Gene Regulatory Networks: Methods and Protocols by Bart DeplanckeGene Regulatory Networks: Methods and Protocols by Bart Deplancke

Gene Regulatory Networks: Methods and Protocols

EditorBart Deplancke, Nele Gheldof

Hardcover | September 22, 2011

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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 BiologyT 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.
Title:Gene Regulatory Networks: Methods and ProtocolsFormat:HardcoverDimensions:457 pagesPublished:September 22, 2011Publisher:Humana PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1617792918

ISBN - 13:9781617792915

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Table of 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 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