Summary
We present a method to predict cis-acting elements by detecting over-represented motifs in promoters of a set of coregulated genes (single-genome, multigenes approach). The method has been used successfully to detect regulating elements in bacteria and yeast. It can be used with higher organisms as well, but with a loss in reliability of the predictions. A web interface is available at the Regulatory Sequence Analysis Tools site (http://rsat.scmbb.ulb.ac.be/rsat/).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
van Helden, J., Andre, B., and Collado-Vides, J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.J. Mol. Biol. 281, 827–842.
van Helden, J., Rios, A. F., and Collado-Vides, J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 28, 1808–1818.
Gasch, A. P., Spellman, P. T., Kao, C. M., et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11, 4241–4257.
van Helden, J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res. 31, 3593–3596.
van Helden, J., Andre, B., and Collado-Vides, J. (2000) A web site for the computational analysis of yeast regulatory sequences. Yeast 16, 177–187.
Acknowledgments
This project was partly supported by the BioSapiens Network of Excellence funded under the sixth Framework programme of the European Communities (LSHG-CT-2003-503265). Genome installation is done on a 40-node PC cluster contributed by various institutions, including the Belgian Fonds pour la Recherche Fondamentale Collective (FRFC grant 2005). We are grateful to Raphaël Leplae for his enthusiasm in obtaining, installing, and maintaining this cluster. JvH acknowledges Stéphane Vissers for an inspiring discussion on the importance of good quality protocols for teaching and practicing good science. We are thankful to Stephan Kurtz for making available his very efficient program vmatch, which is used to purge redundant fragments.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Sand, O., Helden, J.v. (2007). Discovery of Motifs in Promoters of Coregulated Genes. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_21
Download citation
DOI: https://doi.org/10.1007/978-1-59745-514-5_21
Publisher Name: Humana Press
Print ISBN: 978-1-58829-693-1
Online ISBN: 978-1-59745-514-5
eBook Packages: Springer Protocols