title: A systems biology approach toward understanding seed composition in soybean.
abstract: BACKGROUND
  The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks.
  
  
  RESULTS
  With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks.
  
  
  CONCLUSIONS
  This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.forename: Manhoi
authors.initials: M
authors.lastname: Hur
authors.forename: Joon-Yong
authors.initials: JY
authors.lastname: Lee
authors.forename: Wenxu
authors.initials: W
authors.lastname: Zhou
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Song
authors.forename: Nick
authors.initials: N
authors.lastname: Ransom
authors.forename: Cumhur Yusuf
authors.initials: CY
authors.lastname: Demirkale
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.forename: Mark
authors.initials: M
authors.lastname: Westgate
authors.forename: Zebulun
authors.initials: Z
authors.lastname: Arendsee
authors.forename: Vidya
authors.initials: V
authors.lastname: Iyer
authors.forename: Jackie
authors.initials: J
authors.lastname: Shanks
authors.forename: Basil
authors.initials: B
authors.lastname: Nikolau
authors.forename: Eve Syrkin
authors.initials: ES
authors.lastname: Wurtele
mesh_terms: D053263:Gene Regulatory Networks; D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000706:statistics & numerical data; D012639:Seeds / Q000737:chemistry / Q000196:embryology / Q000254:growth & development*; D012984:Software; D013025:Glycine max / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D049490:Systems Biology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014157:Transcription Factors