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
