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In Silico Biology 8, 0027 (2008); ©2008, Bioinformation Systems e.V.  

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics

Kenji Akiyama1, Eisuke Chikayama1, Hiroaki Yuasa2, Yukihisa Shimada1, Takayuki Tohge1, Kazuo Shinozaki1, Masami Yokota Hirai1, Tetsuya Sakurai1*, Jun Kikuchi1* and Kazuki Saito1

1 RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
2 RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan

* Corresponding authors

Edited by E. Wingender; received March 12, 2008; revised June 26 and July 01, 2008; accepted July 01, 2008; published July 09, 2008


PRIMe (, 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.

Keywords: metabolome, transcriptome, correlation analysis, spectrum database, analytical platform