IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

[Arabidopsis] BAR News - November 2012

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Mon Sep 24 13:00:21 EST 2012

Hello Arabidopsis and other Plant Researchers,

1. The Bio-Array Resource's Arabidopsis Interactions Viewer has two new
features enabled by recent updates to the CytoscapeWeb interface it uses:
the ability to group nodes according to their subcellular localization based
on SUBA II data (Heazlewood et al., 2006), and label them according to their
MapMan functional categories (Thimm et al., 2004).

2. The BAR's eFP Browser has two new views, Abiotic Stress II and Root II,
to explore gene expression data from the Campbell, Benfey, Bailey-Serres,
and Pilon-Smits labs.

3. BAR Expressologs: a paper describing our pipeline and results for
identifying homologs with the most similar pattern of expression in
equivalent tissues is out in the September issue of The Plant Journal. We've
also added an eighth plant species, potato, to the framework, now available
for beta testing.

4. Try our Potato eFP Browser for exploring ~2.2 million RNA-seq-based gene
expression measurements in potato developmental and environmental stress
atlases from Robin Buell's group at MSU.

5. Our ePlant tool now has a the ability to view one more level of
biological organization, pathways, with data from the Arabidopsis Reactome
database, curated by Gramene.

6. A predicted rice interactome generated by Matt Geisler and colleagues at
Southern Illinois University and published recently in the journal Rice is
accessible with our Rice Interactions Viewer. Easily view 37472 predicted
and 430 experimentally-determined interactions with the click of a mouse.

7. 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 (2,3,4,5), Rohan Patel (3,4), Anjali Silva (2,4),
Matthew Ierullo (1), Hans Yu (5), Joe Wu (6), for implementing these items;
to the researchers mentioned above for providing feedback; and also to
Bjoern Usadel at RWTH-Aachen for implementing a MapMan webservice feed, and
Anjali Iyer-Pascuzzi at Duke for help with the Root II data sets.

As always, any suggestions or comments are welcome!


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.

More information about the Arab-gen mailing list

Send comments to us at biosci-help [At] net.bio.net