title: Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.
abstract: Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Ohtana
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Azian Azamimi
authors.initials: AA
authors.lastname: Abdullah
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Ming
authors.initials: M
authors.lastname: Huang
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Sato
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Tadao
authors.initials: T
authors.lastname: Sugiura
authors.affiliation: Electronic and Computer Engineering, Ibaraki National College of Technology, 866 Nakane, Hitachinaka, Ibaraki 312-8508, Japan.
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Horai
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Aki
authors.initials: A
authors.lastname: Morita Hirai
authors.affiliation: Department of Experimental Psychology, University of Regensburg, 93040 Regensburg, Germany.
authors.forename: Klaus W
authors.initials: KW
authors.lastname: Lange
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Nelson K
authors.initials: NK
authors.lastname: Kibinge
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Katsuragi
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan. t_shirai@nagahama-i-bio.ac.jp.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Shirai
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. skanaya@gtc.naist.jp.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
keywords: Biological activities; Clustering of 3D-structure similarity; KNApSAcK family databases; Metabolites; Network of secondary metabolites; Phytochemistry; Structureproperty relationships; Visualization, Cheminformatics; ′Bioinformatics