i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

Nucleic Acids Res. 2012 Aug;40(15):e114. doi: 10.1093/nar/gks543. Epub 2012 Jun 20.


The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one analysis, being either TF motifs or 'in vivo' chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Animals
  • Drosophila melanogaster / genetics
  • Enhancer Elements, Genetic
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Genomics / methods*
  • Nucleotide Motifs
  • Regulatory Elements, Transcriptional*
  • Transcription Factors / metabolism


  • Transcription Factors