Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila

  • Delphine Potier
  • Zeynep Kalender Atak
  • Marina Naval Sanchez
  • Carl Herrmann
  • Stein AertsEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 786)


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

Key words

cis-Regulatory module Gene regulatory network Motif discovery Drosophila cisTargetX Transcriptional targets 



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://


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Delphine Potier
    • 1
    • 2
  • Zeynep Kalender Atak
    • 3
  • Marina Naval Sanchez
    • 3
  • Carl Herrmann
    • 4
    • 5
  • Stein Aerts
    • 3
    Email author
  1. 1.TAGC Inserm U928 and Université de la MediterranéeMarseilleFrance
  2. 2.IBDML CNRS UMR 6216 and Université de la MediterranéeMarseilleFrance
  3. 3.Laboratory of Computational Biology, Center for Human GeneticsK. U. LeuvenLeuvenBelgium
  4. 4.TAGC Inserm U928MarseilleFrance
  5. 5.Université de la MediterranéeMarseilleFrance

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