[Gramene] Collaboration on gene expression integration and comparison

[Marc Robinson-Rechavi]

Dear Lincoln Stein,

We are developing Bgee (http://bgee.unil.ch/), a database which allows  
the comparison of gene expression patterns between different species.  
At present, Bgee only contains animal data (indeed, mostly vertebrate  
data). We would be interested in collaborating with the Gramene team  
to develop a plant version. Bgee integrates in situ, microarray and  
EST based expression data (RNA-seq in the pipeline), and links it to  
homologous genes and to homologous organs. I believe that a plant  
version would be very timely, given the large increase in plant  
related data which is occuring beyond Arabidopsis.

If you are interested, we could submit a proposal together to the DoE  
call on Computational Biology and Bioinformatics:
http://www.science.doe.gov/grants/FOA-0000143.html

I will be sending a presubmission next week, as the deadline is  
November 5. It would be great if I could hear from you before that,  
but I understand that this is very last moment. Otherwise, we can  
discuss after I get the answer to the presubmission. I apologize for  
not contacting you earlier, but this call came to my attention very  
recently.

Bgee can also be viewed through links from Uniprot, which look like  
this:
http://bgee.unil.ch/bgee/bgee?page=gene&action=summary&gene_id=ENSMUSG00000038253

Or in the Ensembl browser, through DAS:
http://www.ensembl.org/Mus_musculus/geneview?gene=ENSMUSG00000038253;gene_summary=das:http://bgee.unil.ch/das/bgee=label

Which gives an idea of how our approach could be integrated with  
Gramene.

I am attaching a conference proceeding which describes Bgee, for your  
information.

I look forward to hearing from you.

Best regards,
Marc
____
Marc Robinson-Rechavi
Department of Ecology and Evolution
Biophore 3219, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4220    fax: +41 21 692 4165
http://bioinfo.unil.ch/

Swiss Institute of Bioinformatics
http://www.isb-sib.ch/groups/lausanne/evolutionary-bioinformatics-m-robinson-rechavi.html

La liberte ne s'use que quand on ne s'en sert pas
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