Table 3.
Top 10 most enriched (based on NES) up- and downregulated pathways related to the intestine in induced pluripotent stem cell derived intestinal epithelial cell layers exposed to 10 mM butyrate compared with the control.
| KEGG pathway name | KEGG category | KEGG category subgroup | Genes | NES | P-value | FDR |
|---|---|---|---|---|---|---|
| Upregulated pathwaysa | ||||||
| DNA replication | Genetic Information Processing | Replication and repair | 36 | 2.43 | 0.000 | 0.000 |
| Mismatch repair | Genetic Information Processing | Replication and repair | 23 | 2.18 | 0.000 | 0.000 |
| Fanconi anemia pathway | Genetic Information Processing | Replication and repair | 54 | 2.15 | 0.000 | 0.000 |
| Homologous recombination | Genetic Information Processing | Replication and repair | 41 | 1.99 | 0.000 | 0.004 |
| RNA polymerase | Genetic Information Processing | Transcription | 29 | 1.72 | 0.007 | 0.058 |
| Fatty acid biosynthesis | Metabolism | Lipid metabolism | 16 | 1.59 | 0.027 | 0.142 |
| Nucleotide excision repair | Genetic Information Processing | Replication and repair | 46 | 1.59 | 0.012 | 0.128 |
| Endocrine and other factor regulated calcium reabsorption | Organismal Systems | Excretory system | 48 | 1.55 | 0.012 | 0.135 |
| Alanine, aspartate and glutamate metabolism | Metabolism | Amino acid metabolism | 35 | 1.48 | 0.035 | 0.150 |
| Mineral absorption | Organismal Systems | Digestive system | 56 | 1.47 | 0.022 | 0.143 |
| Downregulated pathwaysa | ||||||
| P53 signaling pathway | Cellular Processes | Cell growth and death | 73 | − 1.99 | 0.000 | 0.010 |
| Pathogenic Escherichia Coli infection | Human Diseases | Infectious disease: bacterial | 179 | − 1.97 | 0.000 | 0.007 |
| Steroid hormone biosynthesis | Metabolism | Lipid metabolism | 49 | − 1.95 | 0.000 | 0.007 |
| Shigellosis | Human Diseases | Infectious disease: bacterial | 224 | − 1.91 | 0.000 | 0.010 |
| ECM receptor interaction | Environmental Information Processing | Signaling molecules and interaction | 78 | − 1.86 | 0.000 | 0.013 |
| NF kappa B signaling pathway | Environmental Information Processing | Signal transduction | 94 | − 1.83 | 0.000 | 0.020 |
| Glutathione metabolism | Metabolism | Metabolism of other amino acids | 46 | − 1.81 | 0.001 | 0.023 |
| Hippo signaling pathway multiple species | Environmental Information Processing | Signal transduction | 29 | − 1.80 | 0.003 | 0.019 |
| Regulation of actin cytoskeleton | Cellular Processes | Cell motility | 194 | − 1.74 | 0.000 | 0.030 |
| JAK STAT signaling pathway | Environmental Information Processing | Signal transduction | 110 | − 1.73 | 0.000 | 0.030 |
aReferences indicating their role or relationship to the intestine for the selected pathways are given in the supplementary files; Table S1.