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Open Access Software

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

Gregor Rot1, Anup Parikh23, Tomaz Curk1, Adam Kuspa34, Gad Shaulsky23 and Blaz Zupan13*

Author Affiliations

1 Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia

2 Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA

3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

4 Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA

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BMC Bioinformatics 2009, 10:265  doi:10.1186/1471-2105-10-265

Published: 25 August 2009

Abstract

Background

Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability.

Results

We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment.

Conclusion

dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.