title: Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network.
abstract: LncRNAs play pivotal roles in many important biological processes, but research on the functions of lncRNAs in human disease is still in its infancy. Therefore, it is urgent to prioritize lncRNAs that are potentially associated with diseases. In this work, we developed a novel algorithm, LncPriCNet, that uses a multi-level composite network to prioritize candidate lncRNAs associated with diseases. By integrating genes, lncRNAs, phenotypes and their associations, LncPriCNet achieves an overall performance superior to that of previous methods, with high AUC values of up to 0.93. Notably, LncPriCNet still performs well when information on known disease lncRNAs is lacking. When applied to breast cancer, LncPriCNet identified known breast cancer-related lncRNAs, revealed novel lncRNA candidates and inferred their functions via pathway analysis. We further constructed the human disease-lncRNA landscape, revealed the modularity of the disease-lncRNA network and identified several lncRNA hotspots. In summary, LncPriCNet is a useful tool for prioritizing disease-related lncRNAs and may facilitate understanding of the molecular mechanisms of human disease at the lncRNA level.
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200031, China.
authors.forename: Qianlan
authors.initials: Q
authors.lastname: Yao
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200031, China.
authors.forename: Leilei
authors.initials: L
authors.lastname: Wu
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Li Guang
authors.initials: LG
authors.lastname: Yang
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Yidi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200031, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: He
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Fangyoumin
authors.initials: F
authors.lastname: Feng
authors.affiliation: CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200031, China.|CAS Key Laboratory for Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.|Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China.
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D005260:Female; D053263:Gene Regulatory Networks; D006801:Humans; D008954:Models, Biological; D010641:Phenotype; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012372:ROC Curve
chemical_list: D062085:RNA, Long Noncoding