MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

BackgroundImprovements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments.DescriptionMeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues.ConclusionMeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

[1]  P. Pieri,et al.  Microclimate influence on mineral and metabolic profiles of grape berries. , 2006, Journal of agricultural and food chemistry.

[2]  Nigel W. Hardy,et al.  Plant Metabolomics , 2002, The Plant Cell Online.

[3]  Nigel W. Hardy,et al.  Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  David S. Wishart,et al.  Phenol-Explorer: an online comprehensive database on polyphenol contents in foods , 2010, Database J. Biol. Databases Curation.

[5]  Akira Oikawa,et al.  Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture , 2007, Planta.

[6]  Junjun Zhang,et al.  BioMart Central Portal—unified access to biological data , 2009, Nucleic Acids Res..

[7]  David S. Wishart,et al.  MetaboAnalyst: a web server for metabolomic data analysis and interpretation , 2009, Nucleic Acids Res..

[8]  Mark R Viant,et al.  International NMR-based environmental metabolomics intercomparison exercise. , 2009, Environmental science & technology.

[9]  J. Keurentjes,et al.  Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry , 2007, Nature Protocols.

[10]  Robert D. Hall,et al.  Biology of plant metabolomics , 2011 .

[11]  Yves Gibon,et al.  GMD@CSB.DB: the Golm Metabolome Database , 2005, Bioinform..

[12]  Ute Roessner,et al.  Plant metabolomics reveals conserved and divergent metabolic responses to salinity. , 2007, Physiologia plantarum.

[13]  Ute Roessner,et al.  Minimum reporting standards for plant biology context information in metabolomic studies , 2007, Metabolomics.

[14]  N. Kruger,et al.  Metabolite fingerprinting and profiling in plants using NMR. , 2004, Journal of experimental botany.

[15]  J. W. Allwood,et al.  1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon. , 2009, Analytical chemistry.

[16]  Jens Stoye,et al.  MeltDB: a software platform for the analysis and integration of metabolomics experiment data , 2008, Bioinform..

[17]  Susumu Goto,et al.  LIGAND: database of chemical compounds and reactions in biological pathways , 2002, Nucleic Acids Res..

[18]  Egon L. Willighagen,et al.  The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports , 2010, Bioinform..

[19]  F Baganz,et al.  Systematic functional analysis of the yeast genome. , 1998, Trends in biotechnology.

[20]  Cécile Cabasson,et al.  Quantitative metabolic profiles of tomato flesh and seeds during fruit development: complementary analysis with ANN and PCA , 2007, Metabolomics.

[21]  Kenneth Levenberg.  A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[22]  Yves Gibon,et al.  Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. , 2011, The New phytologist.

[23]  Nigel W. Hardy,et al.  A proposed framework for the description of plant metabolomics experiments and their results , 2004, Nature Biotechnology.

[24]  R. Dixon,et al.  Plant metabolomics: large-scale phytochemistry in the functional genomics era. , 2003, Phytochemistry.

[25]  Martin Scholz,et al.  Pacific Symposium on Biocomputing 12:169-180(2007) SETUP X – A PUBLIC STUDY DESIGN DATABASE FOR METABOLOMIC PROJECTS , 2022 .

[26]  R. Hall,et al.  Plant metabolomics: from holistic hope, to hype, to hot topic. , 2006, The New phytologist.

[27]  David S. Wishart,et al.  HMDB: a knowledgebase for the human metabolome , 2008, Nucleic Acids Res..

[28]  Ilya Venger,et al.  The Transcript and Metabolite Networks Affected by the Two Clades of Arabidopsis Glucosinolate Biosynthesis Regulators1[W] , 2008, Plant Physiology.

[29]  Aalim M Weljie,et al.  Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures , 2008, BMC Plant Biology.

[30]  G. Harrigan,et al.  Metabolomics, metabolic diversity and genetic variation in crops , 2007, Metabolomics.

[31]  Jane L. Ward,et al.  NMR Spectroscopy in Plant Metabolomics , 2006 .

[32]  Nigel W. Hardy,et al.  Proposed minimum reporting standards for chemical analysis , 2007, Metabolomics.

[33]  Koji Otsuka,et al.  Signal denoising and baseline correction by discrete wavelet transform for microchip capillary electrophoresis , 2003, Electrophoresis.

[34]  Nigel W. Hardy,et al.  Toward Supportive Data Collection Tools for Plant Metabolomics[w] , 2005, Plant Physiology.

[35]  B. Denoyes-Rothan,et al.  Quantitative metabolic profiling by 1-dimensional 1H-NMR analyses: application to plant genetics and functional genomics. , 2004, Functional plant biology : FPB.

[36]  Lloyd W Sumner,et al.  Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period , 2005, BMC Plant Biology.

[37]  Ying Zhang,et al.  HMDB: the Human Metabolome Database , 2007, Nucleic Acids Res..

[38]  John M. Baker,et al.  An inter-laboratory comparison demonstrates that [1H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection , 2010, Metabolomics.

[39]  A. Fernie,et al.  Metabolomics-assisted breeding: a viable option for crop improvement? , 2009, Trends in genetics : TIG.

[40]  Nigel W. Hardy,et al.  The Metabolomics Standards Initiative , 2007, Nature Biotechnology.

[41]  Kazuki Saito,et al.  Metabolomics for functional genomics, systems biology, and biotechnology. , 2010, Annual review of plant biology.

[42]  R. A. van den Berg,et al.  Centering, scaling, and transformations: improving the biological information content of metabolomics data , 2006, BMC Genomics.

[43]  Y. Choi,et al.  NMR-based metabolomic analysis of plants , 2010, Nature Protocols.

[44]  B. Usadel,et al.  Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. , 2008, The Plant journal : for cell and molecular biology.

[45]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[46]  Kazuki Saito,et al.  Potential of metabolomics as a functional genomics tool. , 2004, Trends in plant science.

[47]  Robert D Hall,et al.  Plant metabolomics and its potential application for human nutrition. , 2007, Physiologia plantarum.

[48]  B. Hammock,et al.  Mass spectrometry-based metabolomics. , 2007, Mass spectrometry reviews.

[49]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[50]  Tetsuya Sakurai,et al.  PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics , 2008, Silico Biol..

[51]  Miron Livny,et al.  BioMagResBank , 2007, Nucleic Acids Res..

[52]  Douglas N. Rutledge,et al.  Fruit juice authentication by 1H NMR spectroscopy in combination with different chemometrics tools , 2008, Analytical and bioanalytical chemistry.

[53]  Oliver Hofmann,et al.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level , 2010, Bioinform..

[54]  M. Hirai,et al.  Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks in Arabidopsis by Integration of Metabolomics and Transcriptomics* , 2005, Journal of Biological Chemistry.

[55]  J. W. Allwood,et al.  Plant metabolomics and its potential for systems biology research background concepts, technology, and methodology. , 2011, Methods in Enzymology.

[56]  Nigel W. Hardy,et al.  Summary recommendations for standardization and reporting of metabolic analyses , 2005, Nature Biotechnology.