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Open Access Research article

Clustering under the line graph transformation: application to reaction network

Jose C Nacher*, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa and Tatsuya Akutsu

Author Affiliations

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan

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BMC Bioinformatics 2004, 5:207  doi:10.1186/1471-2105-5-207

Published: 24 December 2004



Many 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.


We have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient C(k) is calculated for the transformed network. C(k) indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While C(k) follows the scaling law C(k) ~ k-1.1 for the initial hierarchical network, C(k) scales weakly as k0.08 for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement.


The 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.