ArticleBMC genomics2015
Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 50 citations in OpenAlex.
- Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.Nature methods · 2023Article
- CScience advances · 2023Article
- Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation.Nature communications · 2023Article
- TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile.PLoS computational biology · 2022Article
- A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses.Journal of cell science · 2022Article
- Hypermethylation at the CXCR5 gene locus limits trafficking potential of CD8+ T cells into B-cell follicles during HIV-1 infection.Blood advances · 2022Article
- Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma.Nature communications · 2021Article
- Reactivation of a developmentally silenced embryonic globin gene.Nature communications · 2021Article
- Analytical Approaches for ATAC-seq Data Analysis.Current protocols in human genetics · 2020Article
- From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.Genome biology · 2020Review
- Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf.Cell reports · 2019Article
- Genome-Wide Transcription Factor Binding in Leaves from CThe Plant cell · 2019Article
- Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions.Genes & development · 2019Article
- BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test.Nucleic acids research · 2019Article
- Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.BMC genomics · 2018Article
- Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid.Scientific reports · 2018Article
- A metabolic interplay coordinated by HLX regulates myeloid differentiation and AML through partly overlapping pathways.Nature communications · 2018Article
- Bringing numerous methods for expression and promoter analysis to a public cloud computing service.Bioinformatics (Oxford, England) · 2018Article
- Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.Nucleic acids research · 2018Article
- Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.Genome research · 2017Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe 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.
resultsIn 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.
conclusionsOur new tool, Wellington-bootstrap, will enable the detection of differential TF binding facilitating the study of gene regulatory systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.