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[Gohelp] GO Help query (from website)

Rebecca Foulger rfoulger at ebi.ac.uk
Thu Apr 14 01:27:14 PDT 2011


Dear Karim,

Thank you for writing to GO.

For grouping your genes based on their annotations, you will probably 
want to use one of the GO slims: GO slims are cut-down versions of the 
GO ontologies containing a subset of the terms in the whole GO.  You can 
then map the granular annotations of your query set of genes to one or 
more high-level, broader GO Slim terms. This will allow you to include 
the child terms you're not currently seeing with your direct mapping.

You can use one of the pre-created GO slims (for example, the generic GO 
slim created by the GO consortium, or you can tailor your own). There is 
more information on the GO slims on the Gene Ontology website: 
http://www.geneontology.org/GO.slims.shtml.

You can run a map2slim.pl script on your mouse annotation file to 
produce the GO slim mappings: there is documentation on how to do this 
at: http://search.cpan.org/~cmungall/go-perl/

Alternatively, there is a web-based version at: 
http://amigo.geneontology.org/cgi-bin/amigo/slimmer. The description of 
this tool is available at: 
http://wiki.geneontology.org/index.php/AmiGO_Manual:_Slimmer

I hope this helps with your query. Please let us know if you have 
further questions.

With best wishes,
Rebecca (GO help desk).



> Subject:
> GO Help query (from website)
> From:
> helmyk at mskcc.org
> Date:
> Wed, 13 Apr 2011 09:31:27 -0700
>
> To:
> gohelp at genome.stanford.edu
>
>
> Email:helmyk at mskcc.org
> Name: Annotation (from Karim Helmy)
> Text: Dear GO:
>
> I wonder if there is a file available of ontology categories and all genes that are members of that GO category. I would like to create updated genesets for Gene Set Enrichment Analysis (GSEA). I have accessed the ontology OBO files and also the Annotation files (MGI for mouse). I have been able to map the genes from the annotation file to the GO category in the OBO file, but my category sets tend to be very small because I think I am not including genes in the children GO categories. Is there a way to obtain the current comprehensive list of all genes within a given GO category?  Thanks for your help.
>
> Best,
>
> Karim


-- 
Dr Rebecca Foulger
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492523
f: +44 1223 494468

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