Table 2.
Most enriched gene sets representing pathways associated with intestinal cell function, core signaling and cell survival in Caco-2 cells cultured under dynamic conditions compared to static conditions.
| KEGG pathway name | KEGG category | KEGG category subgroup | Size | NES | p-value | FDR |
|---|---|---|---|---|---|---|
| Upregulated gene sets | ||||||
| Endocytosis | Cellular processes | Transport and catabolism | 243 | 1.42 | 3.4E−03 | 7.8E−02 |
| NOD-like receptor signaling pathway | Organismal system | Immune system | 168 | 1.93 | 0.00E+00 | 5.6E−04 |
| RIG-I-like receptor signaling pathway | Organismal system | Immune system | 67 | 1.60 | 3.8E−03 | 2.8E−02 |
| Cytosolic DNA-sensing pathway | Organismal system | Immune system | 58 | 2.01 | 0.0E+00 | 1.7E−04 |
| IL-17 signaling pathway | Organismal system | Immune system | 93 | 1.72 | 3.7E−04 | 9.5E−03 |
| MAPK signaling pathway | Environmental information processing | Signal transduction | 292 | 1.60 | 0.0E+00 | 2.7E−02 |
| TGF-beta signaling pathway | Environmental information processing | Signal transduction | 92 | 1.47 | 1.3E−02 | 5.9E−02 |
| Jak-STAT signaling pathway | Environmental information processing | Signal transduction | 158 | 1.41 | 1.1E−02 | 8.3E−02 |
| NF-kappa B signaling pathway | Environmental information processing | Signal transduction | 97 | 1.96 | 0.0E+00 | 3.5E−04 |
| TNF signaling pathway | Environmental information processing | Signal transduction | 110 | 2.00 | 0.0E+00 | 2.2E−04 |
| Cell cycle | Cellular processes | Cell growth and death | 124 | 1.92 | 0.0E+00 | 6.5E−04 |
| Apoptosis | Cellular processes | Cell growth and death | 133 | 1.66 | 1.8E−04 | 1.6E−02 |
| Necroptosis | Cellular processes | Cell growth and death | 128 | 1.77 | 0.0E+00 | 6.2E−03 |
| p53 signaling pathway | Cellular processes | Cell growth and death | 72 | 1.70 | 1.1E−03 | 1.1E−02 |
| Cellular senescence | Cellular processes | Cell growth and death | 158 | 1.39 | 1.4E−02 | 9.3E−02 |
| Downregulated gene sets | ||||||
| Drug metabolism-cytochrome P450 | Metabolism | Xenobiotics biodegradation and metabolism | 62 | − 2.00 | 0.0E+00 | 4.4E−04 |
| Drug metabolism-other enzymes | Metabolism | Xenobiotics biodegradation and metabolism | 70 | − 1.42 | 2.5E−02 | 8.5E−02 |
| ABC transporters | Environmental information processing | Membrane transport | 45 | − 1.48 | 2.9E−02 | 5.8E−02 |
| Carbohydrate digestion and absorption | Organismal system | Digestive system | 39 | − 2.19 | 0.0E+00 | 5.7E−05 |
| Protein digestion and absorption | Organismal system | Digestive system | 83 | − 2.23 | 0.0E+00 | 1.1E−04 |
| Fat digestion and absorption | Organismal system | Digestive system | 41 | − 2.17 | 0.0E+00 | 3.8E−05 |
| Vitamin digestion and absorption | Organismal system | Digestive system | 23 | − 2.00 | 0.0E+00 | 4.8E−04 |
| Phosphatidylinositol signaling pathway | Environmental information processing | Signal transduction | 99 | − 1.60 | 2.2E−03 | 2.9E−02 |
| AMPK signaling pathway | Environmental information processing | Signal transduction | 119 | − 1.39 | 2.1E−02 | 9.9E−02 |