Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS)

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Staab, Jennifer M ^a,b   O'Connell, Thomas M ^b,c   Gomez, Shawn M ^a,d  

^a Brooks Computer Science Building   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c Hamner UNC Center for Drug Safety Sciences   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETTER PERFORMANCE; CHEMICAL SHIFT POSITION; CHEMICAL SHIFT VARIATIONS; CONSENSUS ALIGNMENT; LONGITUDINAL STUDY; METABOLITE CONCENTRATIONS; PAIR-WISE COMPARISON; REFERENCE SPECTRUM;

CHEMICAL SHIFT;

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

PROTEOME;

ARTICLE; COMPUTER PROGRAM; METABOLOMICS; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STATISTICS;

MAGNETIC RESONANCE SPECTROSCOPY; METABOLOMICS; PROTEOME; SOFTWARE; STATISTICS AS TOPIC;

EID: 77952301941     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-123     Document Type: Article

References (15)

1. Nicholson JK, Lindon JC, Holmes E. Metabonomics: Understanding the Metabolic Responses of Living Systems to Pathophysiological Stimuli via Multivariate Statistical Analysis of Biological NMR Spectroscopic Data. Xenobiotica 1999,
2. Robertson DG. Metabonomics in Toxicology: A Review. Toxicological Sciences 2005,
3. Gartland K, Beddell C, Lindon J, Nicholson J. Application of pattern recognition methods to the analysis and classification of toxicological data derived from proton nuclear magnetic resonance spectroscopy of urine. Mol Pharmacol 1991, 39(5):629-642.
4. Anthony M, Sweatman B, Beddell C, Lindon J, Nicholson J. Pattern recognition classification of the site of nephrotoxicity based on metabolic data derived from proton nuclear magnetic resonance spectra of urine. Mol Pharmacol 1994, 46:199-211.
5. Wong JWH, Durante C, Cartwright HM. Application of Fast Fourier Transform Cross-Correlation for the Alignment of Large Chromatographic and Spectral Datasets. Analytical Chemistry 2005, 77(17):5655-5661. 10.1021/ac050619p, 16131078.
6. America AHP, Cordewener JHG. Comparative LC-MS: A landscape of peaks and valleys. Proteomics 2008, 8(4):731-749. 10.1002/pmic.200700694, 18297651.
7. Wu W, Daszykowski M, Walczak B, Sweatman BC, Connor SC, Haselden JN, Crowther DJ, Gill RW, Lutz MW. Peak Alignment of Urine NMR Spectra Using Fuzzy Warping. Journal of Chemical Information and Modeling 2006, 46(2):863-875. 10.1021/ci050316w, 16563018.
8. Kim S, Wang Z, Duran CM. A Bayesian Approach for the Alignment of High-Resolution NMR spectra. Proceedings of the INFORMS Artificial Intelligence and Data Mining Workshop, Pittsburgh, PA, USA 2006, 1-6.
9. Torgrip RJO, Åberg KM, Karlberg B, Jacobsson SP. Peak alignment using reduced set mapping. Journal of Chemometrics 2003, 17(11):573-582.
10. Veselkov KA, Lindon JC, Ebbels TMD, Crockford D, Volynkin VV, Holmes E, Davies DB, Nicholson JK. Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery. Analytical Chemistry 2009, 81:56-66. 10.1021/ac8011544, 19049366.
11. Savorani F, Tomasi G, Engelsen S. icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. Journal of Magnetic Resonance 2010, 202(2):190-202. 10.1016/j.jmr.2009.11.012, 20004603.
12. Bradford BU, O'Connell TM, Han J, Kosyk O, Shymonyak S, Ross PK, Winnike J, Kono H, Rusyn I. Metabolomic profiling of a modified alcohol liquid diet model for liver injury in the mouse uncovers new markers of disease. Toxicology and Applied Pharmacology 2008, 232(2):236-243. 10.1016/j.taap.2008.06.022, 2583460, 18674555.
13. Cloarec O, Dumas ME, Craig A, Barton RH, Trygg J, Hudson J, Blancher C, Gauguier D, Lindon JC, Holmes E, Nicholson J. Statistical Total Correlation Spectroscopy: An Exploratory Approach for Latent Biomarker Identification from Metabolic 1H NMR Data Sets. Analytical Chemistry 2005, 77(5):1282-1289. 10.1021/ac048630x, 15732908.
14. Wiklund S, Johansson E, Sjostrom L, Mellerowicz EJ, Edlund U, Shockcor JP, Gottfries J, Moritz J, Trygg J. Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. Analytical Chemistry 2008, 80:115-122. 10.1021/ac0713510, 18027910.
15. Sasic S, Muszynski A, Ozaki Y. A New Possibility of the Generalized Two-Dimensional Correlation Spectroscopy. 1. Sample-Sample Correlation Spectroscopy. Journal of Physical Chemistry A 2000, 104(27):6380-6387.