Table 3.
IPA summary of liver transcriptomes in hatchling chicks–D2FAST48h vs. D2REFED4h contrast
| Top Canonical Pathways | p-value | Overlap | Ratio |
|---|---|---|---|
| Super-pathway of Cholesterol Biosynthesis | 4.68E-09 | 35.7% | 10/28 Cholesterol |
| Biosynthesis I-III | 3.23E-08 | 53.8% | 7/13 |
| Protein Ubiquitination Pathway | 9.27E-07 | 9.4% | 24/255 |
| Tryptophan Degradation III | 5.12E-06 | 28.0% | 7/25 |
| Zymosterol Biosynthesis | 1.01E-05 | 66.7% | 4/6 |
| Top Upstream Regulators | p-value of overlap | # Target genes | |
| HNF4A | 1.64E-16 | 126 | |
| PPARA | 3.12E-15 | 46 | |
| NFE2L2 | 2.26E-13 | 44 | |
| TP53 | 3.37E-13 | 92 | |
| E2F1 | 2.26E-11 | 44 | |
| Top Molecular and Cellular Functions | p-value | # Genes | |
| Cell Death and Survival | 7.95E-03 - 5.11E-10 | 206 | |
| Lipid Metabolism | 7.07E-03 - 6.42E-09 | 118 | |
| Small Molecule Biochemistry | 7.12E-03 - 6.42E-09 | 160 | |
| Vitamin and Mineral Metabolism | 7.07E-03 - 4.29E-08 | 39 | |
| Cellular Growth and Proliferation | 8.01E-03 - 7.35E-08 | 217 | |
| Physiological System Development and Function | p-value | # Genes | |
| Reproductive System Development and Function | 4.46E-05 - 4.46E-05 | 8 | |
| Connective Tissue Development and Function | 7.76E-03 - 6.39E-05 | 89 | |
| Embryonic Development | 5.24E-03 - 1.23E-04 | 29 | |
| Cardiovascular System Development and Function | 5.24E-03 - 1.49E-04 | 10 | |
| Tissue Morphology | 6.24E-03 - 1.99E-04 | 63 | |
| Top Up-regulated genes | FAST48h/REFED4h | Top Down-regulated genes | FAST48h/REFED4h |
| CYP4A22 | 2.53 | THRSPA | −4.89 |
| UPP2 | 2.49 | HKDC1 | −4.17 |
| IGFBP2 | 1.79 | CYP51A1 | −3.60 |
| NDRG1 | 1.77 | MSMO1 | −3.44 |
| TDO2 | 1.68 | PLIN2 | −3.37 |
| VSNL1 | 1.68 | ME1 | −2.78 |
| HAL | 1.56 | UGP2 | −2.72 |
| TDH | 1.53 | AACS | −2.68 |
| CEPT1 | 1.51 | ACSBG2 | −2.50 |
| SLC16A5 | 1.46 | INSIG1 | −2.43 |
Ingenuity Pathway Analysis (IPA) was used for functional analysis of 641 “Analysis Ready” (AR)-DEGs found in the D2FAST48h vs.D2REFED4h contrast. The top 10 up-regulated and down-regulated AR-DEGs are presented along with their respective log2 ratio of treatment conditions