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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2081-4) contains supplementary material, which is available to authorized users.

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