Sparsity as cellular objective to infer directed metabolic networks from steady-state metabolome data: a theoretical analysis

PLoS One. 2013 Dec 31;8(12):e84505. doi: 10.1371/journal.pone.0084505. eCollection 2013.

Abstract

Since metabolome data are derived from the underlying metabolic network, reverse engineering of such data to recover the network topology is of wide interest. Lyapunov equation puts a constraint to the link between data and network by coupling the covariance of data with the strength of interactions (Jacobian matrix). This equation, when expressed as a linear set of equations at steady state, constitutes a basis to infer the network structure given the covariance matrix of data. The sparse structure of metabolic networks points to reactions which are active based on minimal enzyme production, hinting at sparsity as a cellular objective. Therefore, for a given covariance matrix, we solved Lyapunov equation to calculate Jacobian matrix by a simultaneous use of minimization of Euclidean norm of residuals and maximization of sparsity (the number of zeros in Jacobian matrix) as objective functions to infer directed small-scale networks from three kingdoms of life (bacteria, fungi, mammalian). The inference performance of the approach was found to be promising, with zero False Positive Rate, and almost one True positive Rate. The effect of missing data on results was additionally analyzed, revealing superiority over similarity-based approaches which infer undirected networks. Our findings suggest that the covariance of metabolome data implies an underlying network with sparsest pattern. The theoretical analysis forms a framework for further investigation of sparsity-based inference of metabolic networks from real metabolome data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Metabolic Networks and Pathways / genetics*
  • Metabolome / genetics*
  • Models, Genetic*
  • Saccharomyces cerevisiae / genetics
  • Species Specificity

Grant support

The financial support by TUBITAK, The Scientific and Technological Research Council of Turkey, through a career grant (Project Code: 110M464) is gratefully acknowledged. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.