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...

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Detalles Bibliográficos
Autor: Vaquerizas, Juan M.
Tipo de recurso: artículo
Fecha de publicación:2005
País:España
Institución:Universidad Autónoma de Madrid
Repositorio:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglés
OAI Identifier:oai:repositorio.uam.es:10486/678305
Acceso en línea:http://hdl.handle.net/10486/678305
https://dx.doi.org/10.1093/nar/gki500
Access Level:acceso abierto
Palabra clave:Gene Expression
Analysis
GEPAS
Experiments
Microarray data analysis
Medicina
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spelling GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression dataVaquerizas, Juan M.Gene ExpressionAnalysisGEPASExperimentsMicroarray data analysisMedicinaThe 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. © 2005 Oxford University Press.J.M.V. is supported by the Formacion del Personal Investigador fellowship program from the Ministerio de Educación y Ciencia. L.C. is supported by a fellowship from the Fondo de Investigacion Sanitaria (grant PI020919). P.M. is supported by a grant from Genoma España and Canada Genome.This work is partly supported by grants from Fundación Ramón Areces, Fundació La Caixa, Fundación BBVA and RTICCC from the FISOxford University PressDepartamento de BioquímicaFacultad de Medicina20052005-07-01research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/678305https://dx.doi.org/10.1093/nar/gki500reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/6783052026-06-23T12:46:27Z
dc.title.none.fl_str_mv GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
title GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
spellingShingle GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
Vaquerizas, Juan M.
Gene Expression
Analysis
GEPAS
Experiments
Microarray data analysis
Medicina
title_short GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
title_full GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
title_fullStr GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
title_full_unstemmed GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
title_sort GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
dc.creator.none.fl_str_mv Vaquerizas, Juan M.
author Vaquerizas, Juan M.
author_facet Vaquerizas, Juan M.
author_role author
dc.contributor.none.fl_str_mv Departamento de Bioquímica
Facultad de Medicina
dc.subject.none.fl_str_mv Gene Expression
Analysis
GEPAS
Experiments
Microarray data analysis
Medicina
topic Gene Expression
Analysis
GEPAS
Experiments
Microarray data analysis
Medicina
description 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. © 2005 Oxford University Press.
publishDate 2005
dc.date.none.fl_str_mv 2005
2005-07-01
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10486/678305
https://dx.doi.org/10.1093/nar/gki500
url http://hdl.handle.net/10486/678305
https://dx.doi.org/10.1093/nar/gki500
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
repository.name.fl_str_mv
repository.mail.fl_str_mv
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