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The state of the art in the analysis of two-dimensional gel electrophoresis images.

Berth M, Moser FM, Kolbe M, Bernhardt J - Appl. Microbiol. Biotechnol. (2007)

Bottom Line: Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments.We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results.Challenges for analysis software as well as good practices are highlighted.

View Article: PubMed Central - PubMed

Affiliation: DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany.

ABSTRACT
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

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Related in: MedlinePlus

Protein labeling, staining, and tagging techniques for the selective detection of proteins. By multiplexing detection approaches, image analysis may relate different subsets of the proteome such as phosphorylated or glycosylated proteins
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Fig3: Protein labeling, staining, and tagging techniques for the selective detection of proteins. By multiplexing detection approaches, image analysis may relate different subsets of the proteome such as phosphorylated or glycosylated proteins

Mentions: Various techniques are available to make the separated spots detectable (Fig. 3). A direct method that suggests itself is the detection of the UV-induced autofluorescence of proteins (Roegener et al. 2003). Unfortunately, it is still not available for routine analysis, although it generates promising results.Fig. 3


The state of the art in the analysis of two-dimensional gel electrophoresis images.

Berth M, Moser FM, Kolbe M, Bernhardt J - Appl. Microbiol. Biotechnol. (2007)

Protein labeling, staining, and tagging techniques for the selective detection of proteins. By multiplexing detection approaches, image analysis may relate different subsets of the proteome such as phosphorylated or glycosylated proteins
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2279157&req=5

Fig3: Protein labeling, staining, and tagging techniques for the selective detection of proteins. By multiplexing detection approaches, image analysis may relate different subsets of the proteome such as phosphorylated or glycosylated proteins
Mentions: Various techniques are available to make the separated spots detectable (Fig. 3). A direct method that suggests itself is the detection of the UV-induced autofluorescence of proteins (Roegener et al. 2003). Unfortunately, it is still not available for routine analysis, although it generates promising results.Fig. 3

Bottom Line: Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments.We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results.Challenges for analysis software as well as good practices are highlighted.

View Article: PubMed Central - PubMed

Affiliation: DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany.

ABSTRACT
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

Show MeSH
Related in: MedlinePlus