ArticlePlant & cell physiology2013
PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.
Article in Plant & cell physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Quantitative ambient mass spectrometry imaging in plants: A perspective on challenges and future applications.Current opinion in plant biology · 2025Review
- Development of phytochemical genomics: From decoding metabolome to functional genomics and biotechnology of plant metabolism.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Data Science and Plant Metabolomics.Metabolites · 2023Review
- LCMD: Lung Cancer Metabolome Database.Computational and structural biotechnology journal · 2022Article
- Plants Metabolome Study: Emerging Tools and Techniques.Plants (Basel, Switzerland) · 2021Review
- Article
- Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production.Journal of advanced research · 2020Review
- Machine Learning Applications for Mass Spectrometry-Based Metabolomics.Metabolites · 2020Review
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- Metabolome-based discrimination of chrysanthemum cultivars for the efficient generation of flower color variations in mutation breeding.Metabolomics : Official journal of the Metabolomic Society · 2019Article
- Analytical Methods for Detection of Plant Metabolomes Changes in Response to Biotic and Abiotic Stresses.International journal of molecular sciences · 2019Review
- The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance.Frontiers in plant science · 2018Review
- Article
- From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics.GigaScience · 2017Review
- Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes.Plant & cell physiology · 2017Article
- Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy.PloS one · 2017Article
- Illuminating a plant's tissue-specific metabolic diversity using computational metabolomics and information theory.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Combined Metabolomics and Transcriptomics Approaches to Assess the IL-6 Blockade as a Therapeutic of ALS: Deleterious Alteration of Lipid Metabolism.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2016Article
- In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.International journal of molecular sciences · 2015Article
- Analysis of phenolic and cyclic compounds in plants using derivatization techniques in combination with GC-MS-based metabolite profiling.Molecules (Basel, Switzerland) · 2015Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
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.
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