ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.
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.
Klein
Johannes
J
Institute for Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.
Leupold
Stefan
S
Münch
Richard
R
Pommerenke
Claudia
C
Johl
Thorsten
T
Kärst
Uwe
U
Jänsch
Lothar
L
Jahn
Dieter
D
Retter
Ida
I
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
D001426:Bacterial Proteins; D008565:Membrane Proteins