IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity.
Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Liang
L
Cheng
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Hongbo
H
Shi
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Zhenzhen
Z
Wang
School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China.
Yang
Y
Hu
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Haixiu
H
Yang
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Chen
C
Zhou
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Jie
J
Sun
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
Meng
M
Zhou
D002352:Carrier Proteins / Q000235:genetics; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D008957:Models, Genetic; D009687:Nuclear Proteins / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*
D002352:Carrier Proteins; C000624704:MRNIP protein, human; D035683:MicroRNAs; D009687:Nuclear Proteins; D062085:RNA, Long Noncoding
integrated network; lncRNA functional similarity; lncRNA-disease associations; long non-coding RNAs