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[Arabidopsis] BAR News, January 2010

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Mon Jan 18 15:31:42 EST 2010


Hello Arabidopsis Researchers,

The Bio-Array Resource at http://bar.utoronto.ca is pleased to announce
several improvements for working with Arabidopsis functional genomics data
using its tools.

1. More linking between tools: we have enabled small icons in the outputs of
our eFP Browser to subcellular localization, protein-protein interaction,
and annotation data. These icons are active only if the corresponding
information is present. Our eFP and Cell eFP Browsers are now also directly
accessible as LinkOuts from NCBI's GenBank records for Arabidopsis genes and
proteins.

2. Classification SuperViewer now with p-values and MapMan categories: we
have improved our Classification SuperViewer for functionally categorizing
lists of genes. Now you can use either GO terms or MapMan bins from the
Usadel laboratory to classify your genes of interest. We have also included
a p-value score for each term, in addition to an enrichment or depletion
score. 

3. DataMetaFormatter now includes automatic calculation of enrichment for GO
categories for your electronic Northern queries. In addition, we have
improved the ability to explore long heatmap outputs by allowing the
information panel to be detached from the top of the page.

Subcellular localization data are from SUBA (Heazlewood et a., 2007) from A.
Harvey Millar's lab at the University of Western Australia. MapMan bin data
are from the Usadel lab at the Max Planck Institute for Molecular Plant
Physiology in Germany (Thimm et al., 2004; Usadel et al., 2005).

We are experimenting with displaying Google ads on several of our pages to
help fund the BAR. Thanks for your understanding and thanks to Robert Breit
for his work on the improvements described above. As always, comments are
welcome.

All the best in 2010,

Nick

.........................................
Nicholas Provart, PhD
Assistant Professor, Plant Cyberinfrastructure & Systems Biology
Director, Graduate Program in Genome Biology and Bioinformatics
Chair, Bioinformatics SC, Multinational Arabidopsis Steering Committee
Member, Centre for the Analysis of Genome Evolution and Function
Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto
25 Willcocks St., Toronto, ON. M5S 3B2. CANADA

Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878
URL. http://www.csb.utoronto.ca/faculty/provart-nicholas
The Bio-Array Resource. http://www.BAR.utoronto.ca   
email. nicholas.provart from utoronto.ca
TTC. Spadina LRT, Willcocks St.





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