title: PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.
abstract: PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research and analysis workflows ranging from metabolome to transcriptome analysis. The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses (SpinAssign for the identification of metabolites by means of NMR, KNApSAcK for searches within metabolite databases). In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting for the analysis of mRNA expression. Use of the tools and database can contribute to the analysis of biological events at the levels of metabolites and gene expression, and we describe one example of such an analysis for Arabidopsis thaliana using the batch-learning self-organizing map (BL-SOM), which is provided via the Web site.
authors.affiliation: RIKEN Plant Science Center, Yokohama, Kanagawa, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Akiyama
authors.forename: Eisuke
authors.initials: E
authors.lastname: Chikayama
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Yuasa
authors.forename: Yukihisa
authors.initials: Y
authors.lastname: Shimada
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tohge
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Jun
authors.initials: J
authors.lastname: Kikuchi
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
mesh_terms: D003628:Database Management Systems; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D019906:Nuclear Magnetic Resonance, Biomolecular; D012984:Software