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新书资源(2012年8月)

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