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

[摘要] BackgroundThe 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.ResultsIn 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.ConclusionsOur new tool, Wellington-bootstrap, will enable the detection of differential TF binding facilitating the study of gene regulatory systems.

[发布日期] 2015-11-25

[关键词] Transcriptional regulation;Transcription factors binding sites;Digital genomic footprinting;DNase-seq analysis;Gene regulatory networks