ArticleNucleic acids research2022
CircleBase: an integrated resource and analysis platform for human eccDNAs.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 46 citations in OpenAlex.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
- AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.Nature methods · 2026Article
- The potential clinical implications of extrachromosomal circular DNA as a biomarker.Genes & diseases · 2026Review
- The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.Nature communications · 2026Article
- DeepECC: a deep learning framework for genome-wide identification and analysis of human cancer eccDNAs.Nucleic acids research · 2026Article
- Gene4Denovo2: an updated platform for human de novo mutations discovery and interpretation.Nucleic acids research · 2026Article
- CircleBase V2: an eccDNA annotation platform across cancers and species.Nucleic acids research · 2026Article
- eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.Molecular biology and evolution · 2025Article
- Article
- Exploring the potential of extrachromosomal DNA as a novel oncogenic driver.Science China. Life sciences · 2025Review
- Extrachromosomal circular DNA drives dynamic genome plasticity: emerging roles in disease progression and clinical potential.Theranostics · 2025Review
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.Database : the journal of biological databases and curation · 2024Article
- ECGA: A web server to explore and analyze extrachromosomal gene in cancer.Computational and structural biotechnology journal · 2024Article
- Article
- Review
- Review
- CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines.NAR cancer · 2024Article
- Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies.Life (Basel, Switzerland) · 2024Review
- Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer.Biomolecules · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.
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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.