Table 2. Distribution of categories of enriched pathways depending on their association with treatments.
| KEGG Path. | KEGG Path. | KEGG Path. | KEGG Path. | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Metabolism | Cell Growth | Immune | Others | ||||||
| # | % | # | % | # | % | # | % | ||
| All 4 ligands | 4h | 3 | 4.2 | 1 | 2.1 | 3 | 13.0 | 0 | 0.0 |
| combined | 24h | 38 | 52.8 | 17 | 35.4 | 7 | 30.5 | 2 | 20.0 |
| 4h and 24h | 31 | 43.0 | 30 | 62.5 | 13 | 56.5 | 8 | 80.0 | |
| Total | 72 | 100.0 | 48 | 100 | 23 | 100.0 | 10 | 100.0 | |
| FXR-L | alone | 15 | 23.1 | 21 | 47.7 | 16 | 76.2 | 8 | 80.0 |
| sh.with LXR-L | 7 | 10.8 | 15 | 34.1 | 2 | 9.5 | 0 | 0.0 | |
| sh.with PPARα-L | 25 | 38.5 | 8 | 18.2 | 3 | 14.3 | 2 | 20.0 | |
| FXR-L, LXR-L and PPARα-L | 18 | 27.7 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| Total | 65 | 100.0 | 44 | 100 | 21 | 100.0 | 10 | 100.0 | |
| LXR-L | alone | 2 | 6.9 | 0 | 0.0 | 0 | 0.0 | 0 | N/A |
| sh.with FXR-L | 7 | 24.1 | 15 | 100.0 | 2 | 100.0 | 0 | N/A | |
| sh.with PPARα-L | 2 | 6.9 | 0 | 0.0 | 0 | 0.0 | 0 | N/A | |
| FXR-L, LXR-L and PPARα-L | 18 | 62.1 | 0 | 0.0 | 0 | 0.0 | 0 | N/A | |
| Total | 29 | 100.0 | 15 | 100.0 | 2 | 100.0 | 0 | N/A | |
| PPARα-L | alone | 2 | 4.3 | 1 | 11.1 | 1 | 25.0 | 0 | 0.0 |
| sh.with FXR-L | 25 | 53.2 | 8 | 88.9 | 3 | 75.0 | 2 | 100.0 | |
| sh.with LXR-L | 2 | 4.3 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| FXR-L, LXR-L and PPARα-L | 18 | 62.1 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| Total | 47 | 100.0 | 9 | 100.0 | 4 | 100.0 | 2 | 100.0 | |
| CDCA | alone | 1 | 1.9 | 3 | 8.1 | 1 | 6.7 | 0 | 0.0 |
| sh. with FXR-L | 9 | 16.7 | 14 | 37.8 | 10 | 66.7 | 7 | 87.5 | |
| sh.with LXR-L | 1 | 1.9 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| sh.with PPARα-L | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| sh.with FXR-L and LXR-L | 4 | 7.4 | 12 | 32.4 | 1 | 6.7 | 0 | 0.0 | |
| sh.with FXR-L and PPARα-L | 22 | 40.7 | 8 | 21.6 | 3 | 20.0 | 1 | 12.5 | |
| sh.with LXR-L and PPARα-L | 1 | 1.9 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| CDCA, FXR-L, LXR-L, PPARα-L | 16 | 29.6 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | |
| Total | 54 | 100.0 | 37 | 100.0 | 15 | 100.0 | 8 | 100.0 | |
Enriched KEGG pathways were grouped manually into 4 wide categories (“Metabolism”, “Cell growth and death”, “Immune system” and “Other”). Top four rows: Number and percentage of positively enriched KEGG pathways from all treatments combined, found either at a single time point (4h, 24h) or at both time points (4h and 24h) in each category; totals from both time points. Central section: Numbers and percentages of pathways found affected by each of the three synthetic ligands (at any or both time points), with a breakdown of how many DE genes and enriched pathways are exclusive to one treatment and how many are shared between two or all three treatments. Bottom section: Numbers and percentages for the natural ligand CDCA, showing the overlap with pathways affected by the three synthetic ligands. (Due to rounding error, percentages do not add up to exactly 100.0 in some table cells.). sh.: shared