GO annotation file for hsa genes

Question

[wsciekly.maciek]

Dear All,

I am trying to perform a GO analysis with Ontologizer tool. I cannot find any .gaf files with gene-term annotation anymore...
http://current.geneontology.org/products/pages/downloads.html

At the official website there are only files for protein-term and rna-term associations (for homo sapienes). Is there any other resource? Or should I manually convert the protein IDs to gene IDs and create my own .gaf file?
Regards,

[Arup Ghosh]

If a solution involving R will be helpful you can try "EnrichmentBrowser" package.

Tutorial: 9.9 Gene sets

Also you can try PantherDB.

Answer 1

[geneontologyhelp]

Hi, Sorry to be late to answer, but there's a reason for this. The Gene Ontology is used to describe the function(s) of a gene product (typically but not always a protein)- the gene doesn't perform the action, the gene product does. Also, since GO is used for all organisms, we can't ignore alternative splicing. Some MODs even account for isoforms. Annotating directly to the gene would lose a lot of detail- and since you're interested in humans, this definitely affects your organism.

So you are correct, your best bet would be to take an official GAF from the GO site, then convert the protein IDs to your desired gene IDs. Hope this clarifies things!