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Correcting Distortions in 2D Gels - A Survey

Jussi Salmi, Tero Aittokallio, Tuula A. Nyman, Olli S. Nevalainen, Correcting Distortions in 2D Gels - A Survey. TUCS Technical Reports 653, Turku Centre for Computer Science, 2004.

Abstract:

Two-dimensional electrophoresis (2-DE) provides a rapid means for separating thousands of proteins from cell and tissue samples in one run. Although this powerful research tool has been enthusiastically applied in many fields of biomedical research, accurate analysis and interpretation of the data have provided many challenges. Several analysis steps are needed to convert the large amount of noisy data obtained with 2-DE into reliable and interpretable biological information. The goals of such analysis steps include accurate protein detection and quantification, as well as the identification of differentially expressed proteins between samples run on different gels. To achieve these goals, systematic errors such as geometric distortions between the gels must be corrected by using computer-assisted methods. A wide range of computer software has been developed, but no general consensus exists as standard for 2-DE data analysis protocol. The choice of the analysis approach is an important element depending both on the data and on the goals of the experiment. Therefore, basic understanding of the algorithms behind the software is required for optimal results. This review highlights some of the common themes in 2-DE data analysis, including protein spot detection and geometric image warping using both spot- and pixel-based approaches. Several computational strategies are overviewed and their relative merits and potential pitfalls discussed. This review is a preliminary and detailed version of our paper in the Journal of Chromatography [ASN04] concerning the warping techniques.

BibTeX entry:

@TECHREPORT{tSaAiNyNe04a,
  title = {Correcting Distortions in 2D Gels - A Survey},
  author = {Salmi, Jussi and Aittokallio, Tero and Nyman, Tuula A. and Nevalainen, Olli S.},
  number = {653},
  series = {TUCS Technical Reports},
  publisher = {Turku Centre for Computer Science},
  year = {2004},
  keywords = {2D gel electrophoresis, image registration, spot matching, spot detection},
  ISBN = {952-12-1487-2},
}

Belongs to TUCS Research Unit(s): Algorithmics and Computational Intelligence Group (ACI), Biomathematics Research Unit (BIOMATH)

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