Comparison of different approaches for identifying subnetworks in metabolic networks

Abstract

A metabolic network model provides a computational framework for studying the metabolism of a cell at the system level. The organization of metabolic networks has been investigated in different studies. One of the organization aspects considered in these studies is the decomposition of a metabolic network. The decompositions produced by different methods are very different and there is no comprehensive evaluation framework to compare the results with each other. In this study, these methods are reviewed and compared in the first place. Then they are applied to six different metabolic network models and the results are evaluated and compared based on two existing and two newly proposed criteria. Results show that no single method can beat others in all criteria but it seems that the methods introduced by Guimera and Amaral and Verwoerd do better on among metabolite-based methods and the method introduced by Sridharan et al. does better among reaction-based ones. Also, the methods are applied to several artificial networks, each constructed from merging a few KEGG pathways. Then, their capability to recover those pathways are compared. Results show that among metabolite-based methods, the method of Guimera and Amaral does better again, however, no notable difference between the performances of reaction-based methods was detected.

In silicoidentification of switching nodes in metabolic networks

“…Finally, ISIS could also be used to decompose the whole network into different modules connecting the switch nodes, in order to analyze the metabolism or to develop dynamical model as proposed in [2, 1]. This would give a new approach for network splitting, complementing a set of methods (reviewed in [25]) based on network topology, flux coupling, or elementary flux mode. A specificity of our approach in that case is that the set of selected conditions defines the node identification.…”

Visual exploration of large metabolic models

“…metabolic flux measurements (Yoon et al, 2007), in order to derive a decomposition. The interested reader may find several of these methods in the reviews by Rezvan and Eslahchi (2017) and Singh and Lercher (2020).…”

“…In particular, this can be seen in our use case, where the decomposition by Schuster et al (2002) results in a median subsystem size of 1, meaning that at least half of the resulting subsystems only contain a single reaction. In this case, the decomposition may not be considered in its entirety but rather used to find individual meaningful subsystems that are part of it (Rezvan and Eslahchi, 2017) Paradigm: While the compartment decomposition is a spatial decomposition, the KEGG decomposition is a functional one. Different computational methods in addition, may aim for both paradigms, or even further ones.…”