Sean is right, If you have better information about how a set of IDs match up with known gene IDs (entrez gene IDs), then you can create a custom chip package using the instructions in the SQLForge vignette found here: http://www.bioconductor.org/packages/2.10/bioc/html/AnnotationDbi.html Marc On 04/18/2012 03:12 PM, array chip wrote: > Ok, thank you Sean! > > John > > > > ________________________________ > From: Sean Davis<sdavis2@mail.nih.gov> > > Cc: "bioconductor@r-project.org"<bioconductor@r-project.org> > Sent: Wednesday, April 18, 2012 1:03 PM > Subject: Re: [BioC] retrieve gene symbol/description > > >> Thank you Sean. You are right there is no annotation of this gene in GenBank >> or Ensemble. But if we dig into more, you can see that both GenBank (section >> "Reference sequence information" on the right panel) >> and EMBL ("Ensemble Genes" in the "Navigation" section) point to the gene >> Pannexin 3 (PANX3) for this clone, and BLAST confirms that this clone aligns >> 100% to PANX3. >> >> Is there a package/function in bioconductor that still allows me to retrieve >> the gene information for this ID? I have a bunch of GenBank/EMBL IDs in this >> situation, just want to automate the retrieval if possible. > I do not know of a single resource that is complete in this regard. > You could try using the AnnotationDbi package to build an annotation > package if that is your use case. Otherwise, you might try using > Unigene or NCBI Entrez Gene to get some more mapping down. > > Sean > > >> ________________________________ >> From: Sean Davis<sdavis2@mail.nih.gov> >> Cc: "bioconductor@r-project.org"<bioconductor@r-project.org> >> Sent: Wednesday, April 18, 2012 12:16 PM >> Subject: Re: [BioC] retrieve gene symbol/description >> > e: >>> Hi, I am trying to retrieve gene symbol/description with GenBank/EMBL IDs >>> using biomaRt. I was successful with some IDs, but not with others. For >>> example: >>> >>>> library(biomaRt) >>>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>> >>>> getBM(attributes=c('embl', 'description','hgnc_symbol'), filters = >>>> 'embl', values = c('AF133587','AA456140'), mart = ensembl) >>> embl >>> description hgnc_symbol >>> 1 AF133587 rhabdoid tumor deletion region gene 1 [Source:HGNC >>> Symbol;Acc:13437] RTDR1 >>> >>> >>> As you can see, the first ID returns gene symbol/description successfully, >>> but the 2nd one did not. What is the reason for the 2nd one not working? Is >>> there other ways to get it to work? >>> >> Hi, John. >> >> This query is working as expected. The genbank accession "AA456140" >> is not associated with any gene in the Ensembl gene collection. Try >> typing your two accessions into the ensembl search box. You'll note >> that one the first is associated with a gene while the second is >> simply a genomic alignment (and not associated with a gene). >> >> Sean >> >> > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]