title: iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment.
abstract: Gene expression profiling is often used to identify genes that are co-expressed in a biological process or disease. Downstream analyses of co-expressed gene sets using bioinformatics methods can reveal candidate transcription factors (TF) that co-regulate these genes, based on the presence of shared TF binding sites. Drawing gene regulatory networks that connect TFs to their predicted target genes can uncover gene modules that implement a particular function. Here, we describe several protocols to analyze any set of co-expressed genes using iRegulon and i-cisTarget. These tools perform regulatory sequence analysis (motif discovery) and integrate and mine large collections of existing regulatory data, such as ChIP-Seq, DHS-seq, and FAIRE-seq (track discovery). While iRegulon focuses on sets of co-expressed genes, i-cisTarget also analyses genomic regions as input. The following protocols describe how to install and use these tools, how to interpret the obtained results, and will thus help to create meaningful regulatory networks.
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium.
authors.forename: Annelien
authors.initials: A
authors.lastname: Verfaillie
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium.
authors.forename: Hana
authors.initials: H
authors.lastname: Imrichova
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium.
authors.forename: Rekins
authors.initials: R
authors.lastname: Janky
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium.
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
mesh_terms: D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics*; D018085:Regulon / Q000235:genetics*; D012984:Software
keywords: gene regulatory networks; motif discovery; track enrichment