Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors

作者：Piper Jason; Assi Salam A; Cauchy Pierre; Ladroue Christophe; Cockerill Peter N^*; Bonifer Constanze; Ott Sascha

来源：BMC Genomics, 2015, 16(1): 1000.

DOI：10.1186/s12864-015-2081-4

• Transcriptional regulation
• Transcription factors binding sites
• Digital genomic footprinting
• DNase-seq analysis
• Gene regulatory networks

Background: The analysis of differential gene expression is a fundamental tool to relate gene regulation with specific biological processes. Differential binding of transcription factors (TFs) can drive differential gene expression. While DNase-seq data can provide global snapshots of TF binding, tools for detecting differential binding from pairs of DNase-seq data sets are lacking.
Results: In order to link expression changes with changes in TF binding we introduce the concept of differential footprinting alongside a computational tool. We demonstrate that differential footprinting is associated with differential gene expression and can be used to define cell types by their specific TF occupancy patterns.
Conclusions: Our new tool, Wellington-bootstrap, will enable the detection of differential TF binding facilitating the study of gene regulatory systems.

• 出版日期2015-11-25