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Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2007 35(Database issue):D841-D845; doi:10.1093/nar/gkl835
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Nucleic Acids Research, 2007, Vol. 35, Database issue D841-D845
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PathoPlant®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses

Lorenz Bülow*, Martin Schindler1 and Reinhard Hehl

Institut für Genetik, Technische Universität Braunschweig Spielmannstraße 7, D-38106 Braunschweig, Germany 1 Software Systems Engineering Institute, Technische Universität Braunschweig Mühlenpfordtstraße 23, D-38106 Braunschweig, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5783; Fax: +49 531 391 5765; Email: l.buelow{at}tu-braunschweig.de

Received August 15, 2006. Revised October 5, 2006. Accepted October 6, 2006.

Plants react to pathogen attack by expressing specific proteins directed toward the infecting pathogens. This involves the transcriptional activation of specific gene sets. PathoPlant®, a database on plant–pathogen interactions and signal transduction reactions, has now been complemented by microarray gene expression data from Arabidopsis thaliana subjected to pathogen infection and elicitor treatment. New web tools enable identification of plant genes regulated by specific stimuli. Sets of genes co-regulated by multiple stimuli can be displayed as well. A user-friendly web interface was created for the submission of gene sets to be analyzed. This results in a table, listing the stimuli that act either inducing or repressing on the respective genes. The search can be restricted to certain induction factors to identify, e.g. strongly up- or down-regulated genes. Up to three stimuli can be combined with the option of induction factor restriction to determine similarly regulated genes. To identify common cis-regulatory elements in co-regulated genes, a resulting gene list can directly be exported to the AthaMap database for analysis. PathoPlant is freely accessible at http://www.pathoplant.de.


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L. Bulow, S. Engelmann, M. Schindler, and R. Hehl
AthaMap, integrating transcriptional and post-transcriptional data
Nucleic Acids Res., October 8, 2008; (2008) gkn709v1.
[Abstract] [Full Text] [PDF]


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