Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data

BMC Bioinformatics

Ola Kristoffer Øye³  Katarina M Jørgensen¹  Sigrun M Hjelle¹  André Sulen¹  Dag Magne Ulvang³  Bjørn Tore Gjertsen² 

[1] Department of Clinical Science, Hematology Section, University of Bergen, Bergen, Norway

[2] Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway

[3] Christian Michelsen Research AS, P.O. Box 60315892 Bergen, Norway

关键词: p53 activation;    Spearman rank correlation;    Pixel-by-pixel analysis;    Two-dimensional gel electrophoresis;   

Others  :  1087821
DOI  :  10.1186/1471-2105-14-215

 received in 2013-03-15, accepted in 2013-07-01,  发布年份 2013

【 摘 要 】

Background

Two-dimensional gel electrophoresis (2DE) is a powerful technique for studying protein isoforms and their modifications. Existing commercial 2D image analysis tools rely on spot detection that limits analysis of complex protein profiles, e.g. spot appearance/disappearance or overlapping spots. Pixel-by-pixel correlation analysis, an analysis technique for identifying relations between protein patterns in gel images and external variables, can overcome such limitations in spot analysis.

Results

We have implemented the first publically available pixel-by-pixel correlation analysis tool, the software Gel2DE. 2D immunoblot time course analysis of p53 protein stabilization in response to ionizing irradiation shows that pixel-by-pixel analysis can yield an overall activation biosignature for p53, despite changing spots shape, size and position.

Conclusions

Pixel-by-pixel correlation of aligned 2D images permits analysis of complex protein patterns. We anticipate that the Gel2DE correlation software will be a useful tool for future bioinformatics discoveries through 2D gel electrophoresis.

【 授权许可】

   
2013 Øye et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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