Protocol abstract
Nature Protocols 4, - 992 - 1005 (2009)
Published online: 4 June 2009 | doi:10.1038/nprot.2009.81
Subject Categories: Computational and theoretical biology | Microbiology and virology | Model organisms
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet
Jan Baumbach1, Tobias Wittkop1,2,3, Christiane Katja Kleindt2,4 & Andreas Tauch5
Abstract
CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. It provides web-based access to integrated data on gene regulatory interactions of corynebacteria relevant to human medicine and biotechnology, Escherichia coli and Mycobacterium tuberculosis. To facilitate the analysis and reconstruction of the corresponding networks, CoryneRegNet provides user-friendly interfaces for bioinformatics analysis and network visualization tools. This protocol describes four major workflows: (1) querying the regulatory network of a gene of interest, (2) prediction and interspecies transfer of gene regulatory interactions, (3) visualization and comparison of predicted or known networks and (4) integration of gene expression data analysis and visualization. This protocol guides the user through the most important features of CoryneRegNet and takes 45–60 min to complete.
- Algorithms Group, International Computer Science Institute, Berkeley, California, USA.
- International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany.
- Graduiertenkolleg Bioinformatik, Bielefeld University, Bielefeld, Germany.
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Correspondence to: Jan Baumbach1 e-mail: jbaumbac@icsi.berkeley.edu
