Plant systems biology / edited by Dmitry A. Belostotsky. — New York ; London : Humana, c2009. – (58.17/M592/v.553) |
Contents
CONTENTS
Foreword
Preface
Contributors
SECTION I SYSTEMS BIOLOGY OF PLANT GENE EXPRESSION
1. Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks
2. Genome-Wide Analysis of RNA-Protein Interactions in Plants
3. Whole-Genome Microarrays: Applications and Technical Issues
4. Manipulating Large-Scale Arabidopsis Microarray Expression Data: Identifying Dominant Expression Patterns and Biological Process Enrichment 57
5. Applications of Ultra-high-Throughput Sequencing
6. Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification Methods 109
7. Chromatin Charting: Global Mapping of Epigenetic Effects 127
8. Clone-Based Functional Genomics
SECTION II: NETWORKS, PATHWAYS, STATISTICAL ISSUES, AND NOVEL COMPUTATIONAL TOOLS
9. Challenges and Approaches to Statistical Design and Inference in High-Dimensional Investigations
10. Discrete Dynamic Modeling with Asynchronous Update, or How to Model Complex Systems in the Absence of Quantitative Information 207
11. Quantification of Variation in Expression Networks
12. Co-expression Analysis of Metabolic Pathways in Plants
13. Integration of Metabolic Reactions and Gene Regulation
14. Applying Word-Based Algorithms: The IMEter
SECTION III: IMAGING
15. Live-Imaging and Image Processing of Shoot Apical Meristems of Arabidopsis thaliana
16. Computer Vision as a Tool to Study Plant Development
SECTION IV: CHEMICAL GENETIC, METABOLOMIC, AND INTEGRATIVE METHODS FOR PLANT SYSTEMS BIOLOGY
17. Metabolomics of Plant Volatiles 329
18. Chemical Genomics Approaches in Plant Biology 345
19. Comparison of Quantitative Metabolite Imaging Tools and Carbon-13 Techniques for Fluxomics 355
20. Democratization and Integration of Genomic Profiling Tools 373
Index