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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 09:41:27 PDT 2012


Dear Stefan,

Many thanks for your useful suggestion. I'm forwarding it to our user, 
so he may get in touch with you directly if needed.

Best regards,
Paola

On 6/28/12 5:29 PM, Stefan Götz wrote:
> Hello,
> with Blast2GO you can simply upload your GO term assignments (a table 
> with ID <tab> GO, one per row, extension: .annot) and than perform a 
> enrichment analysis (Menu -> Analysis -> Enrichment) providing a test 
> and reference set (list of your IDs, plain txt file, one id per row). 
> Start Blast2GO from here: http://www.blast2go.com/b2glaunch (you need 
> Java installed).
> Best regards,
> Stefan
>
> On 28 June 2012 17:48, Paola Roncaglia <paola at ebi.ac.uk 
> <mailto:paola at ebi.ac.uk>> wrote:
>
>     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 <tel:%2B44%201223%20492600>
>     f: +44 1223 494468 <tel:%2B44%201223%20494468>
>
>     _______________________________________________
>     go-friends mailing list
>     go-friends at lists.stanford.edu <mailto:go-friends at lists.stanford.edu>
>     https://mailman.stanford.edu/mailman/listinfo/go-friends
>
>

-- 
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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