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[Arabidopsis] [BAR News] Updates to the Arabidopsis electronic Fluorescent Protein (eFP) Browser and other BAR tools

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart At utoronto.ca)
Tue Jan 2 17:02:01 EST 2007


Happy New Year!

We have updated and expanded many of the tools of the BAR, the Botany Array
Resource, located at http://bbc.botany.utoronto.ca, and added one more tool
called the Arabidopsis Genetic Uniquess and Redundancy Revealer, AGURR.

1. Expression Angler: It is now possible to identify anti-correlated genes
in the gene expression data sets generated by the AtGenExpress consortium,
as well as genes that are correlated. You can also now enter either an ATH1
probe set identifier or an AGI identifier against which you'd like to "fish"
for coregulated or anti-coregulated genes.

2. eFP Browser: In addition to the AtGenExpress data sets, we have started
collecting cell-type-specific expression data sets from the literature and
making these available for viewing with the eFP (electronic Fluorescent
Protein) Browser. It is possible to "zoom in" to view, for example, the
expression levels of a gene in the cell types of the root (based on data
generated by Birnbaum, Benfey and others, Science, 2003), developing pollen
(Honys and Twell), embryo parts (Lindsey lab), and xylem and cork (Campbell
and Dubos). New filtering options have also been added. See
http://bbc.botany.utoronto.ca/efp/. 

3. We are beta-testing a tool called AGURR, the Arabidopsis Genetic
Uniqueness and Redundancy Revealer, available at
http://bbc.botany.utoronto.ca/agurr/, for identifying samples in which one
gene of a gene family is uniquely expressed, or samples in which several
genes are potentially redundantly expressed, in order to guide phenotyping
and high-order mutant generation efforts. It is linked from the output of
Expression Browser, so just enter a list of AGI IDs for a gene family into
the Expression Browser and run AGURR afterwards by clicking on the link in
the Expression Browser output.

4. Expression Browser: It is now possible to perform electronic Northerns on
the cell-type-specific data sets described above. We also provide a link to
AGURR (see above) for identifying potential gene redundancies or uniqueness
of expression patterns for members of a gene family.

5. Annotation and lookups for the AGI identifiers have been updated, as well
as some minor bug fixes to BlastDigester, for easy CAPS marker generation.
We have also moved to GCOS/MAS5.0 normalization, TGT100, for most gene
expression data sets, to allow better cross-set comparison.

Much success to all in 2007,

Best regards, 

The BAR team - Kiana Toufighi, Hardeep Nahal and Nicholas Provart, with
additional programming by Debbie Winter and Ben Vinegar.

.........................................
Nicholas Provart, PhD
Assistant Professor, Plant Bioinformatics
Director, 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/
Arabidopsis Tools. http://bbc.botany.utoronto.ca   
email. nicholas.provart At utoronto.ca
TTC. Spadina LRT, Willcocks St.



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