Description
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. 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 Andr 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 PPAR-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
