Table 1.
Altered pathways identified by Gene Set Enrichment Analysis in high-RFI compared to low-RFI beef steers.
| Pathway | FDR | NES | Gene set size (# of leading edge genes) | Leading edge genes |
|---|---|---|---|---|
| Binding and uptake of ligands by scavenger receptors | 0.01 | 1.82 | 4 (3) | HBB, HBA1, HBA |
| Scavenging of heme from plasma | 0.01 | 1.82 | 4 (3) | HBB, HBA1, HBA |
| Erythrocytes take up carbon dioxide and release oxygen | 0.01 | 1.68 | 3 (3) | HBB, HBA1, HBA |
| Erythrocytes take up oxygen and release carbon dioxide | 0.01 | 1.68 | 3 (3) | HBB, HBA1, HBA |
| O2/CO2 exchange in erythrocytes | 0.01 | 1.68 | 3 (3) | HBB, HBA1, HBA |
| Metabolism of proteins | 0.01 | −1.70 | 248 (85) | LOC101907518, RPL39, LOC101902490, UBE2D1, FUCA2, B4GALT6, FBXL3, SOCS3, COMMD8, RPLP2, RPL34 |
| Cellular responses to external stimuli | 0.01 | −1.99 | 69 (19) | HSPA1A, HSPH1, BAG2, DNAJA1, JUN, HSPA4, UBE2D1, DNAJB1, H3C13, H2BC7, H4C2, ELOC, ELOB, H2AC8, SIRT1, FLCN, ATP6V1G1, HSPA14, H2BU1 |
| Cellular responses to stress | 0.01 | −1.99 | 69 (19) | HSPA1A, HSPH1, BAG2, DNAJA1, JUN, HSPA4, UBE2D1, DNAJB1, H3C13, H2BC7, H4C2, ELOC, ELOB, H2AC8, SIRT1, FLCN, ATP6V1G1, HSPA14, H2BU1 |
| Cellular response to heat stress | 0.01 | −2.05 | 16 (5) | HSPA1A, HSPH1, BAG2, HSPA4, DNAJB1 |
| Regulation of HSF1-mediated heat shock response | 0.01 | −2.05 | 16 (5) | HSPA1A, HSPH1, BAG2, HSPA4, DNAJB1 |
High-RFI, feed inefficient beef steers; low-RFI, feed-efficient beef steers; False discovery rate (FDR) ≤ 0.01; NES, normalized enrichment score (high-RFI vs. low-RFI). Leading edge genes are those that are enriched within the gene set. See Supplementary Table 3 for the full list of leading edge genes associated with metabolism of proteins. #Means number.