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

hal.structure.identifierLomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou] [MSU]
hal.structure.identifierInstitute for Information Transmission Problems [IITP]
dc.contributor.authorNIKULOVA, Anna A
hal.structure.identifierJohns Hopkins University School of Medicine [Baltimore]
dc.contributor.authorFAVOROV, Alexander V
hal.structure.identifierLomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou] [MSU]
dc.contributor.authorSUTORMIN, Roman A
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorMAKEEV, Vsevolod J
hal.structure.identifierLomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou] [MSU]
hal.structure.identifierInstitute for Information Transmission Problems [IITP]
dc.contributor.authorMIRONOV, Andrey A
dc.date.accessioned2024-04-15T09:45:27Z
dc.date.available2024-04-15T09:45:27Z
dc.date.issued2012-03-15
dc.identifier.issn0305-1048
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197921
dc.description.abstractEnIdentification 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.
dc.language.isoen
dc.publisherOxford University Press
dc.title.enCORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.
dc.typeArticle de revue
dc.identifier.doi10.1093/nar/gks235
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.journalNucleic Acids Research
bordeaux.page1-10
bordeaux.volume40
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.issue12
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.peerReviewedoui
hal.identifierhal-00696900
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00696900v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nucleic%20Acids%20Research&rft.date=2012-03-15&rft.volume=40&rft.issue=12&rft.spage=1-10&rft.epage=1-10&rft.eissn=0305-1048&rft.issn=0305-1048&rft.au=NIKULOVA,%20Anna%20A&FAVOROV,%20Alexander%20V&SUTORMIN,%20Roman%20A&MAKEEV,%20Vsevolod%20J&MIRONOV,%20Andrey%20A&rft.genre=article


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