title: Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks.
abstract: Physiological responses, developmental programs, and cellular functions rely on complex networks of interactions at different levels and scales. Systems biology brings together high-throughput biochemical, genetic, and molecular approaches to generate omics data that can be analyzed and used in mathematical and computational models toward uncovering these networks on a global scale. Various approaches, including transcriptomics, proteomics, interactomics, and metabolomics, have been employed to obtain these data on the cellular, tissue, organ, and whole-plant level. We summarize progress on gene regulatory, cofunction, protein interaction, and metabolic networks. We also illustrate the main approaches that have been used to obtain these networks, with specific examples from Arabidopsis thaliana, and describe the pros and cons of each approach.
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
authors.forename: George W
authors.initials: GW
authors.lastname: Bassel
authors.forename: Allison
authors.initials: A
authors.lastname: Gaudinier
authors.forename: Siobhan M
authors.initials: SM
authors.lastname: Brady
authors.forename: Lars
authors.initials: L
authors.lastname: Hennig
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
authors.forename: Ive
authors.initials: I
authors.lastname: De Smet
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D053263:Gene Regulatory Networks; D023281:Genomics; D053858:Metabolic Networks and Pathways; D055432:Metabolomics; D008954:Models, Biological; D040901:Proteomics; D049490:Systems Biology / Q000379:methods*; D014158:Transcription, Genetic