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 Confidentiality Notice: This e-mail message, including a...{{dropped:10}}

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 > Confidentiality Notice: This e-mail message, including > a...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Al, Thank you for your suggestion. EBI has this strain GO-annotated: http://www.ebi.ac.uk/integr8/OrganismHomePage.do?orgProteomeId=74352&c urrentclicked=ORGANISM_HOME Finally it appeared to be easy! Best regards Galina -----Original Message----- From: Al Ivens [gmail account] [mailto:al.c.ivens@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 > Confidentiality Notice: This e-mail message, including > a...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > Confidentiality Notice: This e-mail message, including a...{{dropped:7}}