[Arabidopsis] BAR News - December 2011

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Tue Dec 20 16:39:54 EST 2011

Dear Arabidopsis Researchers,

1. Our Arabidopsis Interactions Viewer now contains 1,090 new G-protein
interactions from Kopffleish et al. (2011), along with 32 ARF-Aux/IAA
protein-protein interactions from Jian-Feng Li and colleagues (2011), for a
total of 28,522 experimentally-determined interactions. New features include
the ability to paint on expression data and to upload your own .CYS files
from Cytoscape.

2. Try our Maize eFP Browser for exploring ~12.2 million gene expression
measurements in a maize developmental atlas from Shawn Kaeppler's group at
UW-Madison (from Sehkon et al., 2011 - select Sehkon et al. from the Data
Source drop down).

3. Our new Guard Cell eFP now contains data for early GC meristemoids from
Keiko Torii's group at U. Washington (Pillitteri et al., 2011).

4. BAR Expressologs: we have computed the most likely expressolog
(expression homolog) for most genes across 7 plant species (including
maize), based expression profile similarity in the gene expression
developmental atlases available for these species. An icon will appear at
the top of the eFP pages - click on the icon if it is not greyed out to see
a combined sequence and expression pattern similiarity tree across these

5. We've added new data sets to our eFP Browser: in the Tissue Specific view
there are data for trichomes from David Marks group at UMN (Marks et al.,
2009; and Gilding & Marks, 2010), and a new Biotic Stress II series
containing LCM powdery mildew infection data from Mary Wildermuth's group at
Berkeley (Chandran et al., 2010) and downy mildew infection data from
Xinnian Dong's group at Duke (Wang et al., 2011). New biotic and abiotic
stress sets will be added in the new year.

6. ePlant now has a MAFFT download feature, plus the ability to see
coexpression neighbours from Takeshi Obayashi's ATTED II database in the
expression view.

7. We're looking for volunteers to beta-test our "My-eFP" tool for creating
your own eFP views in a very easy way, using any sort of quantitative data
(RNA-seq, microarray, etc.) and your own image. Let me know if you're

8. Keep up-to-date with BAR news by liking us on Facebook  - this will also
hopefully help the BAR get more secure funding!

Thanks to Hardeep Nahal (1,3,5,6), Rohan Patel (2,4), Joe Wu (1), Anjali
Silva (5), Robert Breit (7) and Garon La (6) for implementing these items,
and to the researchers mentioned above for providing feedback.

All the best to you in 2012!


Nicholas Provart, PhD
Associate Professor, Plant Cyberinfrastructure & Systems Biology
Chair, Bioinformatics SC, Multinational Arabidopsis Steering Committee
Member, North American 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, Skype. nicholas.provart, 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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