title: PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.
abstract: PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a website that was designed and implemented to support research and analyses ranging from metabolomics to transcriptomics. To achieve functional genomics and annotation of unknown metabolites, we established the following PRIMe contents: MS2T, a library comprising >1 million entries of untargeted tandem mass spectrometry (MS/MS) data of plant metabolites; AtMetExpress LC-MS, a database of transcriptomics and metabolomics approaches in Arabidopsis developmental stages (AtMetExpress Development LC-MS) and a data set of the composition of secondary metabolites among 20 Arabidopsis ecotypes (AtMetExpress 20 ecotypes LC-MS); and ReSpect, hybrid reference MS/MS data resources (acquisitions and literature). PRIMeLink is a new web application that allows access to the innovative data resources of PRIMe. The MS2T library was generated from a set of MS/MS spectra acquired using the automatic data acquisition function of mass spectrometry. To increase the understanding of mechanisms driving variations in metabolic profiles among plant tissues, we further provided the AtMetExpress Development LC-MS database in PRIMe, facilitating the investigation of relationships between gene expression and metabolite accumulation. This information platform therefore provides an integrative analysis resource by linking Arabidopsis transcriptome and metabolome data. Moreover, we developed the ReSpect database, a plant-specific MS/MS data resource, which allows users to identify candidate structures from the suite of complex phytochemical structures. Finally, we integrated the three databases into PRIMeLink and established a walk-through link between transcriptome and metabolome information. PRIMeLink offers a bi-directional searchable function, from the gene and the metabolite perspective, to search for targets seamlessly and effectively.
authors.affiliation: RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan. stetsuya@psc.riken.jp
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Yamada
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sawada
authors.forename: Fumio
authors.initials: F
authors.lastname: Matsuda
authors.forename: Kenji
authors.initials: K
authors.lastname: Akiyama
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D062126:Databases, Chemical; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D020407:Internet; D055432:Metabolomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D012984:Software; D053719:Tandem Mass Spectrometry; D059467:Transcriptome