TABLE 4.
Results of annotation enrichment analysis for the lists of differentially regulated genes at 1.5 h postinfection
| Overrepresented functional family or pathwaya | No. of genes | No. of genes in group/no. of genes in genome (%) | P valueb |
|---|---|---|---|
| Upregulated inside macrophages at 1.5 h | |||
| Citrate cycle (TCA cycle) | 16 | 3.3 | 2.4E−10 |
| ABC transporters, general | 54 | 11.1 | 1.1E−08 |
| Carboxylic acid metabolic process | 39 | 8.0 | 9.6E−07 |
| Cellular respiration/coenzyme catabolic process | 8 | 1.7 | 6.1E−06 |
| Branched-chain-family amino acid metabolic process | 9 | 1.9 | 1.4E−05 |
| Oxidoreductase | 25 | 5.2 | 2.5E−05 |
| Amino acid biosynthetic process | 20 | 4.1 | 4.2E−05 |
| Flavoprotein | 11 | 2.3 | 3.7E−04 |
| Fatty acid metabolism/valine, leucine and isoleucine degradation | 7 | 1.4 | 1.1E−03 |
| Glutamine family amino acid biosynthetic process | 7 | 1.4 | 2.4E−03 |
| Glyoxylate and dicarboxylate metabolism | 7 | 1.4 | 3.8E−03 |
| Hydrolyase | 7 | 1.4 | 3.9E−03 |
| Anion transport | 7 | 1.4 | 7.4E−03 |
| Carbohydrate metabolic process | 23 | 4.7 | 1.5E−02 |
| Glyoxylate metabolic process | 3 | 0.6 | 2.0E−02 |
| Vitamin binding/thiamine pyrophosphate | 6 | 1.2 | 2.4E−02 |
| Downregulated inside macrophages at 1.5 h | |||
| Virulence (ysc and lcr genes) | 10 | 3.9 | 7.0E−07 |
| Iron ion transport | 9 | 3.5 | 1.3E−05 |
| Protein biosynthesis | 10 | 3.9 | 7.3E−05 |
| Purine metabolism | 13 | 5.1 | 3.5E−03 |
| tRNA metabolic process | 10 | 3.9 | 7.0E−03 |
| Translation | 14 | 5.5 | 9.7E−03 |
| Pyrimidine metabolism | 9 | 3.5 | 1.1E−02 |
| TonB-dependent receptor, plug | 4 | 1.6 | 1.2E−02 |
| Ribonucleoside metabolic process | 4 | 1.6 | 1.6E−02 |
a
Underlined categories are overrepresented only at 1.5 h postinfection and not at 4 or 8 h postinfection.
b
P values were calculated using Fisher's exact test (see Materials and Methods for details).