Hello, I have been trying on the UCSC table browser to find a table that links kgIDs with gene IDs, but I did not find that. With the package GenomicFeatures, when constructing a TranscriptDB object from UCSC, one can group the transcripts by gene, the gene names being the Entrez gene IDs, which is quite neat. > txdb <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "knownGene") > txbygene <- transcriptsBy(txdb, by="gene") > head(names(txbygene)) [1] "1" "10" "100" "1000" "10000" "100009676" I would like to know how the the kgID have been associated with Entrez gene IDs. Thanks ! Arnaud The information in this e-mail is intended only for the ...{{dropped:11}}

Hi Arnaud, I am glad that you like this feature. The ultimate source of this information is by linking the known gene table to the knownToLocusLink table at UCSC. http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=184855093&hgta_doSchemaD b=hg19&hgta_doSchemaTable=knownToLocusLink Marc On 01/26/2011 01:31 PM, Arnaud Amzallag, Ph.D wrote: > Hello, > > I have been trying on the UCSC table browser to find a table that links kgIDs with gene IDs, but I did not find that. With the package GenomicFeatures, when constructing a TranscriptDB object from UCSC, one can group the transcripts by gene, the gene names being the Entrez gene IDs, which is quite neat. > > >> txdb <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "knownGene") >> txbygene <- transcriptsBy(txdb, by="gene") >> head(names(txbygene)) >> > [1] "1" "10" "100" "1000" "10000" "100009676" > > I would like to know how the the kgID have been associated with Entrez gene IDs. > > Thanks ! > > Arnaud > > > > The information in this e-mail is intended only for the ...{{dropped:11}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >