The role of bioinformatics in two-dimensional gel electrophoresis

Andrew W. Dowsey, Michael J. Dunn, Guang Zhong Yang*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

153 Citations (Scopus)

Abstract

Over the last two decades, two-dimensional electrophoresis (2-DE) gel has established itself as the de facto approach to separating proteins from cell and tissue samples. Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research topic. The results of these analyses include accurate protein quantification, isoelectric point and relative molecular mass-estimation, and the detection of differential expression between samples run or different gels. Systematic errors such as current leakage and regional expression inhomogeneities are corrected for, followed by each protein spot in the gel being segmented and modelled for quantification. To assess differential expression of protein spots in different samples run on a series of two-dimensional gels, a number of image registration techniques for correcting geometric distortion have been proposed. This paper provides a comprehensive review of the computation techniques used in the analysis of 2-DE gels, together with a discussion of current and future trends in large scale analysis. We examine the pitfalls of existing techniques and highlight some of the key areas that need to be developed in the coming years, especially those related to statistical approaches based on multiple gel runs and image mining techniques through the use of parallel processing based on cluster computing and the grid technology.

Original languageEnglish
Pages (from-to)1567-1596
Number of pages30
JournalProteomics
Volume3
Issue number8
DOIs
Publication statusPublished - 1 Aug 2003

Keywords

  • Bioinformatics
  • Data mining
  • Review
  • Spot detection
  • Spot matching
  • Two-dimensional gel electrophoresis

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