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Methods to Reconstruct and Compare Transcriptional Regulatory Networks

  • M. Madan Babu
  • Benjamin Lang
  • L. Aravind
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 541)

Abstract

The availability of completely sequenced genomes and the wealth of literature on gene regulation have enabled researchers to model the transcriptional regulation system of some organisms in the form of a network. In order to reconstruct such networks in non-model organisms, three principal approaches have been taken. First, one can transfer the interactions between homologous components from a model organism to the organism of interest. Second, microarray experiments can be used to detect patterns in gene expression that stem from regulatory interactions. Finally, knowledge of experimentally characterized transcription factor binding sites can be used to analyze the promoter sequences in a genome in order to identify potential binding sites. In this chapter, we will focus in detail on the first approach and describe methods to reconstruct and analyze the transcriptional regulatory networks of uncharacterized organisms by using a known regulatory network as a template.

Key words

Transcriptional regulatory network network reconstruction template-based method network motif lifestyle statistical significance 

Notes

Acknowledgments

MMB acknowledges the Medical Research Council, UK, for financial support. LA acknowledges the Intramural Research Program of the NIH, NLM, NCBI, USA, for funding. We thank Arthur Wuster for critically reading this manuscript.

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • M. Madan Babu
    • 1
  • Benjamin Lang
    • 1
  • L. Aravind
    • 2
  1. 1.MRC Laboratory of Molecular BiologyUK
  2. 2.National Center for Biotechnology InformationNational Library of Medicine, National Institutes of HealthBethesdaUSA

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