DNALinux

DNALinux logo

DNALinux is a Live Linux for bioinformatic use. Just boot your computer and have several bioinformatic software. Download and use it free.

Collaboration on gene expression integration and comparison PDF Print E-mail
Written by Virginia Gonzalez   
Monday, 02 November 2009 13:33

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.

More information:

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/