title: Integrated network analysis and effective tools in plant systems biology.
abstract: One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1) network visualization tools, (2) pathway analyses, (3) genome-scale metabolic reconstruction, and (4) the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.
authors.affiliation: RIKEN Center for Sustainable Resource Science Tsurumi, Yokohama, Japan ; Japan Science and Technology Agency, National Bioscience Database Center Tokyo, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Fukushima
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology Nara, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
authors.affiliation: Japan Science and Technology Agency, National Bioscience Database Center Tokyo, Japan ; Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center Osaka, Japan.
authors.forename: Kozo
authors.initials: K
authors.lastname: Nishida
keywords: flux balance analysis; genome-scale metabolic reconstruction; network visualization; pathway analysis; plant metabolism