Abstract
Accumulating evidence indicates that the regulation of long non-coding RNAs (lncRNAs) is closely related to a variety of diseases. Identifying meaningful lncRNA–disease associations will help to contribute to the understanding of the molecular mechanisms underlying these diseases. However, only a limited number of associations between lncRNAs and diseases have been inferred from traditional biological experiments due to the high cost and highly specialized. Therefore, computational methods are increasingly used to reduce time of biological experiments and complement biological research. In this paper, a computational method called HBRWRLDA is proposed to predict lncRNA–disease associations. First, HBRWRLDA models the relationships between multiple nodes using hypergraphs, which allows HBRWRLDA to integrate the expression similarity of lncRNAs and the semantic similarity of diseases to construct hypergraphs. Then, a bi-random walk on hypergraphs is used to predict potential lncRNA–disease associations. HBRWRLDA achieves a higher area under the curve value of 0.9551 and \(0.9488\pm 0.0013\), respectively, compared with the other five advanced methods under the framework of one-leave cross validation (LOOCV) and five-fold cross-validation (5-fold CV). In addition, the prediction effect of HBRWRLDA was confirmed case studies of three diseases: renal cell carcinoma, gastric cancer, and hepatocellular carcinoma. Case studies demonstrates the capacity of HBRWRLDA to identify potentially disease-associated lncRNAs. Overall, HBRWRLDA is excellent at predicting potential lncRNA–disease associations and could be useful in conducting further biological experiments by helping researchers identify candidates of lncRNA–disease association.
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The source codes used in this work could be freely downloaded at https://github.com/yeyetuowoyi/HBRWRLDA.
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This work was supported by the National Natural Science Foundation of China (62002070, 61802072); the Science and Technology Plan Project of Guangzhou City (201902020012, 202102021236, 201902020006); the 315 Opening Project of Guangdong Province Key Laboratory of Computational Science at the Sun Yat-seUniversity (2021013).
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Xie, G., Zhu, Y., Lin, Z. et al. HBRWRLDA: predicting potential lncRNA–disease associations based on hypergraph bi-random walk with restart. Mol Genet Genomics 297, 1215–1228 (2022). https://doi.org/10.1007/s00438-022-01909-y
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DOI: https://doi.org/10.1007/s00438-022-01909-y