The application of MANOVA to analyse Arabidopsis thaliana metabolomic data from factorially designed experiments

Metabolomics

Volumn 3, Issue 4, 2007, Pages 517-530

  Johnson, Helen E ^a   Lloyd, Amanda J ^a   Mur, Luis A J ^a   Smith, Aileen R ^a   Causton, David R ^a  

^a ABERYSTWYTH UNIVERSITY   (United Kingdom)

Author keywords

Arabidopsis; Experimental design; MANOVA; Metabolomics

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; BOTRYOTINIA FUCKELIANA;

EID: 36048932994     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-007-0065-3     Document Type: Article

References (35)

1. Alsberg B.K., Wade W.G., Goodacre R. (1998) Chemometric analysis of diffuse reflectance-absorbance Fourier transform infrared spectra using rule induction methods: Application to the classification of Eubacterium species. Appl. Spectrosc. 52, 823-832
2. Bino R.J., Hall R.D., Fiehn O., et al (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9, 418-425
3. Bleecker A.B., Kende H. (2000) Ethylene: A gaseous signal molecule in plants. Annu. Rev. Cell. Dev. Biol. 16, 1-18
4. Bleecker A.B., Estelle M.A., Somerville C., Kende H. (1988) Insensitivity to ethylene conferred by a dominant mutation in Arabidopsis thaliana. Science 241, 1086-1089
5. Boyes D.C., Zayed A.M., Ascenzi R., et al (2001) Growth stage-based phenotypic analysis of Arabidopsis: A model for high throughput functional genomics in plants. Plant Cell 13, 1499-1510
6. Chatfield, C. and Collins, A.J. (1980) Introduction to Multivariate Analysis. Chapman and Hall
7. Chen J.J., Delongchamp R.R., Tsai C.A., et al (2004) Analysis of variance components in gene expression data. Bioinformatics 20(9), 1436-1446
8. Coombes, K.R. (2007). PCANOVA: Combining principal components with analysis of variance to access group structure. Technical report available online: http://bioinformatics.mdanderson.org/TechReports/ pca.pdf (Downloaded: 15/05/2007)
9. Daoyu Z., Lawes G.S. (2000) MANOVA and discriminant analyses of phenotypic data as a guide for parent selection in kiwifruit (Actinidia deliciosa) breeding. Euphytica 114, 151-157
10. Dunn W.B., Bailey N.J.C., Johnson H.E. (2005) Measuring the metabolome: current analytical technologies. Analyst 130, 606-625
11. Fernie A.R. (2003) Metabolome characterisation in plant system analysis. Funct. Plant Biol. 30, 111-120
12. Fiehn O., Kopka J., Dormann P., Altmann T., Tretheway R.N., Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18, 1157-1161
13. Goodacre R., Timmins E.M., Burton R., et al (1998) Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144, 1157-1170
14. Goodacre R., Timmins E.M., Rooney P.J., Rowland J.J., Kell D.B. (1996) Rapid identification of Streptococcus and Enterococcus species using diffuse reflectance-absorbance Fourier transform infrared spectroscopy and artificial neural networks. FEMS Microbiol. Lett. 140, 233-239
15. Goodacre R., Vaidyanathan S., Dunn W.B., Harrigan G.C., Kell D.B. (2004) Metabolomics by numbers: Acquiring and understanding global metabolite data. Trends Biotechnol. 22, 245-252
16. Gullberg J., Jonsson P., Nordstrom A., Sjostrom M., Moritz T. (2004) 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, 283-295
17. Guzman P., Ecker J.R. (1990) Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. Plant Cell 2, 513-523
18. Holtorf H., Guitton M., Reski R. (2002) Plant functional genomics. Naturwissenschaften 89, 235-249
19. 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. J. Chemometr. 19(9), 469-481
20. Johnson H.E., Broadhurst D., Goodacre R., Smith A.R. (2003) Metabolic fingerprinting of salt-stressed tomatoes. Phytochemistry 62, 919-928
21. Kieber J.J., Rothenberg M., Roman G., Feldmann K.A., Ecker J.R. (1993) CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72, 427-441
22. Langsrud Ø. (2002) 50-50 multivariate analysis of variance for collinear responses. Statistician 51(3), 305-317
23. Otto M. (1999) Chemometrics: Statistics and Computer Application in Analytical Chemistry. Wiley-VCH Weinheim, Germany
24. Quinn G.P., Keough M.J. (2002) Experimental Design and Data Analysis for Biologists. Cambridge University Press, Cambridge, UK
25. Penninckx I.A.M.A., Thomma B.P.H.J., Buchala A., Métraux J.-P., Broekaert W (1998) Cooperative activation of jasmonate and ethylene response pathways in parallel is required for induction of a plant defensin gene in Arabidopsis. Plant Cell 10, 2103-2114
26. Roessner U., Wagner C., Kopka J., Trethewey R.N., Willmitzer L. (2000) Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23, 131-142
27. Seahl H. (1964) Multivariate Statistical Analysis for Biologists. Methuen, London, UK
28. Schulz H., Baranska M., Belz H.H., Rosch P., Strehle M.A., Popp J. (2004) Chemotaxonomic characterisation of essential oil plants by vibrational spectroscopy measurements. Vib. Spectrosc. 35, 81-86
29. Smilde A.K., Jansen J.J., Hoefsloot H.C., Lamers R.J., van der Greef J., Timmerman M.E. (2005) ANOVA-simultaneous component analysis (ASCA): A new tool for analyzing designed metabolomics data. Bioinformatics 21(13), 3043-3048
30. Smith H., Gnanadesikan R., Hughes J.B. (1962) Multivariate analysis of variance (MANOVA). Biometrics 18(1), 22-41
31. Sumner L.W., Mendes P., Dixon R.A. (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62, 817-836
32. Thomma B.P.H.J., Eggermont K., Penninckx I.A.M.A., et al (1998) Separate jasmonate-dependent and salicylated dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens. Proc. Natl. Acad. Sci. U.S.A. 95, 15107-15111
33. Taylor J., King R.D., Altmann T., Fiehn O. (2002) Application of metabolomics to plant genotype discrimination using statistics and machine learning. Bioinformatics 18, S241-S248
34. Winson M.K., Goodacre R., Timmins E.M., et al (1997). Diffuse reflectance absorbance spectroscopy taking in chemometrics (DRASTIC). A hyperspectral FT-IR-based approach to rapid screening for metabolite overproduction. Anal. Chim. Acta 348, 273-282
35. Woeste K., Kieber J.J. (1998) The molecular basis of ethylene signalling in Arabidopsis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 352, 1431-1438