title: Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
abstract: Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.
authors.affiliation: Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
authors.forename: Yu-Fei
authors.initials: YF
authors.lastname: Gao
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
authors.forename: Kai-Yan
authors.initials: KY
authors.lastname: Feng
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Yang
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D055432:Metabolomics; D008954:Models, Biological; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins