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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Pages (from-to)2631-2632
Number of pages2
JournalBioinformatics
Volume23
Issue number19
DOIs
StatePublished - Oct 1 2007
Externally publishedYes

Fingerprint

Gene Expression Data
Gene expression
Pathway
Genes
Databases
Gene
Gene Expression
Intuitive
Information Storage and Retrieval
Fisher's Exact Test
Microarray Data Analysis
Microarray Analysis
Terminology
Microarrays
Graphical user interfaces
Application programs
Ontology
Graphical User Interface
Statistical methods
Software

ASJC Scopus subject areas

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

Cite this

Cavalieri, D., Castagnini, C., Toti, S., Maciag, K., Kelder, T., Gambineri, L., ... Dolara, P. (2007). Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics, 23(19), 2631-2632. https://doi.org/10.1093/bioinformatics/btm333

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. / Cavalieri, Duccio; Castagnini, Cinzia; Toti, Simona; Maciag, Karolina; Kelder, Thomas; Gambineri, Luca; Angioli, Samuele; Dolara, Piero.

In: Bioinformatics, Vol. 23, No. 19, 01.10.2007, p. 2631-2632.

Research output: Contribution to journalArticle

Cavalieri, D, Castagnini, C, Toti, S, Maciag, K, Kelder, T, Gambineri, L, Angioli, S & Dolara, P 2007, 'Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases', Bioinformatics, vol. 23, no. 19, pp. 2631-2632. https://doi.org/10.1093/bioinformatics/btm333
Cavalieri D, Castagnini C, Toti S, Maciag K, Kelder T, Gambineri L et al. Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics. 2007 Oct 1;23(19):2631-2632. https://doi.org/10.1093/bioinformatics/btm333
Cavalieri, Duccio ; Castagnini, Cinzia ; Toti, Simona ; Maciag, Karolina ; Kelder, Thomas ; Gambineri, Luca ; Angioli, Samuele ; Dolara, Piero. / Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. In: Bioinformatics. 2007 ; Vol. 23, No. 19. pp. 2631-2632.
@article{4dbd1926d0d44fcf9eeee834bede782f,
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",
year = "2007",
month = "10",
day = "1",
doi = "10.1093/bioinformatics/btm333",
language = "English (US)",
volume = "23",
pages = "2631--2632",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "19",

}

TY - JOUR

T1 - Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases

AU - Cavalieri, Duccio

AU - Castagnini, Cinzia

AU - Toti, Simona

AU - Maciag, Karolina

AU - Kelder, Thomas

AU - Gambineri, Luca

AU - Angioli, Samuele

AU - Dolara, Piero

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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=35748935228&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35748935228&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btm333

DO - 10.1093/bioinformatics/btm333

M3 - Article

C2 - 17599938

AN - SCOPUS:35748935228

VL - 23

SP - 2631

EP - 2632

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 19

ER -