Baumbach Jan, Brinkrolf Karina, Czaja Lisa F, Rahmann Sven, Tauch Andreas
International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
BMC Genomics. 2006 Feb 14;7:24. doi: 10.1186/1471-2164-7-24.
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.
DNA微阵列技术在细菌基因组序列的后基因组分析中的应用使得能够生成与调控网络相关的大量数据。这些数据连同从文献中获得的关于基因表达调控的知识，为全基因组转录调控网络的重建开辟了道路。这些大规模重建可以转化为细菌细胞的计算机模型，从而能够系统分析网络在不断变化的环境条件下的行为。
CoryneRegNet旨在促进对生物技术和人类医学中相关棒状杆菌转录调控网络的全基因组重建。在导入和整合来自实验研究或文献知识的数据过程中，CoryneRegNet生成与基因组注释、已鉴定的转录因子以及相应顺式调控元件的链接。CoryneRegNet基于转录调控的多层、分层和模块化概念，并通过使用关系数据库管理系统MySQL和基于本体的数据结构来实现。重建的调控网络可以使用yFiles JAVA图形库进行可视化。作为CoryneRegNet的一个应用实例，我们重建了棒状杆菌中参与SOS和应激反应的细胞模块的全局转录调控。
CoryneRegNet是一个基于本体的数据仓库，它允许对调控相互作用进行相关数据管理，并对转录调控网络进行全基因组规模的重建。这些模型可以进一步与代谢网络相结合，以构建包括代谢及其转录调控在内的细胞功能综合模型。
