Table 7.
Top ten biological processes enriched in genes detected in the core haplotypes under positive selection in individual pig breeds
| #Term | ID | Input number | Background number | P-Value | Corrected P-Value |
|---|---|---|---|---|---|
| PL | |||||
| Embryonic skeletal system development | GO:0048706 | 6 | 37 | 8.68E-07 | 0.001 |
| Embryonic skeletal system morphogenesis | GO:0048704 | 5 | 29 | 5.69E-06 | 0.0037 |
| Skeletal system morphogenesis | GO:0048705 | 6 | 65 | 1.71E-05 | 0.0074 |
| Anterior/posterior pattern specification | GO:0009952 | 6 | 70 | 2.53E-05 | 0.0081 |
| Regionalization | GO:0003002 | 7 | 118 | 4.95E-05 | 0.0127 |
| Skeletal system development | GO:0001501 | 7 | 123 | 6.35E-05 | 0.0136 |
| Pattern specification process | GO:0007389 | 7 | 131 | 9.26E-05 | 0.0170 |
| Sequence-specific DNA binding | GO:0043565 | 10 | 305 | 0.00015 | 0.0251 |
| Chordate embryonic development | GO:0043009 | 7 | 171 | 0.0004 | 0.0603 |
| Embryo development ending in birth or egg hatching | GO:0009792 | 7 | 173 | 0.0005 | 0.0603 |
| PUL | |||||
| Regulation of hair cycle | GO:0042634 | 2 | 5 | 0.0005 | 0.2658 |
| Establishment of protein localization to organelle | GO:0072594 | 5 | 151 | 0.0010 | 0.2658 |
| Regulation of protein import | GO:1904589 | 3 | 41 | 0.0013 | 0.2658 |
| Regulation of protein import into nucleus | GO:0042306 | 3 | 41 | 0.0013 | 0.2658 |
| Protein targeting | GO:0006605 | 5 | 162 | 0.0014 | 0.2658 |
| Regulation of nucleocytoplasmic transport | GO:0046822 | 3 | 46 | 0.0018 | 0.2658 |
| Regulation of protein localization to nucleus | GO:1900180 | 3 | 49 | 0.0021 | 0.2658 |
| Negative regulation of peptide hormone secretion | GO:0090278 | 2 | 13 | 0.0024 | 0.2658 |
| Negative regulation of peptide secretion | GO:0002792 | 2 | 13 | 0.0024 | 0.2658 |
| Muscle fiber development | GO:0048747 | 2 | 14 | 0.0028 | 0.2658 |
| ZW | |||||
| Cellular transition metal ion homeostasis | GO:0046916 | 2 | 26 | 0.0032 | 0.4776 |
| Transition metal ion homeostasis | GO:0055076 | 2 | 35 | 0.0056 | 0.4776 |
| Nucleotidase activity | GO:0008252 | 1 | 5 | 0.0180 | 0.4776 |
| Zinc ion homeostasis | GO:0055069 | 1 | 6 | 0.0210 | 0.4776 |
| Negative regulation of innate immune response | GO:0045824 | 1 | 6 | 0.0210 | 0.4776 |
| Glycosphingolipid biosynthetic process | GO:0006688 | 1 | 6 | 0.0210 | 0.4776 |
| Glucosyltransferase activity | GO:0046527 | 1 | 6 | 0.0210 | 0.4776 |
| Negative regulation of T cell apoptotic process | GO:0070233 | 1 | 6 | 0.0210 | 0.4776 |
| Cellular zinc ion homeostasis | GO:0006882 | 1 | 6 | 0.0210 | 0.4776 |
| Response to zinc ion | GO:0010043 | 1 | 6 | 0.0210 | 0.4776 |
| ZS | |||||
| Galactosidase activity | GO:0015925 | 1 | 5 | 0.0087 | 0.3709 |
| Sphingolipid catabolic process | GO:0030149 | 1 | 5 | 0.0087 | 0.3709 |
| Membrane lipid catabolic process | GO:0046466 | 1 | 5 | 0.0087 | 0.3709 |
| Glucosidase activity | GO:0015926 | 1 | 5 | 0.0087 | 0.3709 |
| Activation of NF-kappaB-inducing kinase activity | GO:0007250 | 1 | 6 | 0.0101 | 0.3709 |
| snRNA processing | GO:0016180 | 1 | 7 | 0.012 | 0.3709 |
| Postreplication repair | GO:0006301 | 1 | 8 | 0.0130 | 0.3709 |
| snRNA metabolic process | GO:0016073 | 1 | 9 | 0.0144 | 0.3709 |
| Positive regulation of NIK/NF-kappaB signaling | GO:1901224 | 1 | 9 | 0.0144 | 0.3709 |
| Protein K63-linked ubiquitination | GO:0070534 | 1 | 10 | 0.0159 | 0.3709 |