Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data.
Nucleic Acids Res
; 45(10): 5666-5677, 2017 Jun 02.
Article
em En
| MEDLINE
| ID: mdl-28472398
ABSTRACT
Transcription factors (TFs) play crucial roles in regulating gene expression through interactions with specific DNA sequences. Recently, the sequence motif of almost 400 human TFs have been identified using high-throughput SELEX sequencing. However, there remain a large number of TFs (â¼800) with no high-throughput-derived binding motifs. Computational methods capable of associating known motifs to such TFs will avoid tremendous experimental efforts and enable deeper understanding of transcriptional regulatory functions. We present a method to associate known motifs to TFs (MATLAB code is available in Supplementary Materials). Our method is based on a probabilistic framework that not only exploits DNA-binding domains and specificities, but also integrates open chromatin, gene expression and genomic data to accurately infer monomeric and homodimeric binding motifs. Our analysis resulted in the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase compared to the existing coverage.
Texto completo:
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Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
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Algoritmos
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DNA
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Cromatina
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Regulação da Expressão Gênica
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Modelos Estatísticos
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article