title: ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.
abstract: 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.
authors.affiliation: Institute for Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Klein
authors.forename: Stefan
authors.initials: S
authors.lastname: Leupold
authors.forename: Richard
authors.initials: R
authors.lastname: Münch
authors.forename: Claudia
authors.initials: C
authors.lastname: Pommerenke
authors.forename: Thorsten
authors.initials: T
authors.lastname: Johl
authors.forename: Uwe
authors.initials: U
authors.lastname: Kärst
authors.forename: Lothar
authors.initials: L
authors.lastname: Jänsch
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
authors.forename: Ida
authors.initials: I
authors.lastname: Retter
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics; D003196:Computer Graphics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D020407:Internet; D008565:Membrane Proteins / Q000235:genetics; D053858:Metabolic Networks and Pathways; D009876:Operon; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000378:metabolism; D018085:Regulon; D012984:Software; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins