Table 1.
Enriched KEGG pathways in periodontitis.
| Pathway or module | Background1 | Up2 | Down3 | FDR4 |
|---|---|---|---|---|
| flagellar assembly | 38 | 25 | 0 | 0 |
| rod, hook and filament | 19 | 14 | 0 | 0.001 |
| flagellar export apparatus | 12 | 8 | 0 | 0.047 |
| bacterial chemotaxis | 26 | 12 | 0 | 0.001 |
| type III secretion system | 27 | 8 | 0 | 0.001 |
| SEC (secretion) system | 12 | 3 | 0 | 0.229 |
| aminotransferase, class III | 16 | 3 | 0 | 0.14 |
| arginine and proline metabolism | 90 | 9 | 0 | 0.152 |
| alanine, aspartate and glutamate metabolism | 44 | 6 | 1 | 0.202 |
| gluconeogenesis, oxaloacetate => fructose-6P | 20 | 5 | 0 | 0.162 |
| glycine, serine and threonine metabolism | 67 | 14 | 1 | 0.041 |
| nicotinate and nicotinamide metabolism | 34 | 6 | 0 | 0.156 |
| type III CRISPR-Cas system | 13 | 5 | 0 | 0.089 |
| two component system proteins | 11 | 7 | 0 | 0.095 |
| fatty acid biosynthesis, elongation | 12 | 4 | 0 | 0.159 |
| butanoate metabolism | 69 | 8 | 1 | 0.172 |
| reductive citrate cycle | 37 | 8 | 1 | 0.084 |
| one carbon pool by folate | 21 | 5 | 0 | 0.149 |
Gene sets with FDR ≤ 0.25 and number of expressed genes ≥10 are shown. Gene set enrichment was performed as described in Materials and Methods.
1Number of expressed KO genes in periodontitis for each enriched pathway.
2Number of up-regulated KO genes in periodontitis for each enriched pathway.
3Number of down-regulated KO genes in periodontitis for each enriched pathway.
4FDR of statistical test for the gene set emrichment analysis.