Journal of Computer Science & Systems Biology

Strategy for Exploring Metabolic Pathways: Generation of Hypothetical Metabolic Network

Abstract

Jun Ohta

Development of metabolomics has made completion of metabolic map an important issue. Rational suggestion of specific metabolic pathways as candidates for real pathway will promote study to complete metabolic map. Exploring hypothetical metabolic networks containing candidate pathways enable this. Three different hypothetical metabolic networks abbreviated as BRP-dependent network, metabolite-dependent network and CFB network are considered. BRP-dependent and CFB networks are generated by network expansion from seed compounds via balanced reaction pattern (BRP) and via simple cleavage/formation of chemical bonds, respectively. Concept of network expansion, a term introduced by Heinrich’s group, is generalized and a previous approach by Hatzimanikatis and his colleagues for generation of BRP-dependent network equivalent is re-defined in the context of network expansion. Metabolite dependent network is generated from a given set of metabolites based on stoichiometry. Hypothetical metabolites and BRPs are considered to appear in BRP-dependent and metabolite-dependent networks, respectively. Concept of atom network is introduced.