Table 5 GO-terms mainly enriched by GOEA applied on accessory genes and coregenome variants of Salmonella enterica subsp. enterica serovars associated by microbial GWAS with animal sources (i.e. avian bovine, swine and fish). The GOEA was performed with the workflow ‘fastGSEA’ based on the parent-child approach integrating hypergeometric tests and Bonferroni corrections. The GOEA input sample is a list of corresponding RefSeq identifiers of accessory genes (i.e. RefSeq from Roary) and coregenome variants (i.e. NP from SNPeff 4.1 g) associated by microbial GWAS. The input universe is a list of RefSeq identifiers of all accessory genes (i.e. RefSeq from Roary) and all core genes (i.e. NP from SNPeff 4.1 g). The highest GO-levels presenting the most accurate GO-terms (i.e. ≥ 5) and the lowest Bonferroni corrected p-values representing highly enriched GO-terms (i.e. < 5.0 × 10−2), are presented. BP, MF and CC stand for biological process, molecular function and cellular component, respectively
Animal source | Uniprotkb | Associated Mutations | GO-term identifier | GO-term | Hits | Exp. hits | GO level | Corr. p-value | Ontology |
|---|---|---|---|---|---|---|---|---|---|
avian | Q55434 | gene cph2_2 | GO:0009585 | red, far-red light phototransduction | 1 | 0.01 | 7 | 1 × 10−7 | BP |
avian | Q55434 | gene cph2_2 | GO:0009584 | detection of visible light | 1 | 0.01 | 7 | 1 × 10−7 | BP |
avian | Q55434 | gene cph2_2 | GO:0009883 | red or far-red light photoreceptor activity | 1 | 0.01 | 5 | 1 × 10−7 | MF |
avian | Q9RT63 | gene recD2 | GO:0043141 | ATP-dependent 5′-3′ DNA helicase activity | 1 | 0.01 | 11 | 1 × 10−7 | MF |
avian | Q9RT63 | gene recD2 | GO:0008094 | DNA-dependent ATPase activity | 5 | 0.28 | 10 | 1 × 10−3 | MF |
avian | P0ABN5 | gene dcuA | GO:0015740 | C4-dicarboxylate transport | 3 | 0.13 | 10 | 1 × 10−2 | BP |
bovine | Q7CPA1 | SNP in aspA | GO:0008797 | aspartate ammonia-lyase activity | 1 | 0.01 | 6 | 1 × 10−7 | MF |
fish | Q7A2S0 | gene dapH | GO:0047200 | tetrahydrodipicolinate N-acetyltransferase activity | 1 | 0.01 | 8 | 1 × 10−7 | MF |
fish | P43478 | gene cgkA | GO:0033918 | kappa-carrageenase activity | 1 | 0.01 | 6 | 1 × 10−7 | MF |