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PMID: 16478536 Published · epublish English Journal Article

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.

BMC genomics ·Vol. 7 ·2006-02-14 ·Pages 24

Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A

Abstract

The application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. This data along with literature-derived knowledge on regulation of gene expression has opened the way for genome-wide reconstruction of transcriptional regulatory networks. These large-scale reconstructions can be converted into in silico models of bacterial cells that allow a systematic analysis of network behavior in response to changing environmental conditions. CoryneRegNet was designed to facilitate the genome-wide reconstruction of transcriptional regulatory networks of corynebacteria relevant in biotechnology and human medicine. During the import and integration process of data derived from experimental studies or literature knowledge CoryneRegNet generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure. Reconstructed regulatory networks can be visualized by using the yFiles JAVA graph library. As an application example of CoryneRegNet, we have reconstructed the global transcriptional regulation of a cellular module involved in SOS and stress response of corynebacteria. CoryneRegNet is an ontology-based data warehouse that allows a pertinent data management of regulatory interactions along with the genome-scale reconstruction of transcriptional regulatory networks. These models can further be combined with metabolic networks to build integrated models of cellular function including both metabolism and its transcriptional regulation.

MeSH Terms
Computer Graphics Corynebacterium/genetics,metabolism Database Management Systems Databases, Genetic Gene Expression Regulation, Bacterial Genome, Bacterial Genomics Internet SOS Response, Genetics Software Transcription Factors/genetics,metabolism User-Computer Interface
Chemicals
Transcription Factors
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Baumbach Jan
International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
Brinkrolf Karina
Czaja Lisa F
Rahmann Sven
Tauch Andreas
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-7-24
Published
2006-02-14
Epub
2006-00-14
Pages
24
Language
English
Region
England
NLM ID
100965258
PMCID
PMC1382212
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-7-24 PMC Full Text View journal details
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