Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.
Bioinformatics
; 31(17): 2879-81, 2015 Sep 01.
Article
em En
| MEDLINE
| ID: mdl-25953800
ABSTRACT
UNLABELLED Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys2His2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail. AVAILABILITY AND IMPLEMENTATION RCADE is available as a webserver and also for download at http//rcade.ccbr.utoronto.ca/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT t.hughes@utoronto.ca.
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
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Proteínas Nucleares
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Proteínas de Transporte
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Sequências Reguladoras de Ácido Nucleico
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Dedos de Zinco
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Imunoprecipitação da Cromatina
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Sequenciamento de Nucleotídeos em Larga Escala
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Motivos de Nucleotídeos
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2015
Tipo de documento:
Article
País de afiliação:
Canadá