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Volumn 13, Issue 5-6, 2009, Pages 532-538

Integrated omics approaches in plant systems biology

Author keywords

[No Author keywords available]

Indexed keywords

DATA ANALYSIS; ELECTROSPRAY MASS SPECTROMETRY; GAS CHROMATOGRAPHY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC VARIABILITY; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; METABOLITE; METABOLOMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHENOTYPE; PLANT GENE; PLANT GENETICS; PREDICTION; PROSPECTIVE STUDY; REVIEW;

EID: 70549112091     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2009.09.022     Document Type: Review
Times cited : (177)

References (65)
  • 2
    • 37849020436 scopus 로고    scopus 로고
    • Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'
    • This is a comprehensive critical review focused on strategies, databases, and their applications for gene coexpression. Studies combining transcriptomics and metabolomics data are also presented.
    • 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. This is a comprehensive critical review focused on strategies, databases, and their applications for gene coexpression. Studies combining transcriptomics and metabolomics data are also presented.
    • (2008) Trends Plant Sci , vol.13 , pp. 36-43
    • Saito, K.1    Hirai, M.Y.2    Yonekura-Sakakibara, K.3
  • 3
    • 33749120080 scopus 로고    scopus 로고
    • Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes
    • This work describes the integration of genome-wide transcript profiling, enzyme activity assays, and metabolite measurements in Arabidopsis. The authors argue that the changes in enzyme activity and metabolic levels are much smaller than those in transcription.
    • Gibon Y., Usadel B., Blaesing O.E., Kamlage B., Hoehne M., Trethewey R., and Stitt M. Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol 7 (2006) R76. This work describes the integration of genome-wide transcript profiling, enzyme activity assays, and metabolite measurements in Arabidopsis. The authors argue that the changes in enzyme activity and metabolic levels are much smaller than those in transcription.
    • (2006) Genome Biol , vol.7
    • Gibon, Y.1    Usadel, B.2    Blaesing, O.E.3    Kamlage, B.4    Hoehne, M.5    Trethewey, R.6    Stitt, M.7
  • 6
    • 34447570857 scopus 로고    scopus 로고
    • Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice
    • Kusano M., Fukushima A., Kobayashi M., Hayashi N., Jonsson P., Moritz T., Ebana K., and Saito K. Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. J Chromatogr B Analyt Technol Biomed Life Sci 855 (2007) 71-79
    • (2007) J Chromatogr B Analyt Technol Biomed Life Sci , vol.855 , pp. 71-79
    • Kusano, M.1    Fukushima, A.2    Kobayashi, M.3    Hayashi, N.4    Jonsson, P.5    Moritz, T.6    Ebana, K.7    Saito, K.8
  • 7
    • 48249152281 scopus 로고    scopus 로고
    • Mode of inheritance of primary metabolic traits in tomato
    • The paper reports inter-inference between molecular QTL (quantitative trait loci) and phenotypic traits in tomato, revealing naturally occurring variations in metabolite compositions.
    • Schauer N., Semel Y., Balbo I., Steinfath M., Repsilber D., Selbig J., Pleban T., Zamir D., and Fernie A.R. Mode of inheritance of primary metabolic traits in tomato. Plant Cell 20 (2008) 509-523. The paper reports inter-inference between molecular QTL (quantitative trait loci) and phenotypic traits in tomato, revealing naturally occurring variations in metabolite compositions.
    • (2008) Plant Cell , vol.20 , pp. 509-523
    • Schauer, N.1    Semel, Y.2    Balbo, I.3    Steinfath, M.4    Repsilber, D.5    Selbig, J.6    Pleban, T.7    Zamir, D.8    Fernie, A.R.9
  • 8
    • 33645070537 scopus 로고    scopus 로고
    • Plant metabolomics: from holistic hope, to hype, to hot topic
    • Hall R.D. Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169 (2006) 453-468
    • (2006) New Phytol , vol.169 , pp. 453-468
    • Hall, R.D.1
  • 9
    • 62549159971 scopus 로고    scopus 로고
    • Web-based resources for mass-spectrometry-based metabolomics: a user's guide
    • Tohge T., and Fernie A.R. Web-based resources for mass-spectrometry-based metabolomics: a user's guide. Phytochemistry 70 (2009) 450-456
    • (2009) Phytochemistry , vol.70 , pp. 450-456
    • Tohge, T.1    Fernie, A.R.2
  • 10
    • 17044391118 scopus 로고    scopus 로고
    • Integrating genomics and metabolomics for engineering plant metabolic pathways
    • Oksman-Caldentey K.M., and Saito K. Integrating genomics and metabolomics for engineering plant metabolic pathways. Curr Opin Biotechnol 16 (2005) 174-179
    • (2005) Curr Opin Biotechnol , vol.16 , pp. 174-179
    • Oksman-Caldentey, K.M.1    Saito, K.2
  • 13
    • 24644481093 scopus 로고    scopus 로고
    • High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses
    • Jonsson P., Johansson A.I., Gullberg J., Trygg J., Grung A.J., Marklund B., Sjostrom S., Antti M., and Moritz H.T. High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Anal Chem 77 (2005) 5635-5642
    • (2005) Anal Chem , vol.77 , pp. 5635-5642
    • Jonsson, P.1    Johansson, A.I.2    Gullberg, J.3    Trygg, J.4    Grung, A.J.5    Marklund, B.6    Sjostrom, S.7    Antti, M.8    Moritz, H.T.9
  • 14
    • 33745728711 scopus 로고    scopus 로고
    • MET-IDEA: data extraction tool for mass spectrometry-based metabolomics
    • Broeckling C.D., Reddy I.R., Duran A.L., Zhao X., and Sumner L.W. MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal Chem 78 (2006) 4334-4341
    • (2006) Anal Chem , vol.78 , pp. 4334-4341
    • Broeckling, C.D.1    Reddy, I.R.2    Duran, A.L.3    Zhao, X.4    Sumner, L.W.5
  • 15
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • Smith C.A., Want E.J., O'Maille G., Abagyan R., and Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78 (2006) 779-787
    • (2006) Anal Chem , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 16
    • 40049092920 scopus 로고    scopus 로고
    • TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling experiments
    • Luedemann A., Strassburg K., Erban A., and Kopka J. TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics 24 (2008) 732-737
    • (2008) Bioinformatics , vol.24 , pp. 732-737
    • Luedemann, A.1    Strassburg, K.2    Erban, A.3    Kopka, J.4
  • 17
    • 65249132985 scopus 로고    scopus 로고
    • MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing
    • Lommen A. MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81 (2009) 3079-3086
    • (2009) Anal Chem , vol.81 , pp. 3079-3086
    • Lommen, A.1
  • 18
    • 33644867564 scopus 로고    scopus 로고
    • MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
    • Katajamaa M., Miettinen J., and Oresic M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22 (2006) 634-636
    • (2006) Bioinformatics , vol.22 , pp. 634-636
    • Katajamaa, M.1    Miettinen, J.2    Oresic, M.3
  • 20
    • 34248512719 scopus 로고    scopus 로고
    • Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry
    • De Vos R.C., Moco S., Lommen A., Keurentjes J.J., Bino R.J., and Hall R.D. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc 2 (2007) 778-791
    • (2007) Nat Protoc , vol.2 , pp. 778-791
    • De Vos, R.C.1    Moco, S.2    Lommen, A.3    Keurentjes, J.J.4    Bino, R.J.5    Hall, R.D.6
  • 22
    • 58149110910 scopus 로고    scopus 로고
    • High-resolution direct infusion-based mass spectrometry in combination with whole (13)c metabolome isotope labeling allows unambiguous assignment of chemical sum formulas
    • Giavalisco P., Hummel J., Lisec J., Inostroza A.C., Catchpole G., and Willmitzer L. High-resolution direct infusion-based mass spectrometry in combination with whole (13)c metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal Chem 80 (2008) 9417-9425
    • (2008) Anal Chem , vol.80 , pp. 9417-9425
    • Giavalisco, P.1    Hummel, J.2    Lisec, J.3    Inostroza, A.C.4    Catchpole, G.5    Willmitzer, L.6
  • 23
    • 58849117570 scopus 로고    scopus 로고
    • MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites
    • Matsuda F., Yonekura-Sakakibara K., Niida R., Kuromori T., Shinozaki K., and Saito K. MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J 57 (2009) 555-577
    • (2009) Plant J , vol.57 , pp. 555-577
    • Matsuda, F.1    Yonekura-Sakakibara, K.2    Niida, R.3    Kuromori, T.4    Shinozaki, K.5    Saito, K.6
  • 24
    • 58449134032 scopus 로고    scopus 로고
    • Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants
    • Sawada Y., Akiyama K., Sakata A., Kuwahara A., Otsuki H., Sakurai T., Saito K., and Hirai M.Y. Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol 50 (2009) 37-47
    • (2009) Plant Cell Physiol , vol.50 , pp. 37-47
    • Sawada, Y.1    Akiyama, K.2    Sakata, A.3    Kuwahara, A.4    Otsuki, H.5    Sakurai, T.6    Saito, K.7    Hirai, M.Y.8
  • 25
    • 33845810018 scopus 로고    scopus 로고
    • Data correction strategy for metabolomics analysis using gas chromatography-mass spectrometry
    • Kanani H.H., and Klapa M.I. Data correction strategy for metabolomics analysis using gas chromatography-mass spectrometry. Metab Eng 9 (2007) 39-51
    • (2007) Metab Eng , vol.9 , pp. 39-51
    • Kanani, H.H.1    Klapa, M.I.2
  • 26
    • 3242741850 scopus 로고    scopus 로고
    • Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry
    • Gullberg J., Jonsson P., Nordstrom A., Sjostrom M., and Moritz T. Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331 (2004) 283-295
    • (2004) Anal Biochem , vol.331 , pp. 283-295
    • Gullberg, J.1    Jonsson, P.2    Nordstrom, A.3    Sjostrom, M.4    Moritz, T.5
  • 27
    • 34347384910 scopus 로고    scopus 로고
    • Normalization method for metabolomics data using optimal selection of multiple internal standards
    • Sysi-Aho M., Katajamaa M., Yetukuri L., and Oresic M. Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8 (2007) 93
    • (2007) BMC Bioinformatics , vol.8 , pp. 93
    • Sysi-Aho, M.1    Katajamaa, M.2    Yetukuri, L.3    Oresic, M.4
  • 30
    • 12144291195 scopus 로고    scopus 로고
    • MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    • Thimm O., Blasing O., Gibon Y., Nagel A., Meyer S., Kruger P., Selbig J., Muller L.A., Rhee S.Y., and Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37 (2004) 914-939
    • (2004) Plant J , vol.37 , pp. 914-939
    • Thimm, O.1    Blasing, O.2    Gibon, Y.3    Nagel, A.4    Meyer, S.5    Kruger, P.6    Selbig, J.7    Muller, L.A.8    Rhee, S.Y.9    Stitt, M.10
  • 32
    • 84983633298 scopus 로고    scopus 로고
    • KNApSAcK: a comprehensive species-metabolite relationship database
    • Saito K., Dixon R.A., and Willmitzer L. (Eds), Springer. The authors have constructed a comprehensive database of species-metabolite relationships (URL: http://kanaya.naist.jp/KNApSAcK/). This has great potential for identifying unknown metabolites derived from nontargeted metabolomics.
    • Shinbo Y., Nakamura Y., Altaf-Ul-Amin M., Asahi H., Kurokawa K., Arita M., Saito K., Ohta D., Shibata D., and Kanaya S. KNApSAcK: a comprehensive species-metabolite relationship database. In: Saito K., Dixon R.A., and Willmitzer L. (Eds). Biotechnology in Agriculture and Forestry 57 Plant Metabolomics (2006), Springer 165-184. The authors have constructed a comprehensive database of species-metabolite relationships (URL: http://kanaya.naist.jp/KNApSAcK/). This has great potential for identifying unknown metabolites derived from nontargeted metabolomics.
    • (2006) Biotechnology in Agriculture and Forestry 57 Plant Metabolomics , pp. 165-184
    • Shinbo, Y.1    Nakamura, Y.2    Altaf-Ul-Amin, M.3    Asahi, H.4    Kurokawa, K.5    Arita, M.6    Saito, K.7    Ohta, D.8    Shibata, D.9    Kanaya, S.10
  • 33
    • 46749102552 scopus 로고    scopus 로고
    • Detection of monosaccharide types from coordinates
    • Arita M., and Tokimatsu T. Detection of monosaccharide types from coordinates. Genome Inform 19 (2007) 3-14
    • (2007) Genome Inform , vol.19 , pp. 3-14
    • Arita, M.1    Tokimatsu, T.2
  • 34
    • 41349122884 scopus 로고    scopus 로고
    • Statistical search on the Semantic Web
    • Kobayashi N., and Toyoda T. Statistical search on the Semantic Web. Bioinformatics 24 (2008) 1002-1010
    • (2008) Bioinformatics , vol.24 , pp. 1002-1010
    • Kobayashi, N.1    Toyoda, T.2
  • 35
    • 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 Min 1 (2008) 7
    • (2008) BioData Min , vol.1 , pp. 7
    • Arita, M.1    Suwa, K.2
  • 40
    • 2442647715 scopus 로고    scopus 로고
    • Differential metabolic networks unravel the effects of silent plant phenotypes
    • Weckwerth W., Loureiro M.E., Wenzel K., and Fiehn O. Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci U S A 101 (2004) 7809-7814
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 7809-7814
    • Weckwerth, W.1    Loureiro, M.E.2    Wenzel, K.3    Fiehn, O.4
  • 41
    • 33748475897 scopus 로고    scopus 로고
    • Review: on the analysis and interpretation of correlations in metabolomic data
    • Steuer R. Review: on the analysis and interpretation of correlations in metabolomic data. Brief Bioinform 7 (2006) 151-158
    • (2006) Brief Bioinform , vol.7 , pp. 151-158
    • Steuer, R.1
  • 42
    • 37849016716 scopus 로고    scopus 로고
    • Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana
    • The metabolomic network approach using GC-time-of-flight (TOF)/MS demonstrates a further testable hypothesis on unknown metabolic pathways.
    • Kusano M., Fukushima A., Arita M., Jonsson P., Moritz T., Kobayashi M., Hayashi N., Tohge T., and Saito K. Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Syst Biol 1 (2007) 53. The metabolomic network approach using GC-time-of-flight (TOF)/MS demonstrates a further testable hypothesis on unknown metabolic pathways.
    • (2007) BMC Syst Biol , vol.1 , pp. 53
    • Kusano, M.1    Fukushima, A.2    Arita, M.3    Jonsson, P.4    Moritz, T.5    Kobayashi, M.6    Hayashi, N.7    Tohge, T.8    Saito, K.9
  • 43
    • 60149100804 scopus 로고    scopus 로고
    • Modules of co-regulated metabolites in turmeric (Curcuma longa) rhizome suggest the existence of biosynthetic modules in plant specialized metabolism
    • Xie Z., Ma X., and Gang D.R. Modules of co-regulated metabolites in turmeric (Curcuma longa) rhizome suggest the existence of biosynthetic modules in plant specialized metabolism. J Exp Bot 60 (2009) 87-97
    • (2009) J Exp Bot , vol.60 , pp. 87-97
    • Xie, Z.1    Ma, X.2    Gang, D.R.3
  • 48
  • 50
    • 34248377833 scopus 로고    scopus 로고
    • The metabolic signature related to high plant growth rate in Arabidopsis thaliana
    • This work represents the importance of reverse genetic approaches with GC-MS-based metabolite profiling in capturing interrelationship between phenotypes and metabolites. The authors showed a correlation between biomass and the contribution of multiple metabolic compositions.
    • Meyer R.C., Steinfath M., Lisec J., Becher M., Witucka-Wall H., Torjek O., Fiehn O., Eckardt A., Willmitzer L., Selbig J., et al. The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci U S A 104 (2007) 4759-4764. This work represents the importance of reverse genetic approaches with GC-MS-based metabolite profiling in capturing interrelationship between phenotypes and metabolites. The authors showed a correlation between biomass and the contribution of multiple metabolic compositions.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 4759-4764
    • Meyer, R.C.1    Steinfath, M.2    Lisec, J.3    Becher, M.4    Witucka-Wall, H.5    Torjek, O.6    Fiehn, O.7    Eckardt, A.8    Willmitzer, L.9    Selbig, J.10
  • 51
    • 59149100506 scopus 로고    scopus 로고
    • System-wide molecular evidence for phenotypic buffering in Arabidopsis
    • In this excellent paper, the authors show that an integrative genome-wide strategy could identify six QTL hotspots related to transcripts, proteins, metabolites, and phenotypic traits in Arabidopsis, though the mapping resolution has limitations.
    • Fu J., Keurentjes J.J., Bouwmeester H., America T., Verstappen F.W., Ward J.L., Beale M.H., de Vos R.C., Dijkstra M., Scheltema R.A., et al. System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet 41 (2009) 166-167. In this excellent paper, the authors show that an integrative genome-wide strategy could identify six QTL hotspots related to transcripts, proteins, metabolites, and phenotypic traits in Arabidopsis, though the mapping resolution has limitations.
    • (2009) Nat Genet , vol.41 , pp. 166-167
    • Fu, J.1    Keurentjes, J.J.2    Bouwmeester, H.3    America, T.4    Verstappen, F.W.5    Ward, J.L.6    Beale, M.H.7    de Vos, R.C.8    Dijkstra, M.9    Scheltema, R.A.10
  • 52
    • 54149090305 scopus 로고    scopus 로고
    • Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome
    • Rowe H.C., Hansen B.G., Halkier B.A., and Kliebenstein D.J. Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. Plant Cell 20 (2008) 1199-1216
    • (2008) Plant Cell , vol.20 , pp. 1199-1216
    • Rowe, H.C.1    Hansen, B.G.2    Halkier, B.A.3    Kliebenstein, D.J.4
  • 53
    • 62349101060 scopus 로고    scopus 로고
    • Genetical metabolomics: closing in on phenotypes
    • Keurentjes J.J. Genetical metabolomics: closing in on phenotypes. Curr Opin Plant Biol 12 (2009) 223-230
    • (2009) Curr Opin Plant Biol , vol.12 , pp. 223-230
    • Keurentjes, J.J.1
  • 54
    • 42449106989 scopus 로고    scopus 로고
    • Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1
    • Using the combination of high-throughput expression profiling and systematic experimental design, based on combinatorial design, the authors suggest a candidate for an organic nitrogen-responsive transcription factor. This is the first report of the relationship between the regulation of circadian clock component CCA1 and nitrogen assimilatory genes.
    • Gutierrez R.A., Stokes T.L., Thum K., Xu X., Obertello M., Katari M.S., Tanurdzic M., Dean A., Nero D.C., McClung C.R., et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105 (2008) 4939-4944. Using the combination of high-throughput expression profiling and systematic experimental design, based on combinatorial design, the authors suggest a candidate for an organic nitrogen-responsive transcription factor. This is the first report of the relationship between the regulation of circadian clock component CCA1 and nitrogen assimilatory genes.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 4939-4944
    • Gutierrez, R.A.1    Stokes, T.L.2    Thum, K.3    Xu, X.4    Obertello, M.5    Katari, M.S.6    Tanurdzic, M.7    Dean, A.8    Nero, D.C.9    McClung, C.R.10
  • 55
    • 67649872569 scopus 로고    scopus 로고
    • Starch as a major integrator in the regulation of plant growth
    • This study highlights the potential of molecular phenotyping including metabolite profiling. By combining a species-wide analysis based on 94 Arabidopsis accessions with a multivariate regression approach, the authors found that starch content negatively correlates with leaf biomass. From the results of an integrative approach with transcript profiling and detailed genotyping of leaf samples, two candidate genes associated with increased biomass production were identified.
    • Sulpice R., Pyl E.T., Ishihara H., Trenkamp S., Steinfath M., Witucka-Wall H., Gibon Y., Usadel B., Poree F., Piques M.C., et al. Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci U S A 106 (2009) 10348-10353. This study highlights the potential of molecular phenotyping including metabolite profiling. By combining a species-wide analysis based on 94 Arabidopsis accessions with a multivariate regression approach, the authors found that starch content negatively correlates with leaf biomass. From the results of an integrative approach with transcript profiling and detailed genotyping of leaf samples, two candidate genes associated with increased biomass production were identified.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 10348-10353
    • Sulpice, R.1    Pyl, E.T.2    Ishihara, H.3    Trenkamp, S.4    Steinfath, M.5    Witucka-Wall, H.6    Gibon, Y.7    Usadel, B.8    Poree, F.9    Piques, M.C.10
  • 56
    • 60849098774 scopus 로고    scopus 로고
    • Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen
    • This paper reports that, based on the O2PLS method, multivariate statistical modeling of systematic changes at different functional levels (transcripts, proteins, and metabolites) measured in parallel facilitates the interpretation of the results, indicating that this is the most promising approach for data integration. The possible implications of an integrated approach are also described.
    • Bylesjo M., Nilsson R., Srivastava V., Gronlund A., Johansson A.I., Jansson S., Karlsson J., Moritz T., Wingsle G., and Trygg J. Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen. J Proteome Res 8 (2009) 199-210. This paper reports that, based on the O2PLS method, multivariate statistical modeling of systematic changes at different functional levels (transcripts, proteins, and metabolites) measured in parallel facilitates the interpretation of the results, indicating that this is the most promising approach for data integration. The possible implications of an integrated approach are also described.
    • (2009) J Proteome Res , vol.8 , pp. 199-210
    • Bylesjo, M.1    Nilsson, R.2    Srivastava, V.3    Gronlund, A.4    Johansson, A.I.5    Jansson, S.6    Karlsson, J.7    Moritz, T.8    Wingsle, G.9    Trygg, J.10
  • 57
    • 63049122216 scopus 로고    scopus 로고
    • Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response
    • This paper describes the phenotyping of arrhythmic plants, d975 - knockout of PSEUDO RESPONSE REGULATORS 9, 7, and 5, by using transcriptome analysis. The mutants exhibited significant cold tolerance because of the upregulation of cold-responsive transcription factor genes, for example Dehydration Responsive Element Binding protein 1 (DREB1)/C-repeat Binding Factor (CBF).
    • Nakamichi N., Kusano M., Fukushima A., Kita M., Ito S., Yamashino T., Saito K., Sakakibara H., and Mizuno T. Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 50 (2009) 447-462. This paper describes the phenotyping of arrhythmic plants, d975 - knockout of PSEUDO RESPONSE REGULATORS 9, 7, and 5, by using transcriptome analysis. The mutants exhibited significant cold tolerance because of the upregulation of cold-responsive transcription factor genes, for example Dehydration Responsive Element Binding protein 1 (DREB1)/C-repeat Binding Factor (CBF).
    • (2009) Plant Cell Physiol , vol.50 , pp. 447-462
    • Nakamichi, N.1    Kusano, M.2    Fukushima, A.3    Kita, M.4    Ito, S.5    Yamashino, T.6    Saito, K.7    Sakakibara, H.8    Mizuno, T.9
  • 58
    • 66349124175 scopus 로고    scopus 로고
    • Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination
    • This is the first report on the link between circadian clock and mitochondrial function in Arabidopsis. The authors demonstrated that arrhythmic plants lacking PRR 9, 7, and 5 can be characterized by increases of antioxidant, osmolytes, and intermediates associated with the TCA cycle. The approach used is based on combining GC-MS-based metabolite profiling and microarrays.
    • Fukushima A., Kusano M., Nakamichi N., Kobayashi M., Hayashi N., Sakakibara H., Mizuno T., and Saito K. Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc Natl Acad Sci U S A 106 (2009) 7251-7256. This is the first report on the link between circadian clock and mitochondrial function in Arabidopsis. The authors demonstrated that arrhythmic plants lacking PRR 9, 7, and 5 can be characterized by increases of antioxidant, osmolytes, and intermediates associated with the TCA cycle. The approach used is based on combining GC-MS-based metabolite profiling and microarrays.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 7251-7256
    • Fukushima, A.1    Kusano, M.2    Nakamichi, N.3    Kobayashi, M.4    Hayashi, N.5    Sakakibara, H.6    Mizuno, T.7    Saito, K.8
  • 59
    • 33846050368 scopus 로고    scopus 로고
    • Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana
    • •], this paper demonstrates that a combination of mathematical modeling and experimental data can identify the candidate component for the circadian clock oscillator in Arabidopsis. The authors also provide accessible tools for simulating the model (URL: http://www.amillar.org/).
    • •], this paper demonstrates that a combination of mathematical modeling and experimental data can identify the candidate component for the circadian clock oscillator in Arabidopsis. The authors also provide accessible tools for simulating the model (URL: http://www.amillar.org/).
    • (2006) Mol Syst Biol , vol.2 , pp. 59
    • Locke, J.C.1    Kozma-Bognar, L.2    Gould, P.D.3    Feher, B.4    Kevei, E.5    Nagy, F.6    Turner, M.S.7    Hall, A.8    Millar, A.J.9
  • 65
    • 70350095897 scopus 로고    scopus 로고
    • Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data
    • Redestig H., Fukushima A., Stenlund H., Moritz T., Arita M., Saito K., and Kusano M. Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data. Analytical Chemistry 81 (2009) 7974-7980
    • (2009) Analytical Chemistry , vol.81 , pp. 7974-7980
    • Redestig, H.1    Fukushima, A.2    Stenlund, H.3    Moritz, T.4    Arita, M.5    Saito, K.6    Kusano, M.7


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