LLCLPLDA: a novel model for predicting lncRNA–disease associations

Long noncoding RNAs play a significant role in the occurrence of diseases. Thus, studying the relationship prediction between lncRNAs and disease is becoming more popular. Researchers hope to determine effective treatments by revealing the occurrence and development of diseases at the molecular leve...

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Bibliographic Details
Published in:Molecular genetics and genomics : MGG 2019-12, Vol.294 (6), p.1477-1486
Main Authors: Xie, Guobo, Huang, Shuhuang, Luo, Yu, Ma, Lei, Lin, Zhiyi, Sun, Yuping
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Biochemistry
Biomedical and Life Sciences
Breast cancer
Cervical cancer
Cervix
Disease
Glioma
Human Genetics
Life Sciences
Microbial Genetics and Genomics
Original Article
Plant Genetics and Genomics
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Summary:Long noncoding RNAs play a significant role in the occurrence of diseases. Thus, studying the relationship prediction between lncRNAs and disease is becoming more popular. Researchers hope to determine effective treatments by revealing the occurrence and development of diseases at the molecular level. However, the traditional biological experimental way to verify the association between lncRNAs and disease is very time-consuming and expensive. Therefore, we developed a method called LLCLPLDA to predict potential lncRNA–disease associations. First, locality-constrained linear coding (LLC) is leveraged to project the features of lncRNAs and diseases to local-constraint features, and then, a label propagation (LP) strategy is used to mix up the initial association matrix and the obtained features of lncRNAs and diseases. To demonstrate the performance of our method, we compared LLCLPLDA with five methods in the leave-one-out cross-validation and fivefold cross-validation scheme, and the experimental results show that the proposed method outperforms the other five methods. Additionally, we conducted case studies on three diseases: cervical cancer, gliomas, and breast cancer. The top five predicted lncRNAs for cervical cancer and gliomas were verified, and four of the five lncRNAs for breast cancer were also confirmed.
ISSN:1617-4615
1617-4623
DOI:10.1007/s00438-019-01590-8