Table 5.
Top enriched canonical pathways associated with growth rate, feed intake, and metabolic body weight in Angus, Charolais, and Kinsella Composite (KC) animals
| Trait_breed1 | Ingenuity Canonical Pathways | P-value | Ratio | Z−score2 | Molecules |
|---|---|---|---|---|---|
| ADG_ Angus | Superpathway of Cholesterol Biosynthesis | 1.35E-05 | 0.14 | −2.00 | SQLE, HMGCR, HMGCS1, CYP51A1 |
| Nicotine Degradation II | 2.40E-05 | 0.08 | −2.24 | UGT2B17, FMO2, INMT, CYP51A1, CYP2C19 | |
| LPS/IL-1 Mediated Inhibition of RXR Function | 2.40E-05 | 0.04 | 2.24 | IL1R2, NR0B2, FMO2, CYP7A1, LBP, HMGCS1, SULT2A1, CYP2C19 | |
| Acute Phase Response Signaling | 4.17E-05 | 0.04 | 0.82 | SOCS3, HP, SAA1, SOCS2, SERPINA3, LBP, SERPINE1 | |
| LXR/RXR Activation | 4.37E-05 | 0.05 | −1.00 | IL1R2, SAA1, CYP7A1, LBP, HMGCR, CYP51A1 | |
| ADG_Charolais | LXR/RXR Activation | 1.23E-06 | 0.06 | 0.45 | IL1R2, SCD, RXRG, APOA1, APOA4, FASN, SAA1 |
| LPS/IL-1 Mediated Inhibition of RXR Function | 6.61E-05 | 0.03 | 0.00 | IL1R2, SULT1E1, CPT1B, ALDH3B1, GSTA1, CYP2B6, CYP2C19 | |
| PXR/RXR Activation | 2.09E-04 | 0.06 | NC | SCD, GSTA1, CYP2B6, CYP2C19 | |
| FXR/RXR Activation | 2.63E-04 | 0.04 | NC | APOA1, APOA4, FASN, SAA1, FOXA3 | |
| Glycine Betaine Degradation | 8.71E-04 | 0.20 | NC | SDS, SHMT2 | |
| ADG_KC | PXR/RXR Activation | 3.39E-06 | 0.08 | NC | GSTM1, SCD, CYP7A1, IGFBP1, ALAS1 |
| Interferon Signaling | 7.76E-06 | 0.11 | −2.00 | OAS1, MX1, IFI6, ISG15 | |
| LPS/IL-1 Mediated Inhibition of RXR Function | 1.38E-04 | 0.03 | GSTM1, IL36G, GSTM4, CYP7A1, ALAS1, SOD3 | ||
| 2-amino-3-carboxymuconate Semialdehyde Degradation to Glutaryl-CoA | 3.55E-03 | 1.00 | NC | ACMSD | |
| 4-hydroxybenzoate Biosynthesis | 3.55E-03 | 1.00 | NC | TAT | |
| DMI_ Angus | Pyrimidine Ribonucleotides Interconversion | 1.20E-03 | 0.07 | NC | NUDT5, CMPK2, AK8 |
| Pyrimidine Ribonucleotides De Novo Biosynthesis | 1.38E-03 | 0.07 | NC | NUDT5, CMPK2, AK8 | |
| LXR/RXR Activation | 2.69E-03 | 0.03 | NC | SCD, APOA4, SAA1, CYP7A1 | |
| Activation of IRF by Cytosolic Pattern Recognition Receptors | 3.39E-03 | 0.05 | NC | DHX58, IFIT2, ISG15 | |
| GADD45 Signaling | 3.63E-03 | 0.11 | NC | GADD45B, CDKN1A | |
| DMI_Charolais | LPS/IL-1 Mediated Inhibition of RXR Function | 2.63E-10 | 0.07 | 0.33 | IL1R2, ABCG8, GSTM1, ABCG5, SULT1E1, JUN, SULT1C4, NR0B2, CYP7A1, SLC27A6, IL1B, ALDH3B1, HMGCS1, ABCA1, CYP2C19 |
| Superpathway of Cholesterol Biosynthesis | 2.34E-06 | 0.18 | −2.24 | SQLE, PMVK, IDI1, HMGCR, HMGCS1 | |
| Mevalonate Pathway I | 2.45E-06 | 0.31 | −2.00 | PMVK, IDI1, HMGCR, HMGCS1 | |
| LXR/RXR Activation | 5.13E-06 | 0.07 | −1.34 | IL1R2, ABCG8, ABCG5, SAA1, CYP7A1, IL1B, HMGCR, ABCA1 | |
| Superpathway of Geranylgeranyl diphosphate Biosynthesis I (via Mevalonate) | 7.94E-06 | 0.24 | −2.00 | PMVK, IDI1, HMGCR, HMGCS1 | |
| DMI_KC | Interferon Signaling | 1.00E-10 | 0.22 | 2.83 | OAS1, IFI6, PSMB8, STAT1, TAP1, IRF1, IFITM1, ISG15 |
| Antigen Presentation Pathway | 6.31E-09 | 0.18 | NC | PSMB9, NLRC5, HLA-B, HLA-DQB1, PSMB8, HLA-DQA2, TAP1 | |
| Th1 Pathway | 3.80E-07 | 0.07 | 1.41 | NFIL3, CD3E, HLA-B, CD274, HLA-DQB1, HLA-DQA2, STAT1, CD3D, IRF1 | |
| Th1 and Th2 Activation Pathway | 5.25E-06 | 0.05 | NC | NFIL3, CD3E, HLA-B, CD274, HLA-DQB1, HLA-DQA2, STAT1, CD3D, IRF1 | |
| PKCθ Signaling in T Lymphocytes | 1.82E-05 | 0.05 | 2.45 | CACNA1I, RAC2, CACNG1, CD3E, HLA-B, HLA-DQB1, CD3D, LCP2 | |
| MWT_Angus | LPS/IL-1 Mediated Inhibition of RXR Function | 1.38E-05 | 0.03 | −2.00 | IL1R2, SULT1E1, CYP2B6, LBP, HMGCS1, SULT2A1, CYP2C19 |
| Melatonin Degradation I | 8.13E-05 | 0.06 | 1.00 | SULT1E1, CYP2B6, SULT2A1, CYP2C19 | |
| Superpathway of Melatonin Degradation | 1.10E-04 | 0.06 | 1.00 | SULT1E1, CYP2B6, SULT2A1, CYP2C19 | |
| IGF-1 Signaling | 6.46E-04 | 0.04 | NC | CTGF, IGF1, CYR61, IGFBP2 | |
| Mevalonate Pathway I | 9.33E-04 | 0.15 | NC | HMGCR, HMGCS1 | |
| MWT_Charolais | Neuroinflammation Signaling Pathway | 1.45E-04 | 0.02 | 1.89 | HMOX1, VCAM1, HLA-B, IL1B, HLA-DQB1, CSF1R, GRIN3A |
| Prostanoid Biosynthesis | 4.68E-04 | 0.22 | NC | PTGS1, TBXAS1 | |
| Granulocyte Adhesion and Diapedesis | 5.37E-04 | 0.03 | NC | VCAM1, SELL, IL1B, MMP11, SDC3 | |
| Graft-versus-Host Disease Signaling | 7.24E-04 | 0.06 | NC | HLA-B, IL1B, HLA-DQB1 | |
| Altered T-Cell and B-Cell Signaling in Rheumatoid Arthritis | 4.47E-03 | 0.03 | NC | HLA-B, IL1B, HLA-DQB1 | |
| MWT_KC | Antigen Presentation Pathway | 3.39E-04 | 0.08 | NC | HLA-B, HLA-DQB1, HLA-DQA2 |
| Pathogenesis of Multiple Sclerosis | 4.47E-04 | 0.22 | NC | CXCL10, CXCL9 | |
| Nicotine Degradation III | 1.07E-03 | 0.05 | NC | UGT2B17, CYP2B6, CYP2C19 | |
| Th1 Pathway | 1.41E-03 | 0.03 | NC | SOCS3, HLA-B, HLA-DQB1, HLA-DQA2 | |
| Melatonin Degradation I | 1.62E-03 | 0.05 | NC | UGT2B17, CYP2B6, CYP2C19 |
1ADG = average daily gain; DMI = average daily dry matter intake; MWT = metabolic body weight.
2The Z-score indicates activation (+) or inactivation (−) of the process in high-ADG, low-DMI, or low-MWT steers. NC = not calculated.