Analyzing ChIP-seq data

Preprocessing, normalization, differential identification, and binding pattern characterization

Cenny Taslim, Kun Huang, Hui-ming Huang, Shili Lin

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages275-291
Number of pages17
Volume802
DOIs
StatePublished - 2012
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume802
ISSN (Print)10643745

Fingerprint

Chromatin Immunoprecipitation
Genome
Guidelines
DNA-Binding Proteins
Binding Sites
Technology
Antibodies

Keywords

  • ChIP-seq
  • Differential analysis
  • Finite mixture model
  • Model-based classification
  • Nonlinear normalization

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Taslim, C., Huang, K., Huang, H., & Lin, S. (2012). Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization. In Methods in Molecular Biology (Vol. 802, pp. 275-291). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_18

Analyzing ChIP-seq data : Preprocessing, normalization, differential identification, and binding pattern characterization. / Taslim, Cenny; Huang, Kun; Huang, Hui-ming; Lin, Shili.

Methods in Molecular Biology. Vol. 802 2012. p. 275-291 (Methods in Molecular Biology; Vol. 802).

Research output: Chapter in Book/Report/Conference proceedingChapter

Taslim, C, Huang, K, Huang, H & Lin, S 2012, Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization. in Methods in Molecular Biology. vol. 802, Methods in Molecular Biology, vol. 802, pp. 275-291. https://doi.org/10.1007/978-1-61779-400-1_18
Taslim C, Huang K, Huang H, Lin S. Analyzing ChIP-seq data: Preprocessing, normalization, differential identification, and binding pattern characterization. In Methods in Molecular Biology. Vol. 802. 2012. p. 275-291. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-400-1_18
Taslim, Cenny ; Huang, Kun ; Huang, Hui-ming ; Lin, Shili. / Analyzing ChIP-seq data : Preprocessing, normalization, differential identification, and binding pattern characterization. Methods in Molecular Biology. Vol. 802 2012. pp. 275-291 (Methods in Molecular Biology).
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