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Gene Regulatory Networks

  • Kartonierter Einband
  • 460 Seiten
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Beschreibung

This timely and authoritative book aims to provide a comprehensive toolkit to study gene regulatory networks from the point of data generation to processing, visualization, and modeling. The book is intended for novices and experienced researchers alike.


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.



Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts



Inhalt

Part I. Regulatory State Components

1. How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome

Juan M. Vaquerizas, Sarah A. Teichmann, and Nicholas M. Luscombe

2. Expression Pattern Analysis of Regulatory Transcription Factors in Caenorhabditis elegans

Huiyun Feng, Hannah L. Craig, and Ian A. Hope

3. High-throughput SELEX Determination of DNA Sequences Bound by Transcription Factors In vitro

Nobuo Ogawa and Mark D. Biggin

4. Convenient Determination of Protein-Binding DNA Sequences using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein

Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, and Yeon-Ki Kim

5. Analysis of Specific Protein-DNA Interactions by Bacterial One-Hybrid Assay

Marcus B. Noyes

6. MITOMI- A Microdluidic Platform for In vitro Characterization of Transcription Factor DNA Interaction

Sylvie Rockel, Marcel Geertz, and Sebastian J. Maerkl

7. Detecting Protein-protein Interactions with the Split-Ubiquitin Sensor

Alexander Dünkler, Judith Müller, and Nils Johnsson

8. Genome-wide Dissection of Post-transcriptional and Post-translational Interactions

Mukesh Bansal and Andrea Califano

9. Linking Cellular Signalling to Gene Expression using EXT Encoded Reporter Libraries

Anna Botvinik and Moritz J. Rossner

10. Sample Preparation for Small RNA Massive Parallel Sequencing

Willemijn M. Gommans and Eugene Berezikov

Part II. Genomic Components

11. CAGE-Cap Analysis Gene Expression: A Protocol for the Detection of Promoter and Transcriptional Networks

Hazuki Takahashi, Sachiko Kato, Mitsuyoshi Murata, and Piero Carninci

12. Detecting DNasel-hypersensitivity Sites with MLPA

Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White

13. Detecting Long-range Chromatin Interactions using the Chromosome Conformation Capture Sequencing (3C-seq) Method

Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, and Alexandre Reymond

Part III. Mapping Protein-DNA Interactions

14. Analyzing Transcription Factor Occupancy during Embryo Development using ChIP-seq

Yad Ghavi-Helm and Eileen E.M. Furlong

15. Genome-wide Profiling of DNA Binding Proteins using Barcode-based Multiplex Solexa Sequencing

Bart Deplancke

16. Computational Analysis of Protein-DNA Interactions from ChIP-seq Data

Jacques Rougemont and Felix Naef

17. Using a Yeast Inverse One-hybrid System to Identify Functional Binding Sites of Transcription Factors

Jizhou Yan and Shawn M. Burgess

18. Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila

Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann, and Stein Aerts

19. Proteomic Methodologies to Study Transcription Factor Function

Harry W. Jarrett

20. A High-throughput Gateway-compatible Yeast One-hybrid Screen to Detect Protein-DNA Interactions

Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke

Part IV. Visualitzation of GRNs

21. BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks

William J. R. Longabaugh

Part V. Modeling of GRNs

22. Implicit Methods for Qualitative Modeling of Gene Regulatory Networks

Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, and Ioannis Xenarios

Produktinformationen

Titel: Gene Regulatory Networks
Untertitel: Methods and Protocols
Editor:
EAN: 9781493958382
ISBN: 1493958380
Format: Kartonierter Einband
Herausgeber: Humana Press
Anzahl Seiten: 460
Gewicht: 858g
Größe: H254mm x B178mm x T24mm
Jahr: 2016
Untertitel: Englisch
Auflage: Softcover reprint of the original 1st ed. 2012

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