H i Team I have set of genes protein and transcripts from ensembl for homo sapiens and I have to map these ensembl gene , protein and transcript ID to the coressponding gene ID from NCBI I heard that bio conductor do this. Can you explain where I got this . how can i do that -- *Thanks & Regards,* *Neeba Sebastian* [[alternative HTML version deleted]]

Hi Neeba, On 6/21/2013 3:21 AM, Neeba Dijo wrote: > H > i Team > > I have set of genes protein and transcripts from ensembl for homo sapiens > and > > I have to map these ensembl gene , protein and > transcript ID to the coressponding gene ID from NCBI If I assume that you mean Gene ID (what used to be called the Entrez Gene ID), then this is a simple thing to do. You will need the org.Hs.eg.db package, and will need to use the select function. As an example, let's say I have a vector of Ensembl transcript IDs, like so: > trans [1] "ENST00000596924" "ENST00000263100" "ENST00000595014" "ENST00000598345" [5] "ENST00000600966" "ENST00000543436" And you want to know the Gene ID. You just do: > library(org.Hs.eg.db) > select(org.Hs.eg.db, trans, "ENTREZID", "ENSEMBLTRANS") ENSEMBLTRANS ENTREZID 1 ENST00000596924 1 2 ENST00000263100 1 3 ENST00000595014 1 4 ENST00000598345 1 5 ENST00000600966 1 6 ENST00000543436 2 As it appears you are new to R, I would highly recommend reading An Introduction To R (http://cran.r-project.org/doc/manuals/r-release/R-intro.html) and the vignette for AnnotationDbi (http://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi /inst/doc/IntroToAnnotationPackages.pdf). Best, Jim > > > I heard that bio conductor do this. Can you explain where I got this . how > can i do that > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099