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Wellington-bootstrap : differential DNase-seq footprinting identifies cell-type determining transcription factors
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Piper, Jason, Assi, Salam A., Cauchy, Pierre, Ladroue, Christophe, Cockerill, Peter N., Bonifer, Constanze and Ott, Sascha (2015) Wellington-bootstrap : differential DNase-seq footprinting identifies cell-type determining transcription factors. BMC Genomics, 16 (1). pp. 1-8. doi:10.1186/s12864-015-2081-4 ISSN 1471-2164.
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Official URL: http://dx.doi.org/10.1186/s12864-015-2081-4
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.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QR Microbiology | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre | ||||||||
Library of Congress Subject Headings (LCSH): | Genetic transcription -- Regulation, Transcription factors, Gene regulatory networks | ||||||||
Journal or Publication Title: | BMC Genomics | ||||||||
Publisher: | BioMed Central Ltd. | ||||||||
ISSN: | 1471-2164 | ||||||||
Official Date: | 25 November 2015 | ||||||||
Dates: |
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Volume: | 16 | ||||||||
Number: | 1 | ||||||||
Number of Pages: | 8 | ||||||||
Page Range: | pp. 1-8 | ||||||||
DOI: | 10.1186/s12864-015-2081-4 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 28 January 2016 | ||||||||
Date of first compliant Open Access: | 8 February 2016 | ||||||||
Funder: | Engineering and Physical Sciences Research Council (EPSRC) | ||||||||
Grant number: | EP/P50578X/1 (EPSRC) |
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