Open Access Highly Accessed Software

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

Ola Kristoffer Øye1, Katarina M Jørgensen2, Sigrun M Hjelle2, André Sulen2, Dag Magne Ulvang1 and Bjørn Tore Gjertsen23*

Author Affiliations

1 Christian Michelsen Research AS, P.O. Box 60315892 Bergen, Norway

2 Department of Clinical Science, Hematology Section, University of Bergen, Bergen, Norway

3 Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway

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BMC Bioinformatics 2013, 14:215  doi:10.1186/1471-2105-14-215

Published: 6 July 2013

Abstract

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.

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