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.
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.|Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Jason
authors.initials: J
authors.lastname: Piper
authors.affiliation: Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Salam A
authors.initials: SA
authors.lastname: Assi
authors.affiliation: Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
authors.forename: Pierre
authors.initials: P
authors.lastname: Cauchy
authors.affiliation: Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Christophe
authors.initials: C
authors.lastname: Ladroue
authors.affiliation: 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.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Cockerill
authors.affiliation: 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.
authors.forename: Constanze
authors.initials: C
authors.lastname: Bonifer
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK. s.ott@warwick.ac.uk.
authors.forename: Sascha
authors.initials: S
authors.lastname: Ott
mesh_terms: D018941:Antigens, CD19 / Q000378:metabolism; D016175:B-Lymphocyte Subsets / Q000378:metabolism; D001665:Binding Sites; D018414:CD8-Positive T-Lymphocytes / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018983:DNA Footprinting / Q000379:methods; D003851:Deoxyribonucleases / Q000378:metabolism*; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009928:Organ Specificity / Q000235:genetics; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D018941:Antigens, CD19; D014157:Transcription Factors; D003851:Deoxyribonucleases