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Open Access Research

Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli

Theresa Scharl12, Gerald Striedner2*, Florentina Pötschacher2, Friedrich Leisch3 and Karl Bayer2

Author Affiliations

1 Department of Statistics and Probability Theory, Vienna University of Technology, Wiedner Hauptstr. 8-10, A-1040 Vienna, Austria

2 Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria

3 Department of Statistics, University of Munich, Ludwigstr. 33, D-80539 Munich, Germany

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Microbial Cell Factories 2009, 8:37  doi:10.1186/1475-2859-8-37

Published: 15 July 2009

Abstract

Background

Interpretation of comprehensive DNA microarray data sets is a challenging task for biologists and process engineers where scientific assistance of statistics and bioinformatics is essential. Interdisciplinary cooperation and concerted development of software-tools for simplified and accelerated data analysis and interpretation is the key to overcome the bottleneck in data-analysis workflows. This approach is exemplified by gcExplorer an interactive visualization toolbox based on cluster analysis. Clustering is an important tool in gene expression data analysis to find groups of co-expressed genes which can finally suggest functional pathways and interactions between genes. The visualization of gene clusters gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results.

Results

In this study the interactive visualization toolbox gcExplorer is applied to the interpretation of E. coli microarray data. The data sets derive from two fedbatch experiments conducted in order to investigate the impact of different induction strategies on the host metabolism and product yield. The software enables direct graphical comparison of these two experiments. The identification of potentially interesting gene candidates or functional groups is substantially accelerated and eased.

Conclusion

It was shown that gcExplorer is a very helpful tool to gain a general overview of microarray experiments. Interesting gene expression patterns can easily be found, compared among different experiments and combined with information about gene function from publicly available databases.