Question: GO annotation file for hsa genes
0
gravatar for wsciekly.maciek
5 weeks ago by
wsciekly.maciek0 wrote:

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,

rna-seq go database • 121 views
ADD COMMENTlink modified 6 days ago by geneontologyhelp20 • written 5 weeks ago by wsciekly.maciek0

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

Tutorial: 9.9 Gene sets

Also you can try PantherDB.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by arup870
1
gravatar for geneontologyhelp
6 days ago by
geneontologyhelp20 wrote:

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!

ADD COMMENTlink written 6 days ago by geneontologyhelp20
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