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

Paola Roncaglia paola at ebi.ac.uk
Thu Jun 28 09:21:37 PDT 2012


Dear Calin,

Many thanks for your prompt reply.
I am forwarding it to the user, as I previously entered his email 
address in an invalid format (apologies).
He may then get in touch with you directly if needed.

With best regards,
Paola Roncaglia

On 6/28/12 5:18 PM, Calin Voichita wrote:
> Hello,
>
> Our tools (Onto-Express / OE2GO) available at
> http://vortex.cs.wayne.edu/ontoexpress/ are able to deal with such
> situations. After logging in, please select OE2GO and an input form will
> appear that requires:
>
> - differentially expressed transcripts (which is available)
> - the list of all transcripts (which should be available as well)
> - the annotation (which I see its available)
> - the ontology (in obo format that can be downloaded at
> http://www.geneontology.org/GO.downloads.ontology.shtml) - currently we
> only support v1.0
>
> Don't hesitate to contact us for any further details.
>
> Sincerely,
> Calin Voichita
>
> -------- Original Message  --------
> Subject: [go-friends] GO enrichment analysis - IDs not in database
> From: Paola Roncaglia<paola at ebi.ac.uk>
> To: go-friends at lists.stanford.edu
> Cc: go-helpdesk at mailman.stanford.edu, "a.weig at
> uni-bayreuth.de"@domain.invalid
> Date: Thu 28 Jun 2012 11:48:06 AM EDT
>
>> 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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