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Nucleic Acids Research Advance Access published online on April 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn217
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© 2008 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.

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ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks

Johannes Klein1, Stefan Leupold1, Richard Münch1, Claudia Pommerenke1,2, Thorsten Johl2, Uwe Kärst2, Lothar Jänsch2, Dieter Jahn1,* and Ida Retter1

1Institute for Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig and 2Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5801; Fax: +49 531 391 5854; Email: d.jahn{at}tu-bs.de

Received February 1, 2008. Revised April 3, 2008. Accepted April 9, 2008.

ProdoNet is a web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. For a given list of genes, the system detects shared operons, identifies co-expressed genes and deduces joint regulators. In addition, the contribution to shared metabolic pathways becomes visible on KEGG maps. Furthermore, the co-occurrence of genes of interest in gene expression profiles can be added to the visualization of the global network. In this way, ProdoNet provides the basis for functional genomics approaches and for the interpretation of transcriptomics and proteomics data. As an example, we present an investigation of an experimental membrane subproteome analysis of Pseudomonas aeruginosa with ProdoNet. The ProdoNet dataset on transcriptional regulation is based on the PRODORIC Prokaryotic Database of Gene Regulation and the Virtual Footprint tool. ProdoNet is accessible at http://www.prodonet.tu-bs.de.


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