I-4. Analyzing Regulatory Regions in Genomes

  1. Prof. Dr. Thomas Lengauer Ph.D.
  1. Dr. Thomas Werner

Published Online: 1 APR 2004

DOI: 10.1002/3527601481.ch4

Bioinformatics ‐ From Genomes to Drugs

Bioinformatics - From Genomes to Drugs

How to Cite

Werner, T. (2001) Analyzing Regulatory Regions in Genomes, in Bioinformatics - From Genomes to Drugs (ed T. Lengauer), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527601481.ch4

Editor Information

  1. Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

Author Information

  1. GSF-National Research Center for Environmental and Health, Institute of Experimental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany

Publication History

  1. Published Online: 1 APR 2004
  2. Published Print: 1 NOV 2001

Book Series:

  1. Methods and Principles in Medicinal Chemistry

Book Series Editors:

  1. Prof. Dr. Raimund Mannhold3,
  2. Prof. Dr. Hugo Kubinyi4 and
  3. Prof. Dr. Gerd Folkers5

Series Editor Information

  1. 3

    Biomedical Research Center, Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstraße 1, D-40225 Düsseldorf, Germany

  2. 4

    BASF AG, Ludwigshaften, c/o Donnersbergstrasse g, D-67256 Weisenheim am Sand, Germany

  3. 5

    Department of Applied Biosciences, ETH Zürich, Winterthurer Str. 190, CH-8057 Zürich, Switzerland

ISBN Information

Print ISBN: 9783527299881

Online ISBN: 9783527601486



  • genomes;
  • eukaryotic genomes;
  • transcription factor binding sites;
  • regulatory regions


This chapter contains sections titled:

  • General features of regulatory regions in eukaryotic genomes

  • General functions of regulatory regions

    • Transcription factor binding sites (TF-sites)

    • Sequence features

    • Structural elements

    • Organizational principles of regulatory regions

    • Bioinformatics models for the analysis and detection of regulatory regions

  • Methods for element detection

    • Detection of transcription factor binding sites

    • Detection of structural elements

    • Assessment of other elements

  • Analysis of regulatory regions

    • Training set selection

    • Statistical and biological significance

    • Context dependency

  • Methods for detection of regulatory regions

    • Types of regulatory regions

    • Programs for recognition of regulatory sequences

  • Annotation of large genomic sequences

    • The balance between sensitivity and specificity

    • The larger context

    • Aspects of comparative genomics

    • Analysis of data sets from high throughput methods

  • Conclusions