A Probability based Pair Extension Method in Protein 2-DE Gel Image Analysis

Authors: Yanhua Jin, Won Suk Lee

Abstract:

The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

Keywords: Proteomics, spot-matching, two-dimensionalelectrophoresis.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1071446

References:

[1] Rabilloud T., "Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains", Proteomics, 2002, Vol. 2, pp.3-10.
[2] Mann, M., Hendrickson, R.C.; Pandey, A., "Analysis of Proteins and proteomes by mass spectrometry", Annu. Rev. Biochem. 2001, 70, pp.437-473.
[3] Steven P. G, Garry L. C., Y. Zhang, Y. Rochon and R. Aebersold. "Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology". PNAS, 2000, Vol. 97, No. 17, pp.9390-9395
[4] Rosengren A.T., Salmi J.M., Aittokallio T., Westerholm J.j Lahesmaa R., Nyman T.A and Nevalaien O.S., "Comparison of PDQuest and Progenesis software package in the analysis of two-dimensional electrophoresis gels", Proteomics, 2003, Vol. 3, pp.1936-1946.
[5] Rman B., Cheung A. and Martern M.R., "Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software package, Z3 and Melanie", Electrophoresis, 2001, Vol.23, pp.283-291.
[6] Aittokallio T., Salmi J., Nyman TA., Nevalainen OS, "Geometrical distortions in two-dimensional gels applicable correction methods", Journal o f Chromatography, 2005, Vol.815/1-2, pp.25-37.
[7] Gustafsson J.S., Blomberg A. and Rudemo M., "Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern", Electrophoresis, 2002, Vol.23, pp.1731-1744.
[8] R. Agrawal, R. Srikant, "Fast algorithms for Mining Association Rules", 1994, VLDB conference, Santiago, Chile.
[9] J. Han, J. Pei, J. Yin, "Mining Frequent Patterns without Candidate Generation", Proc. of SIGMOD, 2000, pp. 1-12.
[10] E. Omiecinski, "Alternative interest measures for mining associations", IEEE Trans. Knowledge and Data Engineering, 2003.
[11] Y. Jin, J. E. Shim and W. S. Lee, "Error Spot Filtering Method in Protein 2-DE Image Spot-Matching Operation", IADIS International Conference, 2007.