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[Arabidopsis] BAR News, May 2010

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Wed May 5 15:51:18 EST 2010

Hello Arabidopsis Researchers,

We're pleased to announce several additions to the BAR at

1. New data sets: a seed development series based on laser-capture
microdissection of pre-globular to mature green seed parts is now available
in the "Seed" view of our eFP Browser. These data come from an NSF-funded
Gene Networks in Seed Development project in the Goldberg (UCLA) and Harada
(UCD) labs, see seedgenenetwork.org.

2. New chart feature in our eFP Browser: a link to generate a
publication-quality chart at 300 dpi is now present at the bottom of the eFP
Browser page. This feature and the next were implemented by Robert Breit in
my lab.

3. New links in our eFP Browser: icon links to TAIR and GeneMANIA now appear
at the top of eFP Browser outputs. Click on the to either go to TAIR or to
activate GeneMANIA, a fast online gene function prediction tool that uses
large-scale data sets from Arabidopsis (coexpression, localization,
protein-protein interaction, etc.) to try to predict gene function.
GeneMANIA was developed by Quaid Morris' laboratory at the Centre for
Cellular and Biomolecular Research in Toronto.

4. "Proto-alert" warning flags in our eFP Browser: around 370 genes are
induced by the protoplasting method used to generate specific cell
populations for expression profiling (identified in Birnbaum et al., 2003).
A small alert now appears beside samples prepared in such a way if your
query gene belongs to this set.

5. Updated protein-protein interaction data sets in our Arabidopsis
Interactions Viewer: we've updated our data set to include those
interactions recently announced for N-Browse. Our AIV currently indexes more
than 8,600 literature-documented PPIs, and more than 70,000 predicted PPIs,
generated by the Geisler Lab at Southern Illinois University (Geisler-Lee et
al., 2007). These interactions also appear in queries of expression data (in
Expression Browser as "loops" between genes, and in the eFP Browser as an

6. BAR now on Facebook: join the Bio-Array Resource's Facebook page by
clicking on the FaceBook icon on the BAR homepage and then clicking on the
"Like" link. We'll post minor update news here in the future, and monitor
the page for feedback.

As always we welcome criticisms and comments. Thanks for your support - our
eFP Browser surpassed one million uses this week since going online in 2007.
We're grateful to the community for the high quality data sets we present.
Keep 'em coming!

Best regards,


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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