Table 2.
Functional Evaluation of the E. coli Expression Classes.
| E. coli expression class | Ecl1 | Ecl2 | Ecl3 |
|---|---|---|---|
| No. genes | 1,094 genes | 734 genes | 1,058 genes |
| GO enrich.a | Chemotaxis | Cell division | Multiorganism processes |
| Energy metabolism | Cell wall assembly | Cell adhesion | |
| Amino acid metabolism | Carbohydrate biosynthesis | Carbohydrate catabolism | |
| Nucleotide metabolism | Nucleotide biosynthesis | Transport proteins | |
| Cation/osmotic stress | Transcription | Acidity stress | |
| Translation | Starvation stress | ||
| Toxin stress | |||
| Oxidative stress | |||
| Funct. div.b | Anabolism | Anabolism | Catabolism |
| 2.43E-12 enrich. p-val | 2.2E-3 enrich. p-val | 8.51E-6 enrich. p-val | |
| Central metabolism | |||
| 8.51E-6 enrich. p-val | |||
| Ess. genesc | 60 essential genes | 204 essential genes | 8 essential genes |
| 3.3E-9 depl. p-val | 2.4E-12 enrich. p-val | 9.8E-45 depl. p-val | |
| TF targetsd | FlhDC | LexA | CRP |
| (TrpR) | SoxS | IHF | |
| (TyrR) | DnaA | FhlA | |
| (Lrp) | PurR | NarP | |
| GadE | CysB | ||
| SF targetsd | σ28 | σ70 | σ38 |
| (σ70) | (σ24) | ||
| SF presente | σ28 | σ54 | σ24 |
| σ32 | σ38 | ||
| σ70 |
aSummary of GO enrichment results, full listing available in supplementary table S2, Supplementary Material online.
bEnriched functional divisions using the annotation provided by Seshasayee et al. (2009).
cEssential E. coli genes.
dTarget genes for given TF or SF enriched in cluster, TFs in parenthesis were not significant according to multiple testing criterion, full listing available in supplementary table S3, Supplementary Material online.
eGene encoding for SF present in cluster.