Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization

Cenny Taslim, Kun Huang, Tim Huang, Shili Lin

Producción científica: Chapter

11 Citas (Scopus)

Resumen

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a high-throughput antibody-based method to study genome-wide protein-DNA binding interactions. ChIP-seq technology allows scientist to obtain more accurate data providing genome-wide coverage with less starting material and in shorter time compared to older ChIP-chip experiments. Herein we describe a step-by-step guideline in analyzing ChIP-seq data including data preprocessing, nonlinear normalization to enable comparison between different samples and experiments, statistical-based method to identify differential binding sites using mixture modeling and local false discovery rates (fdrs), and binding pattern characterization. In addition, we provide a sample analysis of ChIP-seq data using the steps provided in the guideline.

Idioma originalEnglish (US)
Título de la publicación alojadaNext Generation Microarray Bioinformatics
Subtítulo de la publicación alojadaMethods and Protocols
EditoresJunbai Wang, Tianhai Tian, Aik Choon Tan
Páginas275-291
Número de páginas17
DOI
EstadoPublished - 2012
Publicado de forma externa

Serie de la publicación

NombreMethods in Molecular Biology
Volumen802
ISSN (versión impresa)1064-3745

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

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