Microarrays for an integrative genomics / Isaac S. Kohane, Alvin T. Kho, and Atul J. Butte.

Cambridge, Mass ; London : MIT Press, [2003], ©2003.

xviii, 306 pages : illustrations ; 24 cm.

"Bradford book."

Copy 1. Donor: Wellcome Trust Sanger Institute.

Includes bibliographical references (p. [283]-295) and index.

The Future Is So Bright ... -- Functional Genomics -- Informatics and advances in enabling technology -- Why do we need new techniques? -- Missing the Forest for the Dendrograms -- Sociology of a functional genomics pipeline -- Functional Genomics, Not Genetics -- In silico analysis will never substitute for in vitro and in vivo -- Basic Biology -- Biological caveats in mRNA measurements -- Sequence-level genomics -- Proteomics -- Experimental Design -- The Safe Conception of a Functional Genomic Experiment -- Experiment design space -- Expression space -- Exercising the expression space -- Discarding data and low-hanging fruit -- Gene-Clustering Dogma -- Supervised versus unsupervised learning -- Figure of merit: The elusive gold standard in functional genomics -- Microarray Measurements to Analyses -- Generic Features of Microarray Technologies -- Robotically spotted microarrays -- Oligonucleotide microarrays -- Replicate Experiments, Reproducibility, and Noise -- What is a replicate experiment? A reproducible experimental outcome? -- Reproducibility across repeated microarray experiments: Absolute expression level and fold difference -- Cross-platform (technology) reproducibility -- Pooling sample probes and PCR for replicate experiments -- What is noise? -- Sources and examples of noise in the generic microarray experiment -- Biological variation as noise: The Human Genome Project and irreproducibility of expression measurements -- Managing noise -- Prototypical Objectives and Questions -- Two examples: Inter-array and intra-array.