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[Arabidopsis] BAR news, Feb. 2009: new interaction data sets and promoter tools

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Tue Feb 17 17:06:39 EST 2009

Hello Arabidopsis Researchers,

A couple of news items for the Bio-Array Resource (BAR) at

1. We have updated our Arabidopsis Interactions Viewer (AIV) to include Dr.
Matt Geisler's updated Interactome 2.0, which more than triples the number
of predicted interactions in Arabidopsis to 70,944  by incorporating
interaction data sets from many more organisms to compute Arabidopsis
interologs. We have also added 1,276 MAP Kinase/target interactions
determined using protein microarrays by Sorina Popescu and colleagues in
Dinesh-Kumar's lab at Yale and published recently in Genes and Development,
for a total of 2,779 literature-supported interactions. The AIV images now
link to SVG graphic format files for high quality visualizations.

2. Two new tools, Cistome and Cistome Map, are now available. Cistome
permits cis-element prediction using a variety of 3rd party packages, as
well as with a new version of Promomer, Promomer2, which is an enumerative
program that allows for degeneracy in potential cis-elements. Additionally,
known cis-elements from PLACE may be mapped onto promoter sets. Cistome Map
allows consensus sequences or PSSMs to be mapped onto diagrammatic
representations of TAIR8 promoter sequences with defined transcriptional

Feedback, as always, is welcome. Keep an eye out in the coming months for a
Medicago truncatula eFP Browser, as well as for the Affymetrix Whole Genome
Tiling Array At-TAX data sets from the Weigel laboratory in our existing
Arabidopsis eFP Browser.


Nicholas Provart, PhD
Assistant Professor, Plant Bioinformatics & 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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