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

Jason Piper; Salam A Assi; Pierre Cauchy; Christophe Ladroue; Peter N Cockerill; Constanze Bonifer; Sascha Ott

doi:10.1186/s12864-015-2081-4

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

Jason Piper, Salam A Assi, Pierre Cauchy, Christophe Ladroue, Peter N Cockerill, Constanze Bonifer, Sascha Ott

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

20 Citations (Scopus)

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.

Original language	English
Article number	1000
Journal	BMC Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12864-015-2081-4
Publication status	Published - 25 Nov 2015

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title = "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.",

author = "Jason Piper and Assi, {Salam A} and Pierre Cauchy and Christophe Ladroue and Cockerill, {Peter N} and Constanze Bonifer and Sascha Ott",

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doi = "10.1186/s12864-015-2081-4",

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AU - Piper, Jason

AU - Assi, Salam A

AU - Cauchy, Pierre

AU - Ladroue, Christophe

AU - Cockerill, Peter N

AU - Bonifer, Constanze

AU - Ott, Sascha

PY - 2015/11/25

Y1 - 2015/11/25

N2 - 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.

AB - 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.

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VL - 16

JO - BMC Genomics

JF - BMC Genomics

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ER -

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

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