Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?

Background: Standard graphs, where each edge links two nodes, have been extensively used to represent the connectivity of metabolic networks. It is based on this representation that properties of metabolic networks, such as hierarchical and small-world structures, have been elucidated and null models have been proposed to derive biological organization hypotheses. However, these graphs provide a simplistic model of a metabolic network’s connectivity map, since metabolic reactions often involve more than two reactants. In other words, this map is better represented as a hypergraph. Consequently, a question that naturally arises in this context is whether these properties truly reflect biological organization or are merely an artifact of the representation. Results: In this paper, we address this question by reanalyzing topological properties of the metabolic network of hia coli under a hypergraph representation, as well as standard graph abstractions. We find that when clustering is ...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Wanding Zhou, Luay Nakhleh
• Keywords: Artificial Intelligence, BMCBI 2011, Metabolic Networks, Null Model, Standard Graph