Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies.
AMIA Annu Symp Proc
; 2019: 371-379, 2019.
Article
em En
| MEDLINE
| ID: mdl-32308830
ABSTRACT
ChIP-Seq, a technique that allows for quantification of DNA sequences bound by transcription factors or histones, has been widely used to characterize genome-wide DNA-protein binding at baseline and induced by specific exposures. Integrating results of multiple ChIP-Seq datasets is a convenient approach to identify robust DNA- protein binding sites and determine their cell-type specificity. We developed brocade, a computational pipeline for reproducible analysis of publicly available ChIP-Seq data that creates R markdown reports containing information on datasets downloaded, quality control metrics, and differential binding results. Glucocorticoids are commonly used anti-inflammatory drugs with tissue-specific effects that are not fully understood. We demonstrate the utility of brocade via the analysis of five ChIP-Seq datasets involving glucocorticoid receptor (GR), a transcription factor that mediates glucocorticoid response, to identify cell type-specific and shared GR binding sites across the five cell types. Our results show that brocade facilitates analysis of individual ChIP-Seq datasets and comparative studies involving multiple datasets.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Receptores de Glucocorticoides
/
Conjuntos de Dados como Assunto
/
Sequenciamento de Cromatina por Imunoprecipitação
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article