[Bioperl-l] Database Retrieval

Benoit Ballester benoit at ebi.ac.uk
Tue Aug 8 11:37:46 EDT 2006

Dear Rick

> I have a list of mouse GeneIDs for which I have extracted the RefSeqs for.  
> With these accession numbers I want to know what are the three closest  
> upstream and downstream genes (and orientation, if possible) to my gene of  
> interest. Is these some way of finding this out? Any suggestions?

You can search the Ensembl database with your Refseq IDs.
You can either use the Ensembl Genome Browser (www.ensembl.org)  or the 
Ensembl Perl API.
I have attached a simple script that extract upstream and downstream 
genes for a given human refseq ID. You can start from here and have a 
look to the Ensembl Perl API. 

You will find some tutorials and documentations for each API (Core, 
Compara, Variation) at the address above.

> Also, I would also like to know something about the expression of a  
> particular gene of interest. e.g. ba querying the Novartis Gene Atlas  
> (http://symatlas.gnf.org/SymAtlas/). Is there a module for handling  
> submissions and retrieving results of this sort?

You can get expression data from ArrayExpress and GEO 
(http://www.ebi.ac.uk/arrayexpress/  http://www.ncbi.nlm.nih.gov/geo/). 
ArrayExpress and GEO are public repository for microarray data (MIAME 

Hope this help.

Benoit Ballester
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