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PMID: 18616425 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Review

Systems approaches to identifying gene regulatory networks in plants.

Annual review of cell and developmental biology ·Vol. 24 ·2008-00-00 ·Pages 81-103

Long TA, Brady SM, Benfey PN

Abstract

Complex gene regulatory networks are composed of genes, noncoding RNAs, proteins, metabolites, and signaling components. The availability of genome-wide mutagenesis libraries; large-scale transcriptome, proteome, and metabalome data sets; and new high-throughput methods that uncover protein interactions underscores the need for mathematical modeling techniques that better enable scientists to synthesize these large amounts of information and to understand the properties of these biological systems. Systems biology approaches can allow researchers to move beyond a reductionist approach and to both integrate and comprehend the interactions of multiple components within these systems. Descriptive and mathematical models for gene regulatory networks can reveal emergent properties of these plant systems. This review highlights methods that researchers are using to obtain large-scale data sets, and examples of gene regulatory networks modeled with these data. Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed.

MeSH Terms
Biological Clocks/physiology Circadian Rhythm/physiology Databases, Genetic Gene Expression Regulation, Plant Gene Regulatory Networks Genes, Plant Indoleacetic Acids/metabolism Models, Genetic Plant Development Plants/anatomy & histology,metabolism Systems Biology Transcription, Genetic
Chemicals
Indoleacetic Acids
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Long Terri A
1Department of Biology, Duke University, Durham, North Carolina 27708, USA.
Brady Siobhan M
Benfey Philip N
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Article Info
Journal
Annual review of cell and developmental biology
Abbr.
Annu Rev Cell Dev Biol
ISSN
1081-0706
DOI
10.1146/annurev.cellbio.24.110707.175408
Published
2008-00-00
Pages
81-103
Language
English
Region
United States
NLM ID
9600627
PMCID
PMC2739012
Subset
IM
Grants
NIGMS NIH HHS · P50 GM081883-010003 · United States
NIGMS NIH HHS · R01 GM043778 · United States
NIGMS NIH HHS · R01 GM043778-17 · United States
NIGMS NIH HHS · P50 GM081883-01 · United States
NIGMS NIH HHS · R01 GM043778-18 · United States
NIGMS NIH HHS · P50 GM081883-02 · United States
NIGMS NIH HHS · P50 GM081883 · United States
External Links
PubMed source DOI: 10.1146/annurev.cellbio.24.110707.175408 PMC Full Text View journal details
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