Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (or the LocusLink) in Bioconductor. Obviously, one way is to query Entrez Gene web service ID by ID, but is there any way to get connected to that web service from within R/Bioconductor and retrieve the specific fields only( like gene symbol, Name, Chromosome, MIM etc) of Entrez Gene Records? biomaRt seems to require interactive R, and mine is command-line, and also it doesn't make one-on-one mapping table since multiple ensemble IDs map to one Entrez Gene ID, which is very annoying in making a good-looking annotation table. Thank you so much. Weijun

Luo Weijun wrote: > Hello all, > Is there anyway to retrieve the gene symbols, full > names (discription), or other gene information, given > a list of Entrez Gene IDs (or the LocusLink) in > Bioconductor. Obviously, one way is to query Entrez > Gene web service ID by ID, but is there any way to get > connected to that web service from within > R/Bioconductor and retrieve the specific fields only( > like gene symbol, Name, Chromosome, MIM etc) of Entrez > Gene Records? > biomaRt seems to require interactive R, and mine is > command-line, I don't know what interactive R might be, and how that might differ from command line. As far as I know, there is only one 'type' of R (pretty much command line, unless you are using some tcl/tk widgets), and biomaRt works for that. and also it doesn't make one-on-one > mapping table since multiple ensemble IDs map to one > Entrez Gene ID, which is very annoying in making a > good-looking annotation table. Again, not sure what you are getting at here. There are many things in the annotation world that don't have a neat one-to-one mapping. Anyway, have you looked at the vignette in biomaRt that shows how to make an annotated HTML table using biomaRt and annotate? This cleanly handles any one-to-many annotations, and the result isn't completely horrible to look at... HTH, Jim > Thank you so much. > Weijun > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Luo Weijun wrote: > Hello all, > Is there anyway to retrieve the gene symbols, full > names (discription), or other gene information, given > a list of Entrez Gene IDs (or the LocusLink) in > Bioconductor. Obviously, one way is to query Entrez > Gene web service ID by ID, but is there any way to get > connected to that web service from within > R/Bioconductor and retrieve the specific fields only( > like gene symbol, Name, Chromosome, MIM etc) of Entrez > Gene Records? > biomaRt seems to require interactive R, and mine is > command-line, and also it doesn't make one-on-one > mapping table since multiple ensemble IDs map to one > Entrez Gene ID, which is very annoying in making a > good-looking annotation table. You might want to look at the humanLLMappings package in the metadata section of bioconductor. If I recall, this package is keyed using Entrez Gene IDs. You will probably want to look at the mget() function for extracting information. The annotate vignette also has some information that is relevant. Sean