[Arabidopsis] New eFP Browser Light and Natural Variation views and tissue-specific data sets

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Sun Feb 3 17:31:24 EST 2008


Hi everyone,

We are happy to announce the addition of 2 new views and several new
tissue-specific expression microarray data sets to our eFP Browser, at
http://bar.utoronto.ca/efp/. 

1. eFP Light Series: Several microarray datasets are displayed describing
diurnal, thermocycling, circadian and light treatment experiments generated
by researchers around the world including Todd Michael (Michael et al., PLoS
Genetics, 2008), Mark Stitt (Blaesing et al, 2005), Steve Kay, Joanne Chory,
Stacey Harmer (Covington & Harmer, 2007), Alison Smith (Smith et al., 2004),
Andrew Millar (Edwards & Millar, 2007) as well as the AtGenExpress
Consortium. 

See diurnal and circadian cycling of CCA1 (At2g46830) here:
http://At2g46830.notlong.com 

2. Natural Variation Series: See the expression of your gene of interest
across 34 Arabidopsis ecotypes, in data generated by the Weigel Laboratory.
For example, see the reduced expression of PHYC in the Fr-2 ecotype,
described in Balasubramanian et al. (2006, Nature Genetics), here:
http://At5g35840.notlong.com 

3. Additional tissue-specific data sets from the Schroeder, Ohlrogge and
Preuss labs. The data described in the guard cell set from the Schroeder lab
will be published shortly in Plant Methods, and epidermal and stigma and
ovary expression data from the Ohlrogge and Preuss labs are published.

You can check out epidermal-specific expression of CUT1, a wax biosynthetic
enzyme for the epidermis, here:
http://At1g68530.notlong.com

or guard-cell-specific expression of a potassium channel, KAT1, here:
http://At5g46240.notlong.com 

or a stigma-specific gene, S-locus related 1 (AtS1), here:
http://At3g12000.notlong.com 

Thanks to Todd Michael, Julian Schroeder, Yingzhen Yang, John Ohlrogge, Owen
Rowland, and Detlef Weigel for feedback in putting these views together, and
to Hardeep Nahal for database assistance. Any other feedback or comments are
welcome.

The eFP Browser is described in Winter et al., PLoS One 2(8):e718, see
http://dx.doi.org/10.1371/journal.pone.0000718. 

Best regards,

Nick
.........................................
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/
Arabidopsis Tools. http://www.bar.utoronto.ca   
email. nicholas.provart from utoronto.ca



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