Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
23/08/2012 |
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Data da última atualização: |
08/01/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
LOBO, F. P.; RODRIGUES, M. R.; RODRIGUES, G. O. L.; HILÁRIO, H. O.; SOUZA, R. A.; TAUCH, A.; MIYOSHI, A.; FRANCO, G. C.; AZEVEDO, V.; FRANCO, G. R. |
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Afiliação: |
FRANCISCO PEREIRA LOBO, CNPTIA; MAÍRA R. RODRIGUES, UFMG; GISELE O. L. RODRIGUES, UFMG; HERON O. HILÁRIO, UFMG; RAONI A. SOUZA, Fundação Ezequiel Dias, MG; ANDREAS TAUCH, Bielefeld University; ANDERSON MIYOSHI, UFMG; GLAURA C. FRANCO, UFMG; VASCO AZEVEDO, UFMG; GLÓRIA R. FRANCO, UFMG. |
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Título: |
KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
Nucleic Acids Research, Oxford, v. 40, p. W491-W497, 2012. |
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DOI: |
10.1093/nar/gks490 |
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Idioma: |
Inglês |
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Conteúdo: |
The enrichment analysis is a standard procedure to interpret ?omics? experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org. |
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Palavras-Chave: |
Bioinformática; Ferramenta web; Genomas. |
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Thesagro: |
Atividade Enzimática. |
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Thesaurus NAL: |
Bioinformatics; Genome. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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Marc: |
LEADER 02413naa a2200313 a 4500
001 1932006
005 2020-01-08
008 2012 bl uuuu u00u1 u #d
024 7 $a10.1093/nar/gks490$2DOI
100 1 $aLOBO, F. P.
245 $aKOMODO$ba web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa.$h[electronic resource]
260 $c2012
520 $aThe enrichment analysis is a standard procedure to interpret ?omics? experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org.
650 $aBioinformatics
650 $aGenome
650 $aAtividade Enzimática
653 $aBioinformática
653 $aFerramenta web
653 $aGenomas
700 1 $aRODRIGUES, M. R.
700 1 $aRODRIGUES, G. O. L.
700 1 $aHILÁRIO, H. O.
700 1 $aSOUZA, R. A.
700 1 $aTAUCH, A.
700 1 $aMIYOSHI, A.
700 1 $aFRANCO, G. C.
700 1 $aAZEVEDO, V.
700 1 $aFRANCO, G. R.
773 $tNucleic Acids Research, Oxford$gv. 40, p. W491-W497, 2012.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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