CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

Abstract

CircR2Disease is a manually curated database, which provides a comprehensive resource for circRNA deregulation in various diseases. Increasing evidences have shown that circRNAs play critical roles in transcriptional, post-transcriptional and translational regulation. Therefore, the aberrant expression of circRNAs has been associated with a group of diseases. It is significant to develop a high-quality database to deposit the deregulated circRNAs in diseases. The current version of CircR2Disease contains 725 associations between 661 circRNAs and 100 diseases by reviewing existing literatures. Each entry in the CircR2Disease contains detailed information for the circRNA–disease relationship, including circRNA name, coordinates and gene symbol, disease name, expression patterns of circRNA, experimental techniques, a brief description of the circRNA–disease relationship, year of publication and the PubMed ID. CircR2Disease provides a user-friendly interface to browse, search and download as well as to submit novel disease-related circRNAs. CircR2Disease could be very beneficial for researches to investigate the mechanism of disease-related circRNAs and explore the appropriate algorithms for predicting novel associations. Database URL: http://bioinfo.snnu.edu.cn/CircR2Disease/

BRWSP: Predicting circRNA-Disease Associations Based on Biased Random Walk to Search Paths on a Multiple Heterogeneous Network

“…e datasets of circRNA-disease associations are downloaded from the CircR2Disease database (http://bioinfo.snnu.edu.cn/) [7]. e CircR2Disease database contains 725 circRNA-disease associations consisting of 661 circRNAs and 100 diseases.…”

“…Along with gradually penetrating to the study of circRNAs, more and more circRNAs have been identi ed and published. erefore, various circRNA databases with di erent emphases have been constructed, such as CircR2Disease [7], circBase [8], exoRBase [9], PlantcircBase [10], circAtlas 2.0 [11], and CSCD [12]. In addition, the biological function of circRNAs has also been gradually revealed, such as acting as miRNA sponges [13], interacting with RNA-binding proteins (RBPs) [14], participating in transcriptional regulation [15] and so forth.…”

“…However, the research progression of prediction in miRNAdisease association and lncRNA-disease association would benefit the development of computational models for circRNAs [28][29][30]. Recently, Fan et al [7] constructed CircR2Disease database by using the method of literature retrieval, which provides 661 circRNAs, 100 diseases, and 725 circRNA-disease associations. Another similar database is circRNA-Disease [31], which provides an opportunity to identify circRNA-disease associations by using computational methods.…”

Biomarker2vec: Attribute- and Behavior-driven Representation for Multi-type Relationship Prediction between Various Biomarkers

“…To construct the Molecular Association Network (MAN) comprehensively, 18 different kinds of experimental verified associations or interactions are collected from various databases [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45]. After the unifying identifier, we obtained a total of 8 diverse types of biomarkers.…”

GCNCDA: A New Method for Predicting CircRNA-Disease Associations Based on Graph Convolutional Network Algorithm

“…As the number of detected circRNAs increases, multiple databases have been created to store information on circRNAs, such as Circ2Traits [20], circBase [21], deepBase [22] and CircNet [23]. Furthermore, researchers have gradually collected circRNA-disease associations supported by experiments and established databases, such as circR2Disease [24], circRNADb [25], circRNADisease [26] and Circ2Disease [27]. The accumulation of these data provides an opportunity for computational methods to predict potential circRNA-disease associations.…”