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Volumn 20, Issue 6, 2009, Pages 610-615

What can metabolomics learn from genomics and proteomics?

Author keywords

[No Author keywords available]

Indexed keywords

DATA-DRIVEN; EFFECTIVE MEDIUM; EXPERIMENTAL DATA; GENOMICS; METABOLOMICS; PROTEOMICS; RESEARCH COMMUNITIES; SCIENTIFIC COMMUNITY; WEB INFRASTRUCTURE;

EID: 70449732240     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2009.09.011     Document Type: Review
Times cited : (17)

References (53)
  • 2
    • 37849020436 scopus 로고    scopus 로고
    • Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'
    • Saito K., Hirai M.Y., and Yonekura-Sakakibara K. Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. Trends Plant Sci 13 (2008) 36-43
    • (2008) Trends Plant Sci , vol.13 , pp. 36-43
    • Saito, K.1    Hirai, M.Y.2    Yonekura-Sakakibara, K.3
  • 3
    • 52949093520 scopus 로고    scopus 로고
    • Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin
    • To identify genes related with glycyrrhizin biosynthesis in the nonmodel plant Glycyrrhiza (fabaceae or beans family), the authors searched for candidate ESTs whose expression patterns coincided with the accumulation pattern of glycyrrhizin. The method is labor-intensive, and its acceleration is one of the major goals of metabolomics.
    • Seki H., Ohyama K., Sawai S., Mizutani M., Ohnishi T., Sudo H., Akashi T., Aoki T., Saito K., and Muranaka T. Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin. Proc Natl Acad Sci U S A 105 (2008) 14204-14209. To identify genes related with glycyrrhizin biosynthesis in the nonmodel plant Glycyrrhiza (fabaceae or beans family), the authors searched for candidate ESTs whose expression patterns coincided with the accumulation pattern of glycyrrhizin. The method is labor-intensive, and its acceleration is one of the major goals of metabolomics.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14204-14209
    • Seki, H.1    Ohyama, K.2    Sawai, S.3    Mizutani, M.4    Ohnishi, T.5    Sudo, H.6    Akashi, T.7    Aoki, T.8    Saito, K.9    Muranaka, T.10
  • 6
    • 38949209075 scopus 로고    scopus 로고
    • NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology
    • Coen M., Holmes E., Lindon J.C., and Nicholson J.K. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol 21 (2008) 9-27
    • (2008) Chem Res Toxicol , vol.21 , pp. 9-27
    • Coen, M.1    Holmes, E.2    Lindon, J.C.3    Nicholson, J.K.4
  • 7
    • 61849108201 scopus 로고    scopus 로고
    • 13C-isotopomer-based metabolomics of microbial groups isolated from two forest soils
    • 13C-isotopomer-based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5 (2009) 108-122
    • (2009) Metabolomics , vol.5 , pp. 108-122
    • Fan, W.M.T.1    Bird, J.A.2    Brodie, E.L.3    Lane, A.N.4
  • 10
    • 56049113260 scopus 로고    scopus 로고
    • Understanding the metabolome - challenges for metabolomics
    • Walsh M.C., Nugent A., Brennan L., and Gibney M.J. Understanding the metabolome - challenges for metabolomics. Nutr Bull 33 (2009) 316-323
    • (2009) Nutr Bull , vol.33 , pp. 316-323
    • Walsh, M.C.1    Nugent, A.2    Brennan, L.3    Gibney, M.J.4
  • 11
    • 74449085466 scopus 로고    scopus 로고
    • Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
    • (Epub ahead of print). Presented by eminent scientists in metabolomics research, this review spans topics from the technological foundation of metabolomics to its future challenges. It is highly recommended as an overview of the research trend.
    • Scalbert A., Brennan L., Fiehn O., Hankemeier T., Kristal B.S., van Ommen B., Pujos-Guillot E., Verheij E., Wishart D., and Wopereis S. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics (2009) (Epub ahead of print). Presented by eminent scientists in metabolomics research, this review spans topics from the technological foundation of metabolomics to its future challenges. It is highly recommended as an overview of the research trend.
    • (2009) Metabolomics
    • Scalbert, A.1    Brennan, L.2    Fiehn, O.3    Hankemeier, T.4    Kristal, B.S.5    van Ommen, B.6    Pujos-Guillot, E.7    Verheij, E.8    Wishart, D.9    Wopereis S10
  • 12
    • 36549008292 scopus 로고    scopus 로고
    • The future of metabolic phytochemistry: larger numbers of metabolites, higher resolution, greater understanding
    • Fernie A.R. The future of metabolic phytochemistry: larger numbers of metabolites, higher resolution, greater understanding. Phytochemistry 68 (2007) 2861-2880
    • (2007) Phytochemistry , vol.68 , pp. 2861-2880
    • Fernie, A.R.1
  • 16
    • 0242569355 scopus 로고    scopus 로고
    • Quantitative metabolome analysis using capillary electrophoresis mass spectrometry
    • Soga T., Ohashi Y., Ueno Y., Naraoka H., Tomita M., and Nishioka T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2 (2003) 488-494
    • (2003) J Proteome Res , vol.2 , pp. 488-494
    • Soga, T.1    Ohashi, Y.2    Ueno, Y.3    Naraoka, H.4    Tomita, M.5    Nishioka, T.6
  • 19
    • 38549144166 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
    • Liolios K., Mavromatis K., Tavernarakis N., and Kyrpides N.C. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36 (2008) D475-479
    • (2008) Nucleic Acids Res , vol.36
    • Liolios, K.1    Mavromatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 20
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., and Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 (2002) 399-403
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 21
    • 36949000237 scopus 로고    scopus 로고
    • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    • Huang H., Jedynak B.M., and Bader J.S. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 3 (2007) e214
    • (2007) PLoS Comput Biol , vol.3
    • Huang, H.1    Jedynak, B.M.2    Bader, J.S.3
  • 22
    • 67049132397 scopus 로고    scopus 로고
    • Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra
    • The authors explain five patterns of false-positives that have been overlooked in previous assessments in proteomics. The error patterns can be directly interpreted in terms of metabolomics and are useful for developing better identification algorithms.
    • Chen Y., Zhang J., Xing G., and Zhao Y. Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. J Proteome Res 8 (2009) 3141-3147. The authors explain five patterns of false-positives that have been overlooked in previous assessments in proteomics. The error patterns can be directly interpreted in terms of metabolomics and are useful for developing better identification algorithms.
    • (2009) J Proteome Res , vol.8 , pp. 3141-3147
    • Chen, Y.1    Zhang, J.2    Xing, G.3    Zhao, Y.4
  • 23
    • 34548329975 scopus 로고    scopus 로고
    • Annotation of bacterial and archaeal genomes: improving accuracy and consistency
    • Overbeek R., Bartels D., Vonstein V., and Meyer F. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 107 (2007) 3431-3447
    • (2007) Chem Rev , vol.107 , pp. 3431-3447
    • Overbeek, R.1    Bartels, D.2    Vonstein, V.3    Meyer, F.4
  • 24
    • 34247123157 scopus 로고    scopus 로고
    • Cellular metabolomics of Escherichia coli
    • Rabinowitz J.D. Cellular metabolomics of Escherichia coli. Expert Rev Proteomics 4 (2007) 187-198
    • (2007) Expert Rev Proteomics , vol.4 , pp. 187-198
    • Rabinowitz, J.D.1
  • 26
    • 50849125711 scopus 로고    scopus 로고
    • High-throughput, quantitative analyses of genetic interactions in E. coli
    • In addition to the single knock-out mutant library (KEIO collection in Ref. [25]), the E. coli community has established a library of double mutants. This library will be extremely useful for assessing other data acquired by high-throughput methods or in in silico strains.
    • Typas A., Nichols R.J., Siegele D.A., Shales M., Collins S.R., Lim B., Braberg H., Yamamoto N., Takeuchi R., Wanner B.L., et al. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5 (2008) 781-787. In addition to the single knock-out mutant library (KEIO collection in Ref. [25]), the E. coli community has established a library of double mutants. This library will be extremely useful for assessing other data acquired by high-throughput methods or in in silico strains.
    • (2008) Nat Methods , vol.5 , pp. 781-787
    • Typas, A.1    Nichols, R.J.2    Siegele, D.A.3    Shales, M.4    Collins, S.R.5    Lim, B.6    Braberg, H.7    Yamamoto, N.8    Takeuchi, R.9    Wanner, B.L.10
  • 27
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed J.L., Vo T.D., Schilling C.H., and Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4 (2003) R54
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 28
    • 63249117139 scopus 로고    scopus 로고
    • The role of predictive modelling in rationally re-engineering biological systems
    • Koide T., Pang W.L., and Baliga N.S. The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol 7 (2009) 297-305
    • (2009) Nat Rev Microbiol , vol.7 , pp. 297-305
    • Koide, T.1    Pang, W.L.2    Baliga, N.S.3
  • 32
    • 66149174897 scopus 로고    scopus 로고
    • Web-queryable large-scale data sets for hypothesis generation in plant biology
    • •] contains useful and up-to-date lists of accessible web resources in metabolomics.
    • •] contains useful and up-to-date lists of accessible web resources in metabolomics.
    • (2009) Plant Cell , vol.21 , pp. 1034-1051
    • Brady, S.M.1    Provart, N.J.2
  • 35
    • 1242319556 scopus 로고    scopus 로고
    • The metabolic world of Escherichia coli is not small
    • Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U S A 101 (2004) 1543-1547
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 1543-1547
    • Arita, M.1
  • 36
    • 33747853260 scopus 로고    scopus 로고
    • APID: Agile Protein Interaction DataAnalyzer
    • Prieto C., and De Las Rivas J. APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res 34 (2006) W298-302
    • (2006) Nucleic Acids Res , vol.34
    • Prieto, C.1    De Las Rivas, J.2
  • 39
    • 67149130077 scopus 로고    scopus 로고
    • Cellular Open Resource (COR): current status and future directions
    • Garny A., Noble D., Hunter P.J., and Kohl P. Cellular Open Resource (COR): current status and future directions. Philos Trans A Math Phys Eng Sci 367 (2009) 1885-1905
    • (2009) Philos Trans A Math Phys Eng Sci , vol.367 , pp. 1885-1905
    • Garny, A.1    Noble, D.2    Hunter, P.J.3    Kohl, P.4
  • 40
    • 21544461263 scopus 로고    scopus 로고
    • PAX of mind for pathway researchers
    • Luciano J.S. PAX of mind for pathway researchers. Drug Discov Today 10 (2005) 937-942
    • (2005) Drug Discov Today , vol.10 , pp. 937-942
    • Luciano, J.S.1
  • 43
    • 65949115307 scopus 로고    scopus 로고
    • Database and information-retrieval methods for knowledge discovery
    • Weikum G., Kasneci G., Ramanath M., and Suchanek F. Database and information-retrieval methods for knowledge discovery. Commun ACM 52 (2009) 56-64
    • (2009) Commun ACM , vol.52 , pp. 56-64
    • Weikum, G.1    Kasneci, G.2    Ramanath, M.3    Suchanek, F.4
  • 44
    • 33847132279 scopus 로고    scopus 로고
    • Key biology databases go wiki
    • Giles J. Key biology databases go wiki. Nature (News) 445 (2007) 691
    • (2007) Nature (News) , vol.445 , pp. 691
    • Giles, J.1
  • 45
    • 64749098176 scopus 로고    scopus 로고
    • Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database
    • Arita M., and Suwa K. Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database. BioData Mining 1 (2008) 7
    • (2008) BioData Mining , vol.1 , pp. 7
    • Arita, M.1    Suwa, K.2
  • 47
    • 70350755839 scopus 로고    scopus 로고
    • Mediator infrastructure for information integration and semantic data integration environment for biomedical research
    • Grethe J.S., Ross E., Little D., Sanders B., Gupta A., and Astakhov V. Mediator infrastructure for information integration and semantic data integration environment for biomedical research. Methods Mol Biol 569 (2009) 33-53
    • (2009) Methods Mol Biol , vol.569 , pp. 33-53
    • Grethe, J.S.1    Ross, E.2    Little, D.3    Sanders, B.4    Gupta, A.5    Astakhov, V.6
  • 48
    • 49949099664 scopus 로고    scopus 로고
    • Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
    • Although the words cyberinfrastructure and e-Science have become familiar, their definition or purpose is usually unknown. This article explains their underlying concepts and their benefits by introducing the ongoing iPlant (URL: http://www.iplantcollaborative.org/) and CaBIG (URL: https://cabig.nci.nih.gov/) projects.
    • Stein L.D. Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 9 (2008) 678-688. Although the words cyberinfrastructure and e-Science have become familiar, their definition or purpose is usually unknown. This article explains their underlying concepts and their benefits by introducing the ongoing iPlant (URL: http://www.iplantcollaborative.org/) and CaBIG (URL: https://cabig.nci.nih.gov/) projects.
    • (2008) Nat Rev Genet , vol.9 , pp. 678-688
    • Stein, L.D.1
  • 49
    • 50449088836 scopus 로고    scopus 로고
    • A wiki for the life sciences where authorship matters
    • Hoffmann R. A wiki for the life sciences where authorship matters. Nat Genet 40 (2008) 1047-1051
    • (2008) Nat Genet , vol.40 , pp. 1047-1051
    • Hoffmann, R.1
  • 53
    • 67649785231 scopus 로고    scopus 로고
    • How large is the metabolome? A critical analysis of data exchange practices in chemistry
    • Kind T., Scholz M., and Fiehn O. How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS One 4 (2009) e5440
    • (2009) PLoS One , vol.4
    • Kind, T.1    Scholz, M.2    Fiehn, O.3


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