Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.

TitleDecomposing complex reaction networks using random sampling, principal component analysis and basis rotation.
Publication TypeJournal Article
Year of Publication2009
AuthorsBarrett CL, Herrgard MJ, Palsson BØ
JournalBMC systems biology
Volume3
Pagination30
PubMed Date2009
ISSN1752-0509
KeywordsEscherichia coli, Gene Regulatory Networks, Metabolic Networks and Pathways, Monte Carlo Method, Principal Component Analysis, Systems Biology
Abstract

BACKGROUND: Metabolism and its regulation constitute a large fraction of the molecular activity within cells. The control of cellular metabolic state is mediated by numerous molecular mechanisms, which in effect position the metabolic network flux state at specific locations within a mathematically-definable steady-state flux space. Post-translational regulation constitutes a large class of these mechanisms, and decades of research indicate that achieving a network flux state through post-translational metabolic regulation is both a complex and complicated regulatory problem. No analysis method for the objective, top-down assessment of such regulation problems in large biochemical networks has been presented and demonstrated.

RESULTS: We show that the use of Monte Carlo sampling of the steady-state flux space of a cell-scale metabolic system in conjunction with Principal Component Analysis and eigenvector rotation results in a low-dimensional and biochemically interpretable decomposition of the steady flux states of the system. This decomposition comes in the form of a low number of small reaction sets whose flux variability accounts for nearly all of the flux variability in the entire system. This result indicates an underlying simplicity and implies that the regulation of a relatively low number of reaction sets can essentially determine the flux state of the entire network in the given growth environment.

CONCLUSION: We demonstrate how our top-down analysis of networks can be used to determine key regulatory requirements independent of specific parameters and mechanisms. Our approach complements the reductionist approach to elucidation of regulatory mechanisms and facilitates the development of our understanding of global regulatory strategies in biological networks.

Alternate JournalBMC Syst Biol
PubMed ID19267928

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