CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. - CNRS - Centre national de la recherche scientifique Accéder directement au contenu
Article Dans Une Revue Nucleic Acids Research Année : 2012

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

Résumé

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.

Dates et versions

hal-00696900 , version 1 (14-05-2012)

Identifiants

Citer

Anna A Nikulova, Alexander V Favorov, Roman A Sutormin, Vsevolod J Makeev, Andrey A Mironov. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.. Nucleic Acids Research, 2012, 40 (12), pp.1-10. ⟨10.1093/nar/gks235⟩. ⟨hal-00696900⟩
101 Consultations
2 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More