Chicken skeletal muscle-associated macroarray for gene discovery

Detalhes bibliográficos
Autor(a) principal: Jorge, E. C.
Data de Publicação: 2010
Outros Autores: Melo, C. M. R., Rosario, M. F., Rossi, J. R. S., Ledur, M. C., Moura, Ana Silvia Alves Meira Tavares [UNESP], Coutinho, L. L.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.4238/vol9-1gmr712
http://hdl.handle.net/11449/14420
Resumo: Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.
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spelling Chicken skeletal muscle-associated macroarray for gene discoveryGallusGene expressionSkeletal muscleTissue-specific expressionMacro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Univ São Paulo, Dept Zootecnia, Escola Super Agr Luiz de Queiroz, Piracicaba, SP, BrazilUniversidade Federal de Santa Catarina (UFSC), Dept Aquicultura, Florianopolis, SC, BrazilEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Suinos & Aves, Genet & Melhoramento Anim, Concordia, SC, BrazilUniv Estadual Paulista, Dept Anim Prod, Fac Med Vet & Zootecnia Botucatu, Botucatu, SP, BrazilUniv Estadual Paulista, Dept Anim Prod, Fac Med Vet & Zootecnia Botucatu, Botucatu, SP, BrazilFunpec-editoraUniversidade de São Paulo (USP)Universidade Federal de Santa Catarina (UFSC)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Estadual Paulista (Unesp)Jorge, E. C.Melo, C. M. R.Rosario, M. F.Rossi, J. R. S.Ledur, M. C.Moura, Ana Silvia Alves Meira Tavares [UNESP]Coutinho, L. L.2013-09-30T18:28:27Z2014-05-20T13:41:38Z2013-09-30T18:28:27Z2014-05-20T13:41:38Z2010-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article188-207application/pdfhttp://dx.doi.org/10.4238/vol9-1gmr712Genetics and Molecular Research. Ribeirao Preto: Funpec-editora, v. 9, n. 1, p. 188-207, 2010.1676-5680http://hdl.handle.net/11449/1442010.4238/vol9-1gmr712WOS:000277326200014WOS000277326200014.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenetics and Molecular Research0,439info:eu-repo/semantics/openAccess2024-09-09T13:01:51Zoai:repositorio.unesp.br:11449/14420Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462024-09-09T13:01:51Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Chicken skeletal muscle-associated macroarray for gene discovery
title Chicken skeletal muscle-associated macroarray for gene discovery
spellingShingle Chicken skeletal muscle-associated macroarray for gene discovery
Jorge, E. C.
Gallus
Gene expression
Skeletal muscle
Tissue-specific expression
title_short Chicken skeletal muscle-associated macroarray for gene discovery
title_full Chicken skeletal muscle-associated macroarray for gene discovery
title_fullStr Chicken skeletal muscle-associated macroarray for gene discovery
title_full_unstemmed Chicken skeletal muscle-associated macroarray for gene discovery
title_sort Chicken skeletal muscle-associated macroarray for gene discovery
author Jorge, E. C.
author_facet Jorge, E. C.
Melo, C. M. R.
Rosario, M. F.
Rossi, J. R. S.
Ledur, M. C.
Moura, Ana Silvia Alves Meira Tavares [UNESP]
Coutinho, L. L.
author_role author
author2 Melo, C. M. R.
Rosario, M. F.
Rossi, J. R. S.
Ledur, M. C.
Moura, Ana Silvia Alves Meira Tavares [UNESP]
Coutinho, L. L.
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de São Paulo (USP)
Universidade Federal de Santa Catarina (UFSC)
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Jorge, E. C.
Melo, C. M. R.
Rosario, M. F.
Rossi, J. R. S.
Ledur, M. C.
Moura, Ana Silvia Alves Meira Tavares [UNESP]
Coutinho, L. L.
dc.subject.por.fl_str_mv Gallus
Gene expression
Skeletal muscle
Tissue-specific expression
topic Gallus
Gene expression
Skeletal muscle
Tissue-specific expression
description Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.
publishDate 2010
dc.date.none.fl_str_mv 2010-01-01
2013-09-30T18:28:27Z
2013-09-30T18:28:27Z
2014-05-20T13:41:38Z
2014-05-20T13:41:38Z
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.uri.fl_str_mv http://dx.doi.org/10.4238/vol9-1gmr712
Genetics and Molecular Research. Ribeirao Preto: Funpec-editora, v. 9, n. 1, p. 188-207, 2010.
1676-5680
http://hdl.handle.net/11449/14420
10.4238/vol9-1gmr712
WOS:000277326200014
WOS000277326200014.pdf
url http://dx.doi.org/10.4238/vol9-1gmr712
http://hdl.handle.net/11449/14420
identifier_str_mv Genetics and Molecular Research. Ribeirao Preto: Funpec-editora, v. 9, n. 1, p. 188-207, 2010.
1676-5680
10.4238/vol9-1gmr712
WOS:000277326200014
WOS000277326200014.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Genetics and Molecular Research
0,439
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 188-207
application/pdf
dc.publisher.none.fl_str_mv Funpec-editora
publisher.none.fl_str_mv Funpec-editora
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv repositoriounesp@unesp.br
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