Gene regulatory networks : methods and protocols / edited by Bart Deplancke, Nele Gheldof. — New York : Humana Press ; Springer, c2012. – (58.17/M592/v.786) |
Contents
Contents
Preface
Contributors
PART I REGULATORY STATE COMPONENTS
1 How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome
2 Expression Pattern Analysis of Regulatory Transcription Factors in Caenorhabditis elegans
3 High-Throughput SELEX Determination of DNA Sequences Bound by Transcription Factors In Vitro
4 Convenient Determination of Protein-Binding DNA Sequences Using Quadruple 9-Mer-Bascd Microarray and DsRed-Monomer Fusion Protein
5 Analysis of Specific Protein-DNA Interactions by Bacterial One-Hybrid Assay 79
6 MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor-DNA Interaction
7 Detecting Protein-Protein Interactions with the Split-Ubiquitin Sensor
8 Genome-Wide Dissection of Posttranscriptional and Posttranslational Interactions
9 Linking Cellular Signalling to Gene Expression Using EXT-Encoded Reporter Libraries
10 Sample Preparation for Small RNA Massive Parallel Sequencing
PART II GENOMIC COMPONENTS
11 CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection of Promoter and Transcriptional Networks
12 Detecting DNaseI-Hypersensitivity Sites with MLPA
13 Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method
PART III MAPPING PROTEIN-DNA INTERACTIONS
14 Analyzing Transcription Factor Occupancy During Embryo Development Using ChIP-seq
15 Genome-Wide Profiling of DNA-Binding Proteins Using Barcode-Based Multiplex Solexa Sequencing
16 Computational Analysis of Protein-DNA Interactions from ChIP-seq Data 263
17 Using a Yeast Inverse One-Hybrid System to Identify Functional Binding Sites of Transcription Factors 275
18 Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila
19 Proteomic Methodologies to Study Transcription Factor Function 315
20 A High-throughput Gateway-Compatible Yeast One-Hybrid Screen to Detect Protein-DNA Interactions
PART IV VISUALIZATION OF GRNs
21 BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks 359
PART V MODELING OF GRNs
22 Implicit Methods for Qualitative Modeling of Gene Regulatory Networks 397
Index 445