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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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Related in: MedlinePlus

Consensus spot pattern applied to four gel images (a–d), before remodeling of spot shapes. The consensus spot pattern is generated by spot detection on the synthetic fusion image (e) which was computed from the original images
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Fig2: Consensus spot pattern applied to four gel images (a–d), before remodeling of spot shapes. The consensus spot pattern is generated by spot detection on the synthetic fusion image (e) which was computed from the original images

Mentions: For spot quantitation and building expression profiles, the consensus spot pattern is applied to all gel images of the experiment (Fig. 2). The image transformation (step 4) assures that all spots of the consensus pattern arrive at their correct position. A remodeling step makes sure that the predetermined spot boundaries from the consensus are adapted to the real gray levels observed on the target image. All boundaries of the consensus pattern can be found on every gel.


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)

Consensus spot pattern applied to four gel images (a–d), before remodeling of spot shapes. The consensus spot pattern is generated by spot detection on the synthetic fusion image (e) which was computed from the original images
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: Consensus spot pattern applied to four gel images (a–d), before remodeling of spot shapes. The consensus spot pattern is generated by spot detection on the synthetic fusion image (e) which was computed from the original images
Mentions: For spot quantitation and building expression profiles, the consensus spot pattern is applied to all gel images of the experiment (Fig. 2). The image transformation (step 4) assures that all spots of the consensus pattern arrive at their correct position. A remodeling step makes sure that the predetermined spot boundaries from the consensus are adapted to the real gray levels observed on the target image. All boundaries of the consensus pattern can be found on every gel.

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