GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76 000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 33; no. suppl-2; pp. W616 - W620
Main Authors:	Vaquerizas, Juan M., Conde, Lucía, Yankilevich, Patricio, Cabezón, Amaya, Minguez, Pablo, Díaz-Uriarte, Ramón, Al-Shahrour, Fátima, Herrero, Javier, Dopazo, Joaquín
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-07-2005 Oxford Publishing Limited (England)
Subjects:	Algorithms Gene Expression Profiling - methods Internet Oligonucleotide Array Sequence Analysis - methods Software Systems Integration User-Computer Interface
Online Access:	Get full text
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Summary:	The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76 000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.
Bibliography:	local:gki500 To whom correspondence should be addressed. Tel: +34 96 328 96 80; Fax: +34 96 328 97 01; Email: jdopazo@ochoa.fib.es ark:/67375/HXZ-MS17G7ZN-C istex:22533D886EE638B71BCDC4EDF029F009B2F539E1 ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 Present address: Juan M. Vaquerizas, Lucía Conde, Pablo Minguez, Fátima Al-Shahrour and Joaquín Dopazo, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013, Valencia, Spain
ISSN:	0305-1048 1362-4962
DOI:	10.1093/nar/gki500