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

Kenji Akiyama1, Eisuke Chikayama, Hiroaki Yuasa

  • 1RIKEN Plant Science Center, Yokohama, Kanagawa, Japan.

In Silico Biology
|November 27, 2008
PubMed
Summary
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PRIMe is a web platform for metabolomics and transcriptomics analysis. It offers tools and standardized data for metabolite identification and gene expression analysis, aiding biological event studies.

Area of Science:

  • Metabolomics
  • Transcriptomics
  • Bioinformatics

Background:

  • Metabolomics and transcriptomics are crucial for understanding biological events.
  • Integrated analysis of metabolite and gene expression data is complex.
  • A centralized platform is needed to streamline these analyses.

Purpose of the Study:

  • To introduce PRIMe, a web platform for integrated metabolome and transcriptome analysis.
  • To provide access to standardized metabolomics data and analysis tools.
  • To offer transcriptomics tools for mRNA expression analysis.

Main Methods:

  • Utilized Nuclear Magnetic Resonance (NMR), Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-Mass Spectrometry (LC-MS), and Capillary Electrophoresis-Mass Spectrometry (CE-MS) for metabolomics data acquisition.

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  • Implemented SpinAssign for NMR-based metabolite identification and KNApSAcK for metabolite database searches.
  • Developed Correlated Gene Search and Cluster Cutting tools for transcriptomics analysis.
  • Employed batch-learning self-organizing map (BL-SOM) for integrated analysis.

    • Main Results:

    • PRIMe provides a comprehensive resource for metabolomics and transcriptomics data.
    • Integrated analysis of metabolite and gene expression data is facilitated.
    • Demonstrated the utility of PRIMe with an example analysis of Arabidopsis thaliana.

    Conclusions:

    • PRIMe serves as a valuable platform for researchers in metabolomics and transcriptomics.
    • The integrated approach aids in the comprehensive analysis of biological events.
    • The platform supports diverse research workflows from metabolite to transcriptome analysis.