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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: Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments.Challenges for analysis software as well as good practices are highlighted.We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

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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Gel image tiles before (a) and after (b) multiway histogram equalization. After the equalization, the difference in the highlighted spot (middle row, left and right images) is clearly visible as shown in the expression profile (c)
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Fig16: Gel image tiles before (a) and after (b) multiway histogram equalization. After the equalization, the difference in the highlighted spot (middle row, left and right images) is clearly visible as shown in the expression profile (c)

Mentions: For the presentation of an analysis, as well as throughout the whole process, going back to original images is often useful. Showing whole images or sections thereof in combination with the processed spot data (Fig. 16) is therefore a feature offered by all analysis packages. Let us start with the display of a single gel image. The gray level resolution of current imaging devices (usually 16 bit for 65,536 different values) is much higher than what a computer screen can display. Therefore, the 2-D gel images have to be adapted or enhanced by histogram manipulations that cause a certain loss of information.Fig. 16


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)

Gel image tiles before (a) and after (b) multiway histogram equalization. After the equalization, the difference in the highlighted spot (middle row, left and right images) is clearly visible as shown in the expression profile (c)
© Copyright Policy
Related In: Results  -  Collection

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

Fig16: Gel image tiles before (a) and after (b) multiway histogram equalization. After the equalization, the difference in the highlighted spot (middle row, left and right images) is clearly visible as shown in the expression profile (c)
Mentions: For the presentation of an analysis, as well as throughout the whole process, going back to original images is often useful. Showing whole images or sections thereof in combination with the processed spot data (Fig. 16) is therefore a feature offered by all analysis packages. Let us start with the display of a single gel image. The gray level resolution of current imaging devices (usually 16 bit for 65,536 different values) is much higher than what a computer screen can display. Therefore, the 2-D gel images have to be adapted or enhanced by histogram manipulations that cause a certain loss of information.Fig. 16

Bottom Line: Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments.Challenges for analysis software as well as good practices are highlighted.We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

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