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Briefings in Bioinformatics Advance Access originally published online on December 12, 2008
Briefings in Bioinformatics 2009 10(1):75-83; doi:10.1093/bib/bbn055
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks

Jan Baumbach, Andreas Tauch and Sven Rahmann

Corresponding author. Jan Baumbach, International Computer Science Institute, Berkeley, USA. E-mail: jbaumbac{at}icsi.berkeley.edu

To handle changing environmental surroundings and to manage unfavorable conditions, microbial organisms have evolved complex transcriptional regulatory networks. To comprehensively analyze these gene regulatory networks, several online available databases and analysis platforms have been implemented and established. In this article, we address the typical cycle of scientific knowledge exploration and integration in the area of procaryotic transcriptional gene regulation. We briefly review five popular, publicly available systems that support (i) the integration of existing knowledge, (ii) visualization capabilities and (iii) computer analysis to predict promising wet lab targets. We exemplify the benefits of such integrated data analysis platforms by means of four application cases exemplarily performed with the corynebacterial reference database CoryneRegNet.

Keywords: data integration, systems biology, gene regulation, transcription factor, database

Submitted: April 26, 2008. Received (in revised form): November 6, 2008.


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