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Bioinformatics Advance Access published online on June 28, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm333
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases.

Duccio Cavalieri 1,*, Cinzia Castagnini 1,#, Simona Toti 1,2,#, Karolina Maciag 1, Thomas Kelder 3, Luca Gambineri 4, Samuele Angioli 4 and Piero Dolara 1

1Department of Preclinical and Clinical Pharmacology, University of Florence, Florence, Italy
2Department of Statistics, University of Florence, Florence, Italy
3BIGCAT Bioinformatics, University of Maastricht, Maastricht, The Netherlands
4Inspect.it, Capolona (Arezzo), Italy

*To whom correspondence should be addressed. Prof. Duccio Cavalieri, E-mail: duccio.cavalieri{at}unifi.it


  Abstract

Motivation: Eu.Gene Analyzer is an easy-to-use, standalone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Eu.Gene supports a variety of array platforms, organisms and pathway ontologies, transparently deals with multiple nomenclature systems and seamlessly integrates data from different sources. Two different statistical methods, the Fisher Exact Test and the Gene Set Enrichment Analysis (GSEA), are implemented to identify biological pathways transcriptionally affected under experimental conditions. A suite of tools is offered to define, visualize and share custom non-redundant pathway sets.

In conclusion, Eu.Gene Analyzer is a new software application that takes advantage of information from multiple pathway databases to build a comprehensive interpretation of experimental results in a simple, intuitive environment.

Availability: Download of Eu.Gene Analyzer Java version is available free of charge for academic users. Please visit the web page: http://www.ducciocavalieri.org/bio/Eugene.htm

Supplementary information: http://www.ducciocavalieri.org/bio/Eugene/Suppl_Inf.

Associate Editor: Prof. David Rocke

# These authors equally contributed to this work.

Received on April 19, 2007; revised on June 15, 2007; accepted on June 17, 2007

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