How To Retrieve All Go Terms Associated To The Zebrafish In Order To Perform An Enrichment Test ?

Question

[Bioch'Ti]

Hi all,

I would like to perform an enrichment test (Fisher test) with contrasting a reference set of GO terms (in my case, all GO terms associated to the zebrafish) and a test set of genes to highlight over/under represented biological functions. So, I still haven't found any solution to retrieve all the GO terms associated to this species from NCBI, Ensembl or ZFIN?

Does anyone has an idea how to do it?

Best regards, Christopher

[David Quigley]

Incidentally, you may want to consider using the hypergeometric test rather than Fisher exact. This is normally the test used to determine if a set of values drawn more frequently has a given label than would be expected by chance from the total distribution.

Answer 1

[Khader Shameer]

As you mentioned you should have a list of of background and a list of 'hits' for performing GO based enrichment analysis. For full set of annotated genes from Zebra fish you may use the GOA (Gene Ontology Annotation) for Zebra fish from GOA project website at EBI.

[Bioch'Ti]

@Khader - Thanks for your answer!

[biobot 0.0.77.a.1099]

Yes, that's a better suggestion than mine.

Answer 2

[biobot 0.0.77.a.1099]

The GO consortium maintain a list derived from ZFIN, described here. From Ensembl, they can be obtained through the Ensembl Biomart linked at the top of the D.rerio index page. The GO terms are found under the attributes section. I'm not so familiar with NCBI, so I can't offer any help there.

Unless you already know that a particular source of annotation is most reliable, I would obtain the data from all of them and make a comparison. You are not really measuring over/under represented biological functions, you're measuring over/under represented annotation of biological functions, which we hope is similar, but often isn't.

[Bioch'Ti]

I agree that, in the way I perform my enrichment test, I measure over/under representation of "annotated" biological functions ! Many thanks