TY  - JOUR
A1  - Koch, Ina
A1  - Ackermann, Jörg
T1  - On functional module detection in metabolic networks
T2  - Metabolites : open access journal
N2  - 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.
KW  - metabolic networks
KW  - functional module
KW  - Petri net
KW  - t-invariant
KW  - Fourier-Motzkin algorithm
KW  - elementary mode
KW  - maximal common transition set
KW  - t-cluster
KW  - minimal cut set
KW  - community
KW  - Q-modularity
Y1  - 2013
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/31469
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-314699
SN  - 2218-1989
N1  - © 2013 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
VL  - 3
SP  - 673
EP  - 700
PB  - MDPI
CY  - Basel
ER  -