Gene Regulatory Networks

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