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[go-helpdesk] Enrichment GO Help query

Paola Roncaglia paola at ebi.ac.uk
Tue Jun 26 06:46:13 PDT 2012


Dear Alfons,

Thank you for writing to GO.

I have a few questions so I may provide you with better indications. Do 
you have a gene association file for the fungal species you're working 
on? That is, a file that includes both the full list of genes in your 
fungus' genome (and/or the genes on the microarray) and the GO terms 
associated to each gene. Is the microarray you're using a commercial one?

For your reference, a list of GO tools for enrichment analysis is 
available here:
http://www.geneontology.org/GO.tools_by_type.term_enrichment.shtml

With best regards,

Paola Roncaglia, for GO help.


> Subject:
> GO Help query (from website)
> From:
> a.weig at uni-bayreuth.de
> Date:
> Tue, 26 Jun 2012 00:14:36 -0700
>
> To:
> go-helpdesk at mailman.stanford.edu
>
>
> Email:a.weig at uni-bayreuth.de
> Name: Ontology (from Alfons Weig)
> Text: Hello,
> I have identified induced/repressed genes by microarray analysis from a fully sequenced fungus. Most of these genes were already annotated with GO terms during the sequencing and annotation project. However, this organims is not included in the reference organisms in AMIGO's GO Term enrichment.
> I am looking for a tool where I can enter GO terms directly to see whether some term are enriched. My hope was to use GO Slimmer using the fungal or Aspergillus slims, but - again - genes are required for input.
>
> Is there any tool where I can analyse a subset of GO terms for enrichment/slim analyses.
>
> Best regards
> Alfons Weig

-- 
Dr Paola Roncaglia
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492600
f: +44 1223 494468

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