Discovery of metabolite features for the modelling and analysis of high-resolution NMR spectra

International Journal of Data Mining and Bioinformatics

Volumn 2, Issue 2, 2008, Pages 176-192

  Cho, Hyun Woo ^a   Kim, Seoung Bum ^b   Jeong, Myong K ^c   Park, Youngja ^d   Miller, Nana Gletsu ^d   Ziegler, Thomas R ^d   Jones, Dean P ^d  

^a University of Tennessee Knoxville   (United States)

^b The University of Texas at Arlington   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics; Data mining; Feature selection; Metabolomics; Multivariate statistical analysis; NMR; Nuclear magnetic resonance; Orthogonal signal correction; OSC

Indexed keywords

EID: 47149086566     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2008.019097     Document Type: Article

References (35)

1. Barker, M. and Rayens, W. (2003) 'Partial least squares for discrimination', Journal of Chemometrics, Vol. 17, pp.166-173.
2. Bathen, T.F., Krane, J., Engan, T., Bjerve, K.S. and Axelson, D. (2000) 'Quantification of plasma lipids and apolipoproteins by use of proton NMR spectroscopy, multivariate and neural network analysis', NMR Biomed., Vol. 13, pp.271-288.
3. Beckonert, O., Bollard, M.E., Ebbels, T.M.D., Keun, H.C., Antti, H., Holmes, E., Lindon, J.C. and Nicholson, J.K. (2003) 'NMR-based metabonomic toxicity classification: Hierarchical cluster analysis and k-nearest-neighbour approaches', Analytica Chimica Acta, Vol. 490, pp.3-15.
4. Blanco, M., Coello, J., Eustaquio, A., Iturriaga, H. and Maspoch, S. (2000) 'Development and validation of a method for the analysis of a pharmaceutical preparation by near-infrared diffuse reflectance spectroscopy', Journal of Pharmaceutical Sciences, Vol. 88, pp.551-556.
5. Chen, L-F., Lio, H-Y.M., Ko, M-T., Lin, J-C. and Yu, G-J. (2000) 'A new LDA-based face recognition system which can solve the small sample size problem', Pattern Recognition, Vol. 33, pp.1713-1726.
6. Chiang, L.H., Russell, E.L. and Braatz, R.D. (2000) 'Fault diagnosis in chemical processes using Fisher discriminant analysis, discriminant partial least squares, and principal component analysis', Chemometrics and Intelligent Laboratory Systems, Vol. 50, pp.243-252.
7. Cortes, C. and Vapnik, V.N. (1995) 'Support vector networks', Machine Learning, Vol. 20, pp.273-297.
8. 1H NMR data', Chemometrics and Intelligent Laboratory Systems, Vol. 81, pp.50-59.
9. Fearn, T. (2000) 'On orthogonal signal correction', Chemometrics and Intelligent Laboratory Systems, Vol. 50, pp.47-52.
10. Goodarcre, R., York, E.V., Heald, J.K. and Scott, I.M. (2003) 'Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry', Phytochemistry, Vol. 62, pp.859-863.
11. Holmes, E. and Antti, H. (2002) 'Chemometric contributions to the evolution of metabonomics: Mathematical solutions to characterising and interpreting complex biological NMR spectra', Analyst, Vol. 127, pp.1549-1557.
12. Holmes, E., Nicholson, J.K. and Tranter, G. (2001) 'Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks', Chemical Research in Toxicology, Vol. 14, pp.182-191.
13. Hoskuldsson, A. (1998) 'PLS regression methods', Journal of Chemometrics, Vol. 2, pp.211-228.
14. Jansen, J.J., Hoefsloot, H.C.J., Boelens, H.F.M., Greef, J.V.D. and Smilde, A.K. (2004) 'Analysis of longitudinal metabolomics data', Bioinformatics, Vol. 20, pp.2438-2446.
15. Johnson, R.A. and Wichern, D.W. (2002) Applied Multivariate Statistical Analysis, Prentice-Hall, New York.
16. Kourti, T. (2005) 'Application of latent variable methods to process control and multivariate statistical process control in industry', International Journal of Adaptive Control and Signal Processing, Vol. 19, pp.213-246.
17. Kourti, T. and MacGregor, J.F. (1996) 'Multivariate SPC methods for process and product monitoring', Journal of Quality Technology, Vol. 28, pp.409-428.
18. Lee, G.C. and Woodruff, D.L. (2004) 'Beam search for peak alignment of NMR signals', Analytica Chimica Acta, Vol. 513, pp.413-416.
19. Lindon, J.C. (2004) 'Metabonomics - techniques and applications', Business Briefing: Future Drug Discovery, Vol. 2004, pp.1-6.
20. Lindon, J.C., Holmes, E. and Nicholson, J.K. (2001) 'Pattern recognition methods and applications in biomedical magnetic resonance', Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 39, pp.1-40.
21. Musumarra, G., Barresi, V., Condorelli, D.F., Fortuna, C.G. and Scire, S. (2004) 'Potentialities of multivariate approaches in genome-based cancer research: Identification of candidate genes for new diagnostics by PLS discriminant analysis', Journal of Chemometrics, Vol. 18, pp.125-132.
22. Nicholson, J.K., Connelly, J., Lindon, J.C. and Holmes, E. (2002) 'Metabonomics: A platform for studying drug toxicity and gene function', Nature Reviews Drug Discovery, Vol. 1, pp.153-161.
23. Nicholson, J.K., Lindon, J.C. and Holms, E. (1999) 'Metabonomics: Understanding the metabolic responses of living systems to pathophysiological stimuli via multi-variate statistical analysis of biological NMR spectroscopic data', Xenobiotica, Vol. 29, pp.1181-1189.
24. Qin, S.J. (2003) 'Statistical process monitoring: Basics and beyond', Journal of Chemometrics, Vol. 17, pp.480-502.
25. Shao, X., Wang, F., Chen, D. and Su, Q. (2004) 'A method for near-infrared spectral clibration of complex plant samples with wavelet transform and elimination of uninformative variables', Analytical and Bioanalytical Chemistry, Vol. 378, pp.1382-1387.
26. Sjoblom, J., Svensson, O., Josefson, M., Kullberg, H. and Wold, S. (1998) 'An evaluation of orthogonal signal correction applied to calibration transfer of near infrared spectra', Chemometrics and Intelligent Laboratory Systems, Vol. 44, pp.229-244.
27. 1H nuclear magnetic resonance-based metabonomic technique for the analysis of the biochemical effects of dietary isoflavones on human plasma profile', Analytical Biochemistry, Vol. 323, pp.197-204.
28. Sun, J. (1997) 'Statistical analysis of NIR data: Data pretreatment', Journal of Chemometrics, Vol. 11, pp.525-532.
29. Tapp, H.S., Defernez, M. and Kemsley, E.K. (2003) 'FTIR spectroscopy and multivariate analysis can distinguish geographical origin of extra virgin olive oil', Journal of Agricultural and Food Chemistry, Vol. 51, pp.6110-6115.
30. Umetrics AB (2005) SIMCA-P and SIMCA-P+ User Guide and Tutorial, Umetrics, Umeå, Sweden.
31. Wang, Y.L., Bollard, M.E., Keun, H., Antti, H., Beckonert, O., Ebbels, T.M., Lindon, J.C., Holmes, E., Tang, H.R. and Nicholson, J.K. (2003) 'Spectral editing and pattern recognition methods applied to high-resolution magic-angle spinning H-1 nuclear magnetic resonance spectroscopy of liver tissues', Analytical Biochemistry, Vol. 322, pp.26-32.
32. Wang, Y.L., Holmes, E., Nicholson, J.K., Cloarec, O., Chollet, J., Tanner, M., Singer, B.H. and Utzinger, J. (2004) 'Metabonomic investigations in mice infected with Schistosoma mansoni: An approach for biomarker identification', Proc. Natl. Acad. Sci. USA, Vol. 101, pp.12676-12681.
33. Westerhuis, J.A., de Jong, S. and Smilde, A.K. (2001) 'Direct orthogonal signal correction', Chemometrics and Intelligent Laboratory Systems Vol. 56, pp.13-25.
34. Wold, S., Antti, H., Lindgren, F. and Öhman, J. (1998) 'Orthogonal signal correction of near-infrared spectra', Chemometrics and Intelligent Laboratory Systems, Vol. 44, pp.175-185.
35. Yang, J., Frangia, A.F. and Yang, J. (2004) 'A new kernel Fisher discriminant algorithm with application to face recognition', Neurocomputing, Vol. 56, pp.415-421.