CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes

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doi doi:10.2390/biecoll-jib-2006-24
submission July 21, 2006
published August 28, 2006

Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch and Sven Rahmann

Correspondence should be addressed to:
Jan Baumbach
Welle 5, 33602 Bielefeld, Germany
ed.dlefeleib-inu.cetibec@nullhcabmuab.naj


Abstract

CoryneRegNet is an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Now we integrated the genomes and transcriptional interactions of three other corynebacteria, C. diphtheriae, C. efficiens, and C. jeikeium into CoryneRegNet; providing comparative analysis and visualization with GraphVis. We also integrated the high-performance PSSM search tool PoSSuMsearch to detect potential transcription factor binding sites within and across species. As an application, we reconstruct in silico the regulatory network of the iron metabolism regulator DtxR in the four corynebacteria. CoryneRegNet is freely accessible at https://www.cebitec.uni-bielefeld.de/ groups/gi/software/coryneregnet/. The final slash (/) is mandatory. In order to use the GraphVis feature, Java (at least version 1.4.2) is required.

Reference

Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch and Sven Rahmann. CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006. Online Journal: http://journal.imbio.de/index.php?paper_id=24
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