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• W2071952037 abstract "The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used to raise hypotheses about regulation. However, these tools are generally used as black boxes, with default parameters. A systematic evaluation of optimal parameters for a footprint discovery strategy can bring a sizeable improvement to the predictions. We evaluate the performances of a footprint discovery approach based on the detection of over-represented spaced motifs. This method is particularly suitable for (but not restricted to) Bacteria, since such motifs are typically bound by factors containing a Helix-Turn-Helix domain. We evaluated footprint discovery in 368 Escherichia coli K12 genes with annotated sites, under 40 different combinations of parameters (taxonomical level, background model, organism-specific filtering, operon inference). Motifs are assessed both at the levels of correctness and significance. We further report a detailed analysis of 181 bacterial orthologs of the LexA repressor. Distinct motifs are detected at various taxonomical levels, including the 7 previously characterized taxon-specific motifs. In addition, we highlight a significantly stronger conservation of half-motifs in Actinobacteria, relative to Firmicutes, suggesting an intermediate state in specificity switching between the two Gram-positive phyla, and thereby revealing the on-going evolution of LexA auto-regulation. The footprint discovery method proposed here shows excellent results with E. coli and can readily be extended to predict cis-acting regulatory signals and propose testable hypotheses in bacterial genomes for which nothing is known about regulation." @default.
• W2071952037 created "2016-06-24" @default.
• W2071952037 creator A5054447627 @default.
• W2071952037 creator A5056821549 @default.
• W2071952037 date "2008-01-23" @default.
• W2071952037 modified "2023-10-07" @default.
• W2071952037 title "Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution" @default.
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• W2071952037 cites W1594677737 @default.
• W2071952037 cites W1639189531 @default.
• W2071952037 cites W1644055901 @default.
• W2071952037 cites W1777388788 @default.
• W2071952037 cites W1783384641 @default.
• W2071952037 cites W1897119929 @default.
• W2071952037 cites W1961265293 @default.
• W2071952037 cites W1974614108 @default.
• W2071952037 cites W1979136055 @default.
• W2071952037 cites W1984053739 @default.
• W2071952037 cites W1984984816 @default.
• W2071952037 cites W1993450828 @default.
• W2071952037 cites W1998300401 @default.
• W2071952037 cites W2003967338 @default.
• W2071952037 cites W2008900336 @default.
• W2071952037 cites W2009566340 @default.
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• W2071952037 cites W2025853251 @default.
• W2071952037 cites W2028487413 @default.
• W2071952037 cites W2032231928 @default.
• W2071952037 cites W2035895654 @default.
• W2071952037 cites W2037652809 @default.
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• W2071952037 cites W2096525273 @default.
• W2071952037 cites W2097396311 @default.
• W2071952037 cites W2097525601 @default.
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• W2071952037 doi "https://doi.org/10.1186/1471-2105-9-37" @default.
• W2071952037 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2248561" @default.
• W2071952037 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18215291" @default.
• W2071952037 hasPublicationYear "2008" @default.
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