ArticleBriefings in bioinformatics2022
CRAFT: a bioinformatics software for custom prediction of circular RNA functions.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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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
18 citing papers in PubMed.
- Dysregulated circRNA expression profile and associated miRNA sponging in abnormal lung development in congenital diaphragmatic hernia.Clinical and translational medicine · 2026Article
- Review
- Circular RNA as emerging precision therapeutics: from RNA regulation to peptide translation.Precision clinical medicine · 2026Review
- Coding circular RNA in human cancer.Genes & diseases · 2025Review
- Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications.Molecular psychiatry · 2025Review
- Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.Briefings in functional genomics · 2025Review
- Mechanisms and recent advances in non-coding RNAs and RNA modifications in antiplatelet drug resistance.Frontiers in genetics · 2025Review
- Circular RNAs perspective: exploring the direction of immunotherapy for colorectal cancer.Frontiers in oncology · 2025Review
- Investigation of the Circular Transcriptome in Alzheimer's Disease Brain.Journal of molecular neuroscience : MN · 2024Article
- Functional relevance of circRNA aberrant expression in pediatric acute leukemia with KMT2A::AFF1 fusion.Blood advances · 2024Article
- Discovery of dysregulated circular RNAs in whole blood transcriptomes from cystic fibrosis patients - implication of a role for cellular senescence in cystic fibrosis.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2023Article
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
- Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion.Briefings in bioinformatics · 2023Article
- Newly discovered circRNAs encoding proteins: recent progress.Frontiers in genetics · 2023Review
- Tumor Cell-Derived Exosomal circ-PRKCI Promotes Proliferation of Renal Cell Carcinoma via Regulating miR-545-3p/CCND1 Axis.Cancers · 2022Article
- Circular RNAs Activity in the Leukemic Bone Marrow Microenvironment.Non-coding RNA · 2022Review
- Editorial: Machine learning-based methods for RNA data analysis-Volume II.Frontiers in genetics · 2022Article
- Circular RNA and Its Roles in the Occurrence, Development, Diagnosis of Cancer.Frontiers in oncology · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular RNAs (circRNAs), transcripts generated by backsplicing, are particularly stable and pleiotropic molecules, whose dysregulation drives human diseases and cancer by modulating gene expression and signaling pathways. CircRNAs can regulate cellular processes by different mechanisms, including interaction with microRNAs (miRNAs) and RNA-binding proteins (RBP), and encoding specific peptides. The prediction of circRNA functions is instrumental to interpret their impact in diseases, and to prioritize circRNAs for functional investigation. Currently, circRNA functional predictions are provided by web databases that do not allow custom analyses, while self-standing circRNA prediction tools are mostly limited to predict only one type of function, mainly focusing on the miRNA sponge activity of circRNAs. To solve these issues, we developed CRAFT (CircRNA Function prediction Tool), a freely available computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBP, along with their coding potential. Analysis of a set of circRNAs with known functions has been used to appraise CRAFT predictions and to optimize its setting. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, and extensive functional enrichment analysis. Moreover, it originally combines the predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the modulation of biological processes.
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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.