ILNCSIM: improved lncRNA functional similarity calculation model
Huang, Yu-An1; Chen, Xing2,3; You, Zhu-Hong4; Huang, De-Shuang5; Chan, Keith C. C.6
Source PublicationONCOTARGET
AbstractIncreasing observations have indicated that lncRNAs play a significant role in various critical biological processes and the development and progression of various human diseases. Constructing lncRNA functional similarity networks could benefit the development of computational models for inferring lncRNA functions and identifying lncRNA-disease associations. However, little effort has been devoted to quantifying lncRNA functional similarity. In this study, we developed an Improved LNCRNA functional SIMilarity calculation model (ILNCSIM) based on the assumption that lncRNAs with similar biological functions tend to be involved in similar diseases. The main improvement comes from the combination of the concept of information content and the hierarchical structure of disease directed acyclic graphs for disease similarity calculation. ILNCSIM was combined with the previously proposed model of Laplacian Regularized Least Squares for lncRNA-Disease Association to further evaluate its performance. As a result, new model obtained reliable performance in the leave-one-out cross validation (AUCs of 0.9316 and 0.9074 based on MNDR and Lnc2cancer databases, respectively), and 5-fold cross validation (AUCs of 0.9221 and 0.9033 for MNDR and Lnc2cancer databases), which significantly improved the prediction performance of previous models. It is anticipated that ILNCSIM could serve as an effective lncRNA function prediction model for future biomedical researches.
KeywordlncRNAs functional similarity disease cancer directed acyclic graph
Funding ProjectNational Natural Science of Foundation of China[11301517] ; National Natural Science of Foundation of China[61572506] ; National Center for Mathematics and Interdisciplinary Sciences, CAS
WOS Research AreaOncology ; Cell Biology
WOS SubjectOncology ; Cell Biology
WOS IDWOS:000377722300077
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Document Type期刊论文
Corresponding AuthorChen, Xing; You, Zhu-Hong
Affiliation1.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen 518060, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
3.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China
4.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou 221116, Peoples R China
5.Tongji Univ, Sch Elect & Informat Engn, Shanghai 201804, Peoples R China
6.Hong Kong Polytech Univ, Dept Comp, Hong Kong, Hong Kong, Peoples R China
Recommended Citation
GB/T 7714
Huang, Yu-An,Chen, Xing,You, Zhu-Hong,et al. ILNCSIM: improved lncRNA functional similarity calculation model[J]. ONCOTARGET,2016,7(18):25902-25914.
APA Huang, Yu-An,Chen, Xing,You, Zhu-Hong,Huang, De-Shuang,&Chan, Keith C. C..(2016).ILNCSIM: improved lncRNA functional similarity calculation model.ONCOTARGET,7(18),25902-25914.
MLA Huang, Yu-An,et al."ILNCSIM: improved lncRNA functional similarity calculation model".ONCOTARGET 7.18(2016):25902-25914.
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