Reverse engineering of metabolic networks, a critical assessment

Mol Biosyst. 2011 Feb;7(2):511-20. doi: 10.1039/c0mb00083c. Epub 2010 Nov 10.

Abstract

Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.

Publication types

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

MeSH terms

  • Animals
  • Escherichia coli / metabolism
  • Feasibility Studies
  • Humans
  • Metabolomics*
  • Yeasts / metabolism