Integrating Bipartite Network Projection and KATZ Measure to Identify Novel CircRNA-Disease Associations

Accumulating biological experiments have shown that circRNAs are closely related to the occurrence and development of many complex human diseases. During recent years, the associations of circRNA with disease have caused more and more researchers to pay attention and to analyze their correlation mechanisms. However, experimental methods for determining the associations of circRNA with a particular disease are still expensive, difficult, and time consuming. Moreover, the available databases related to circRNA-disease correlations have only recently been updated, and only a few computational methods are constructed to predict potential circRNA-disease correlations. Taking into account the limitations of experimental studies, we develop a novel computational method, named IBNPKATZ, for predicting potential circRNA-disease associations, which integrates the bipartite network projection algorithm and KATZ measure. This model is based on the known circRNA-disease associations, combining circRNA similarity and disease similarity. Specifically, the circRNA similarity is derived from the average of the semantic similarity and the Gaussian interaction profile (GIP) kernel similarity of circRNA. Similarly, disease similarity is the mean of the semantic similarity and the GIP kernel similarity of disease. Furthermore, it is semi-supervised and does not require negative samples. Finally, IBNPKATZ achieves reliable AUC of 0.9352 in the leave-one-out cross validation, and case studies show that the circRNA-disease correlations predicted by our method can be successfully demonstrated by relevant experiments. The IBNPKATZ is expected to be a useful biomedical research tool for predicting potential circRNA-disease associations.