Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks

Plant Cell. 2012 Oct;24(10):3859-75. doi: 10.1105/tpc.112.100776. Epub 2012 Oct 30.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis / physiology*
  • Gene Regulatory Networks
  • Genomics
  • Metabolic Networks and Pathways*
  • Metabolomics
  • Models, Biological*
  • Proteomics
  • Systems Biology / methods*
  • Transcription, Genetic*