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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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