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BMC Genomics. 2015 Nov 25;16:1000. doi: 10.1186/s12864-015-2081-4.

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

Author information

1
Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.
2
Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
3
Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK.
4
Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK. P.N.Cockerill@bham.ac.uk.
5
Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK. C.Bonifer@bham.ac.uk.
6
Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK. s.ott@warwick.ac.uk.

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.

PMID:
26608661
PMCID:
PMC4658755
DOI:
10.1186/s12864-015-2081-4
[Indexed for MEDLINE]
Free PMC Article

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