Book Volume 553 2009

Plant Systems Biology

Editors:

ISBN: 978-1-60327-562-0 (Print) 978-1-60327-563-7 (Online)

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xv

  2. Part I: Systems Biology of Plant Gene Expression

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 3-12

      Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks

    3. No Access

      Protocol

      Pages 13-37

      Genome-Wide Analysis of RNA-Protein Interactions in Plants

    4. No Access

      Protocol

      Pages 39-56

      Whole-Genome Microarrays: Applications and Technical Issues

    5. No Access

      Protocol

      Pages 57-77

      Manipulating Large-Scale Arabidopsis Microarray Expression Data: Identifying Dominant Expression Patterns and Biological Process Enrichment

    6. No Access

      Protocol

      Pages 79-108

      Applications of Ultra-high-Throughput Sequencing

    7. No Access

      Protocol

      Pages 109-126

      Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification Methods

    8. No Access

      Protocol

      Pages 127-139

      Chromatin Charting: Global Mapping of Epigenetic Effects

    9. No Access

      Protocol

      Pages 141-177

      Clone-Based Functional Genomics

  3. Part II: Networks, Pathways, Statistical Issues, and Novel Computational Tools

    1. Front Matter

      Pages 179-179

    2. No Access

      Protocol

      Pages 181-206

      Challenges and Approaches to Statistical Design and Inference in High-Dimensional Investigations

    3. No Access

      Protocol

      Pages 207-225

      Discrete Dynamic Modeling with Asynchronous Update, or How to Model Complex Systems in the Absence of Quantitative Information

    4. No Access

      Protocol

      Pages 227-245

      Quantification of Variation in Expression Networks

    5. No Access

      Protocol

      Pages 247-264

      Co-expression Analysis of Metabolic Pathways in Plants

    6. No Access

      Protocol

      Pages 265-285

      Integration of Metabolic Reactions and Gene Regulation

    7. No Access

      Protocol

      Pages 287-301

      Applying Word-Based Algorithms: The IMEter

  4. Part III: Imaging

    1. Front Matter

      Pages 303-303

    2. No Access

      Protocol

      Pages 305-316

      Live-Imaging and Image Processing of Shoot Apical Meristems of Arabidopsis thaliana

    3. No Access

      Protocol

      Pages 317-326

      Computer Vision as a Tool to Study Plant Development

  5. Part IV: Chemical Genetic, Metabolomic, and Integrative Methods for Plant Systems Biology

    1. Front Matter

      Pages 327-327

    2. No Access

      Protocol

      Pages 329-343

      Metabolomics of Plant Volatiles

    3. No Access

      Protocol

      Pages 345-354

      Chemical Genomics Approaches in Plant Biology

    4. No Access

      Protocol

      Pages 355-372

      Comparison of Quantitative Metabolite Imaging Tools and Carbon-13 Techniques for Fluxomics

    5. No Access

      Protocol

      Pages 373-393

      Democratization and Integration of Genomic Profiling Tools

  6. Back Matter

    Pages 395-408