Analysis of Binary Relations and Hierarchies of Enzymes in the Metabolic Pathways

Hiroyuki Ogata (
Hidemasa Bono (
Wataru Fujibuchi (
Susumu Goto (
Minoru Kanehisa (

Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611 Japan


In conjunction with a new database system that efficiently organizes the metabolic pathway data from various organisms, we are developing computational methodologies using binary relations and hierarchies of enzymes. Biological knowledge integrated in the system includes genes, gene products, chemical compounds, enzyme reactions and metabolic pathway diagrams. By automatically mapping the enzymes of a specific organism on the pathway diagrams, it becomes possible to visualize the characteristic features of the organism-specific metabolic pathways. With the aid of the computational methodology implemented in the system, it becomes again possible to analyze and investigate the pathways in terms of their function and evolution. In this paper, we describe the outline of the system and present new biological features of metabolic pathways revealed by the system.