Table 2.
IPA summary of liver transcriptomes in hatchling chicks-D2FED48h vs. D2FAST48h contrast
| Top Canonical Pathways | p-value | Overlap | Ratio |
|---|---|---|---|
| Superpathway of Cholesterol Biosynthesis | 1.36E-09 | 42.9% | 12/28 |
| Protein Ubiquitination Pathway | 2.83E-08 | 13.3% | 34/255 |
| Tryptophan Degradation III (Eukaryotic) | 1.65E-07 | 42.9% | 9/21 |
| NRF2-mediated Oxidative Stress Response | 2.46E-07 | 14.4% | 26/180 |
| Cholesterol Biosynthesis I | 5.92E-07 | 53.8% | 7/13 |
| Top Upstream Regulators | p-value of overlap | # Target genes | |
| HNF4A | 1.32E-24 | 174 | |
| PPARA | 1.48E-24 | 69 | |
| TP53 | 2.81E-19 | 119 | |
| NFE2L2 | 3.18E-15 | 51 | |
| MYC | 1.73E-14 | 95 | |
| Top Molecular and Cellular Functions | p-value | # Genes | |
| Lipid Metabolism | 1.83E-03 - 3.91E-15 | 195 | |
| Small Molecule Biochemistry | 2.08E-03 - 3.91E-15 | 277 | |
| Cell Cycle | 2.07E-03 - 1.26E-11 | 175 | |
| Amino Acid Metabolism | 2.08E-03 - 4.78E-11 | 41 | |
| Cell Death and Survival | 1.13E-03 - 5.19E-11 | 31 | |
| Physiological System Development and Function | p-value | # Genes | |
| Tissue Morphology | 2.00E-03 - 4.53E-06 | 92 | |
| Tissue Development | 1.77E-03 - 9.24E-06 | 76 | |
| Connective Tissue Development and Function | 2.00E-03 - 1.09E-05 | 116 | |
| Organismal Survival | 2.13E-05 - 2.13E-05 | 200 | |
| Organismal Development | 1.77E-03 - 4.61E-05 | 28 | |
| Top up-regulated genes | D2FED48h/D2FAST48h | Top down-regulated genes | D2FED48h/D2FAST48h |
| THRSPA | 6.19 | IGFBP2 | −3.45 |
| ME1 | 4.74 | ADSL | −3.18 |
| SCD | 4.74 | CYP3A7 | −3.07 |
| FADS2 | 3.63 | CYP4A22 | −2.74 |
| LGALS2 | 3.47 | CYP2C44 | −2.66 |
| CYP2C44 | 3.24 | LDHB | −2.62 |
| PLIN2 | 3.23 | UPP2 | −2.48 |
| MSMO1 | 2.49 | EHHADH | −2.41 |
| ELOVL6 | 2.43 | HADHB | −2.31 |
| INSIG1 | 2.33 | BHMT | −2.15 |
Ingenuity Pathway Analysis (IPA) was used for functional analysis of 968 Analysis Ready (AR)-DEGs from the D2FED48h vs. D2FAST48h contrast. The top 10 up-regulated and down-regulated AR-DEGs are presented along with their respective log2 ratio of treatment conditions