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[go-helpdesk] Fwd: GO enrichment analysis - IDs not in database

Paola Roncaglia paola at ebi.ac.uk
Thu Jun 28 08:54:41 PDT 2012


Dear Alfons,

With regard to the GO term enrichment question that you sent to 
GO-helpdesk yesterday, I've just posted it on the GO-friends mailing 
list, where someone may have suggestions about tools that you can use 
when the gene product IDs are not present in any public database, as is 
your case.

I hope this helps. My message to the GO-friends mailing list is below 
(your email address was entered in an invalid format, apologies).

Best regards,
Paola Roncaglia, for GO help.

-------- Original Message --------
Subject: 	[go-helpdesk] GO enrichment analysis - IDs not in database
Date: 	Thu, 28 Jun 2012 16:48:06 +0100
From: 	Paola Roncaglia <paola at ebi.ac.uk>
To: 	go-friends at mailman.stanford.edu
CC: 	go-helpdesk at mailman.stanford.edu, "a.weig at 
uni-bayreuth.de"@domain.invalid



Hello,

We have a GO user (cc'd on this email) who would like to perform GO term
enrichment analysis on a newly sequenced species, from in-house
microarray results. The genomic data is public (released by DOE-JGI),
but not available from a public database yet, therefore the gene product
IDs are not recognized by e.g. AmiGO's enrichment tool. The user has a
list of IDs of differentially expressed transcript, and a table provided
by the sequencing lab that contains all transcript IDs and
automatically-generated GO term assignments. Could anyone please
recommend a tool?

The latest email on this subject (containing most of the pertaining
GO-help correspondence, bottom to top) is here:
https://mailman.stanford.edu/pipermail/go-helpdesk/2012-June/005212.html

Many thanks,
Paola Roncaglia

-- 
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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