This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Gene Ontology - Why Is There The Same Gene Name, Same Go Id Occurring Multiple Times In A Go Record?

Hello all.
I downloaded the gene association record for genes associated with the GO "antioxidative pathway" for arabidopsis (from AmiGO db). Why are there 3 instances of the same gene APX1 in the same record (there are many other similar cases in the same record for other genes)? Differences are mainly for the date and the database fields. Is there a reason for this? Thanks.

=>TAIR locus:2026616 APX1 GO:0016688 TAIR:Communication:501714663|InterPro:IPR002207|NCBI_gi:16173 ISS InterPro:IPR002207; NCBI_gi:16173 F ascorbate peroxidase 1 ASCORBATE PEROXIDASE|AT1G07890|AT1G07890.1|ATAPX01|ATAPX1|CS1|F24B9.2|F24B9_2|maternal effect embryo arrest 6|MEE6 protein taxon:3702 20020710 TIGR
=>TAIR locus:2026616 APX1 GO:0016688 PMID:15608336 IMP F ascorbate peroxidase 1 ASCORBATE PEROXIDASE|AT1G07890|AT1G07890.1|ATAPX01|ATAPX1|CS1|F24B9.2|F24B9_2|maternal effect embryo arrest 6|MEE6 protein taxon:3702 20100719 TAIR
=>TAIR locus:2026616 APX1 GO:0016688 PMID:9291097 TAS F ascorbate peroxidase 1 ASCORBATE PEROXIDASE|AT1G07890|AT1G07890.1|ATAPX01|ATAPX1|CS1|F24B9.2|F24B9_2|maternal effect embryo arrest 6|MEE6 protein taxon:3702 20040210 TAIR

gene ontology
• 4,199 views • link
updated by Sean Davis Sean Davis • written by Olivier Olivier

1 answer

I believe the answer is simply because there are multiple sources of evidence for the association.

• 82 views • link
written by Sean Davis Sean Davis

I think Sean is correct - if you look at the 5th(?) column in your results, you see 3 different evidence codes: ISS (Inferred by Sequence Similarity), IMP (Inferred by Mutant Phenotype) and TAS (Traceable Author Statement).

see http://www.geneontology.org/GO.evidence.shtml for explanation of the evidence codes

and

http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q05431 for the full set of GO annotations for this protein (contains duplicates, for the reason outlined above)

• 0 views • link
written by sarahhunter sarahhunter

Log in to answer this question.

More posts like this

No similar posts found.