[BioC] GO enrichment analysis for Salmonella enterica

[Glazko, Galina V]

Al,

Thank you for your suggestion. EBI has this strain GO-annotated:
http://www.ebi.ac.uk/integr8/OrganismHomePage.do?orgProteomeId=74352&currentclicked=ORGANISM_HOME
Finally it appeared to be easy!

Best regards
Galina

-----Original Message-----
From: Al Ivens [gmail account] [mailto:al.c.ivens at gmail.com] 
Sent: Wednesday, July 27, 2011 3:26 AM
To: Glazko, Galina V; bioconductor at r-project.org
Cc: nrt at sanger.ac.uk
Subject: RE: [BioC] GO enrichment analysis for Salmonella enterica

Hi Galina,

An option might be to access the data from the Sanger Institute, e.g. 

www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html

I couldnt see any GO information there, but if you contact Nick
Thompson, he may well be better placed to help you.

Cheers,

Al



> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of 
> Glazko, Galina V
> Sent: 26 July 2011 17:52
> To: bioconductor at r-project.org
> Subject: [BioC] GO enrichment analysis for Salmonella enterica
> 
> 
> Dear all,
> 
> I would like to do GO enrichment analysis for Salmonella 
> enterica (serovar Typhimurium strain SL1344); I was trying to 
> find GO annotations for it, but it is not in 
> 'bacteria_mart_10', and it is also absent from NCBI  
> gene2go.gz. Could someone point me to the right direction, 
> how I can do GO enrichment in this case? I have Salmonella 
> lists of GenBank Identifiers to start with.
> 
> I would appreciate your advises, thank you!
> 
> Best regards
> Galina
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