ReviewBriefings in bioinformatics2021
Closing the circle: current state and perspectives of circular RNA databases.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 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
71 citing papers in PubMed, 109 citations in OpenAlex.
- Circular RNAs: Unlocking new avenues in cardiometabolic disease management.The Journal of physiology · 2026Review
- MIFNDRA: an innovative knowledge-enhanced multimodal fusion and graph learning framework for predicting drug resistance-related ncRNAs.Briefings in bioinformatics · 2026Article
- Circular RNAs in Intestinal Mucosal Homeostasis and Pathologies.Non-coding RNA · 2026Review
- Article
- circRNA_Atp8a1 Promotes Glycolytic Reprogramming in Damage of Intestinal Mucosal Barrier by Upregulating IGF2 through miR-200b-3p.Tissue engineering and regenerative medicine · 2025Article
- The role of circular RNAs in regulating cytokine signaling in cancer.FEBS open bio · 2025Review
- MVGNCDA: Identifying Potential circRNA-Disease Associations Based on Multi-view Graph Convolutional Networks and Network Embeddings.Interdisciplinary sciences, computational life sciences · 2025Article
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy.Biomolecules · 2025Review
- Circular RNAs in cancer stem cells: Insights into their roles and mechanisms (Review).International journal of molecular medicine · 2025Review
- Geometry-enhanced graph neural networks accelerate circRNA therapeutic target discovery.Frontiers in genetics · 2025Article
- Circular RNA in liver cancer research: biogenesis, functions, and roles.Frontiers in oncology · 2025Review
- Circular RNAs in inflammatory bowel disease: a review of mechanisms, biomarkers and therapeutic potential.Frontiers in immunology · 2025Review
- Online Databases in Circular RNAs.Advances in experimental medicine and biology · 2025Review
- CircRNA: Functions, Applications and Prospects.Biomolecules · 2024Article
- Article
- Acupuncture may play a key role in anti-depression through various mechanisms in depression.Chinese medicine · 2024Review
- Importance of Studying Non-Coding RNA in Children and Adolescents with Type 1 Diabetes.Biomedicines · 2024Review
- CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs.Scientific reports · 2024Article
- Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals.Naunyn-Schmiedeberg's archives of pharmacology · 2024Article
11 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
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules that have been linked to various diseases, including cancer. However, a precise function and working mechanism are lacking for the larger majority. Following many different experimental and computational approaches to identify circRNAs, multiple circRNA databases were developed as well. Unfortunately, there are several major issues with the current circRNA databases, which substantially hamper progression in the field. First, as the overlap in content is limited, a true reference set of circRNAs is lacking. This results from the low abundance and highly specific expression of circRNAs, and varying sequencing methods, data-analysis pipelines, and circRNA detection tools. A second major issue is the use of ambiguous nomenclature. Thus, redundant or even conflicting names for circRNAs across different databases contribute to the reproducibility crisis. Third, circRNA databases, in essence, rely on the position of the circRNA back-splice junction, whereas alternative splicing could result in circRNAs with different length and sequence. To uniquely identify a circRNA molecule, the full circular sequence is required. Fourth, circRNA databases annotate circRNAs' microRNA binding and protein-coding potential, but these annotations are generally based on presumed circRNA sequences. Finally, several databases are not regularly updated, contain incomplete data or suffer from connectivity issues. In this review, we present a comprehensive overview of the current circRNA databases and their content, features, and usability. In addition to discussing the current issues regarding circRNA databases, we come with important suggestions to streamline further research in this growing field.
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.