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

[Hotz, Hans-Rudolf]

On 3/17/09 6:58 AM, "Wei Shi" <shi at wehi.edu.au> wrote:

> 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:
> 
> library(org.Mm.eg.db)
> mget("Tff1", org.Mm.egSYMBOL2EG)
> $Tff1
> [1] "21784"
> mget("21784", org.Mm.egCHRLOC)
> $`21784`
>         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.

The files on "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/" should contain all the
data you want. 


Regards, Hans

>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=
> English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
> 
> 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
> 
> 
> Thanks,
> Wei
> 
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