title: Identification of Candidate Functional Elements in the Genome from ChIP-seq Data.
abstract: ChIP-seq datasets provide a wealth of information for the identification of candidate regulatory elements in the genome. For this potential to be fully realized, methods for evaluating data quality and for distinguishing reproducible signal from technical and biological noise are necessary. Here, the computational methods for addressing these challenges developed by the ENCODE Consortium are described and the key considerations for analyzing and interpreting ChIP-seq data are discussed.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN, 47405, USA. marinovg@iu.edu.
authors.forename: Georgi K
authors.initials: GK
authors.lastname: Marinov
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods; D019295:Computational Biology / Q000379:methods; D016678:Genome; D015698:Genomic Library; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006657:Histones / Q000378:metabolism; D006801:Humans; D011485:Protein Binding; D020218:Response Elements; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D064878:Web Browser; D057188:Workflow
chemical_list: D006657:Histones; D014157:Transcription Factors
keywords: Chromatin immunoprecipitation; High-throughput sequencing; Histone modifications; Regulatory elements; Transcription factors