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

Duccio Cavalieri; Cinzia Castagnini; Simona Toti; Karolina Maciag; Thomas Kelder; Luca Gambineri; Samuele Angioli; Piero Dolara

doi:10.1093/bioinformatics/btm333

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

Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, Piero Dolara

School of Medicine

Research output: Contribution to journal › Article › peer-review

34 Scopus citations

Abstract

Motivation: Eu.Gene Analyzer is an easy-to-use, stand-alone 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.

Original language	English (US)
Pages (from-to)	2631-2632
Number of pages	2
Journal	Bioinformatics
Volume	23
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/btm333
State	Published - Oct 1 2007

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btm333

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title = "Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases",

abstract = "Motivation: Eu.Gene Analyzer is an easy-to-use, stand-alone 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.",

author = "Duccio Cavalieri and Cinzia Castagnini and Simona Toti and Karolina Maciag and Thomas Kelder and Luca Gambineri and Samuele Angioli and Piero Dolara",

note = "Funding Information: This work was funded by the European Networks of Excellence NuGO (FOOD-2003-5063-60), Dc Thera (LSHB-CT-2004-512074), by a year 2007 grant from Cassa di Risparmio di Firenze at the {\textquoteleft}Noi per Voi{\textquoteright} association and by a grant from AIRC Milan, Italy. We thank Prof. Bruce Conklin, Dr Chris Evelo and Dr Andre Boorsma for the useful discussions.",

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doi = "10.1093/bioinformatics/btm333",

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AU - Cavalieri, Duccio

AU - Castagnini, Cinzia

AU - Toti, Simona

AU - Maciag, Karolina

AU - Kelder, Thomas

AU - Gambineri, Luca

AU - Angioli, Samuele

AU - Dolara, Piero

N1 - Funding Information: This work was funded by the European Networks of Excellence NuGO (FOOD-2003-5063-60), Dc Thera (LSHB-CT-2004-512074), by a year 2007 grant from Cassa di Risparmio di Firenze at the ‘Noi per Voi’ association and by a grant from AIRC Milan, Italy. We thank Prof. Bruce Conklin, Dr Chris Evelo and Dr Andre Boorsma for the useful discussions.

PY - 2007/10/1

Y1 - 2007/10/1

N2 - Motivation: Eu.Gene Analyzer is an easy-to-use, stand-alone 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.

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

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