Predicting circRNA–Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data

Abstract

With the development of high-throughput techniques, various biological molecules are discovered, which includes the circular RNAs (circRNAs). Circular RNA is a novel endogenous noncoding RNA that plays significant roles in regulating gene expression, moderating the microRNAs transcription as sponges, diagnosing diseases, and so on. Based on the circRNA particular molecular structures that are closed-loop structures with neither 5′-3′ polarities nor polyadenylated tails, circRNAs are more stable and conservative than the normal linear coding or noncoding RNAs, which makes circRNAs a biomarker of various diseases. Although some conventional experiments are used to identify the associations between circRNAs and diseases, almost the techniques and experiments are time-consuming and expensive. In this study, we propose a collaboration filtering recommendation system–based computational method, which handles the “cold start” problem to predict the potential circRNA–disease associations, which is named ICFCDA. All the known circRNA–disease associations data are downloaded from circR2Disease database (). Based on these data, multiple data are extracted from different databases to calculate the circRNA similarity networks and the disease similarity networks. The collaboration filtering recommendation system algorithm is first employed to predict circRNA–disease associations. Then, the leave-one-out cross validation mechanism is adopted to measure the performance of our proposed computational method. ICFCDA achieves the areas under the curve of 0.946, which is better than other existing methods. In order to further illustrate the performance of ICFCDA, case studies of some common diseases are made, and the results are confirmed by other databases. The experimental results show that ICFCDA is competent in predicting the circRNA–disease associations.

An Overview of Recommendation Techniques and Their Applications in Healthcare

“…After years of development, there is a lot of work to show that recommendation techniques have been successfully applied to disease prediction, disease prevention, medical diagnosis, and so on [62], [65], [85], [112], [113], [143], [161], [166]. Moreover, recent work has indicated that health RS has developed from the applications of basic recommendation techniques to the algorithm improvement and model innovation [13], [19], [67], [122], [146].…”

“…CircR-NA, as a marker of many diseases, is often used to identify the correlation with diseases. Lei et al [85] have employed a CFbased recommendation algorithm to predict circRNAdisease associations. Based on the assumption that similar cell lines and similar drugs exhibit similar drug responses, a hybrid interpolation weighted CF method has been adopted to predict the missing drug response [166].…”

Emerging Function and Clinical Significance of Exosomal circRNAs in Cancer

“… 15 Since circRNAs do not have 5′ caps and 3′ polyadenylated tails, they are more stable than linear RNAs. 16 However, circRNAs were initially regarded as non-functional byproducts of aberrant RNA splicing. 17 With the development of high-throughput RNA sequencing (RNA-seq) technology, circRNAs have been proven to be widely present in eukaryotic cells.…”

The circRNA_102911/miR‑129‑5p/SOX6 axis is involved with T lymphocyte immune function in elderly patients with laparoscopic left hepatectomy for hepatolithiasis

“…However, in the case of immune dysfunction, the temporary post-traumatic or post-operative immune suppression predisposes the patient for septic complications, especially for elderly patients as a result of immunosenescence ( 5 ). Studies have shown that circular RNA (circRNA) plays an important role in immune regulation ( 6 , 7 ). circRNAs show tissue-specific expression profiles and are abnormally expressed in various diseases.…”

“…They also participate in post-transcriptional cutting, editing, translocation, translation and degradation ( 8 ). Studies have shown that circRNAs are involved in the development of various disease, including liver cancer, cholangiocarcinoma, leukemia, acute kidney transplantation, Alzheimer's disease and rheumatoid arthritis ( 6 , 7 ). However, the role of (circRNA)_102911 (102911) in T lymphocytes immune function in elderly patients with laparoscopic left hepatectomy (LLH) for hepatolithiasis has not been elucidated.…”