Table 3.
Overlap between gene expression and cis-eQTL with selection signatures. To test for enrichment of genes under selection in genes over-expressed in distinctive tissues (a), a Chi-squared test was performed between genes that overlapped with a selection signature in at least one breed (n = 350) and the top 5% of genes that were over-expressed in 22 distinctive tissues. To test for enrichment of selection signatures within cis-eQTL (b), a permutation test was performed
| Tissue | a) Enrichment of selection candidate genes in tissue-specific over-expressed genes (Chi-squared test) | b) Enrichment of selection signatures in cis-eQTL (permutation test) | p-value |
|---|---|---|---|
| p-value | z-score | ||
| Adipose | 1.20E-03* | 4.39 | 6.00E-04* |
| Blood | 1.72E-73* | 5.76 | 1.00E-04* |
| Embryo | 1.32E-01 | 2.63 | 1.34E-02 |
| Hypothalamus | 1.45E-01 | 3.57 | 4.20E-03 |
| Ileum | 3.87E-03 | 2.07 | 5.97E-02 |
| Jejunum | 3.43E-02 | 7.68 | 1.00E-04* |
| Leukocyte | 2.38E-02 | 6.73 | 1.00E-04* |
| Liver | 1.48E-01 | 3.43 | 2.70E-03 |
| Lung | 4.73E-04* | 2.77 | 8.90E-03 |
| Lymph node | 3.56E-03 | 5.08 | 2.00E-04* |
| Macrophage | 2.70E-02 | 2.41 | 1.86E-02 |
| Mammary | 3.08E-03 | 5.05 | 1.00E-04* |
| Monocytes | 5.25E-03 | 6.17 | 1.00E-04* |
| Muscle | 6.73E-01 | 4.18 | 1.00E-03* |
| Ovary | 6.13E-03 | 5.27 | 1.00E-04* |
| Oviduct | 1.57E-02 | 3.26 | 9.70E-03 |
| Pituitary | 7.75E-03 | 4.22 | 2.60E-03 |
| Rumen | 1.61E-01 | 6.69 | 1.00E-04* |
| Salivary gland | 6.39E-03 | 2.58 | 2.45E-02 |
| Skin fibroblast | 4.06E-03 | -0.11 | 6.09E-01 |
| Testis | 3.17E-04* | 1.71 | 7.75E-02 |
| Uterus | 1.56E-03* | 9.1 | 1.00E-04* |
*Significantly enriched for Bonferroni-corrected p-value (0.05/22)
Tissues in bold had a significant result in both analyses.