Preface
1 A brief history of gnomics
2 DNA array formats
In situ synthesized oligonucleotide arrays
Pre-synthesized DNA arrays
Filter-based DNA arrays
Non-conventional gene expression profiling technologies
3 DNA array teadout methods
Reading data from a fluorescent signal
Reading data from a radioactive signal
4 Gene expression profiling experiments:problems,pitfalls,and solutions
Primary sources of experimental and biological varization
Special considerations for gene expression profiling in bacteria
Problems associated with target preparation with polyadenylated mRNA from eukaryotic cells
A total RNA solution for targert preparation from eukaryotic cells
Target cDNA solution for target preparation from eukaryotic cells
Data acquisition for nylon filter experiments
Data acquisition for Affymetrix GeneChipTM glass slide experiments
Normalization methods
5 Statistical analysis of array data:Ingerring changes
Problems and common approaches
Probablilistic modeling of array data
Simulations
Extensions
6 Statistical analysis of array data:Dimensionality reduction,clustering,and regulatory regions
Problems and approaches
Visualization,dimensionality reduction,and principal component analysis
Clustering overview
Hierarchical clustering
K-means,mixture models,and EM algorithms
DNA arrays and regulatory regions
7 The design,analysis,and interpretation of gene expression profiling experiments
Experimental design
Identification of differentially expressed genes
Determination of the source of errors in DNA array experiments
Estimation of the global false positive level for a DNA array experiment
Improved statistical inference from DNA array data using a Bayseian statistical framework
Nylon filter data vs.Affymetrix GeneChipTM data
Modeling probe pair set data from Affymetrix GeneChipsTM
Application of clustering and visualization methods
Identification of defferential gene expression patterns resulting form two-variable perturbation experiments
8 Systems biology
Introduction
The molecular worle:Representation and Simulation
Computational models of regulatory networks
Software and databases
The search for general principles
Appendix A Experimental protocols
Appendix B Mathematical complements
Appendix C Internet resoutces
Appendix D CyberT:An online program for the statistical analysis of DNA array data
Index
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