title: Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.
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.
authors: Department of Molecular Virology, Immunology & Medical Genetics, The Ohio State University, Columbus, OH, USA.
authors: Cenny
authors: C
authors: Taslim
authors: Kun
authors: K
authors: Huang
authors: Tim
authors: T
authors: Huang
authors: Shili
authors: S
authors: Lin
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software