Plant metabolomics: Large-scale phytochemistry in the functional genomics era

Phytochemistry

Volumn 62, Issue 6, 2003, Pages 817-836

  Sumner, Lloyd W ^a   Mendes, Pedro ^b   Dixon, Richard A ^a  

^a PLANT BIOLOGY DIVISION   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Analytical instrumentation; Bioinformatics; Mass spectrometry; Medicago truncatula; Metabolic profiling; Metabolite databases; Metabolite profiling; Metabolomics; MS

Indexed keywords

ARABIDOPSIS; BIOINFORMATICS; DATA BASE; DNA MICROARRAY; GENOMICS; INFRARED SPECTROSCOPY; INTERNET; MASS SPECTROMETRY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PHYTOCHEMISTRY; PLANT METABOLISM; PRINCIPAL COMPONENT ANALYSIS; REVIEW; THIN LAYER CHROMATOGRAPHY; TRANSGENIC PLANT;

MEDICAGO; MEDICAGO TRUNCATULA;

EID: 0345270397     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0031-9422(02)00708-2     Document Type: Review

References (150)

1. Aharoni, A., Ric de Vos, C.H., Verhoeven, H.A., Maliepaard, C.A., Kruppa, G., Bino, R., Goodenowe, D., 2002. Non-targeted metabolomic profiling using Fourier transform ion cyclotron mass spectrometry (FTMS). OMICS: A Journal of Integrative Biology 6, 217-234.
2. Arlt, K., Brandt, S., Kehr, J., 2001. Amino acid analysis in five pooled single plant cell samples using capillary electrophoresis coupled to laser-induced fluorescence detection. Journal of Chromatography A 926, 319-325.
3. Asimov, D., 1985. The grand tour: a tool for viewing multi-dimensional data. SIAM Journal on Scientific and Statistical Computing 6, 128-143.
4. Baggett, B.R., Cooper, J.D., Hogan, E.T., Carper, J., Paiva, N.L., Smith, J.T., 2002. Profiling isoflavonoids found in legume root extracts using capillary electrophoresis. Electrophoresis 23, 1642-1651.
5. Bailey, N.J., Stanley, P.D., Hadfield, S.T., Lindon, J.C., Nicholson, J.K., 2000a. Mass spectrometrically detected directly coupled high performance liquid chromatography/nuclear magnetic resonance spectroscopy/mass spectrometry for the identification of xenobiotic metabolites in maize plants. Rapid Communications in Mass Spectrometry 14, 679-684.
6. Bailey, N.J., Cooper, P., Hadfield, S.T., Lenz, E.M., Lindon, J.C., Nicholson, J.K., Stanley, P.D., Wilson, I.D., Wright, B., Taylor, S.D., 2000b. Application of directly coupled HPLC-NMR-MS/MS to the identification of metabolites of 5-trifluoromethylpyridone (2-hydroxy-5-trifluoromethylpyridine) in hydroponically grown plants. Journal of Agriculture and Food Chemistry 48, 42-46.
7. Bairoch, A., 2000. The ENZYME database in 2000. Nucleic Acids Research 28, 304-305.
8. Bales, J.R., Bell, J.D., Nicholson, J.K., Sadler, P.J., Timbrell, J.A., Hughes, R.D., Bennett, P.N., Williams, R., 1988. Metabolic profiling of body fluids by proton NMR: self-poisoning episodes with paracetamol (acetominophen). Magnetic Resonance in Medicine 6, 300-306.
9. Bales, J.R., Higham, D.P., Howe, I., Nicholson, J.K., Sadler, P.J., 1984, Use of high resoution proton nuclear magnetic resonance spectroscopy for rapid multi-component analysis of urine. Clinical Chemistry 30, 426-432.
10. Baulcombe, D.C., 1999. Fast forward genetics based on virus-induced gene silencing. Current Opinion in Plant Biology 2, 109-113.
11. Bednarek, P., Franski, R., Kerhoas, L., Einhorn, J., Wojtaszek, P., Stobiecki, M., 2001. Profiling changes in metabolism of isoflavonoids and their conjugates in Lupinus albus treated with biotic elicitor. Phytochemistry 56, 77-85.
12. Blackstock, W.P., Weir, M.P., 1999. Proteomics: quantitative and physical mapping of cellular protiens. Trends in Biotechnology 17, 121-127.
13. Bligny, R., Douce, R., 2001. NMR and plant metabolism. Current Opinion in Plant Biology 4, 191-196.
14. Bochner, B.R., Gadzinski, P., Panomitros, E., 2001. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Research 11, 1246-1255.
15. Boyes, D.C., Zayed, A.M., Ascenzi, R., McCaskill, A.J., Hoffman, N.E., Davis, K.R., 2001. Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 13, 1499-1510.
16. Brazma, A., Sarkans, U., Robinson, A., Vilo, J., Vingron, M., Hoheisel, J., Fellenberg, K., 2002. Microarray data representation, annotation and storage, Advances in Biochemical Engineering and Biotechnology 77, 113-139.
17. Bundy, J.B., Spurgeon, D.J., Svendsen, C., Hankard, P.K., Osborn, D., Lindon, J.C., Nicholson, J.K., 2002. Earthworm species of the genus Eisenia can be phenotypically differentiated by metabolic profiling. FEBS Letters 521, 115-120.
18. Burton, R.A.D.M.G., Bacic, A., Findlay, K., Roberts, K., Hamilton, A., Baulcombe, D.C., Fincher, G.B., 2000. Virus-induced silencing of a plant cellulose synthase gene. Plant Cell 12, 691-705.
19. Chong, J., Pierrel, M.A., Atanassova, R., WerckReithhart, D., Fritig, B., Saindrenan, P., 2001. Free and conjugated benzoic acid in tobacco plants and cell cultures. Induced accumulation upon elicitation of defense responses and role as salicylic acid precursors. Plant Physiology 125, 318-328.
20. Cornish-Bowden, A., Eisenthal, R., 1974. Statistical considerations in the estimation of enzyme kinetic parameters by the direct linear plot and other methods. Biochemal Journal 139, 721-730.
21. Cowan, J.D., Sharp, D.H., 1988. Neural nets. Quarterly Review of Biophysics 21, 365-427.
22. Cristianini, N., Shawe-Taylor, J., 2000. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods. Cambridge University Press, Cambridge.
23. Cunnick, W.R., Cromie, J.B., Cortell, R., Wright, B., Beach, E., Seltzer, F., Miller, S., 1972. Value of biochemical profiling in a periodic health examination program: analysis of 1,000 cases. Bulletin of New York Academy of Medicine 18, 5-22.
24. Davis, S.C., Makarov, A.A., Hughes, J.D., 1999. Ultrafast gas chromtography using time-of-flight mass spectrometer. Rapid Communications in Mass Spectrometry 13, 237-241.
25. Devaux, P.G., Horning, M.G., Horning, E.C., 1971. Benyzl-oxime derivative of steroids; a new metabolic profile procedure for human urinary steroids. Analytical Letters 4, 151.
26. Deyl, Z., Hyanek, J., Jorakova, M., 1986. Profiling of amino acids in body fluids and tissues by means of liquid chromatography. Journal of Chromatography 379, 177-250.
27. Edgar, R., Domrachev, M., Lash, A.E., 2002. Gene expression omnibus: NCBIgene expression and hybridization array data repository. Nucleic Acids Research 30, 207-210.
28. Ellis, L.B., Hershberger, C.D., Bryan, E.M., Wackett, L.P., 2001. The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes. Nucleic Acids Research 29, 340-343.
29. Farré, E.M., Tiesssen, A., Roessner, U., Geigenberger, P., Trethewey, R.N., Willmitzer, L., 2001. Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method. Plant Physiology 127, 685-700.
30. Fiehn, O., 2002. Metabolomics - the link between genotypes and phenotypes. Plant Molecular Biology 48, 155-171.
31. Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R.N., Willmitzer, L., 2000. Metabolite profiling for plant functional genomics. Nature Biotechnology 18, 1157-1161.
32. Fraser, P.D., Pinto, M.E., Holloway, D.E., Bramley, P.M., 2000. Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant Journal 24, 551-558.
33. Fridland, G.H., Desiderio, D.M., 1986. Profiling of neuropeptides using gradient reversed-phase high-performance liquid chromatography with novel detection methodologies. Journal of Chromatography 379, 251-268.
34. Gates, S.C., Sweeley, C.C., 1978. Quantitative metabolic profiling based on gas chromatography. Clinical Chemistry 24, 1663-1673.
35. Gerding, T.K., Drenth, B.F., Rossenstein, H.J., de Zeeuw, R.A., Tepper, P.G., Horn, A.S., 1990. The metabolic fate of the dopamine agonist 2-(N-propyl-N-2-thienylethylamino)-5-hydroxytetralin in rats after intravenous and oral administration. I. Disposition and metabolic profiling. Xenobioctica 20, 515-524.
36. Goff, S.A., et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100.
37. Goldberg, D.E., 1989. Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, Reading, Mass.
38. Goodacre, R., Kell, D.B., 1996. Pyrolysis mass spectrometry and its applications in biotechnology. Current Opinion in Biotechnology 7, 20-28.
39. Gorinstein, S., Zemser, M., Vargasalbores, F., Ochoa, J.L., 1995. Classification of seven species of cactaceae based on their chemical and biochemical properties. Bioscience, Biotechnology, and Biochemistry 59, 2022-2027.
40. Goto, S., Okuno, Y., Hattori, M., Nishioka, T., Kanehisa, M., 2002. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Research 30, 402-404.
41. Graham, T.L., 1991. A rapid, high resolution high performance liquid chromatography profiling procedure for plant and microbial aromatic secondary metabolites. Plant Physiology 95, 584-593.
42. Guo, D., Chen, F., Inoue, K., Blount, J.W., Dixon, R.A., 2000. Down-regulation of caffeic acid 3-O-methyltransferase and caffeoyl CoA 3-O-methyltransferase in transgenic alfalfa (Medicago sativa L.): impacts on lignin structure and implications for the biosynthesis of G and S lignin. Plant Cell 13, 73-88.
43. Gygi, S.P., Rochon, Y., Franza, B.R., Aebersold, R., 1999. Correlation between protein and mRNA abundance in yeast. Molecular and Cell Biology 1720-1730.
44. Halket, J.M., Przyborowska, A., Stein, S.E., Mallard, W.G., Down, S., Chalmers, R.A., 1999. Deconvolution gas chromatography/mass spectrometry of urinary organic acids - potential for pattern recognition and automated identification of metabolic disorders. Rapid Communications in Mass Spectrometry 13, 279-284.
45. Hall, R., Beale, M., Fiehn, O., Hardy, N., Sumner, L., Bino, R., 2002. Plant metabolomics as the missing link in functional genomics strategies. Plant Cell 14, 1437-1440.
46. Harrison, M.J., Dixon, R.A., 1993. Isoflavonoid accumulation and expression of defense gene transcripts during the establishment of vesicular arbuscular mycorrhizal associations in roots of Medicago truncatula. Molecular Plant-Microbe Interactions 6, 643-654.
47. Hofmeyr, J.H.S., Cornish-Bowden, A., Rohwer, J.M., 1993. Taking enzyme kinetics out of control - putting control into regulation. European Journal of Biochemistry 212, 833-837.
48. Hofmeyr, J.H., Cornish-Bowden, A., 1996. Co-response analysis: a new experimental strategy for metabolic control analysis. Journal of Theoretical Biology 182, 371-380.
49. Holland, J.F., Leary, J.J., Sweeley, C.C., 1986. Advanced instrumentation and strategies for metabolic profiling. Journal Chromatography 1279, 313-345.
50. Holtorf, H., Guitton, M.-C., Reski, R., 2002. Plant functional genomics. Naturwissenschaften 89, 235-249.
51. Horning, E.C., Horning, M.G., 1970. Metabolic profiles: chromatographic methods for isolation and characterization of a variety of metabolites in man. In: Olson, R.E. (Ed.), Methods in Medical Research. Year Book Medical Publishers, Chicago, p. 369.
52. Horning, E.C., Horning, M.G., 1971a. Human metabolic profiles obtained by GC and GC/MS. Journal of Chromatographic Science 9, 129-140.
53. Horning, E.C., Horning, M.G., 1971b. Metabolic profiles: gas-phase methods for analysis of metabolites. Clinical Chemistry 17, 802-809.
54. Hotellin, H., 1933. Analysis of a complex of statistical variables into principal components. Journal of Educational Psychology 24, 417-441.
55. Huhman, D.V., Sumner, L.W., 2002. Metabolioc profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectometer. Phytochemistry 59, 347-360.
56. Humphreys, J.M., Chapple, C., 2002. Rewriting the lignin roadmap. Current Opinion in Plant Biology 5, 224-229.
57. Ideker, T., Galitski, T., Hood, L., 2001. A new approach to decoding life: sytems biology. Annual Review of Genomics and Human Genetics 2, 343-372.
58. Jung, W., Yu, O., Lau, S.-M.C., O'Keefe, D.P., Odell, J., Fader, G., McGonigle, B., 2000. Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nature Biotechnology 18, 208-212.
59. Kanehisa, M., Goto, S., Kawashima, S., Nakaya, A., 2002. The KEGG databases at GenomeNet. Nucleic Acids Research 30, 42-46.
60. Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collaado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., Gama-Castro, S., 2002. The EcoCyc Database. Nucleic Acids Research 30, 56-58.
61. Katona, Z.F., Sass, P., Molnár-Perl, I., 1999. Simultaneous determination of sugars, sugar alcohols, acids and amino acids in apricots by gas chromatography-mass spectrometry. Journal of Chromatography 847, 91-102.
62. Kehoe, D.M., Villand, P., Somerville, S., 1999. DNA microarrays for studies of higher plants and other photosynthetic organisms. Plant Science 4, 38-41.
63. Kehr, J., 2001. High resolution spatial analysis of plant systems. Current Opinion in Plant Biology 4, 197-201.
64. Kitano, H., 2000. Perspectives on systems biology. New Generation Computing 18, 199-216.
65. Kleter, G.A., van der Krieken, W.M., Kok, E.J., Bosch, D., Jordi, W., Gilissen, L.J.W.L., 2001. Regulation and exploitation of genetically modified crops. Nature Biotechnology 19, 1105-1110.
66. Klose, J., Kobalz, U., 1995. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16, 1034-1059.
67. Kohonen, T., 1982. Self-organized formation of topologically correct feature maps. Biological Cybernetics 43, 59-69.
68. Kohonen, T. In: Kohonen, T., Schroeder, M.R., Huang, T.S. (Eds.), 1995. In Self-Organizing Maps, 3rd Ed. Springer-Verlag, New York.
69. Korolev, A.V., Tomos, A.D., Bowtell, R., Farras, J.F., 2000. Spatial and temporal distribution of solutes in the developing carrot taproot measured at single-cell resolution. Journal of Experimental Botany 51, 567-577.
70. Kose, F., Weckwerth, W., Linke, T., Fiehn, O., 2001. Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 17, 1198-1208.
71. Koosis, D.J., 1997. Statistics A Self-Teaching Guide, 4th Ed. John Wiley & Sons, New York.
72. Koza, J.R., 1992, Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, Cambridge Mass.
73. Lachenbruch, P.A., 1975. Discriminant Analysis. Hafner Press, New York.
74. Larson, T.R., Graham, I.A., 2001. A novel technique for the sensitive quantification of acyl CoA esters from plant tissues. The Plant Journal 25, 115-125.
75. Liebich, H.M., 1986. Gas chromatographic profiling of ketone bodies and organic acids in diabetes. Journal of Chromatography 379, 347-366.
76. Lin, L.Z., He, X.G., Lindenmaier, M., Yang, J., Cleary, M., Qiu, S.X., Cordell, G.A., 2000. LC-ESI-MS study of the flavonoid glycoside malonates of red clover (Trifolium pratense). Journal of Agricultural and Food Chemistry 48, 354-365.
77. Liu, C.-J., Blount, J.W., Steele, C.L., Dixon, R.A., 2002. Bottlenecks for metabolic engineering of isoflavone glycoconjugates in Arabidopsis. Proceedings of the National Academy of Sciences, USA 99, 14578-14583.
78. Lois, R., 1994. Accumulation of UV-absorbing flavonoids induced by UV-B radiation in Arabidopsis thaliana L. Planta 194, 498-503.
79. Longman, P.J., 1999. The curse of Frankenfood. Genetically modified crops stir up controversy at home and abroad. U.S. News & World Report July 16, 39-41.
80. Maier, W., Schmidt, J., Wray, V., Walter, M.H., Strack, D., 1999. The arbuscular mycorrhizal fungus, Glomus intraradices, induces the accumulation of cyclohexenone derivatives in tobacco roots. Planta 207, 620-623.
81. May, G.D., 2002. An integrated approach to Medicago functional genomics. In: Romeo, J.T., Dixon, R.A. (Eds.), Recent Advances in Phytochemistry, Vol. 36. Pergamon, Oxford, UK, pp. 179-195.
82. McGovern, A.C., Broadhurst, D., Taylor, J., Kaderbhai, N., Winson, M.K., Small, D.A., Rowland, J.J., Kell, D.B., Goodacre, R., 2002, Monitoring of complex industrial bioprocesses for metabolite concentrations using modern spectroscopies and machine learning: application to gibberellic acid production. Biotechnology and Bioengineering 78, 527-538.
83. Mendes, P., 2002. Emerging bioinformatics for the metabolome. Briefings in Bioinformatics 3, 134-145.
84. Mendes, P., 2001. Modeling large scale biological systems from functional genomic data: parameter estimation. In: Kitano, H. (Ed.), Foundations of Systems Biology. MIT Press, Cambridge, MA, pp. 163-186.
85. Mendes, P., Bulmore, D.L., Farmer, A.D., Steadman, P.A., Waugh, M.E., Wlodek, S.T., 2000. PathDB: a second generation metabolic database. In: Hofmeyr, J.-H.S., Rohwer, J.M., Snoep, J.L. (Eds.), Animating the Cellular Map. Stellenbosch University Press, Stellenbosch, pp. 207-212.
86. Mendes, P., Kell, D.B., 1998. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883.
87. Meyer, R.D., Cook, D., 2000. Visualization of data. Current Opinion in Biotechnology 11, 89-96.
88. Meyermans, H., Morrell, K., Lapierre, C., Pollet, B., De Bruyn, A., Busson, R., Herdewijn, P., Devresse, B., Van Beeumen, J., Marita, J.M., Ralph, J., Chen, C., Burggraeve, B., Van Montagu, M., Messens, E., Boerjan, W., 2000. Modifications in lignin and accumulation of phenolic glycosides in poplar xylem upon down-regulation of caffeoyl coenzyme A O-methyltransferase, an enzyme involved in lignin biosynthesis. Journal of Biological Chemistry 275, 36899-36909.
89. Michal, G., 1999. Biochemical Pathways. An Atlas of Biochemistry and Molecular Biology. John Wiley & Sons, New York.
90. Miller, J.N., Miller, J.C., 2000. Statistic and Chemometrics for Analytical Chemistry, 4th Ed. Prentice Hall, New York.
91. Mroczek, W.J., 1972. Biochemical profiling and the natural history of hypertensive diseases. Circulation 45, 1332-1333.
92. Muir, S.R., Collins, G.J., Robinson, S., Hughes, S., Bovy, A., De Vos, C.H.R., van Tunen, A.J., Verhoeyen, M.E., 2001. Overexpression of petunia chalcone isomerase in tomato results in fruit containing increased levels of flavonols. Nature Biotechnology 19, 470-474.
93. Nicholson, J.K., Connelly, J., Lindon, J.C., Names, E., 2002. Metabonomics: a platform for studying drug toxicity and gene function. Nature Reviews Drug Discovery 1, 153-161.
94. Nicholson, J.K., Lindon, J.C., Holmes, E., 1999. "Metabonomics" understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181-1189.
95. Nicholson, J.K., O'Flynn, M., Sadler, P.J., Macleod, A., Juul, S.M., Sonksen, P.H., 1984. Proton NMR studies of serum, plasma and urine from fasting normal, and diabetic subjects. Biochemical Journal 217, 275-365.
96. Nikiforow, A., Schlick-Steiner, B., Steiner, F., Kalb, R., and Mistrik, R., 2001. Classification of GC-MS data of epicuticular hydrocarbon from Tetramorium ants by self-organizing maps for morphological determinations. In Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics. Chicago, IL, A011287.
97. Niwa, T., 1986. Metabolic profiling with gas chromatography - mass spectrometry and its application to clinical medicine. Journal of Chromatography 379, 3-26.
98. Oliver, D.J., Nikolau, B., Wurtele, E.S., 2002. Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metabolic Engineering 4, 98-106.
99. Oliver, S., 2002. Demand management in cells. Nature 418, 33-34.
100. Oliver, S., 1997. Yeast as a navigational aid in genome analysis. Microbiololgy 143, 1483-1487.
101. Oliver, S.G., Winson, M.K., Kell, D.B., Baganz, F., 1998. Systematic functional analysis of the yeast genome. Trends in Biotechnology 16, 373-378.
102. Palsson, B., 2000. The challenges of in silico biology. Nature Biotechnology 18, 1147-1150.
103. Pritchard, L., Kell, D.B., 2002. Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. European Journal of Biochemistry 269, 3894-3904.
104. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., Berden, J.A., Brindle, K.M., Kell, D.B., Rowland, J.J., Westerhoff, H.V., van Dam, K., Oliver, S.G., 2001. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnology 19, 45-50.
105. Ratcliffe, R.G., Shachar-Hill, Y., 2001. Probing plant metabolism with NMR. Annual Review of Plant Physiology and Plant Molecular Biology 52, 499-526.
106. Roberts, J.K.M., 2000. NMR adventures in the metabolic labyrinth within plants. Trends in Plant Science 5, 30-34.
107. Roessner, U., Luedemann, A., Brust, D., Fiehn, O., Linke, T., Willmitzeer Fernie, A.R., 2001. Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. The Plant Cell 13, 11-29.
108. Roessner, U., Wagner, C., Kopka, J., Trethewey, R.N., Willmitzer, L., 2000. Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. The Plant Journal 23, 131-142.
109. Sauter, H., Lauer, M., Fritsch, H., 1991. Metabolic profiling of plants a new diagnostic technique. In: Baker, D.R., Fenyes, J.G., Moberg, W.K. (Eds.), American Chemical Society Symposium Series No. 443. American Chemical Society, Washington DC, pp. 288-299.
110. Schomburg, I., Chang, A., Schomburg, D., 2002. BRENDA, enzyme data and metabolic information. Nucleic Acids Research 30, 47-49.
111. Selkov, E., Basmanova, S., Gaasterland, T., Goryanin, I., Gretchkin, Y., Maltsev, N., Nenashev, V., Overbeek, R., Panyushkina, E., Pronevitch, L., Selkov Jr., E., Yunus, I., 1996. The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Research 24, 26-28.
112. Shaw, A.D., Winson, M.K., Woodward, A.M., McGovern, A.C., Davey, H.M., Kaderbhai, N., Broadhurst, D., Gilbert, R.J., Taylor, J., Timmins, E.M., Goodacre, R., Kell, D.B., Alsberg, B.K., Rowland, J.J., 2000. Rapid analysis of high-dimensional bioprocesses using multivariate spectroscopies and advanced chemometrics. Advances in Biochemical Engineering/Biotechnology 66, 83-113.
113. Smith, R.D., Loo, J.A., Ogorzalek-Loo, R.R., Busman, M., Udseth, H.R., 1991. Principles and practice of electrospray ionization-mass spectrometry for large polypeptides and proteins. Mass Spectrometry Reviews 31, 472-485.
114. Soga, Y., Ueno, Y., Naraoka, H., Ohashi, Y., Tomita, M., Nishioka, T., 2002. Simultaneous determination of anionic intermediates for Bcillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Analytical Chemistry 74, 2233-2239.
115. Somerville, C., Dangl, J., 2000. Plant biology in 2010. Science 290, 2077-2078.
116. Somerville, C., Somerville, S., 1999. Plant functional genomics. Science 285, 380-383.
117. Srere, P.A., Ovádi, J., 1990. Enzyme-enzyme interactions and their metabolic role. FEBS Letters 268, 360-364.
118. Stashenko, E.E., Acosta, R., Martinez, J.R., 2000. High-resolution gas-chromatographic analysis of the secondary metabolites obtained by subcritical-fluid extraction from Colombian rue (Ruta graveolens L.). Journal of Biochemical and Biophysical Methods 43, 379-390.
119. Stitt, M., Lilley, R.M., Gerhardt, R., Heldt, H.W., 1989. Metabolite levels in specific cells and subcellular comparments of plant leaves. Methods in Enzymology 174, 518-550.
120. Sumner, L.W., Duran, A.L., Huhman, D.H., Smith, J.T., 2002. Metabolomics: a developing and integral component in functional genomic studies of Medicago truncatula. In: Romeo, J.T., Dixon, R.A. (Eds.), Recent Advances in Phytochemistry, Vol. 36. Pergamon, Oxford, UK, pp. 31-61.
121. Sumner, L.W., Paiva, N.L., Dixon, R.A., Geno, P.W., 1996. HPLC-Continuous-flow liquid secondary ion mass spectrometry of flavonoid glycosides in leguminous plant extracts. Journal of Mass Spectrometry 31, 472-485.
122. Swayne, D.F., Cook, D., Buja, A., 1998. XGobi: interactive dynamic data visualization in the X Window System. Journal of Computational and Graphical Statistics 7, 113-130.
123. Tabachnick, B. G., Fidell, L. S., 1983. Using Multivariate Statistics. Harper & Row, New York, pp. 509.
124. Teusink, B., Baganz, F., Westerhoff, H.V., Oliver, S.G., 1998. Metabolic control analysis as a tool in the elucidation of the function of novel genes. Methods in Microbiology 26, 297-336.
125. Teusink, B., Passarge, J., Reijenga, C.A., Esgalhado, E., van der Weijden, C.C., Schepper, M., Walsh, M.C., Bakker, B.M., van Dam, K., Westerhoff, H.V., Snoep, J.L., 2000. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. European Journal of Biochemistry 267, 5313-5329.
126. The Arabidopsis Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
127. The EU Arabidopsis Genome Project, 1998. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485-488.
128. Thiellement, H., Bahrman, N., Damerval, C., Plomion, C., Rossingnol, M., Santoni, V., de Vienne, D., Zivy, M., 1999. Proteomics for genetic and physiological studies in plants. Electrophoresis 20, 2013-2026.
129. Thompson, J.A., Markey, S.P., 1975. Quantitative metabolic profiling of urinary organic acids by gas chromatography-mass spectrometry: comparison of isolation methods. Analytical Chemistry 47, 1313-1321.
130. Tolstikov, V.V., Fiehn, O., 2002. Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Analytical Biochemistry 301, 298-307.
131. Törönen, P., Kolehmainen, M., Wong, G., Castrén, E., 1999. Analysis of gene expression data using self-organizing maps. FEBS Letters 451, 142-146.
132. Trethewey, R.N., Krotzky, A.J., Willmitzer, L., 1999. Metabolic profiling: a Rosetta Stone for genomics? Current Opinion in Plant Biology 2, 83-85.
133. Trethewey, R.N., 2001. Gene discovery via metabolic profiling. Current Opinions in Biotechnology 12, 135-138.
134. Tweeddale, H., Notley-McRobb, L., Ferenci, T., 1998. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("Metabolome") analysis. Journal of Bacteriology 180, 5109-5116.
135. Umbreit, W.W., 1952. Metabolic Maps. Burgess Publishing Company, Minneapolis, MN.
136. Vaidyanathan, S., Kell, D.B., Goodacre, R., 2001. Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification. Journal of the American Society for Mass Spectrometry 13, 118-128.
137. van Wijk, K.J., 2001. Update on plant proteomics. Challenges and prospects of plant proteomics. Plant Physiology 126, 501-508.
138. Velculescu, V.E., Zhang, L., Vogelstein, B., Kinzlet, K.W., 1995. Serial analysis of gene expression. Science 270, 484-487.
139. Venter, J.C., et al., 2001. The Human Genome. Science 291, 1304-1351.
140. Voirin, B., Bayet, C., 1996. Developmental changes in the monoterpene composition of Menthaxpiperita leaves from individual peltate trichomes. Phytochemistry 43, 573-580.
141. Voit, E.O., Radivoyevithc, T., 2000. Biochemical systems analysis of genome-wide expression data. Bioinformatics 16, 1023-1037.
142. von Röpenack, E., Parr, A., Schulze-Lefert, P., 1998. Structural analyses and dynamics of soluble and cell wall-bound phenolics in a broad spectrum resistance to the powdery mildew fungus in barley. Journal of Biological Chemistry 273, 9013-9022.
143. Vrbanac, J.J., Braselton, W.E.J., Holland, J.F., Sweeley, C.C., 1982. Automated qualitative and quantitative metabolic profiling analysis of urinary steroids by gas chromatography-mass spectrometry-data system. Journal of Chromatography 239, 265-276.
144. Weigel, D., Ahn, J.H., Blazquez, M.A., Borewitz, J., Christensen, S.K., Fankhauser, C., Ferrandiz, C., Kardailsky, I., Malanchaurvil, E.J., Neff, M.M., Nguyen, J.T., Sato, S., Wang, Z.-H., Xia, Y., Dixon, R.A., Harrison, M.J., Lamb, C.J., Yanofsky, M.F., Chory, J., 2000. Activation tagging in Arabidopsis. Plant Physiology 122, 1003-1013.
145. Wesley, V.S., Helliwell, C.A., Smith, N.A., Wang, M.B., Rouse, D.T., Liu, Q., Gooding, P.S.S.P.S., Abbott, D., Stoutjesdijk, P.A., Robinson, S.P., Gleave, A.P., Green, A.G., Waterhouse, P.M., 2001. Construct design for efficient, effective and high-throughput gene silencing in plants. The Plant Journal 27, 581-590.
146. Wittig, U., De Beuckelaer, A., 2001. Analysis and comparison of metabolic pathway databases. Briefings in Bioinformatics 2, 126-142.
147. Wolf, D., Gray, C.P., de Saizieu, A., 2000. Visualising gene expression in its metabolic context. Briefings in Bioinformatics 1, 297-304.
148. Woolf, T.F., Black, A., Sedman, A., Chang, T., 1992. Metabolic disposition of the non-steroidal anti-inflammatory agent isoxicam in man. European Journal of Drug Metabolism and Pharmacokinetics 17, 21-27.
149. Yu, J., et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92.
150. Yu, O., Jung, W., Shi, J., Croes, R.A., Fader, G.M., McGonigle, B., Odell, J.T., 2000. Production of the isoflavones genistein and daidzein in non-legume dicot and monocot tissues. Plant Physiology 124, 781-794.