i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.
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.
TAGC - Inserm U1090 and Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France. carl.herrmann@univ-amu.fr
Carl
C
Herrmann
Bram
B
Van de Sande
Delphine
D
Potier
Stein
S
Aerts
D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors