On Functional Module Detection in Metabolic Networks

Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes mor...

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Bibliographic Details
Published in:Metabolites Vol. 3; no. 3; pp. 673 - 700
Main Authors: Koch, Ina, Ackermann, Jörg
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 12.08.2013
MDPI
Subjects:
community
elementary mode
Fourier-Motzkin algorithm
functional module
maximal common transition set
metabolic networks
minimal cut set
Petri net
Q-modularity
t-cluster
t-invariant
ISSN:2218-1989, 2218-1989
Online Access:Get full text
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Summary:Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models.
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ISSN:2218-1989
2218-1989
DOI:10.3390/metabo3030673