GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data

Detalhes bibliográficos
Autor(a) principal: Carvalho, Paulo C.
Data de Publicação: 2009
Outros Autores: Fischer, Juliana S. G., Chen, Emily I., Domont, Gilberto B., Carvalho, Maria G. C., Degrave, Wim M., Yates, John R., Barbosa, Valmir C.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/31032
Resumo: Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de janeiro, RJ, Brasil / The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA.
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spelling Carvalho, Paulo C.Fischer, Juliana S. G.Chen, Emily I.Domont, Gilberto B.Carvalho, Maria G. C.Degrave, Wim M.Yates, John R.Barbosa, Valmir C.2019-01-15T11:38:05Z2019-01-15T11:38:05Z2009CARVALHO, Paulo C. et al. GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Science, v. 7, n. 6, p. 1-11, Feb. 2009.1477-5956https://www.arca.fiocruz.br/handle/icict/3103210.1186/1477-5956-7-6engBioMed CentralGO ExplorerFerramenta de ontologia genéticaDados de proteômica de espingardaInterpretaçãoGO ExplorerGene-ontology toolShotgun proteomics dataInterpretationGO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics datainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de janeiro, RJ, Brasil / The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA.The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA / Universidade Federal do Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil.The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA / Stony Brook University. Department of Pharmacological Sciences. Stony Brook, NY, USA.Universidade Federal do Rio de Janeiro. Instituto de Química. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ. Brasil.The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA.Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de Janeiro, RJ, Brasil.Background: Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge. Results: Here we present a new algorithm, termed GO Explorer (GOEx), that leverages the gene ontology (GO) to aid in the interpretation of proteomic data. GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions. Moreover, it is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. Its usefulness is demonstrated by applying it to help interpret the effects of perillyl alcohol, a natural chemotherapeutic agent, on glioblastoma multiform cell lines (A172). We used a new multi-surfactant shotgun proteomic strategy and identified more than 2600 proteins; GOEx pinpointed key sets of differentially expressed proteins related to cell cycle, alcohol catabolism, the Ras pathway, apoptosis, and stress response, to name a few. Conclusion: GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/31032/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALwimM_degrave_etal_IOC_2009.pdfwimM_degrave_etal_IOC_2009.pdfapplication/pdf4097995https://www.arca.fiocruz.br/bitstream/icict/31032/2/wimM_degrave_etal_IOC_2009.pdf42956ca4de7ccc6e8abba064e396c291MD52TEXTwimM_degrave_etal_IOC_2009.pdf.txtwimM_degrave_etal_IOC_2009.pdf.txtExtracted texttext/plain48661https://www.arca.fiocruz.br/bitstream/icict/31032/3/wimM_degrave_etal_IOC_2009.pdf.txt6aa86510bb421c34d3cbe76c586f5fe7MD53icict/310322023-09-05 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dc.title.pt_BR.fl_str_mv GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
title GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
spellingShingle GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
Carvalho, Paulo C.
GO Explorer
Ferramenta de ontologia genética
Dados de proteômica de espingarda
Interpretação
GO Explorer
Gene-ontology tool
Shotgun proteomics data
Interpretation
title_short GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
title_full GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
title_fullStr GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
title_full_unstemmed GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
title_sort GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
author Carvalho, Paulo C.
author_facet Carvalho, Paulo C.
Fischer, Juliana S. G.
Chen, Emily I.
Domont, Gilberto B.
Carvalho, Maria G. C.
Degrave, Wim M.
Yates, John R.
Barbosa, Valmir C.
author_role author
author2 Fischer, Juliana S. G.
Chen, Emily I.
Domont, Gilberto B.
Carvalho, Maria G. C.
Degrave, Wim M.
Yates, John R.
Barbosa, Valmir C.
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Carvalho, Paulo C.
Fischer, Juliana S. G.
Chen, Emily I.
Domont, Gilberto B.
Carvalho, Maria G. C.
Degrave, Wim M.
Yates, John R.
Barbosa, Valmir C.
dc.subject.other.pt_BR.fl_str_mv GO Explorer
Ferramenta de ontologia genética
Dados de proteômica de espingarda
Interpretação
topic GO Explorer
Ferramenta de ontologia genética
Dados de proteômica de espingarda
Interpretação
GO Explorer
Gene-ontology tool
Shotgun proteomics data
Interpretation
dc.subject.en.pt_BR.fl_str_mv GO Explorer
Gene-ontology tool
Shotgun proteomics data
Interpretation
description Universidade Federal do Rio de Janeiro. Programa de Engenharia de Sistemas e Ciência da Computação. Rio de janeiro, RJ, Brasil / The Scripps Research Institute. Department of Chemical Physiology. La Jolla, USA.
publishDate 2009
dc.date.issued.fl_str_mv 2009
dc.date.accessioned.fl_str_mv 2019-01-15T11:38:05Z
dc.date.available.fl_str_mv 2019-01-15T11:38:05Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv CARVALHO, Paulo C. et al. GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Science, v. 7, n. 6, p. 1-11, Feb. 2009.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/31032
dc.identifier.issn.pt_BR.fl_str_mv 1477-5956
dc.identifier.doi.none.fl_str_mv 10.1186/1477-5956-7-6
identifier_str_mv CARVALHO, Paulo C. et al. GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Science, v. 7, n. 6, p. 1-11, Feb. 2009.
1477-5956
10.1186/1477-5956-7-6
url https://www.arca.fiocruz.br/handle/icict/31032
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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