 genes |
| GO enrich.a | Amino acid biosynthesis | Cell cycle | Transport proteins | Aerobic respiration | Response to stress |
| Sulfur metabolism | Cellular component biosynthesis | Cell adhesion | Nitrogen compound biosynthesis | ||
| Vitamin biosynthesis | Lipid biosynthesis | Cell motility | |||
| Transcription | |||||
| Translation | |||||
| Infection genesb | 11 inf. genes | 5 inf. genes | 28 inf. genes | 5 inf. genes | 7 inf. genes |
| Essential genesc | 30 ess. genes | 64 ess. genes | 28 ess. genes | 28 ess. genes | 12 ess. genes |
| TF pred. targetsd | (FadR) | (ArgP) | IclR | IscR | Fis |
| (TyrR) | (Fur) | NanR | FlhDC | (PhoP) | |
| (GntR) | (DnaA) | (FNR) | (GalR) | (FruR) | |
| (CRP) | (MelR) | (GlpR) | |||
| (ArcA) | |||||
| (H-NS) | |||||
| (SoxS) | |||||
| ArcA pot. targetse | 36 targets | 27 targets | 87 targets | 46 targets | 25 targets |
| SF presentf | σ24 | σ28 | σ32 | ||
| σ54 | σ38 | ||||
| σ70 |
aSummary of GO enrichment results, full listing available in supplementary table S4, Supplementary Material online.
bGenes required for long term infection as identified by Lawley et al. (2006).
cEssential S. Typhimurium genes.
dTarget genes for given TF enriched in cluster, TFs in parenthesis were not significant according to multiple testing criterion, full listing available in supplementary table S5, Supplementary Material online.
eGenes directly or indirectly regulated by ArcA as identified by Evans et al. (2011).
fGene coding for SF present in cluster.