Microarrays for an Integrative Genomics, 3rd edition by Isaac S. Kohane, Alvin Kho, Atul J. Butte

By Isaac S. Kohane, Alvin Kho, Atul J. Butte

Practical genomics--the deconstruction of the genome to figure out the organic functionality of genes and gene interactions--is some of the most fruitful new parts of biology. The growing to be use of DNA microarrays permits researchers to evaluate the expression of tens of millions of genes at a time. This quantitative swap has resulted in qualitative growth in our skill to appreciate regulatory tactics on the mobile level.This ebook presents a scientific creation to using DNA microarrays as an investigative instrument for practical genomics. The presentation is acceptable for readers from biology or bioinformatics. After proposing a framework for the layout of microarray-driven sensible genomics experiments, the ebook discusses the rules for reading microarray information units, genomic data-mining, the production of standardized nomenclature and knowledge versions, medical functions of useful genomics examine, and the way forward for sensible genomics.

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Additional info for Microarrays for an Integrative Genomics, 3rd edition (Computational Molecular Biology)

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If, in the future, as we expect, massively parallel measurements of individual proteins becomes cost-effective, large-scale, and highly reproducible, then we will certainly expand the analysis to address these methodologies. , every kilobase) genome-wide scans of hundreds of individuals will become economically feasible for most clinical research studies. Current estimates have these technologies available on the genomic and population scale within 5 years. A well-prepared genomic investigator will have prepared the pipeline to take advantage of all these measurement technologies.

An example of some of the broad questions that can be asked are: • Which of all the known genes have regulatory mechanisms that appear to be similar to those regulated by the sonic hedgehog transcription factor in the cerebellum? • Given the effect of 5000 drugs on various cancer cell lines, which gene singly is the most predictive of the responsiveness of the cell line to any chemotherapeutic agent? 20 Chapter 1 • Given a known clinical distinction, such as that between acute lymphocytic leukemia and acute myelogenous leukemia, what is the minimal set of genes that can most reliably distinguish these two diseases?

For instance, gene expression profiling and polymerase chain reaction (PCR) are all methods that have been used by molecular biologists for decades. What we hope the reader will obtain from this book is an appreciation of how the near-comprehensive (and soon to be truly comprehensive) nature of the functional genomics approach as permitted by expression microarrays changes qualitatively and fundamentally the nature of biological investigation. Before our potential readers with biological backgrounds become offended by or disgruntled with this assertion, let us assure them that we present an equivalent critique for the purely computationally oriented bioinformatists and genomicists in the following section.

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