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DNA Microarrays and Gene Expression From Experiments to Data Analysis and Modeling

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DNA Microarrays and Gene Expression From Experiments to Data Analysis and Modeling,0521800226,9780521800228

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Book Information

Publisher:Cambridge University Press
Published In:2002
Weight:1.23 lbs
Pages:pp. xvi + 213, 33 Figures, Tables, Index, Appendices, References

The Title "DNA Microarrays and Gene Expression From Experiments to Data Analysis and Modeling" is written by Pierre Baldi. This book was published in the year 2002. This book has total of pp. xvi + 213 (Pages). The publisher of this title is Cambridge University Press. We have about 81936 other great books from this publisher. DNA Microarrays and Gene Expression From Experiments to Data Analysis and Modeling is currently Available with us.

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About the Book

Massive data acquisition technologies, such as genome sequencing, high-throughput drug screening, and DNA arrays are in the process of revolutionizing Biology and medicine. Using the mRNA of a given cell, at a given time, under a given set of conditions, DNA microarrays can provide a snapshot of the level of expression of all the genes in the cell. Such snapshots can be used to study fundamental biological phenomena such as development or evolution, to determine the function of new genes, to infer the role individual genes or groups of genes may play in diseases, and to monitor the effect of drugs and other compounds on gene expression. This inter-disciplinary introduction to DNA arrays will be essential reading for both biology and Computer Science researchers wanting to take advantage of this powerful new technology.

About the Author

Pierre Baldi is Professor and Director of the Institute for Genomics and Bioinformatics in the Department of Information and Computer Science and in the Department of Biological Chemistry at the University of California, Irvine.

Wes Hatfield is a Professor in the Department of Microbiology and Molecular Genetics in the College of Medicine and the Department of Chemical Engineering and Material Sciences in the School of Engineering at the University of California, Irvine.


1. A brief History of genomics
2. DNA array formats
i. In situ synthesized oligonucleotide arrays
ii. Pre-synthesized DNA arrays
iii. Filter-based DNA arrays
iv. Non-conventional gene expression profiling technologies

3. DNA array readout methods
i. Reading data from a fluorescent signal
ii. Reading data from a radioactive signal

4. Gene expression profiling experiments : Problems, pitfalls, and solutions
i. Primary sources of experimental and biological variation
ii. Special considerations for gene expression profiling in bacteria
iii. Problems associated with target preparation with polyadenylated mRNA from eukaryotic cells
iv. A total RNA solution for target preparation from eukaryotic cells
v. Target cDNA synthesis and radioactive labeling for pre-synthesized DNA arrays
vi. Data acquisition for nylon filter experiments
vii. Data acquisition for Affymetrix GeneChipTM glass slide experiments
viii. Normalization methods

5. Statistical analysis of array data : Inferring changes
i. Problems and common approaches
ii. Probabilistic modeling of array data
iii. Simulations
iv. Extensions

6. Statistical analysis of array data: Dimensionality reduction, clustering, and regulatory regions
i. Problems and approaches
ii. Visualization, dimensionality reduction, and principal component analysis
iii. Clustering overview
iv. Hierarchical clustering
v. K-means, mixture models, and EM algorithms
vi. DNA arrays and regulatory regions

7. The design, analysis, and interpretation of gene expression profiling experiments
i. Experimental design
ii. Identification of differentially expressed genes
iii. Determination of The Source of errors in DNA array experiments
iv. Estimation of the global false positive level for a DNA array experiment
v. Improved statistical inference from DNA array data using a Bayesian statistical framework
vi. Nylon filter data vs. Affymetrix GeneChipTM data
vii. Modeling probe pair set data from Affymetrix GeneChipsTM
viii. Application of clustering and visualization methods
ix. Identification of differential gene expression patterns resulting from two-variable perturbation experiments

8. Systems biology
i. Introduction
ii. The molecular world : Representation and simulation
iii. Computational models of regulatory networks
iv. Software and databases
v. The Search for general principles