Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

Journal of Proteome Research

Volumn 7, Issue 3, 2008, Pages 1288-1296

  Jensen, Kristina Nedenskov ^b   Jessen, Flemming ^b   Jørgensen, Bo M ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Foss   (United States)

Author keywords

2D electrophoresis; Jack knife; PLS regression; Proteomics; Scaling

Indexed keywords

PROTEIN;

ARTICLE; AUTOSCALING; DATA ANALYSIS; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MULTIVARIATE ANALYSIS; NONHUMAN; PREFILTERING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SALMON; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; TWO DIMENSIONAL GEL ELECTROPHORESIS; ISOLATION AND PURIFICATION; METHODOLOGY;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; MULTIVARIATE ANALYSIS; PROTEINS;

EID: 44449102829     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr700800s     Document Type: Article

References (25)

1. Dowsey, A. W.; Dunn, M. J.; Yang, G.-Z. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 2003, 3,1567-1596.
2. Gustafsson, J. S.; Caesar, R.; Glasbey, C. A.; Blomberg, A.; Rudemo, M. Statistical exploration of variation in quantitative two-dimensional gel electrophoresis data. Proteomics 2004, 4, 3791-3799.
3. Wheelock, Åμ. M.; Buckpitt, A. R. Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 2005, 26, 4508-4520.
4. Wheelock, Åμ. M.; Goto, S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev. Proteomics 2006, 3, 129-142.
5. Jessen, F.; Lametsch, R.; Bendixen, E.; Kjærsgård, I. V. H.; Jørgensen, B. M. Extracting information from two-dimensional electrophoresis gels by partial least squares regression. Proteomics 2002, 2, 32-35.
6. Radzikowski, L.; Nesic, L; Hansen, H. B.; Jacobsen, S.; Søndergaard, I. Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis. Electrophoresis 2002, 23, 4157-4166.
7. Gottlieb, D. M.; Schultz, J.; Brunn, S. W.; Jacobsen, S.; Søndergaard, I. Multivariate approaches in plant science. Phytochemistry 2004, 65, 1531-1548.
8. Klenø, T. G.; Leonardsen, I. R.; Kjeldal, H. O.; Laursen, S. M.; Jensen, O. N.; Baunsgaard, D. Mechanism of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis. Proteomics 2004, 4, 868-880.
9. Marengo, E.; Robotti, E.; Righetti, P. G.; Campostrini, N.; Pascali, J.; Ponzoni, M.; Hamdan, M.; Astner, H. Study of protomic changes associated with healthy and tumoral murine samples in neuroblastoma by principal component analysis and classification methods. Clin. Chem. Acta 2004, 345, 55-67.
10. Marengo, E.; Robotti, E.; Cecconi, D.; Hamdan, M.; Scarpa, A.; Righetti, P. G. Identification of the regulatory proteins in human pancreatic cancers treated with trichostatin A by 2D-PAGE maps and multivariate statistical analysis. Anal. Bioanal. Chem. 2004, 379, 992-1003.
11. Schultz, J.; Gottlieb, D. M.; Petersen, M.; Nesic, L.; Jacobsen, S.; Søndergaard, I. Explorative data analysis of two-dimensional electrophoresis gels. Electrophoresis 2004, 25, 502-511.
12. Verhoeckx, K. C. M.; Caspari, M.; Bijlsma, S.; van der Greef, J.; Witkamp, R. F.; Doornbos, R. P.; Rodenburg, R. J. T. In search of secreted protein biomarkers for the anti-inflammatory effect of β2-adrenergic receptor agonists: Application of DIGE technology in combination with multivariate and univariate data analysis tools. J. Proteome Res. 2005, 4, 2015-2023.
13. Grove, H.; Hollung, K.; Uhlen, A. K.; Martens, H.; Faergestad, E. M. Challenges related to analysis of protein spot volumes from two-dimensional gel electrophoresis as revealed by replicate gels. J. Proteome Res. 2006, 5, 3399-3410.
14. Kjærsgård, I. V. K.; Nørrelykke, M. R.; Jessen, F. Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis. Proteomics 2006, 6, 1606-1618.
15. Jacobsen, S.; Grove, H.; Jensen, K. N.; Sørensen, H. A.; Jessen, F.; Hollung, K.; Uhlen, A. K.; Jørgensen, B. M.; Faergestad, E. M. Sondergaard, I. Multivariate analysis of two-dimensional gel electrophoresis protein patterns-Practical approaches. Electrophoresis 2007, 28, 1289-1299.
16. Karp, N. A.; Griffin, J. L.; Lilley, K. S. Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics. Proteomics 2005, 5, 81-90.
17. Martens, H.; Martens, M. Multivariate Analysis of Quality - an Introduction; John Wiley & Sons Ltd.: Chichester, 2001.
18. Martens, H.; Martens, M. Modified jack-knife estimation of parameter uncertainty in bilinear modeling by partial least squares regression (PLSR). Food Qual. Prefer. 2000, 11, 5-16.
19. Kjærsgård, I. V. K.; Jessen, F. Proteome analysis elucidating post mortem changes in cod (Gadus morhua) muscle proteins. J. Agric. Food Chem. 2003, 51, 3985-3991.
20. Whelehan, O. P.; Earll, M. E.; Johansson, E.; Toft, M.; Eriksson, L. Detection of ovarian cancer using chemometric analysis of proteomic profiles. Chemom. Intell. Lab. Syst. 2006, 84, 82-87.
21. Andersen, 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.
22. Jia, X.; Hildrum, K. I.; Westad, F.; Kummen, E.; Aass, L.; Hollung, K. Changes in enzymes associated with energy metabolism during the early post mortem period in Longissimus Thoracis bovine muscle analyzed by proteomics. J. Proteome Res. 2006, 5, 1763-1769.
23. Lilley, K. S.; Friedman, D. B. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1, 401-409.
24. Reinikainen, S.-P.; Höskuldsson, A. COVPROC method: strategy in modelling dynamic systems. J. Chemom. 2003, 17, 130-139.
25. Marengo, E.; Robotti, E.; Antonucci, F.; Gecconi, D.; Campostroni, N.; Righetti, P. G. Numerical approaches for the quantitative analysis of two-dimensinal maps: A review of commercial software and home-made systems. Proteomics 2005, 5, 654-666.