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Identification of cis-Regulatory Elements in Gene Co-expression Networks Using A-GLAM

  • Leonardo Mariño-Ramírez
  • Kannan Tharakaraman
  • Olivier Bodenreider
  • John Spouge
  • David Landsman
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 541)

Abstract

Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology–derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes.

Key words

Promoter sequences transcription factor–binding sites co-expression networks gene ontology Gibbs sampling 

Notes

Acknowledgments

The authors would like to thank King Jordan for important suggestions and helpful discussions and Alex Brick for his assistance in obtaining intergenic regions during his internship at NCBI. This research was supported by the Intramural Research Program of the NIH, NLM, NCBI.

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Copyright information

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

Authors and Affiliations

  • Leonardo Mariño-Ramírez
    • 1
  • Kannan Tharakaraman
    • 1
  • Olivier Bodenreider
    • 2
  • John Spouge
    • 1
  • David Landsman
    • 1
  1. 1.Computational Biology Branch, National Center for Biotechnology InformationNational Institutes of HealthBethesdaUSA
  2. 2.National Library of MedicineNational Institutes of HealthBethesdaUSA

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