TABLE 1.
Ontology analysis of epithelial cell pathways impacted by infection with F. nucleatum or S. gordoniia
| Impacted pathwayb | Impact factorc | No. of input genes/no. of pathway genesd |
|---|---|---|
| F. nucleatum-infected cells | ||
| Phosphatidylinositol signaling pathway | 178.648 | 11/79 |
| MAPK signaling pathway | 173.395 | 43/273 |
| Toll-like receptor signaling pathway | 105.509 | 13/91 |
| Regulation of actin cytoskeleton | 91.253 | 31/206 |
| Cell cycle | 75.558 | 20/112 |
| Wnt signaling pathway | 69.173 | 26/147 |
| Cytokine-cytokine receptor interaction | 61.258 | 24/256 |
| Focal adhesion | 55.455 | 25/194 |
| S. gordonii-infected cells | ||
| MAPK signaling pathway | 248.404 | 57/273 |
| Toll-like receptor signaling pathway | 179.365 | 20/91 |
| Phosphatidylinositol signaling pathway | 172.608 | 9/79 |
| Cell cycle | 95.198 | 30/112 |
| Regulation of actin cytoskeleton | 93.062 | 39/206 |
| Wnt signaling pathway | 74.227 | 31/147 |
| Cytokine-cytokine receptor interaction | 72.52 | 29/256 |
| Focal adhesion | 72.117 | 37/194 |
| Tight junction | 64.433 | 21/119 |
| Jak-STAT signaling pathway | 56.993 | 25/153 |
| Apoptosis | 52.94 | 20/84 |
a
The epithelial cell pathways were determined by Pathway Express (33).
b
Kyoto Encyclopedia of Genes and Genomes pathways (http://www.genome.jp/kegg/).
c
The impact factor measures the pathways most affected by changes in gene expression by considering the proportion of differentially regulated genes, the perturbation factors of all pathway genes, and the propagation of these perturbations throughout the pathway. Only pathways with an impact factor greater than 50 are included.
d
Number of regulated genes in a pathway/total number of genes currently mapped to this pathway.