Bookedited by Bart Deplancke, Nele Gheldof.
Contents:
pt. 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 microfluidic 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 posttranscriptional and posttranslational 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
pt. II. Genomic components. 11. CAGE (cap analysis of gene expression) : a protocol for the detection of promoter and transcriptional networks / Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, and Piero Carninci. 12. Detecting DNaseI-hypersensitivity sites with MLPA / Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White. 13. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method / Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, and Alexandre Reymond
pt. 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 / Sunil Kumar Raghav and 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. High-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions / Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke
pt. IV. Visualization GRNs. 21. BioTapestry : a tool to visualize the dynamic properties of gene regulatory networks / William J.R. Longabaugh
pt. V. Modeling of GRNs. 22. Implicit methods for qualitative modeling of gene regulatory networks / Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, and Ioannis Xenarios.