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Predicting circRNA-Disease Associations Based on circRNA Expression Similarity and Functional Similarity
- Source :
- Frontiers in Genetics, Vol 10 (2019), Frontiers in Genetics
- Publication Year :
- 2019
- Publisher :
- Frontiers Media SA, 2019.
-
Abstract
- Circular RNAs (circRNAs) are a novel class of endogenous noncoding RNAs that have well-conserved sequences. Emerging evidence has shown that circRNAs can be novel biomarkers or therapeutic targets for many diseases and play an important role in the development of various pathological conditions. Therefore, identifying potential disease-related circRNAs is helpful in improving the efficiency of finding therapeutic targets for diseases. Here, we propose a computational model (PreCDA) to predict potential circRNA–disease associations. First, we calculated the circRNA expression similarity based on circRNA expression profiles. The circRNA functional similarity is calculated based on cosine similarity, and the disease similarity is used as the dimension of each circRNA vector. The associations between circRNAs and diseases are defined based on the circRNA functional similarity and expression similarity. We constructed a disease-related circRNA association network and used a graph-based recommendation algorithm (PersonalRank) to sort candidate disease-related circRNAs. As a result, PreCDA has an average area under the receiver operating characteristic curve value of 78.15% in predicting candidate disease-related circRNAs. In addition, we discuss the factors that affect the performance of this method and find some unknown circRNAs related to diseases, with several common diseases used as case studies. These results show that PreCDA has good performance in predicting potential circRNA–disease associations and is helpful for the diagnosis and treatment of human diseases.
- Subjects :
- 0301 basic medicine
disease
lcsh:QH426-470
PersonalRank
Cosine similarity
Disease
Computational biology
Biology
Expression (mathematics)
circRNA functional similarity
lcsh:Genetics
03 medical and health sciences
030104 developmental biology
0302 clinical medicine
Similarity (network science)
030220 oncology & carcinogenesis
circRNA expression similarity
Genetics
Molecular Medicine
circRNA
Functional similarity
Genetics (clinical)
Original Research
Subjects
Details
- ISSN :
- 16648021
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- Frontiers in Genetics
- Accession number :
- edsair.doi.dedup.....1c2c0709af6bf8c9301e8db8e0b7102e