[BioC] How to get NCBI's gene annotation?
hans-rudolf.hotz at fmi.ch
Tue Mar 17 09:11:35 CET 2009
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:
> mget("Tff1", org.Mm.egSYMBOL2EG)
>  "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.
The files on "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/" should contain all the
data you want.
> R version 2.8.1 (2008-12-22)
> attached base packages:
>  tools stats graphics grDevices utils datasets
> methods base
> other attached packages:
>  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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