Table 8.
Gene ontology enrichments analysis for differential variants – Female birds.
| GO | Go term | Description and frequency | Overlapping genes | Chr | Type |
|---|---|---|---|---|---|
| Molecular function | 0005198 | Structural molecule activity (7%) | PSMD13 (Ile118Thr) | 5 | SNV |
| 0035312 | 5′-3′ exodeoxyribonuclease activity (14%) | DCLRE1C | 1 | Deletion | |
| 0005049 | Nuclear export signal receptor activity (3%) | RANBP17 | 13 | SNV | |
| 0008536 | Ran GTPase binding (7%) | ||||
| 0042393 | Histone binding (13%) | ATAD2 | 2 | SNV | |
| 0008453 | Alanine-glyoxylate transaminase activity (14%) | AGXT2 (Ala436Gly) | Z | SNV | |
| 0030170 | Pyridoxal phosphate binding (12%) | ||||
| 0004222 | Metalloendopeptidase activity (9%) | UQCRC1 (Arg211Gln) | 12 | SNV | |
| 0050839 | Cell adhesion molecule binding (8%) | CD200 (His135Asn) | 1 | SNV | |
| 0004872 | Receptor activity (13%) | ||||
| Cellular component | 0070545 | PeBoW complex (3%) | PES1 | 15 | Deletion |
| 0005750 | Mitochondrial respiratory chain complex III (9%) | UQCRC1 (Arg211Gln) | 12 | SNV | |
| 0022624 | Proteasome accessory complex (9%) | PSMD13 (Ile118Thr) | 5 | SNV | |
| 0008541 | Proteasome regulatory particle (6%) | ||||
| 0070419 | Nonhomologous end joining complex (12%) | DCLRE1C | 1 | Deletion | |
| 0000784 | Nuclear chromosome, telomeric region (13%) | ||||
| 0005769 | Early endosome (2%) | ZFYVE9 | 8 | SNV | |
| 0031410 | Cytoplasmic vesicle (17%) | ||||
| 0005840 | Ribosome (12%) | HSPA14 (Leu397Va) | 1 | SNV | |
| 0005913 | Cell-cell adherens junction (17%) | CD200 (His135Asn) | 1 | SNV | |
| Biological process | 0006835 | Dicarboxylic acid transport (3%) | SLC13A2 | 19 | SNV |
| 0000463 | Maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (7%) | PES1 | 15 | Deletion | |
| 0006611 | Protein export from nucleus (8%) | RANBP17 | 13 | SNV | |
| 0006303 | Double-strand break repair via non-homologous end joining (9%) | DCLRE1C | 1 | Deletion | |
| 0036297 | Inter strand cross-link repair (3%) | ||||
| 0031848 | Protection from non-homologous end joining at telomere (4%) | ||||
| 0090305 | Nucleic acid phosphodiester bond hydrolysis (15%) | ||||
| 0007156 | Homophilic cell adhesion (8%) | CD200 His135Asn | 1 | SNV | |
| 0007157 | Heterophilic cell-cell adhesion (8%) | ||||
| 0008037 | Cell recognition (5%) | ||||
| 0006511 | Ubiquitin-dependent protein catabolic process (15%) | PSMD13 Ile118Thr | 5 | SNV | |
| 0043248 | Proteasome assembly (3%) | ||||
| 0009060 | Aerobic respiration (9%) | UQCRC1 (Arg211Gln) | 12 | SNV | |
| 0006122 | Mitochondrial electron transport, ubiquinol to cytochrome c (3%) |
Results of the GO analysis are given in Tables 7 and 8. The output of amino acid change analysis for differential variants was used for gene ontology enrichment analyses in three parts, including biological process, molecular function and cellular component. The gene ontology (GO) association file, which includes gene names and associated gene ontology terms, were downloaded from the gene ontology consortium (http://geneontology.org/) and imported to CLC Genomic Workbench (8.5.1). The significance level of GO analysis was also determined as 0.01.