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[Arabidopsis] BAR News: new eFP Browser cell-type-specific data sets and views for other species, and protein structures in ePlant

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Thu Nov 19 18:09:59 EST 2009

Hello Arabidopsis and other Plant Researchers,

The Bio-Array Resource is pleased to announce the inclusion of several new
cell-type-specific expression data sets in our Arabidopsis eFP Browser at

These cell-type-specific data sets in the Tissue Specific view include:

-a floral meristem set from Venu Reddy's lab at UCR; 
-pollen germination data from Mark Johnson (Brown) and Ravishankar
Palanivelu (Arizona); 

and in a new Root view:

-salt and iron-deficiency root cell-type-response data from the Benfey Lab
-high-resolution root spatiotemporal expression data, again from the Benfey
-nitrogen root cell-type-responses from the Birnbaum Lab (NYU); 

Many thanks to Siobhan Brady, Benfey lab members, Venu Reddy, Mark Johnson
and others for input in the creation of these eFP views. The Root view alone
provides a snapshot of 196 different combinations of cell-types versus
environmental responses or developmental stages (xylem and phloem pole
pericycle, procambium, xylem, phloem, phloem companion cells and other cell
types in 13 different sections generated by Dustin Cartwright and Hardeep
Nahal using an EM algorithm from Cartwright et al. 2009: try it out with
PIN1, At1g73590, as a nice example!), from 268 data sets across 6.1 million
data points.

We're also premiering eFP Browsers for barley and rice in beta - find the
links to these on the BAR homepage at http://bar.utoronto.ca. In addition,
it is now possible to explore Poplar data from the Campbell Lab's
PopGenExpress data sets using our Expression Angler and Expression Browser
tools. The links are also on the BAR homepage.

Finally, our ePlant now contains predicted protein structures for
approximately 72% of the Arabidopsis proteome, based on work carried out in
collaboration with Lawrence Kelley at Imperial College London using his
Phyre algorithm. Check it out at http://bar.utoronto.ca/eplant. 

Feedback as always is welcome!

Best regards,


Nicholas Provart, PhD
Assistant Professor, Plant Cyberinfrastructure & Systems Biology
Director, Graduate Program in Genome Biology and Bioinformatics
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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