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

BMC Genomics

Methodology Article

Christophe Ladroue¹  Constanze Bonifer²  Salam A. Assi²  Peter N. Cockerill²  Pierre Cauchy²  Sascha Ott³  Jason Piper⁴ 

[1] Department of Computer Science, University of Warwick, CV4 7AL, Coventry, UK;Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, B15 2TT, Birmingham, UK;Warwick Systems Biology Centre, University of Warwick, CV4 7AL, Coventry, UK;Warwick Systems Biology Centre, University of Warwick, CV4 7AL, Coventry, UK;Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, B15 2TT, Birmingham, UK;

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

DOI  :  10.1186/s12864-015-2081-4

 received in 2015-05-12, accepted in 2015-10-13,  发布年份 2015

来源: Springer

【 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.

【 授权许可】

CC BY   
© Piper et al. 2015