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

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.

SUBMITTER: Piper J

PROVIDER: S-EPMC4658755 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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

Piper Jason J Assi Salam A SA Cauchy Pierre P Ladroue Christophe C Cockerill Peter N PN Bonifer Constanze C Ott Sascha S

BMC genomics 20151125

<h4>Background</h4>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.<h4>Results</h4>In order to link expression changes with changes in TF binding we introduce the concept of d ...[more]

PMID: 26608661

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