Transcription Factor Regulatory Networks: Methods and Protocols

ISBN-13: 9781493908042 / Angielski / Twarda / 2014 / 220 str.

Etsuko Miyamoto-Sato; Hiroyuki Ohashi; Hiroshi Yanagawa

Opis

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.

Spis treści

1. Detecting Protein-protein Interactions/Complex Components using Mass Spectrometry Coupled Techniques

Zhibin Ning, Brett Hawley, Cheng-Kang Chiang, Deeptee Seebun and Daniel Figeys

2. The Analysis of Transcription Factor Networks using the IVV Method

Hiroyuki Ohashi, Shigeo Fujimori, Hirai Naoya, Hiroshi Yanagawa  and Etsuko Miyamoto-Sato

3. Next-generation Sequencing Coupled with a Cell-free Display Technology

for Reliable Interactome of Translational Factors

Etsuko Miyamoto-Sato

4. Chromatin Immunoprecipitation Protocol for Mammalian Cells

Makiko Komata, Yuki Katou, Hiroshi Tanaka, Ryuichiro Nakato, Katsuhiko Shirahige, and Masashige Bando

5. Detecting Protein–DNA Interactions using a Modified Yeast One-hybrid System

Kazuhisa Ota, Shu-Ying Feng and Takashi Ito

6. RNA Sequencing: From Sample Preparation to Analysis

Sho Maekawa, Ayako Suzuki, Sumio Sugano and Yutaka Suzuki

7. Detecting Expressed Genes using CAGE

Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Miki Kojima-Ishiyama, Piero Carninci^, Yoshihide Hayashizaki and Masayoshi Itoh

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

André Fujita and Satoru Miyano

 9. Inference of TERNs (2)

Hideo Matsuda

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

Ahmed Essaghir

11. Modeling and Simulation using CellDesigner

Yukiko Matsuoka, Akira Funahashi, Samik Ghosh and Hiroaki Kitano

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

N. Monma, T. Gojobori and K. Ikeo

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

Taishin Akiyama, Junwen Qin, Daisuke Ohshima and Jun-ichiro Inoue

14. Analysis of NFATc1-centered Transcription Factor Regulatory Networks in Osteoclast Formation

Masahiro Shinohara and  Hiroshi Takayanagi

15. Transcriptional Regulation in Adipogenesis through PPARγ-dependent and –Independent Mechanisms by Prostaglandins

Ko Fujimori and Yoshihiro Urade

16. Analysis of TFRNs Associated with Steroid Hormone-related Cancers

Kazuhiro Ikeda, Kuniko Horie-Inoue and Satoshi Inoue

17. Repositioning Monocyte TFRN into Fibroblasts

 Takahiro Suzuki, Jay W. Shin and Harukazu Suzuki