Genomic signal processing: from matrix algebra to genetic networks.

Genomic signal processing: from matrix algebra to genetic networks. Research Abstract Details 

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Genomic signal processing: from matrix algebra to genetic networks. Abstract Text:

Orly Alter,

DNA microarrays make it possible, for the first time, to record the complete genomic signals that guide the progression of cellular processes. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment, and drug development. This chapter reviews the first data-driven models that were created from these genome-scale data, through adaptations and generalizations of mathematical frameworks from matrix algebra that have proven successful in describing the physical world, in such diverse areas as mechanics and perception: the singular value decomposition model, the generalized singular value decomposition model comparative model, and the pseudoinverse projection integrative model. These models provide mathematical descriptions of the genetic networks that generate and sense the measured data, where the mathematical variables and operations represent biological reality. The variables, patterns uncovered in the data, correlate with activities of cellular elements such as regulators or transcription factors that drive the measured signals and cellular states where these elements are active. The operations, such as data reconstruction, rotation, and classification in subspaces of selected patterns, simulate experimental observation of only the cellular programs that these patterns represent. These models are illustrated in the analyses of RNA expression data from yeast and human during their cell cycle programs and DNA-binding data from yeast cell cycle transcription factors and replication initiation proteins. Two alternative pictures of RNA expression oscillations during the cell cycle that emerge from these analyses, which parallel well-known designs of physical oscillators, convey the capacity of the models to elucidate the design principles of cellular systems, as well as guide the design of synthetic ones. In these analyses, the power of the models to predict previously unknown biological principles is demonstrated with a prediction of a novel mechanism of regulation that correlates DNA replication initiation with cell cycle-regulated RNA transcription in yeast. These models may become the foundation of a future in which biological systems are modeled as physical systems are today.

Genomic signal processing: from matrix algebra to genetic networks. Publishing Authors By Initials

O Alter,

For similar biological phenomena, cell phenomena, and immunity: cell physiology: cell communication: signal transduction research abstracts see: biological phenomena, cell phenomena, and immunity: cell physiology: cell communication: signal transduction research

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Genomic signal processing: from matrix algebra to genetic networks. Journal Published:

PUBLICATION TYPE: Review

Journal: Methods in molecular biology (Clifton, N.J.)

VOLUME: 377

Page Numbers: 17-60

Journal Abbreviation: Methods Mol. Biol.

ISSN: 1064-3745

DAY: 3

MONTH: 12

YEAR: 2007

Genomic signal processing: from matrix algebra to genetic networks. Information

Number of References: 64

LANGUAGE: eng

NlmUniqueID: 9214969

Genomic signal processing: from matrix algebra to genetic networks. Keywords Mesh Terms:

KEYWORDS: Signal Transduction

MESH TERMS: metabolism

Chemical & Substance for Abstract: Genomic signal processing: from matrix algebra to genetic networks. Information

Substance Name: RNA, Fungal

Registry Number: 0

Grant and Affiliation Information for Genomic signal processing: from matrix algebra to genetic networks.

AFFILIATION: Department of Biomedical Engineering, Institute for Cellular and Molecular Biology and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA.

Country: United States

AGENCY: United States NHGRI

GRANT: K01 HG00038-05

ACRONYM: HG

MEDLINETA: Methods Mol Biol

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