ReviewBriefings in bioinformatics2016
In the loop: promoter-enhancer interactions and bioinformatics.
Review in Briefings in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
79 citing papers in PubMed.
- Enhancer-based gene therapy: a new path for precision medicine.Hereditas · 2026Review
- UniChrom: a universal deep learning architecture for cross-scale chromatin interaction prediction.BMC genomics · 2026Article
- Phase-Separation of YAP Mediates AJUBA Super Enhancer Activation to Promote Aberrant Mitosis in Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Enhancer-mediated NR2F2 recruitment activates BGN to promote tumor growth and shape tumor microenvironment in papillary thyroid cancer.Theranostics · 2026Article
- Systematic identification of Oct4 transcriptional targets in embryonic stem cells using the auxin-inducible degron system and nascent RNA sequencing.Cell regeneration (London, England) · 2025Article
- DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations.BMC bioinformatics · 2025Article
- Super-enhancer MYCNOS-SE promotes chemoresistance in small cell lung cancer by recruiting transcription factors CTCF and KLF15.Oncogene · 2025Article
- RUNX2 Phase Separation Mediates Long-Range Regulation Between Osteoporosis-Susceptibility Variant and XCR1 to Promote Osteoblast Differentiation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Mapping of chromatin architecture and enhancer-promoter interactions in the cochlea.Frontiers in molecular biosciences · 2025Article
- DeepEPI: CNN-transformer-based model for extracting TF interactions through predicting enhancer-promoter interactions.Bioinformatics advances · 2025Article
- Active enhancers: recent research advances and insights into disease.Biology direct · 2024Review
- A deep learning model for DNA enhancer prediction based on nucleotide position aware feature encoding.iScience · 2024Article
- Mechanistic analysis of enhancer sequences in the estrogen receptor transcriptional program.Communications biology · 2024Article
- KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma.Journal of experimental & clinical cancer research : CR · 2024Article
- rs71327024 Associated with COVID-19 Hospitalization ReducesInternational journal of molecular sciences · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- Role of non-coding variants in cardiovascular disease.Journal of cellular and molecular medicine · 2023Review
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancer-promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter-enhancer interactions (PEIs). In the recent years, genome-wide analyses have identified signatures and mapped novel enhancers; however, being able to precisely identify their target gene(s) requires massive biological and bioinformatics efforts. In this review, we give a short overview of the chromatin landscape and transcriptional regulation. We discuss some key concepts and problems related to chromatin interaction detection technologies, and emerging knowledge from genome-wide chromatin interaction data sets. Then, we critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction. Lastly, we provide specific examples of how PEIs have been used to elucidate a functional role of non-coding single-nucleotide polymorphisms. The topic is at the forefront of epigenetic research, and by highlighting some future bioinformatics challenges in the field, this review provides a comprehensive background for future PEI studies.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.