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Transcription Factor Regulatory Networks

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Etsuko Miyamoto-Sato

    1. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Japan

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  2. Hiroyuki Ohashi

    1. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Japan

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  3. Hirotaka Sasaki

    1. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Japan

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  4. Jun-ichi Nishikawa

    1. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Japan

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  5. Hiroshi Yanagawa

    1. Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku-ku, Yokohama, Japan

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1164)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Detecting Protein–Protein Interactions/Complex Components Using Mass Spectrometry Coupled Techniques

    • Zhibin Ning, Brett Hawley, Cheng-Kang Chiang, Deeptee Seebun, Daniel Figeys
    Pages 1-13

  3. Analysis of Transcription Factor Networks Using IVV Method

    • Hiroyuki Ohashi, Shigeo Fujimori, Naoya Hirai, Hiroshi Yanagawa, Etsuko Miyamoto-Sato
    Pages 15-22

  4. Next-Generation Sequencing Coupled with a Cell-Free Display Technology for Reliable Interactome of Translational Factors

    • Etsuko Miyamoto-Sato
    Pages 23-32

  5. Chromatin Immunoprecipitation Protocol for Mammalian Cells

    • Makiko Komata, Yuki Katou, Hiroshi Tanaka, Ryuichiro Nakato, Katsuhiko Shirahige, Masashige Bando
    Pages 33-38

  6. Detecting Protein–DNA Interactions Using a Modified Yeast One-Hybrid System

    • Kazuhisa Ota, Shu-Ying Feng, Takashi Ito
    Pages 39-50

  7. RNA Sequencing: From Sample Preparation to Analysis

    • Sho Maekawa, Ayako Suzuki, Sumio Sugano, Yutaka Suzuki
    Pages 51-65

  8. Detecting Expressed Genes Using CAGE

    • Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Miki Kojima-Ishiyama, Piero Carninci, Yoshihide Hayashizaki, Masayoshi Itoh
    Pages 67-85

  9. A Tutorial to Identify Nonlinear Associations in Gene Expression Time Series Data

    • André Fujita, Satoru Miyano
    Pages 87-95

  10. Inference of TFRNs (2)

    • Hideo Matsuda
    Pages 97-107

  11. Identification of the Minimal Connected Network of Transcription Factors by Transcriptomic and Genomic Data Integration

    • Ahmed Essaghir
    Pages 109-120

  12. Modeling and Simulation Using CellDesigner

    • Yukiko Matsuoka, Akira Funahashi, Samik Ghosh, Hiroaki Kitano
    Pages 121-145

  13. Human Genome Network Platform: A Resource for TFRN Analysis

    • Norikazu Monma, Takashi Gojobori, Kazuho Ikeo
    Pages 147-162

  14. Identification of Transcription Factors Activated in Thymic Epithelial Cells During Embryonic Thymus Development

    • Taishin Akiyama, Junwen Qin, Daisuke Ohshima, Jun-ichiro Inoue
    Pages 163-170

  15. Analysis of NFATc1-Centered Transcription Factor Regulatory Networks in Osteoclast Formation

    • Masahiro Shinohara, Hiroshi Takayanagi
    Pages 171-176

  16. Transcriptional Regulation in Adipogenesis Through PPARγ-Dependent and -Independent Mechanisms by Prostaglandins

    • Ko Fujimori, Yoshihiro Urade
    Pages 177-196

  17. Analysis of TFRNs Associated with Steroid Hormone-Related Cancers

    • Kazuhiro Ikeda, Kuniko Horie-Inoue, Satoshi Inoue
    Pages 197-209

  18. Repositioning Monocyte TFRN into Fibroblasts

    • Takahiro Suzuki, Jay W. Shin, Harukazu Suzuki
    Pages 211-218

  19. Back Matter

    Pages 219-220
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Keywords

About this book

Transcription Factor Regulatory Methods details various techniques ranging from cutting-edge to general techniques use to study transcription factor regulatory networks. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Transcription Factor Regulatory Methods aids scientists in the further study into post-genomic or the personal genomic era.

Editors and Affiliations

  • Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Japan

    Etsuko Miyamoto-Sato, Hiroyuki Ohashi, Hirotaka Sasaki, Jun-ichi Nishikawa

  • Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku-ku, Yokohama, Japan

    Hiroshi Yanagawa

Bibliographic Information

  • Book Title: Transcription Factor Regulatory Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Etsuko Miyamoto-Sato, Hiroyuki Ohashi, Hirotaka Sasaki, Jun-ichi Nishikawa, Hiroshi Yanagawa

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-0805-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, New York 2014

  • Hardcover ISBN: 978-1-4939-0804-2Published: 14 June 2014

  • Softcover ISBN: 978-1-4939-5445-2Published: 17 September 2016

  • eBook ISBN: 978-1-4939-0805-9Published: 13 June 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 220

  • Number of Illustrations: 14 b/w illustrations, 53 illustrations in colour

  • Topics: Human Genetics, Gene Function

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