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[Software-group] GO term enrichment (fwd)

Midori Harris midori at ebi.ac.uk
Wed Feb 3 08:36:54 PST 2010


Another question from a user - is there any way to do many Term Enrichment 
analyses with some automation?

thanks,
m

---------- Forwarded message ----------
Date: Wed, 3 Feb 2010 08:21:42 -0800
From: Luqman Hodgkinson <luqman at berkeley.edu>
To: Midori Harris <midori at ebi.ac.uk>
Subject: Re: GO term enrichment





Dear Midori,

Thank you for your speedy reply! I had seen the AmiGO browser and it seems very 
useful. However I must perform this process 300 times. Is there a way of 
automating the AmiGO method? Or is there another method you would recommend in 
order to automate the process of performing this many GO enrichment requests?

 		With best wishes,
 		Luqman




On Feb 3, 2010, at 8:19 AM, Midori Harris wrote:

> Dear Luqman,
> 
> The Term Enrichment tool that is available on the web with the AmiGO browser 
> allows you to specify an input set of genes of interest simply by 
> typing/pasting them into the query form, or by uploading them in a file that 
> contains a simple list (using the gene_association file format is optional, 
> not required).
> 
> http://amigo.geneontology.org/cgi-bin/amigo/term_enrichment
> 
> Although we recommend using your own background gene set, it is also possible 
> to use the  database filter selection to choose a set from the annotation 
> sets in the GO repository. If you do upload your own background set, it can 
> be in the form of a simple list.
> 
> The web-based Term Enrichment tool does not require you to upload a .obo 
> file; it uses GO ontology data from the AmiGO database.
> 
> I hope this addresses your question, but please let us know if you have any 
> others.
> 
> Regards,
> Midori
> 
> ============================
> Midori A. Harris, Ph.D.
> GO Editor
> EMBL - EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD UK
> 
> Tel: +44 (0) 1223 494667
> Fax: +44 (0) 1223 494468
> Email: midori at ebi.ac.uk
> 
>> Date: Wed, 3 Feb 2010 07:59:08 -0800
>> Email: luqman at berkeley.edu Name: Software (from Luqman Hodgkinson)
>> Text: Dear Sir or Madam,
>> 
>> What is the best way for me to find enrichment of GO terms in a small set of 
>> genes represented by UniProtKB IDs? I also have a large set of genes that 
>> represent the entire universe over which I am searching. I wanted to use 
>> GO:TermFinder, but it requires both an annotation file an a .obo file. How 
>> may I obtain these files: annotation and .obo for my large set of genes?
>> 
>> With best wishes,
>> Luqman



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