Individual differences in metabolomics: Individualised responses and between-metabolite relationships

Metabolomics

Volumn 8, Issue , 2012, Pages 94-104

  Jansen, Jeroen J ^a,b,c   Szymańska, Ewa ^a,b   Hoefsloot, Huub C J ^a,b   Smilde, Age K ^a,b  

^a NETHERLANDS METABOLOMICS CENTRE   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

Chemometrics; Glucosinolate; Herbivory; Individual difference; INDSCAL; Induced response; Multivariate data analysis; PARAFAC; Simultaneous component analysis

Indexed keywords

GLUCOBRASSICIN; GLUCOSINOLATE; NEOGLUCOBRASSICIN; UNCLASSIFIED DRUG;

ARTICLE; CABBAGE; CORRELATION COEFFICIENT; HERBIVORY; METABOLIC PARAMETERS; METABOLOMICS; MULTIVARIATE ANALYSIS; NONHUMAN; PERSONALIZED MEDICINE; PLANT METABOLISM; PLANT RESPONSE; PLANT ROOT; PLANT STRESS; PRINCIPAL COMPONENT ANALYSIS; SHOOT; SHOOT GROWTH; SIMULTANEOUS COMPONENT ANALYSIS; SPECIES DIFFERENCE;

BRASSICA OLERACEA VAR. CAPITATA;

EID: 84860380019     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-012-0414-8     Document Type: Article

References (36)

1. Bodnaryk, R. P. (1994). Potent effect of jasmonates on indole glucosinolates in oilseed rape and mustard. Phytochemistry, 35(2), 301-305.
2. Broeckling, C. D., Huhman, D. V., Farag, M. A., Smith, J. T., May, G. D., Mendes, P., et al. (2005). Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. Journal of Experimental Botany, 56(410), 323-336. doi: 10. 1093/jxb/eri058.
3. Carroll, J. D., & Chang, J. J. (1970). Analysis of individual differences in multidimensional scaling via an N-way generalization of "eckart-young" decomposition. Psychometrika, 35, 283-319.
4. Dall, S. R. X., Houston, A. I., & McNamara, J. M. (2004). The behavioural ecology of personality: Consistent individual differences from an adaptive perspective. Ecology Letters, 7(8), 734-739. doi: 10. 1111/j. 1461-0248. 2004. 00618. x.
5. Dunn, W. B., & Ellis, D. I. (2005). Metabolomics: Current analytical platforms and methodologies. Trac-Trends In Analytical Chemistry, 24(4), 285-294.
6. Dyrby, M., Baunsgaard, D., Bro, R., & Engelsen, S. B. (2005). Multiway chemometric analysis of the metabolic response to toxins monitored by NMR. Chemometrics and Intelligent Laboratory Systems, 76(1), 79.
7. Fahey, J. W., Zhang, Y. S., & Talalay, P. (1997). Broccoli sprouts: An exceptionally rich source of inducers of enzymes that protect against chemical carcinogens. P Natl Acad Sci USA, 94(19), 10367-10372.
8. Fisher, R. A. (1918). The correlation between relatives on the supposition of mendelian inheritance. Transactions of the Royal Society of Edinburgh, 52, 399-433.
9. Harshman, R. A., & Lundy, M. E. (1984). The PARAFAC model for three-way factor analysis and multidimensional scaling. In H. G. Law, C. W. Snyder, J. A. Hattie, & R. P. McDonald (Eds.), Research methods for multimode data analysis. New York: Praeger Publishers.
10. Herms, D. A., & Mattson, W. J. (1992). The dilemma of plants: To grow or defend. Quarterly Review of Biology, 67(3), 283-335.
11. Hopkins, R. J., van Dam, N. M., & van Loon, J. J. A. (2009). Role of glucosinolates in insect-plant relationships and multitrophic interactions. Annual Review of Entomology, 54(1), 57.
12. Jansen, J. J., Hoefsloot, H. C. J., Boelens, H. F. M., van der Greef, J., & Smilde, A. K. (2004). Analysis of longitudinal metabolomics data. Bioinformatics, 20, 2438-2446.
13. Jansen, J. J., Hoefsloot, H. C. J., van der Greef, J., Timmerman, M. E., Westerhuis, J. A., & Smilde, A. K. (2005). ASCA: Analysis of multivariate data obtained from an experimental design. Journal of Chemometrics, 19(9), 469-481.
14. Jansen, J. J., Smit, S., Hoefsloot, H. C. J., & Smilde, A. K. (2009a). The photographer and the greenhouse: How to analyze plant metabolomics data. Phytochemical Analysis, 21(1), 48-60.
15. Jansen, J. J., Szymańska, E., Hoefsloot, H. C. J., Jacobs, D., Strassburg, K., & Smilde, A. (2011). Between metabolite relationships: An essential aspect of metabolic change. Metabolomics, 1-11. doi: 10. 1007/s11306-011-0316-1.
16. Jansen, J. J., van Dam, N. M., Hoefsloot, H. C. J., & Smilde, A. K. (2009b). Crossfit analysis: a novel method to characterize the dynamics of induced plant responses. BMC Bioinformatics, 10(1), 425.
17. Kiers, H. A. L., & Ten Berge, J. M. F. (1994). Hierarchical relations between methods for simultaneous component analysis and a technique for rotation to a simple simultaneous structure. Brit J Math Stat Psy, 47, 109-126.
18. Lindon, J. C., Holmes, E., & Nicholson, J. K. (2000). Pattern Recognition methods and applications in biomedical magnetic resonance. Progress in Nuclear Magnetic Resonance Spectroscopy, 39, 1-40.
19. Millsap, R., & Meredith, W. (1988). Component analysis in cross-sectional and longitudinal data. Psychometrika, 53(1), 123-134. doi: 10. 1007/bf02294198.
20. Picard, F. J., & Bergeron, M. G. (2002). Rapid molecular theranostics in infectious diseases. [Review]. Drug Discovery Today, 7(21), 1092-1101.
21. Smilde, A. K., Bro, R., & Geladi, P. (2004). Multi-way analysis: Applications in the Chemical sciences (1st ed.). New York: Wiley.
22. Smilde, A. K., Jansen, J. J., Hoefsloot, H. C. J., Lamers, R., Greef, J., & Timmerman, M. E. (2005a). ANOVA-simultaneous component analysis (ASCA): A new tool for analyzing designed metabolomics data. Bioinformatics, 21, 3043-3048.
23. Smilde, A. K., Jansen, J. J., Hoefsloot, H. C. J., Lamers, R., van der Greef, J., & Timmerman, M. E. (2005b). ANOVA-simultaneous component analysis (ASCA): A new tool for analyzing designed metabolomics data. Bioinformatics, 21(13), 3043-3048.
24. Smit, S., Hoefsloot, H. C. J., & Smilde, A. K. (2008). Statistical data processing in clinical proteomics. Journal of Chromatography B, 866(1-2), 77-88.
25. Sokal, R. R., & Rohlf, F. J. (1995). Biometry (A series of books in biology). San Francisco: W. H Freeman and company.
26. Steppan, S. J., Phillips, P. C., & Houle, D. (2002). Comparative quantitative genetics: evolution of the G matrix. Trends in Ecology & Evolution, 17(7), 320-327.
27. Steuer, R., Kurths, J., Fiehn, O., & Weckwerth, W. (2003). Observing and interpreting correlations in metabolomic networks. Bioinformatics, 19(8), 1019-1026.
28. Ten Berge, J. M. F., Kiers, H. A. L., & van der Stel, V. (1992). Simultaneous component analysis. Statistica Applicata, 4, 377-392.
29. Timmerman, M. E., & Kiers, H. A. L. (2003). Four simultaneous component models of multivariate time series from more than one subject to model intraindividual and interindividual differences. Psychometrika, 86, 105-122.
30. Trygg, J., Holmes, E., & Lundstedt, T. (2007). Chemometrics in metabonomics. Journal of Proteome Research, 6(2), 469-479.
31. van Dam, N., Qiu, B.-L., Hordijk, C., Vet, L., & Jansen, J. (2010). Identification of biologically relevant compounds in aboveground and belowground induced volatile blends. Journal of Chemical Ecology, 36(9), 1006-1016. doi: 10. 1007/s10886-010-9844-9.
32. van Leur, H., Raaijmakers, C. E., & van Dam, N. M. (2006). A heritable glucosinolate polymorphism within natural populations of Barbarea vulgaris. Phytochemistry, 67(12), 1214-1223.
33. Ward, J. L., Forcat, S., Beckmann, M., Bennett, M., Miller, S. J., Baker, J. M., et al. (2010). The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv tomato. The Plant Journal, 63(3), 443-457. doi: 10. 1111/j. 1365-313X. 2010. 04254. x.
34. Weckwerth, W., Loureiro, M. E., Wenzel, K., & Fiehn, O. (2004). Differential metabolic networks unravel the effects of silent plant phenotypes. Proceedings of the National academy of Sciences of the United States of America, 101(20), 7809-7814.
35. Wu, W., Yuan, M., Zhang, Q., Zhu, Y., Yong, L., Wang, W., et al. (2011). Chemotype-dependent metabolic response to methyl jasmonate elicitation in Artemisia Annua. Planta Medica, 77(10), 1048-1053. doi: 10. 1055/s-0030-1250744.
36. Zwanenburg, G., Hoefsloot, H. C. J., Westerhuis, J. A., Jansen, J. J., & Smilde, A. K. (2010). ANOVA-principal component analysis and ANOVA-simultaneous component analysis: A comparison. Journal of Chemometrics, 25, 561-567. doi: 10. 1002/cem. 1400.