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Registros recuperados: 12
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A comprehensive manually-curated compendium of bovine transcription factors. Repositório Alice
SOUZA, M. M. de; ZERLOTINI NETO, A.; GEISTLINGER, L.; TIZIOTO, P. C.; TAYLOR, J. F.; ROCHA, M. I. P.; DINIZ, W. J. S.; COUTINHO, L. L.; REGITANO, L. C. de A..
Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a contextdependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: DNA bovino; Expressão gênica; Gene expression in cattle; Gene expression regulation.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1102174
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A comprehensive manually-curated compendium of bovine transcription factors. Repositório Alice
SOUZA, M. M. de; ZERLOTINI NETO, A.; GEISTLINGER, L.; TIZIOTO, P. C.; TAYLOR, J. F.; ROCHA, M. I. P.; DINIZ, W. J. S.; COUTINHO, L. L.; REGITANO, L. C. de A..
Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a contextdependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: DNA bovine; Gene expression in cattle; Gene expression regulation.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1101203
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CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes. Repositório Alice
SILVA, V. da; RAMOS, M.; GROENEN, M.; CROOIJMANS, R.; JOHANSSON, A.; REGITANO, L. C. de A.; COUTINHO, L.; ZIMMER, R.; WALDRON, L.; GEISTLINGER, L..
Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied acrossdifferent species for association with diseases and production traits. Established protocols for experimental detection andcomputational inference of CNVs from SNP array and next-generation sequencing data are available. We present theCNVRangerR/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis ofCNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with func-tional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genomic hybridization; Structural genomic; Expressão gênica; Fenótipos quantitativos; Quantitative phenotypes.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115536
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Co-expression network analysis identifies genes associated with iron content in bovine muscle. Repositório Alice
DINIZ, W. J. da S.; CESAR, A. S. M.; GEISTLINGER, L.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; ROCHA, M. I. P.; LIMA, A. O. de; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..
Editores: Luiz Lehmann Coutinho, ESALQ/USP; Luciana Correia de Almeida Regitano, Embrapa Pecuária Sudeste; Gerson Barreto Mourão, ESALQ/USP; Aline Silva Mello Cesar, ESALQ/USP; Bárbara Silva Vignato, FZEA/USP; Mirele Daiana Poleti, ESALQ/USP; Wellison Jarles da Silva Diniz, UFSCar.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Gene expression; Network analysis; Systems biology.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075630
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Co-expression network analysis identifies genes associated with meat tenderness. Repositório Alice
DINIZ, W. J. da S.; CESAR, A. S. M.; GEISTLINGER, L.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; ROCHA, M. I. P.; LIMA, A. O. de; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..
Tenderness is an important trait of meat quality and is known to be influenced by several factors including genetic composition.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Gene expression; Network analysis; System biology.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1080848
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Detection of Co-expressed pathway modules associated with mineral concentration and meat quality in nelore cattle. Repositório Alice
DINIZ, W. J. S.; MAZZONI, G.; COUTINHO; BANERJEE, P.; GEISTLINGER, L.; CESAR, A. S. M.; BERTOLINI. F.; AFONSO, J.; OLIVEIRA, P. S. N.; TIZIOTO, P. C.; KADARMIDEEN, H. N.; REGITANO, L. C. de A..
Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: AMPK pathway; Co-expression analysis; RNA sequencing; Tenderness; Gordura Animal; Gado de Corte; Intramuscular fat; Beef quality; Beef cattle.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1107117
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Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. Repositório Alice
SILVA, V. H. da; REGITANO, L. C. de A.; GEISTLINGER, L.; PÉRTILLE, F.; GIACHETTO, P. F.; BRASSALOTI, R. A.; MOROSINI, N. S.; ZIMMER, R.; COUTINHO, L. L..
Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina1 High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing 6.5% of the genome. Comparing our results with previous studies revealed an overlap in 1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genômica; Maciez da carne; CNV; Nelore; Gado Nelore; Meat tenderness.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1055112
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Identification of a pleiotropic locus for beef quality and feed efficiency in cattle using bi-trait genome-wide association analysis. Repositório Alice
BUSS, C. E.; PETRINI, J.; MOURAO, G. B.; GEISTLINGER, L.; WOLF, J. B.; DINIZ, W. J. da S.; ROCHA, M. I. P.; AFONSO, J.; LIMA, A. O. de; TIZIOTO, P. C.; TULLIO, R. R.; ANDRADE, B. G.; COUTINHO, L. L.; REGITANO, L. C. de A..
Editores: Luiz Lehmann Coutinho, ESALQ/USP; Luciana Correia de Almeida Regitano, Embrapa Pecuária Sudeste; Gerson Barreto Mourão, ESALQ/USP; Aline Silva Mello Cesar, ESALQ/USP; Bárbara Silva Vignato, FZEA/USP; Mirele Daiana Poleti, ESALQ/USP; Wellison Jarles da Silva Diniz, UFSCar.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Lipolysis; Feed efficiency; Pleiotropy; Genome?wide association.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075651
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Identification of pleiotropic loci for daily weight gain and intramuscular fat in cattle using bivariate genome-wide association analysis. Repositório Alice
BUSS, C. E.; DINIZ, W. J. da S.; ANDRADE, B. G.; LIMA, A. O. de; GEISTLINGER, L.; AFONSO, J.; TULLIO, R. R.; TIZIOTO, P. C.; PETRINI, J.; COUTINHO, L. L.; WOLF, J. B.; MOURAO, G. B.; REGITANO, L. C. de A..
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Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Feed efficiency; Pleiotropy; Transcription factor.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1079239
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Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. Repositório Alice
CESAR, A. S. M.; REGITANO, L. C. de A.; REECY, J. M.; POLETI, M. D.; OLIVEIRA, P. S. N.; OLIVEIRA, G. B. de; MOREIRA, G. C. M.; MUDADU, M. de A.; TIZIOTO, P. L.; KOLTES, J. E.; Fritz-Waters, E.; KRAMER, L.; GARRICK, D.; BEIKI, H.; GEISTLINGER, L.; MOURÃO, G. B.; ZERLOTINI NETO, A.; COUTINHO, L. L..
Background: Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Expressão gênica; EQTL; Ácidos graxos; Doenças metabólicas; Expression quantitative trait loci; Gene expression; Fatty acids; Mammals; Metabolic diseases.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1102203
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Potential regulatory elements on PCDH7 gene affecting residual feed intake in Nelore cattle. Repositório Alice
LIMA, A. O. de; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; GEISTLINGER, L.; ROCHA, M. I. P.; DINIZ, W. J. da S.; AFONSO, J.; BUSS, C. E.; PETRINI, J.; MOURAO, G. B.; COUTINHO, L. L.; REGITANO, L. C. de A..
Editores: Luiz Lehmann Coutinho, ESALQ/USP; Luciana Correia de Almeida Regitano, Embrapa Pecuária Sudeste; Gerson Barreto Mourão, ESALQ/USP; Aline Silva Mello Cesar, ESALQ/USP; Bárbara Silva Vignato, FZEA/USP; Mirele Daiana Poleti, ESALQ/USP; Wellison Jarles da Silva Diniz, UFSCar.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Residual feed intake; Promoter; Transcription factor; SNPs.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075636
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Widespread modulation of gene expression by copy number variation in skeletal muscle. Repositório Alice
GEISTLINGER, L.; SILVA, V. H. da; CESAR, A. S. M.; TIZIOTO, P. C.; WALDRON, L.; ZIMMER, R.; REGITANO, L. C. de A.; COUTINHO, L. L..
Copy number variation (CNV) is a frequently observed deviation from the diploid state due to duplication or deletion of genomic regions. Although intensively analyzed for association with diseases and production traits, the specific mechanisms and extent by which such variations affect the phenotype are incompletely understood. We present an integrative study on CNV and genome-wide gene expression in Brazilian Bos indicus cattle. We analyzed CNVs inferred from SNP-chip data for effects on gene expression measured with RNA-seq in skeletal muscle samples of 183 steers. Local effects, where expression changes coincided with CNVs in the respective genes, were restricted to immune genes. Distal effects were attributable to several high-impact CNVs that...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Agricultural genetics; Nellore cattle; Gene expression.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086932
Registros recuperados: 12
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