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

James F. Reid james.reid at ifom-ieo-campus.it
Tue Mar 17 10:56:42 CET 2009


the pointer should be for Mouse:
or here I believe

The reason that the org.Mm.eg.db package is giving you two locations is 
because it uses the alignment given by UCSC of the Refseq(s) of your gene.
In this particular case NM_009362 aligns with 100% identity on both 
chr5:143285577-143289234 and chr17:31298341-31301998.
By aligning this sequence by hand using BLAT you can see that the chr5 
hit appeared as of the July 2007 assembly.
Maybe this kind of information is worth keeping in mind.


Sean Davis wrote:
> On Tue, Mar 17, 2009 at 1:58 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.
> Try here:
> ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/
> Sean
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