Platform for RIKEN Metabolomics

About PRIMe

PRIMe, the Platform for RIKEN Metabolomics, is a Web-based service for metabolomics and transcriptomics as systems for understanding life. This project measures standard metabolites by means of multi-dimensional NMR spectroscopy, GC/MS, LC/MS, and CE/MS. We also provide unique tools for metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.

Sections

What's New?

2008-06-26: [Standard spectrum search] Dramatically changed standard data, ex. 300% increase of NMR data, and version up of "current status" metabolic map.; [SpinAssign] Modified example input data to experimental plant extract, measured by our laboratory. Searching total of more than 500 of ¹³C-HSQC cross peaks with our new NMR data base.
2006-12-29: [SpinAssign] Released a stable service.; [Standard Spectrum Search] Released a stable service.; [Cluster Cutting] Changed the service name.; [Correlated Gene Search] Changed the service name.
2006-08-30: [Site Map] Added a page.; [Cluster Extract] Updated "Using Cluster Extract"; [Cluster Extract] Revised the cutting program.; [Coexpression Gene Search] Released a stable service.; [Coexpression Gene Search] Updated "Using Coexpression Gene Search"
2006-08-17: [Coexpression Gene Search] Added a Biolayout-compatible output format and revised the Pajek-compatible output format.

Web Applications

Standard Spectrum Search: A database of the standardized spectra of a range of compounds based on NMR chemical shifts and on GC and LC mass spectrometer
MS/MS spectral tag (MS2T) viewer: MS/MS spectral libraries of plant secondary metabolites created for LC-MS metabolomics.
ReSpect for Phytochemicals: A collection of literature and in-house MSn spectra data for the plant metabolomics research.
SpinAssign: A large-scale annotation of detection of metabolites by NMR from user 13C-HSQC peaks
Correlated Gene Search: A search tool for finding correlated gene pairs in the AtGenExpress data, with conversion to network-viewer software format
Cluster Cutting: A tool for cutting our AtGenExpress hierarchical clustering data

Distibution and Redistribution

DROP Met: Contains various datasets obtained from mass spectrometer-based metabolome analyses
KNApSAcK: A comprehensive species-metabolite relationships database
Simple BL-SOM: An application for creating a batch-learning self-organizing map

Publications

Akiyama K. et al. (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 8, 0027. </isb/2008/08/0027/> [Abstract]

Modified: 2008-12-03

Comments and questions:
RIKEN Plant Science Center