Table 1 Significantly over- and underrepresented gene ontology (GO) terms in protein-coding genes with loss-of-function variants
From: Porcine single nucleotide polymorphisms and their functional effect: an update
Ontology term | Gene set (n genes) | LOF genes expected | Over (+) or under (−) | P-valuea | |
|---|---|---|---|---|---|
Annotated genes (22,191) | LOF genes (592) | ||||
Biological process | |||||
 Meiotic cell cycle (GO: 0051321) | 103 | 13 | 2.87 | + | 4.38E−02 |
 Cellular process (GO:0009987) | 8666 | 319 | 241.73 | + | 3.26E−06 |
 Localization (GO: 0051179) | 2853 | 123 | 79.58 | + | 5.12E−03 |
Molecular function | |||||
 Phospholipid-translocating ATPase activity (GO:0004012) | 15 | 5 | 0.42 | + | 2.48E−02 |
 Intracellular ligand-gated ion channel activity (GO:0005217) | 17 | 5 | 0.47 | + | 3.20E−02 |
 ATPase activity, coupled (GO:0042623) | 159 | 16 | 4.44 | + | 4.31E−03 |
 ATPase activity (GO:0016887) | 205 | 17 | 5.72 | + | 2.16E−02 |
 Calcium ion binding (GO:0005509) | 483 | 29 | 13.47 | + | 3.35E−02 |
 Pyrophosphatase activity (GO:0016462) | 512 | 30 | 14.28 | + | 3.29E−02 |
 ATP binding (GO:0005524) | 1080 | 63 | 30.13 | + | 5.98E−05 |
 Hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides (GO:0016818) | 515 | 30 | 14.37 | + | 3.27E−02 |
 Hydrolase activity, acting on acid anhydrides (GO:0016817) | 516 | 30 | 14.39 | + | 3.13E−02 |
 Adenyl nucleotide binding (GO:0030554) | 1121 | 64 | 31.27 | + | 8.65E−05 |
 Drug binding (GO:0008144) | 1219 | 69 | 34 | + | 5.16E−05 |
 Adenyl ribonucleotide binding (GO:0032559) | 1115 | 63 | 31.1 | + | 9.88E−05 |
 Carbohydrate derivative binding (GO:0097367) | 1569 | 84 | 43.77 | + | 2.92E−05 |
 Purine nucleotide binding (GO:0017076) | 1391 | 74 | 38.8 | + | 1.09E−04 |
 Purine ribonucleoside triphosphate binding (GO:0035639) | 1344 | 71 | 37.49 | + | 1.89E−04 |
 Purine ribonucleotide binding (GO:0032555) | 1385 | 73 | 38.63 | + | 1.24E−04 |
 Ribonucleotide binding (GO:0032553) | 1398 | 73 | 39 | + | 1.82E−04 |
 Nucleotide binding (GO:0000166) | 1565 | 76 | 43.65 | + | 1.26E−03 |
 Nucleoside phosphate binding (GO:1901265) | 1565 | 76 | 43.65 | + | 1.19E−03 |
 Small molecule binding (GO:0036094) | 1801 | 87 | 50.24 | + | 2.89E−04 |
 Anion binding (GO:0043168) | 1927 | 93 | 53.75 | + | 1.33E−04 |
 Hydrolase activity (GO:0016787) | 1605 | 76 | 44.77 | + | 2.04E−03 |
 Metal ion binding (GO:0046872) | 2142 | 90 | 59.75 | + | 2.43E−02 |
 Ion binding (GO:0043167) | 3701 | 155 | 103.24 | + | 9.19E−05 |
 Cation binding (GO:0043169) | 2186 | 91 | 60.98 | + | 2.57E−02 |
 Catalytic activity (GO:0003824) | 3731 | 148 | 104.07 | + | 2.03E−03 |
 Organic cyclic compound binding (GO:0097159) | 3718 | 140 | 103.71 | + | 3.02E−02 |
 Molecular_function (GO:0003674) | 10,828 | 398 | 302.04 | + | 4.04E−11 |
 Binding (GO:0005488) | 7828 | 287 | 218.36 | + | 2.47E−05 |
Cellular component | |||||
 Integral component of membrane (GO: 0016021) | 4022 | 151 | 112.19 | + | 3.21E−02 |
 Intrinsic component of membrane (GO: 0031224) | 4068 | 152 | 113.47 | + | 3.60E−02 |
 Membrane (GO: 0016020) | 5874 | 210 | 163.85 | + | 1.95E−02 |
 Cell part (GO: 0044464) | 9798 | 330 | 273.31 | + | 3.10E−03 |
 Cell (GO: 0005623) | 9847 | 332 | 274.67 | + | 3.43E−03 |