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BMC Bioinformatics

, 5:207

First Online: 24 December 2004Received: 14 October 2004Accepted: 24 December 2004


BackgroundMany real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. In general, the second network may be related to the first one by a technique called line graph transformation i.e., edges in an initial network are transformed into nodes. Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. While the chemical compound network has been classified as hierarchical network, a detailed study of the chemical reaction network had not been carried out.

ResultsWe have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient Ck is calculated for the transformed network. Ck indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While Ck follows the scaling law Ck ~ k for the initial hierarchical network, Ck scales weakly as k for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement.

ConclusionsThe weak scaling found for the transformed network indicates that the reaction network can be identified as a degree-independent clustering network. By using this result, the hierarchical classification of the reaction network is discussed.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-207 contains supplementary material, which is available to authorized users.

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Autor: Jose C Nacher - Nobuhisa Ueda - Takuji Yamada - Minoru Kanehisa - Tatsuya Akutsu


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