title: Using cisTargetX to predict transcriptional targets and networks in Drosophila.
abstract: Gene expression regulation is a fundamental biological process leading to complete organism development by controlling processes like cell type specification and differentiation. The accuracy of this process is -governed by transcription factors (TFs) acting within a complex gene regulatory network. CisTargetX has been developed to enable a user to predict TFs, enhancers, and target genes involved in the regulation of co-expressed genes. It uses a strategy that incorporates the genome-wide prediction of clusters of transcription factor binding sites (TFBSs), starting from a large, unbiased collection of position weight matrices (PWMs) and uses comparative genomics criteria to filter potential TFBS. We describe in this chapter, step-by-step, how to use cisTargetX starting from a set of genes or TF(s) to predict transcriptional targets with their putative binding sites and networks in Drosophila. Next, we illustrate this approach on a particular developmental system, namely, sensory organ development, and identify relevant TFs, DNA regions regulating gene expression, and TF/target gene interactions. CisTargetX is available at http://med.kuleuven.be/lcb/cisTargetX .
authors.affiliation: TAGC Inserm U928 and Université de la Mediterranée, Marseille, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Potier
authors.forename: Zeynep Kalender
authors.initials: ZK
authors.lastname: Atak
authors.forename: Marina Naval
authors.initials: MN
authors.lastname: Sanchez
authors.forename: Carl
authors.initials: C
authors.lastname: Herrmann
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D004331:Drosophila melanogaster / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D059372:Nucleotide Motifs / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*