Table 1.
Ontology analysis of calvarial bone and soft tissue pathways impacted by polymicrobial infection with P. gingivalis+T. denticola+T. forsythia1
| Impacted pathway2 | Impact Factor3 | Input genes/no. of pathway genes4 | P Value |
|---|---|---|---|
| Calvarial bone | |||
| Leukocyte transendothelial migration | 55.967 | 49/119 | 0.000E0 |
| Cell adhesion molecules | 45.448 | 49/159 | 0.000E0 |
| Adherens junction | 31.999 | 37/77 | 3.510E-13 |
| Antigen processing and presentation | 17.26 | 37/100 | 5.829E-7 |
| Phosphatidylinositol signaling system | 15.717 | 28/75 | 2.497E-6 |
| Ribosome | 13.463 | 55/115 | 2.058E-5 |
| DNA replication | 12.825 | 26/36 | 3.723E-5 |
| ECM-receptor interaction | 11.145 | 45/81 | 1.755E-4 |
| Focal adhesion | 9.608 | 94/199 | 7.127E-4 |
| B cell receptor signaling pathway | 7.748 | 35/71 | 3.776E-3 |
| Apoptosis | 6.122 | 41/93 | 1.563E-2 |
| Natural killer cell mediated cytotoxicity | 5.945 | 47/109 | 1.819E-2 |
| Cell cycle | 5.81 | 54/124 | 2.041E-2 |
| Toll-like receptor signaling pathway | 5.591 | 48/101 | 2.459E-2 |
| VEGF signaling pathway | 5.518 | 36/76 | 2.616E-2 |
| Calvarial tissue | |||
| Leukocyte transendothelial migration | 79.756 | 14/119 | 0.000E0 |
| Cell adhesion molecules | 71.416 | 13/159 | 0.000E0 |
| Adherens junction | 22.027 | 13/77 | 6.282E-9 |
| Phosphatidylinositol signaling system | 14.206 | 7/75 | 1.029E-5 |
| Ribosome | 10.313 | 21/115 | 3.756E-4 |
| PPAR signaling pathway | 7.475 | 14/76 | 4.806E-3 |
| mTOR signaling pathway | 7.117 | 11/55 | 6.584E-3 |
| Insulin signaling pathway | 5.621 | 20/140 | 2.397E-2 |
ECM = extracellular matrix; VEGF = vascular endothelial growth factor; PPAR = peroxisome proliferator-activated receptor; mTOR = mammalian target of rapamycin.
The calvarial bone and tissue gene pathways were determined by Pathway Express (Draghici et al. 2007; Khatri et al. 2007).
Kyoto Encyclopedia of genes and genome pathways (http://www.genome.jp/kegg/).
The impact factor measures the pathways most affected by changes in gene expression in calvarial bone and soft tissue 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 5 are included in this table.
Number of regulated genes in a pathway/total number of genes currently mapped to this pathway. First three pathways that are impacted both in bone and tissue are indicated in bold.