Chicken skeletal muscle-associated macroarray for gene discovery
Autor(a) principal: | |
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Data de Publicação: | 2010 |
Outros Autores: | , , , , , |
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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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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1813546612177240064 |