CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.
Nucleic Acids Res
; 40(12): e93, 2012 Jul.
Article
en En
| MEDLINE
| ID: mdl-22422836
ABSTRACT
Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Regulación de la Expresión Génica
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Análisis de Secuencia de ADN
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Elementos Reguladores de la Transcripción
Tipo de estudio:
Diagnostic_studies
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Evaluation_studies
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Prognostic_studies
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Risk_factors_studies
Límite:
Animals
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2012
Tipo del documento:
Article
País de afiliación:
Rusia