Orthogonal filtered recoupled-STOCSY to extract metabolic networks associated with minor perturbations from NMR spectroscopy

Journal of Proteome Research

Volumn 10, Issue 9, 2011, Pages 4342-4348

  Blaise, Benjamin J ^a   Navratil, Vincent ^a,b   Emsley, Lyndon ^a   Toulhoat, Pierre ^a  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

correlation matrix; metabolic network; metabonomics; NMR; OSC filter; SRV; STOCSY

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; MATHEMATICAL ANALYSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHENOTYPE; PRIORITY JOURNAL; RECOUPLED STATISTICAL TOTAL CORRELATION SPECTROSCOPY; SPECTROSCOPY;

ANIMALS; CAENORHABDITIS ELEGANS; LEAST-SQUARES ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; MODELS, BIOLOGICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHENOTYPE; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY OF RESULTS; SYSTEMS BIOLOGY;

CAENORHABDITIS ELEGANS;

EID: 80052449437     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200489n     Document Type: Article

References (26)

1. Nicholson, J. K.; Lindon, J. C.; Holmes, E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Xenobiotica 1999, 29, 1181-1189
2. Bollard, M. E.; Stanley, E. G.; Lindon, J. C.; Nicholson, J. K.; Holmes, E. NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition NMR Biomed. 2005, 18, 143-162 (Pubitemid 40716122)
3. Bocobza, S. E.; Aharoni, A. Switching the light on plant riboswitches Trends Plant Sci. 2008, 13, 526-533
4. Mandal, M.; Breaker, R. R. Gene regulation by riboswitches Nat. Rev. Mol. Cell Biol. 2004, 5, 451-463 (Pubitemid 38745495)
5. Trygg, J.; Wold, S. Orthogonal projections to latent structures J. Chemom. 2002, 16, 119-128
6. Blaise, B. J.; Giacomotto, J.; Triba, M. N.; Toulhoat, P.; Piotto, M. Metabolic profiling strategy of Caenorhabditis elegans by whole-organism nuclear magnetic resonance J. Proteome Res. 2009, 8, 2542-2550
7. Blaise, B. J.; Giacomotto, J.; Elena, B.; Dumas, M. E.; Toullhoat, P. Metabotyping of Caenorhabditis elegans reveals latent phenotypes Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19808-19812
8. Lavine, B.; Workman, J. Chemometrics Anal. Chem. 2010, 82, 4699-4711
9. Lindon, J. C.; Holmes, E.; Bollard, M. E.; Stanley, E. G.; Nicholson, J. K. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis Biomarkers 2004, 9, 1-31 (Pubitemid 38660013)
10. Wold, S.; Esbensen, K.; Geladi, P. Principal component analysis Chemom. Intell. Lab. Syst. 1987, 2, 37-52
11. Wold, S.; Sjostrom, M.; Eriksson, L. PLS-regression: a basic tool of chemometrics Chemom. Intell. Lab. Syst. 2001, 58, 109-130 (Pubitemid 33033283)
12. Trygg, J. O2-PLS for qualitative and quantitative analysis in multivariate calibration J. Chemom. 2002, 16, 283-293
13. Wold, S.; Antti, H.; Lindgren, F.; Ohman, J. Orthogonal signal correction of near-infrared spectra Chemom. Intell. Lab. Syst. 1998, 44, 175-185 (Pubitemid 29016095)
14. Tapp, H. S.; Kemsley, E. K. Notes on the practical utility of OPLS Trends Anal. Chem. 2009, 28, 1322-1327
15. Anderssen, E.; Dyrstad, K.; Westad, F.; Martens, H. Reducing over-optimism in variable selection by cross-model validation Chemom. Intell. Lab. Syst. 2006, 84, 69-74 (Pubitemid 44708396)
16. Ebbels, T. M. D.; Keun, H. C.; Beckonert, O. P.; Bollard, M. E.; Lindon, J. C. Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach J. Proteome Res. 2007, 6, 4407-4422 (Pubitemid 350158516)
17. Blaise, B. J.; Shintu, L.; Elena, B.; Emsley, L.; Dumas, M. E. Statistical recoupling of variables prior to significance testing in nuclear magnetic resonance based metabonomics Anal. Chem. 2009, 81, 6242-6251
18. Cloarec, O.; Dumas, M. E.; Craig, A.; Barton, R. H.; Trygg, J. Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from 1H NMR data sets Anal. Chem. 2005, 77, 1282-1289 (Pubitemid 40327865)
19. Blaise, B. J.; Navratil, V.; Domange, C.; Shintu, L.; Dumas, M. E. Two-dimensional statistical recoupling for the identification of perturbed metabolic networks from NMR spectroscopy J. Proteome Res. 2010, 9, 4513-4520
20. Sands, C. J.; Coen, M.; Maher, A. D.; Ebbels, T. M. D.; Holmes, E. Statistical total correlation spectroscopy editing of 1H NMR spectra of biofluids: applicartion to drug metabolite profile identification and enhanced information recovery Anal. Chem. 2009, 81, 6458-6466
21. Robinette, S. L.; Veselkov, K. A.; Bohus, E.; Coen, M.; Keun, H. C. Cluster analysis statistical spectroscopy using nuclear magnetic resonance generated metabolic data sets from perturbed biological systems Anal. Chem. 2009, 81, 6581-6589
22. Alves, A. C.; Rantalainen, M.; Holmes, E.; Nicholson, J. K.; Ebbels, T. M. D. Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets Anal. Chem. 2009, 81, 2075-2084
23. Maher, A. D.; Cloarec, O.; Patki, P.; Craggs, M.; Holmes, E. Dynamic biochemical information recovery in spontaneous human seminal fluid reactions via 1H NMR kinetic statistical total correlation spectroscopy Anal. Chem. 2009, 81, 288-295
24. Sands, C. J.; Coen, M.; Ebbels, T. M. D.; Holmes, E.; Lindon, J. C. Data-driven approach for metabolite relationship recovery in biological 1H NMR data sets using iterative statistical total correlation spectroscopy Anal. Chem. 2011, 83, 2075-2082
25. Ogata, H.; Goto, S.; Sato, K.; Fujibuchi, W.; Bono, H. KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 1999, 27, 29-34 (Pubitemid 29209394)
26. Gerlee, P.; Lizana, L.; Sneppen, K. Pathway identification by network pruning in the metabolic network of Escherichia coli Bioinformatics 2009, 25, 3282-3288