On Tue, Mar 17, 2009 at 1:58 AM, Wei Shi <shi@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.
>

Try here:


ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/

Sean

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