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

Jason Piper, Salam A Assi, Pierre Cauchy, Christophe Ladroue, Peter N Cockerill, Constanze Bonifer, Sascha Ott

Research output: Contribution to journalArticlepeer-review

20 Citations (Scopus)


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.

Original languageEnglish
Article number1000
JournalBMC Genomics
Issue number1
Publication statusPublished - 25 Nov 2015


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