Beschreibung
InhaltsangabePart 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
Autorenportrait
InhaltsangabePart 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
