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dc.contributor.authorHarari, Oscar
dc.contributor.authorVal, Coral del
dc.contributor.authorRomero-Zaliz, Rocío
dc.contributor.authorShin, Dongwoo
dc.contributor.authorHuang, Henry
dc.contributor.authorGroisman, Eduardo A.
dc.contributor.authorZwir, Igor
dc.date.accessioned2013-10-18T08:49:56Z
dc.date.available2013-10-18T08:49:56Z
dc.date.issued2009
dc.identifier.citationHarari, O.; et al. Identifying promoter features of co-regulated genes with similar network motifs. BMC Bioinformatics 10(sup4): S1 (2009). [http://hdl.handle.net/10481/28447]es_ES
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10481/28447
dc.descriptionProceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2008, Philadelphia, PA, USA. 3–5 November 2008.es_ES
dc.description.abstractBackground: A large amount of computational and experimental work has been devoted to uncovering network motifs in gene regulatory networks. The leading hypothesis is that evolutionary processes independently selected recurrent architectural relationships among regulators and target genes (motifs) to produce characteristic expression patterns of its members. However, even with the same architecture, the genes may still be differentially expressed. Therefore, to define fully the expression of a group of genes, the strength of the connections in a network motif must be specified, and the cis-promoter features that participate in the regulation must be determined.es_ES
dc.description.abstractResults: We have developed a model-based approach to analyze proteobacterial genomes for promoter features that is specifically designed to account for the variability in sequence, location and topology intrinsic to differential gene expression. We provide methods for annotating regulatory regions by detecting their subjacent cis-features. This includes identifying binding sites for a transcriptional regulator, distinguishing between activation and repression sites, direct and reverse orientation, and among sequences that weakly reflect a particular pattern; binding sites for the RNA polymerase, characterizing different classes, and locations relative to the transcription factor binding sites; the presence of riboswitches in the 5'UTR, and for other transcription factors. We applied our approach to characterize network motifs controlled by the PhoP/PhoQ regulatory system of Escherichia coli and Salmonella enterica serovar Typhimurium. We identified key features that enable the PhoP protein to control its target genes, and distinct features may produce different expression patterns even within the same network motif.es_ES
dc.description.abstractConclusion: Global transcriptional regulators control multiple promoters by a variety of network motifs. This is clearly the case for the regulatory protein PhoP. In this work, we studied this regulatory protein and demonstrated that understanding gene expression does not only require identifying a set of connexions or network motif, but also the cis-acting elements participating in each of these connexions.es_ES
dc.description.sponsorshipThis research was supported in part by the Spanish Ministry of Science and Technology under project TIN2006-12879 and by Consejería de Innovacion, Investigación y Ciencia de la de la Junta de Andalucía under project TIC02788.es_ES
dc.language.isoenges_ES
dc.publisherBiomed Centrales_ES
dc.subjectComputational biologyes_ES
dc.subjectDNA-Directed RNA Polymeraseses_ES
dc.subjectEscherichia-colies_ES
dc.subjectRegulatory networkses_ES
dc.subjectSalmonella typhies_ES
dc.subjectTranscription factorses_ES
dc.titleIdentifying promoter features of co-regulated genes with similar network motifses_ES
dc.typeinfo:eu-repo/semantics/articlees_ES
dc.rights.accessRightsinfo:eu-repo/semantics/openAccesses_ES
dc.identifier.doi10.1186/1471-2105-10-S4-S1es_ES


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