Avoiding spots detection in analysis of electrophoretic gel images

Chemometrics and Intelligent Laboratory Systems

Volumn 104, Issue 1, 2010, Pages 2-7

  Daszykowski, M ^a   Bierczynska Krzysik, A ^b   Silberring, J ^c   Walczak, B ^a  

^a UNIVERSITY OF SILESIA   (Poland)

^b INDUSTRIAL CHEMISTRY RESEARCH INSTITUTE   (Poland)

^c JAGIELLONIAN UNIVERSITY   (Poland)

Author keywords

Discriminant PLS; Image segmentation; Significance analysis

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE QUALITY; INFORMATION PROCESSING; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; STATISTICAL SIGNIFICANCE; TWO DIMENSIONAL GEL ELECTROPHORESIS; UNIVARIATE ANALYSIS;

EID: 78650179404     PISSN: 01697439     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemolab.2009.10.001     Document Type: Article

References (19)

1. Wheelock A.W., Buckpitt A.R. Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 2005, 26:4508-4520.
2. Campostrini N., Areces L.B., Rappsilber J., Pietrogrande M.C., Dondi F., Pastorino F., Ponzoni M., Righetti P.G. Spot overlapping in two-dimensional maps: a serious problem ignored for much too long. Proteomics 2005, 5:2385-2395.
3. Grove H., Hollung K., Uhlen A.K., Martens H., Færgestad 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.
4. Daszykowski M., Stanimirova I., Bodzon-Kulakowska A., Silberring J., Lubec G., Walczak B. The start-to-end processing of two-dimensional gel electrophoretic images. J. Chromatogr. A 2007, 1158:306-317.
5. Færgestad E.M., Rye M., Walczak B., Gidskehaug L., Wold J.P., Grove H., Jia X., Hollung K., Indahl U.G., Westad F., van den Berg F., Martens H. Pixel-based analysis of multiple images for the identification of changes: a novel approach applied to unravel proteome patters of 2-D electrophoresis gel images. Proteomics 2007, 7:3450-3461.
6. Rogers M., Graham J., Tonge R.P. Using statistical image models for objective evaluation of spot detection in two-dimensional gels. Proteomics 2003, 3:879-886.
7. Berth M., Moser F.M., Kolbe M., Berrnhardt J. The state of art in the analysis of two-dimensional gel electrophoresis images. App. Microbiol. Biotechnol. 2007, 76:1223-1243.
8. Pleissner K.P., Hoffmann F., Kriegel K., Wenk C., Wegner S., Sahlström A., Oswald H., Alt H., Fleck E. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases. Electrophoresis 1997, 20:755-765.
9. Hoffmann F., Kriegel K., Wenk C. An applied point pattern matching problem: comparing 2D patterns of protein spots. Discrete Appl. Math. 1999, 93:75-88.
10. Veeser S., Dunn M.J., Yang G.-Z. Multiresolution image registration for two-dimensional gel electrophoresis. Proteomics 2001, 1:856-870.
11. http://www.nonlinear.com.
12. Sternberg S.R. Biomedical image processing. IEEE Comput. 1983, 16:22-34.
13. Meyer F. Topographic distance and watershed lines. Signal Process. 1994, 38:113-125.
14. Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:5116-5121.
15. Daszykowski M., Wróbel M.S., Bierczynska-Krzysik A., Silberring J., Lubec G., Walczak B. Automatic preprocessing of electrophoretic images. Chemometr. Intell. Lab. Syst. 2009, 97:132-140.
16. Martens H., Næs T. Mutivariate Calibration 1989, John Wiley & Sons, Chichester, UK.
17. Massart D.L., Vandeginste B.G.M., Buydens L.M.C., de Jong S., Lewi P.J., Smeyers-Verbeke J. Handbook of Chemometrics and Qualimetrics, Part B 1998, 331-342. Elsevier, Amsterdam, The Netherlands.
18. Bierczynska-Krzysik A., Pradeep J.P., Silberring J., Kotlinska J., Dylag T., Cabatic M., Lubec G. Proteomic analysis of rat cerebral cortex, hippocampus and striatum after exposure to morphine. Int. J. Mol. Med. 2006, 18:775-784.
19. Kemsley E.K., Tapp H.S. OPLS filtered data can be obtained directly from non-orthogonalized PLS1. J. Chemom. 2009, 23:263-264.