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.
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Acknowledgments
We thank P.A. Salmand, A. Aubry, C. Oliva for their advice as cisTargetX users. This work is supported by a PhD fellowship from FWO (to M.N.S.) and KULeuven CREA grant 3 M100189 (to S.A.).
Supplementary material is available online at the following URL: http:// med.kuleuven.be/lcb/resources/.
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Potier, D., Atak, Z.K., Sanchez, M.N., Herrmann, C., Aerts, S. (2012). Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila . In: Deplancke, B., Gheldof, N. (eds) Gene Regulatory Networks. Methods in Molecular Biology, vol 786. Humana Press. https://doi.org/10.1007/978-1-61779-292-2_18
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DOI: https://doi.org/10.1007/978-1-61779-292-2_18
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