ArticleCell reports2020
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.
Article in Cell reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.Nature genetics · 2023Pooled it
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.American journal of human genetics · 2025Article
- The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA.EMBO reports · 2025Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes.Science (New York, N.Y.) · 2024Article
- A genome scale transcriptional regulatory model of the human placenta.Science advances · 2024Article
- A transcriptional enhancer regulates cardiac maturation.Nature cardiovascular research · 2024Article
- Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth.Molecular oncology · 2024Article
- Integrative computational analyses implicate regulatory genomic elements contributing to spina bifida.Genetics in medicine open · 2024Article
- Cochlear organoids reveal transcriptional programs of postnatal hair cell differentiation from supporting cells.Cell reports · 2023Article
- Screening for functional regulatory variants in open chromatin using GenIE-ATAC.Nucleic acids research · 2023Article
- Three-dimensional genome rewiring in loci with human accelerated regions.Science (New York, N.Y.) · 2023Article
- Article
- Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies.PLoS computational biology · 2022Article
- Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells.Neuron · 2022Article
- Advances and Trends in Omics Technology Development.Frontiers in medicine · 2022Review
- Posterior cingulate cortex reveals an expression profile of resilience in cognitively intact elders.Brain communications · 2022Article
- Systems modeling of metabolic dysregulation in neurodegenerative diseases.Current opinion in pharmacology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 6 institutions in 1 country.
Funding
Abstract
Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.
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What Socratic holds
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 Socratic graph.