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Prediction of Regulatory Elements

  • Protocol
Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 453))

Abstract

Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene. As wet-lab methods are time consuming and expensive, it is not realistic to identify TFBS for all uncharacterized genes in the genome by purely experimental means. Computational methods aimed at predicting potential regulatory regions can increase the efficiency of wet-lab experiments significantly. Here, methods for building quantitative models describing the binding preferences of transcription factors based on literature-derived data are presented, as well as a general protocol for scanning promoters using cross-species comparison as a filter (phylogenetic footprinting).

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Acknowledgments

Thanks to Ann Karlsson for comments on the text.

Author information

Authors and Affiliations

  1. The Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark

    Albin Sandelin

Authors
  1. Albin Sandelin
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Editor information

Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Sandelin, A. (2008). Prediction of Regulatory Elements. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 453. Humana Press. https://doi.org/10.1007/978-1-60327-429-6_11

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  • DOI: https://doi.org/10.1007/978-1-60327-429-6_11

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-428-9

  • Online ISBN: 978-1-60327-429-6

  • eBook Packages: Springer Protocols

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