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

Jan Baumbach, Andreas Tauch, Sven Rahmann

Research output: Contribution to journalReview articlepeer-review

18 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)75-83
Number of pages9
JournalBriefings in Bioinformatics
Volume10
Issue number1
DOIs
StatePublished - 2009
Externally publishedYes

Keywords

  • Data integration
  • Database
  • Gene regulation
  • Systems biology
  • Transcription factor

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