[BioC] How to get NCBI's gene annotation?

Wei Shi shi at wehi.EDU.AU
Tue Mar 17 06:58:40 CET 2009

Dear list,

   The annotation package "org.Mm.eg.db" provides UCSC's annotation for 
mouse genes. However, this annotation could sometime be different from 
NCBI's annotation. Below is an example:

mget("Tff1", org.Mm.egSYMBOL2EG)
[1] "21784"
mget("21784", org.Mm.egCHRLOC)
        17          5
 -31298340 -143285576

    Two chromosomal locations were found for "Tff1" which are on 
chromosome 17 and chromosome 5 respectively. However, this genes is only 
located on chromosome 17 according to NCBI Entrez gene database. Does 
anybody know if there is any packages or other sources which provide 
NCBI gene annotation? I am working on a large set of genes and NCBI does 
not seem to provide downloadable files which contain gene information 
such as chromosomal locations etc.

 > sessionInfo()
R version 2.8.1 (2008-12-22)


attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  
methods   base    

other attached packages:
[1] org.Mm.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4           
AnnotationDbi_1.4.3 Biobase_2.2.2    


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