MACPET: model-based analysis for ChIA-PET.
Biostatistics
; 21(3): 625-639, 2020 07 01.
Article
em En
| MEDLINE
| ID: mdl-30698663
ABSTRACT
We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution. Furthermore, significant binding sites discovered by MACPET are involved in a higher number of significant three-dimensional interactions than those discovered by MACS. MACPET is freely available on Bioconductor. ChIA-PET; MACPET; Model-based clustering; Paired-end tags; Peak-calling algorithm.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Ligação Proteica
/
Genoma
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Análise de Sequência de DNA
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Imunoprecipitação da Cromatina
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Sequenciamento de Nucleotídeos em Larga Escala
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Sequenciamento de Cromatina por Imunoprecipitação
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Modelos Biológicos
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Biostatistics
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Noruega