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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