title: Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.
abstract: Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara, 630-0192 Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Ikeda
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Nelson
authors.initials: N
authors.lastname: Kibinge
authors.forename: Aki
authors.initials: A
authors.lastname: Hirai Morita
authors.forename: Atsushi
authors.initials: A
authors.lastname: Nakatani
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
authors.forename: Kensuke
authors.initials: K
authors.lastname: Nakamura
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D000470:Alkaloids / Q000378:metabolism; D019883:Alkyl and Aryl Transferases / Q000378:metabolism; D000595:Amino Acid Sequence; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D019992:Databases as Topic; D005419:Flavonoids / Q000378:metabolism; D055432:Metabolomics; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry*; D010944:Plants / Q000201:enzymology / Q000378:metabolism*; D064210:Secondary Metabolism
chemical_list: D000470:Alkaloids; D005419:Flavonoids; D010455:Peptides; D010940:Plant Proteins; D003577:Cytochrome P-450 Enzyme System; D019883:Alkyl and Aryl Transferases; C108877:terpene synthase
keywords: Batch-learning self-organizing map; Big data biology; Database; KNApSAcK family; Secondary metabolic pathway; Species–metabolite relationship