Table 2.
Time course: KEGG cellular pathways and gene ontology
| Time | KEGG cellular pathway name | IF | GO up-regulated genes | GO down-regulated genes |
|---|---|---|---|---|
| 0.5 | No significant genes | No significant genes | No significant genes | |
| 1 | Epithelial cell signaling in Helicobacter pylori infection | 16.6 | No significant GO | No significant genes |
| Cytokine-cytokine receptor interaction | 8.1 | |||
| Bladder cancer | 7.5 | |||
| Toll-like receptor signaling pathway | 6.6 | |||
| Base excision repair | 6.0 | |||
| Primary immunodeficiency | 5.9 | |||
| Pathways in cancer | 5.4 | |||
| 3 | Epithelial cell signaling in Helicobacter pylori infection | 17.8 | anti-apoptosis | No significant GO |
| Pathways in cancer | 16.9 | regulation of retroviral genome | ||
| Small cell lung cancer | 14.2 | replication | ||
| MAPK signaling pathway | 14.2 | T-helper 1 cell differentiation | ||
| Apoptosis | 12.5 | negative regulation of LPS-mediated signaling pathway | ||
| Adipocytokine signaling pathway | 12.3 | negative regulation of smooth muscle cell migration | ||
| Prostate cancer | 11.4 | regulation of MAP kinase activity chemotaxis | ||
| Toll-like receptor signaling pathway | 11.1 | protein amino acid dephosphorylation | ||
| T cell receptor signaling pathway | 10.5 | neutrophil activation | ||
| B cell receptor signaling pathway | 9.9 | entrainment of circadian clock | ||
| 6 | Phosphatidylinositol signaling system | 32.2 | anti-apoptosis | No significant GO |
| Epithelial cell signaling in Helicobacter pylori infection | 15.5 | regulation of retroviral genome | ||
| Small cell lung cancer | 14.2 | replication | ||
| Pathways in cancer | 12.4 | T-helper 1 cell differentiation | ||
| Apoptosis | 11.6 | neutrophil activation | ||
| Adipocytokine signaling pathway | 10.1 | negative regulation of I-kappaB | ||
| Toll-like receptor signaling pathway | 8.9 | kinase/NF-kB cascade | ||
| MAPK signaling pathway | 8.7 | induction of positive chemotaxis | ||
| Bladder cancer | 8.5 | myeloid dendritic cell differentiation | ||
| B cell receptor signaling pathway | 8.3 | |||
| 12 | Leukocyte transendothelial migration | 309.7 | cell cycle arrest | response to unfolded protein |
| Cell adhesion molecules (CAMs) | 75.4 | amino acid transport | S-adenosylmethionine biosynthetic process | |
| DNA replication | 25.0 | positive regulation of transcription | ||
| Cell cycle | 20.0 | response to stress | ||
| Pathways in cancer | 19.4 | regulation of MAP kinase activity | ||
| p53 signaling pathway | 17.0 | |||
| Antigen processing and presentation | 15.7 | |||
| MAPK signaling pathway | 13.2 | |||
| Small cell lung cancer | 12.2 | |||
| Circadian rhythm | 11.9 | |||
| 24 | Leukocyte transendothelial migration | 80.3 | keratinocyte differentiation | cholesterol biosynthetic process |
| Cell cycle | 24.4 | amino acid transport | response to unfolded protein | |
| p53 signaling pathway | 20.9 | keratinization | isoprenoid biosynthetic process | |
| Circadian rhythm | 18.6 | angiogenesis | creatine biosynthetic process | |
| DNA replication | 18.0 | apoptosis | response to oxidative stress | |
| Adherens junction | 16.1 | response to stress | ||
| Pathways in cancer | 14.9 | cell cycle arrest | ||
| Nucleotide excision repair | 14.3 | pyrimidine nucleotide metabolic | ||
| Ubiquitin mediated proteolysis | 14.2 | process | ||
| Phosphatidylinositol signaling system | 13.7 | induction of positive chemotaxis | ||
Significantly impacted KEGG cellular pathways and enriched Gene Ontology terms (biological processes only) (p < 0.05) at different time points following co-culture of H. pylori and AGS cells. Top 10 pathways/ontologies included where number exceeds 10. IF = impact factor