Clustering under the line graph transformation application to reaction network.docVIP

BMC Bioinformatics BioMedCentral Research article Open Access Clustering under the line graph transformation: application to reaction network Jose C Nacher*, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa and Tatsuya Akutsu Address: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan Email: Jose C Nacher* - nacher@kuicr.kyoto-u.ac.jp; Nobuhisa Ueda - ueda@kuicr.kyoto-u.ac.jp; Takuji Yamada - takuji@kuicr.kyoto-u.ac.jp; Minoru Kanehisa - kanehisa@kuicr.kyoto-u.ac.jp; Tatsuya Akutsu - takutsu@kuicr.kyoto-u.ac.jp * Corresponding author Published: 24 December 2004 Received: 14 October 2004 Accepted: 24 December 2004 BMC Bioinformatics 2004, 5:207 doi:10.1186/1471-2105-5-207 This article is available from: /1471-2105/5/207 ? 2004 Nacher et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: 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. Results: We have applied the line graph transformation to a hierarchical network and the degree- dependent clustering coefficient C(k) is calculated for the transform