title: Exploring functions of long noncoding RNAs across multiple cancers through co-expression network.
abstract: In contrast to protein-coding genes, long-noncoding RNAs (lncRNAs) are much less well understood, despite increasing evidence indicating a wide range of their biological functions, and possible roles in various cancers. Based on public RNA-seq datasets of four solid cancer types, we here utilize Weighted Correlation Network Analysis (WGCNA) to propose a strategy for exploring the functions of lncRNAs altered in more than two cancer types, which we call onco-lncRNAs. Results indicate that cancer-expressed lncRNAs show high tissue specificity and are weakly expressed, more so than protein-coding genes. Most of the 236 onco-lncRNAs we identified have not been reported to have associations with cancers before. Our analysis exploits co-expression network to reveal that onco-lncRNAs likely play key roles in the multistep development of human cancers, covering a wide range of functions in genome stability maintenance, signaling, cell adhesion and motility, morphogenesis, cell cycle, immune and inflammatory response. These observations contribute to a more comprehensive understanding of cancer-associated lncRNAs, while demonstrating a novel and efficient strategy for subsequent functional studies of lncRNAs.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, 610064, China.
authors.forename: Suqing
authors.initials: S
authors.lastname: Li
authors.affiliation: Center for Pharmacogenomics, School of Life Sciences, and State Key Laboratory of Genetic Engineering and Shanghai Cancer Center/Cancer Institute, Fudan University, Shanghai, 201203, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: Center for Pharmacogenomics, School of Life Sciences, and State Key Laboratory of Genetic Engineering and Shanghai Cancer Center/Cancer Institute, Fudan University, Shanghai, 201203, China.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China.
authors.forename: Yuanting
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, 610064, China.
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
authors.affiliation: Center for Pharmacogenomics, School of Life Sciences, and State Key Laboratory of Genetic Engineering and Shanghai Cancer Center/Cancer Institute, Fudan University, Shanghai, 201203, China. lemingshi@fudan.edu.cn.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China. lemingshi@fudan.edu.cn.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: College of Chemistry, Sichuan University, Chengdu, 610064, China. xmpuscu@scu.edu.cn.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Pu
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006801:Humans; D058977:Molecular Sequence Annotation; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000401:mortality / Q000473:pathology; D011379:Prognosis; D062085:RNA, Long Noncoding / Q000235:genetics*; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding