Gene Regulatory Networks

Methods and Protocols

  • Bart Deplancke
  • Nele Gheldof

Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Regulatory State Components

    1. Front Matter
      Pages 1-1
    2. Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, Yeon-Ki Kim
      Pages 65-77
    3. Alexander Dünkler, Judith Müller, Nils Johnsson
      Pages 115-130
    4. Willemijn M. Gommans, Eugene Berezikov
      Pages 167-178
  3. Genomic Components

    1. Front Matter
      Pages 179-179
    2. Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, Piero Carninci
      Pages 181-200
    3. Thomas Ohnesorg, Stefanie Eggers, Stefan J. White
      Pages 201-210
    4. Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, Alexandre Reymond
      Pages 211-225
  4. Mapping Protein–DNA Interactions

    1. Front Matter
      Pages 227-227
    2. Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann, Stein Aerts
      Pages 291-314
  5. Visualization of GRNs

    1. Front Matter
      Pages 357-357
  6. Modeling of GRNs

    1. Front Matter
      Pages 395-395
    2. Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, Ioannis Xenarios
      Pages 397-443
  7. Back Matter
    Pages 445-446

About this book


Gene regulatory networks play a vital role in organismal development and function by controlling gene expression. With the availability of complete genome sequences, several novel experimental and computational approaches have recently been developed which promise to significantly enhance our ability to comprehensively characterize these regulatory networks by enabling the identification of respectively their genomic or regulatory state components, or the interactions between these two in unprecedented detail. Divided into five convenient sections, Gene Regulatory Networks: Methods and Protocols details how each of these approaches contributes to a more thorough understanding of the composition and function of gene regulatory networks, while providing a comprehensive protocol on how to implement them in the laboratory. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.


Authoritative and accessible, Gene Regulatory Networks: Methods and Protocols aims to provide novices and experienced researchers alike with a comprehensive and timely toolkit to study gene regulatory networks from the point of data generation to processing, visualization, and modeling.


ChIP-sequencing RNA massive parallel sequencing protein-DNA interactions protein-protein interactions transcription factors

Editors and affiliations

  • Bart Deplancke
    • 1
  • Nele Gheldof
    • 2
  1. 1.Inst. BioengineeringEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
  2. 2.Faculté de Biologie det Médecine, Centre Intégratif de GénomiqueUniversité de LausanneLausanneSwitzerland

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2012
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-61779-291-5
  • Online ISBN 978-1-61779-292-2
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site