Exploring functions of long noncoding RNAs across multiple cancers through co-expression network

• Published in: Scientific reports Vol. 7; no. 1; pp. 754 - 13
• Main Authors: Li, Suqing, Li, Bin, Zheng, Yuanting, Li, Menglong, Shi, Leming, Pu, Xuemei
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07.04.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 38/91; 631/114; 631/208/199; 631/208/514/1949; 631/67/1857; Cancer; Cell adhesion; Cell adhesion & migration; Cell cycle; Computational Biology - methods; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene Ontology; Gene Regulatory Networks; Genomes; Humanities and Social Sciences; Humans; Inflammation; Molecular Sequence Annotation; Morphogenesis; multidisciplinary; Neoplasms - genetics; Neoplasms - metabolism; Neoplasms - mortality; Neoplasms - pathology; Prognosis; Ribonucleic acid; RNA; RNA, Long Noncoding - genetics; Science; Science (multidisciplinary); Signal Transduction; Transcriptome
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-00856-8

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.