ArticleNucleic acids research2024
EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- G-quadruplex structures are key regulators of mammalian spermatogenesis.Cellular & molecular biology letters · 2026Article
- Transcription start sites experience a high influx of heritable variants fueled by early development.Nature communications · 2025Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- GQ-DNABERT reveals GQ proximal enhancer-promoter interactions associated with tissue-specific transcription.Nucleic acids research · 2025Article
- G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration.Bioinformatics (Oxford, England) · 2025Article
- Mammalian conservation of endogenous G-quadruplex reveals their associations with complex traits.Genome biology · 2025Article
- Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.Scientific reports · 2025Article
- The effect of prolonged G-quadruplex stabilization on the functions of human cells.Scientific reports · 2025Article
- Chromatin Immunoprecipitation Reveals p53 Binding to G-Quadruplex DNA Sequences in Myeloid Leukemia Cell Lines.ACS bio & med chem Au · 2025Article
- G-Quadruplex-Based Splice Switching as a Therapeutic Approach in Duchenne Muscular Dystrophy.ACS chemical biology · 2025Article
- Kolmogorov-Arnold networks for genomic tasks.Briefings in bioinformatics · 2025Article
- Flipons enable genomes to learn by intermediating the exchange of energy for information.Journal of the Royal Society, Interface · 2025Review
- G-quadruplex stabilization provokes DNA breaks in human PKD1, revealing a second hit mechanism for ADPKD.Nature communications · 2025Article
- DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins.Genomics, proteomics & bioinformatics · 2024Article
- A Compendium of G-Flipon Biological Functions That Have Experimental Validation.International journal of molecular sciences · 2024Review
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
G-quadruplexes (G4s) are non-canonical four-stranded structures and are emerging as novel genetic regulatory elements. However, a comprehensive genomic annotation of endogenous G4s (eG4s) and systematic characterization of their regulatory network are still lacking, posing major challenges for eG4 research. Here, we present EndoQuad (https://EndoQuad.chenzxlab.cn/) to address these pressing issues by integrating high-throughput experimental data. First, based on high-quality genome-wide eG4s mapping datasets (human: 1181; mouse: 24; chicken: 2) generated by G4 ChIP-seq/CUT&Tag, we generate a reference set of genome-wide eG4s. Our multi-omics analyses show that most eG4s are identified in one or a few cell types. The eG4s with higher occurrences across samples are more structurally stable, evolutionarily conserved, enriched in promoter regions, mark highly expressed genes and associate with complex regulatory programs, demonstrating higher confidence level for further experiments. Finally, we integrate millions of functional genomic variants and prioritize eG4s with regulatory functions in disease and cancer contexts. These efforts have culminated in the comprehensive and interactive database of experimentally validated DNA eG4s. As such, EndoQuad enables users to easily access, download and repurpose these data for their own research. EndoQuad will become a one-stop resource for eG4 research and lay the foundation for future functional studies.
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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 Socratic graph.