ArticleProceedings of the National Academy of Sciences of the United States of America2014
Global view of enhancer-promoter interactome in human cells.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
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Who cites it
174 citing papers in PubMed, 3 syntheses or guidelines pooled it, 292 citations in OpenAlex.
- Identification of susceptibility loci and relevant cell type for IgA nephropathy in Han Chinese by integrative genome-wide analysis.Frontiers of medicine · 2024Pooled it
- Leverage Large-Scale Biological Networks to Decipher the Genetic Basis of Human Diseases Using Machine Learning.Methods in molecular biology (Clifton, N.J.) · 2021Pooled it
- Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.Nature genetics · 2017Pooled it
- Risk variants disrupting enhancers of TProceedings of the National Academy of Sciences of the United States of America · 2019Trial
- Three-dimensional chromatin architecture is rapidly restored after DNA replication.Nature communications · 2026Article
- Overcoming Artificial Structures in Resolution-Enhanced Hi-C Data by Signal Decomposition and Multi-Scale Attention.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Functional noncoding variants within the TBX1 enhancer contribute to tetralogy of Fallot.Science China. Life sciences · 2026Article
- Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel.bioRxiv : the preprint server for biology · 2026Article
- Comparative fine-mapping of breast cancer susceptibility loci using summary statistics methods and multinomial regression.medRxiv : the preprint server for health sciences · 2026Article
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Learning a pairwise epigenomic and transcription factor binding association score across the human genome.Bioinformatics (Oxford, England) · 2026Article
- Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention.American journal of human genetics · 2026Article
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissues.Scientific reports · 2025Article
- EPIFBMC: A New Model for Enhancer-Promoter Interaction Prediction.International journal of molecular sciences · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- Genome-Wide Detection of Leukemia Biomarkers from lincRNA-Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure.Current issues in molecular biology · 2025Article
- SEgene identifies links between super enhancers and gene expression across cell types.NPJ systems biology and applications · 2025Article
114 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Enhancer mapping has been greatly facilitated by various genomic marks associated with it. However, little is available in our toolbox to link enhancers with their target promoters, hampering mechanistic understanding of enhancer-promoter (EP) interaction. We develop and characterize multiple genomic features for distinguishing true EP pairs from noninteracting pairs. We integrate these features into a probabilistic predictor for EP interactions. Multiple validation experiments demonstrate a significant improvement over state-of-the-art approaches. Systematic analyses of EP interactions across 12 cell types reveal several global features of EP interactions: (i) a larger fraction of EP interactions are cell type specific than enhancers; (ii) promoters controlled by multiple enhancers have higher tissue specificity, but the regulating enhancers are less conserved; (iii) cohesin plays a role in mediating tissue-specific EP interactions via chromatin looping in a CTCF-independent manner. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying EP communication.
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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.