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Main description:
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 (TM) 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.
Contents:
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 Dunkler, Judith Muller, 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
PRODUCT DETAILS
Publisher: Springer (Humana Press Inc.)
Publication date: September, 2011
Pages: 457
Weight: 1056g
Availability: Available
Subcategories: Genetics
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