TY - JOUR

T1 - Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition

AU - Barrett, Christian L.

AU - Price, Nathan D.

AU - Palsson, Bernhard O.

PY - 2006/3/13

Y1 - 2006/3/13

N2 - Background: Extreme pathways (ExPas) have been shown to be valuable for studying the functions and capabilities of metabolic networks through characterization of the null space of the stoichiometric matrix (S). Singular value decomposition (SVD) of the ExPa matrix P has previously been used to characterize the metabolic regulatory problem in the human red blood cell (hRBC) from a network perspective. The calculation of ExPas is NP-hard, and for genome-scale networks the computation of ExPas has proven to be infeasible. Therefore an alternative approach is needed to reveal regulatory properties of steady state solution spaces of genome-scale stoichiometric matrices. Results: We show that the SVD of a matrix (W) formed of random samples from the steady-state solution space of the hRBC metabolic network gives similar insights into the regulatory properties of the network as was obtained with SVD of P. This new approach has two main advantages. First, it works with a direct representation of the shape of the metabolic solution space without the confounding factor of a non-uniform distribution of the extreme pathways and second, the SVD procedure can be applied to a very large number of samples, such as will be produced from genome-scale networks. Conclusion: These results show that we are now in a position to study the network aspects of the regulatory problem in genome-scale metabolic networks through the use of random sampling.

AB - Background: Extreme pathways (ExPas) have been shown to be valuable for studying the functions and capabilities of metabolic networks through characterization of the null space of the stoichiometric matrix (S). Singular value decomposition (SVD) of the ExPa matrix P has previously been used to characterize the metabolic regulatory problem in the human red blood cell (hRBC) from a network perspective. The calculation of ExPas is NP-hard, and for genome-scale networks the computation of ExPas has proven to be infeasible. Therefore an alternative approach is needed to reveal regulatory properties of steady state solution spaces of genome-scale stoichiometric matrices. Results: We show that the SVD of a matrix (W) formed of random samples from the steady-state solution space of the hRBC metabolic network gives similar insights into the regulatory properties of the network as was obtained with SVD of P. This new approach has two main advantages. First, it works with a direct representation of the shape of the metabolic solution space without the confounding factor of a non-uniform distribution of the extreme pathways and second, the SVD procedure can be applied to a very large number of samples, such as will be produced from genome-scale networks. Conclusion: These results show that we are now in a position to study the network aspects of the regulatory problem in genome-scale metabolic networks through the use of random sampling.

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U2 - 10.1186/1471-2105-7-132

DO - 10.1186/1471-2105-7-132

M3 - Article

C2 - 16533395

AN - SCOPUS:33645462026

SN - 1471-2105

VL - 7

JO - BMC Bioinformatics

JF - BMC Bioinformatics

M1 - 132

ER -