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Nucleic Acids Research 2006 34(Web Server issue):W486-W491; doi:10.1093/nar/gkl197
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Next station in microarray data analysis: GEPAS

David Montaner1,2, Joaquín Tárraga1,2, Jaime Huerta-Cepas1,2, Jordi Burguet1, Juan M. Vaquerizas1, Lucía Conde1, Pablo Minguez1, Javier Vera3, Sach Mukherjee4, Joan Valls5, Miguel A. G. Pujana5, Eva Alloza1, Javier Herrero6, Fátima Al-Shahrour1 and Joaquín Dopazo1,2,*

1 Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) Autopista del Saler 16, E46013, Valencia, Spain 2 Functional Genomics Node, INB CIPF, Autopista del Saler 16, E46013, Valencia, Spain 3 INB—BSC Jordi Girona 29, Edifici Nexus II, E-08034 Barcelona, Spain 4 Pattern Analysis and Machine Learning Group, Department of Engineering Science University of Oxford Oxford OX1 2JD, UK 5 Translational Research Laboratory, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet 08907 Barcelona, Spain 6 Ensembl Team, EMBL-EBI Hinxton, Cambridge, UK

*To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701; Email: jdopazo{at}cipf.es

Received February 14, 2006. Revised March 21, 2006. Accepted March 21, 2006.

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.


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