Table 4.
IPA summary of liver transcriptomes in hatcling chicks–D2FAST48h vs. D3REFED24h contrast
| Top Canonical Pathways | p-value | Overlap | Ratio |
|---|---|---|---|
| Tryptophan Degradation III | 4.58E-12 | 56.0% | 14/25 |
| NRF2-mediated Oxidative Stress Response | 4.30E-09 | 17.1% | 33/193 |
| Super-pathway of Cholesterol Biosynthesis | 8.44E-09 | 42.9% | 12/28 |
| Protein Ubiquitination Pathway | 1.42E-08 | 14.7% | 39/265 |
| Fatty Acid -oxidation I | 5.11E-08 | 37.5% | 12/32 |
| Top Upstream Regulators | p-value of overlap | # Target genes | |
| HNF4A | 5.44E-22 | 224 | |
| E2F1 | 6.07E-19 | 81 | |
| PPARA | 9.50E-19 | 77 | |
| NFE2L2 | 4.82E-16 | 68 | |
| E2F4 | 7.81E-16 | 48 | |
| Top Molecular and Cellular Functions | p-value | # Genes | |
| Cell Death and Survival | 3.73E-04 - 9.50E-20 | 434 | |
| Cell Cycle | 3.58E-04 - 7.37E-18 | 270 | |
| Cellular Assembly and Organization | 2.92E-04 - 6.25E-17 | 103 | |
| DNA Replication, Recombination, and Repair | 3.58E-04 - 6.25E-17 | 176 | |
| Amino Acid Metabolism | 2.69E-04 - 2.67E-12 | 38 | |
| Physiological System Development and Function | p-value | # Genes | |
| Organismal Survival | 6.21E-09 - 2.57E-09 | 278 | |
| Digestive System Development and Function | 1.35E-04 - 1.47E-07 | 82 | |
| Hepatic System Development and Function | 4.62E-05 - 1.47E-07 | 53 | |
| Organ Morphology | 3.43E-05 - 1.47E-07 | 52 | |
| Organismal Development | 4.62E-05 - 1.47E-07 | 65 | |
| Up-regulated genes | FAST48h-REFED24h | Down-regulated genes | FAST48h-REFED24h |
| IGFBP2 | 3.19 | THRSPA | −5.99 |
| ADSL | 3.19 | ME1 | −4.84 |
| LDHB | 2.90 | SCD | −4.72 |
| MBL2 | 2.85 | LGALS2 | −3.65 |
| ALB | 2.71 | CYP51A1 | −3.30 |
| CYP4A22 | 2.66 | PLIN2 | −3.26 |
| UPP2 | 2.61 | FADS2 | −3.24 |
| BHMT | 2.56 | CDK1 | −3.06 |
| CYP3A7 | 2.40 | RRM2 | −3.03 |
| NEFH | 2.39 | CDCA3 | −2.93 |
Ingenuity Pathway Analysis (IPA) was used for functional analysis of 1198 “Analysis Ready” (AR)-DEGs from the D2FAST48h vs. D3REFED24h contrast. The top 10 up-regulated and down-regulated AR-DEGs are presented along with their respective log2 ratio of treatment conditions