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CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA-disease Associations and Its
Chunyan Fan1, Xiujuan Lei1, Jiaojiao Tie1
1School of Computer Science, Shaanxi Normal University, Xi'an 710119, China.
Abstract:
With accumulating dysregulated circular RNAs (circRNAs) in pathological processes, the regulatory functions of circRNAs, especially circRNAs as microRNA (miRNA) sponges and their interactions with RNA-binding proteins (RBPs), have been widely validated. However, the collected information on experimentally validated circRNA-disease associations is only preliminary. Therefore, an updated CircR2Disease database providing a comprehensive resource and web tool to clarify the relationships between circRNAs and diseases in diverse species is necessary. Here, we present an updated CircR2Disease v2.0 with the increased number of circRNA-disease associations and novel characteristics. CircR2Disease v2.0 provides more than 5-fold experimentally validated circRNA-disease associations compared to its previous version. This version includes 4201 entries between 3077 circRNAs and 312 disease subtypes. Secondly, the information of circRNA-miRNA, circRNA-miRNA-target, and circRNA-RBP interactions has been manually collected for various diseases. Thirdly, the gene symbols of circRNAs and disease name IDs can be linked with various nomenclature databases. Detailed descriptions such as samples and journals have also been integrated into the updated version. Thus, CircR2Disease v2.0 can serve as a platform for users to systematically investigate the roles of dysregulated circRNAs in various diseases and further explore the posttranscriptional regulatory function in diseases. Finally, we propose a computational method named circDis based on the graph convolutional network (GCN) and gradient boosting decision tree (GBDT) to illustrate the applications of the CircR2Disease v2.0 database. CircR2Disease v2.0 is available at http://bioinfo.snnu.edu.cn/CircR2Disease_v2.0 and https://github.com/bioinforlab/CircR2Disease-v2.0.
Insights
The updated CircR2Disease v2.0 database now offers over five times more experimentally validated circular RNA (circRNA) and disease associations. This resource aids in understanding circRNA roles in diseases and their regulatory functions.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Circular RNAs (circRNAs) play regulatory roles in diseases, often acting as microRNA (miRNA) sponges or interacting with RNA-binding proteins (RBPs).
- Existing databases for experimentally validated circRNA-disease associations are preliminary and require expansion.
Purpose of the Study:
- To present an updated CircR2Disease v2.0 database with significantly expanded circRNA-disease associations and novel features.
- To provide a comprehensive resource and web tool for investigating circRNA roles in various diseases across diverse species.
Main Methods:
- Manual curation of experimentally validated circRNA-disease associations, circRNA-miRNA interactions, and circRNA-RBP interactions.
- Integration of gene symbols and disease IDs with nomenclature databases and detailed descriptions (samples, journals).
- Development of a computational method (circDis) using graph convolutional networks (GCN) and gradient boosting decision trees (GBDT) for database application illustration.
Main Results:
- CircR2Disease v2.0 contains 4201 entries linking 3077 circRNAs to 312 disease subtypes, a >5-fold increase from the previous version.
- Includes detailed information on circRNA-miRNA, circRNA-miRNA-target, and circRNA-RBP interactions for various diseases.
- Provides a web tool for systematic investigation of circRNA functions in disease pathogenesis.
Conclusions:
- CircR2Disease v2.0 is a significantly enhanced resource for studying circRNA-disease relationships.
- The database facilitates exploration of circRNA regulatory functions in posttranscriptional regulation and disease.
- The circDis computational method demonstrates the utility of the updated database for disease association prediction.
