title: ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks.
abstract: The first step in the definition of transcriptional regulatory networks is to establish correct relationships between transcription factors (TFs) and their target genes, together with the effect of their regulatory activity (activator or repressor). Fundamental advances in this direction have been made possible by the introduction of experimental techniques such as Chromatin Immunoprecipitation, which, coupled with next-generation sequencing technologies (ChIP-Seq), permit the genome-wide identification of TF binding sites. This chapter provides a survey on how data of this kind are to be processed and integrated with expression and other types of data to infer transcriptional regulatory rules and codes.
authors.affiliation: Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy. giulio.pavesi@unimi.it.
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D014157:Transcription Factors
keywords: ChIP-Seq; RNA-Seq; Transcription factors; Transcription regulation