Abstract
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 language | English |
---|---|
Article number | 1000 |
Journal | BMC Genomics |
Volume | 16 |
Issue number | 1 |
DOIs | |
Publication status | Published - 25 Nov 2015 |