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[Gohelp] GO Help query (from website)
rfoulger at ebi.ac.uk
Thu Apr 14 01:27:14 PDT 2011
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:
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
Alternatively, there is a web-based version at:
http://amigo.geneontology.org/cgi-bin/amigo/slimmer. The description of
this tool is available at:
I hope this helps with your query. Please let us know if you have
With best wishes,
Rebecca (GO help desk).
> GO Help query (from website)
> helmyk at mskcc.org
> Wed, 13 Apr 2011 09:31:27 -0700
> 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.
Dr Rebecca Foulger
GO Editorial Office
Wellcome Trust Genome Campus
p: +44 1223 492523
f: +44 1223 494468
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