title: Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules.
abstract: Long non-coding RNAs (lncRNAs) have been found to play important roles in various biological processes; however, many of their functions remain unclear. In this study, we present a novel approach to identify the lncRNA-associated protein-protein interaction (PPI) modules and ascertain their functions in human lung squamous cell carcinoma. We collected lncRNA and mRNA expression profiles of lung squamous cell carcinoma from The Cancer Genome Atlas. To identify the lncRNA-associated PPI modules, lncRNA-mRNA co-expression networks were first constructed based on the mutual ranks of expression correlations. Next, we examined whether the co-expressed mRNAs of a specific lncRNA were closely connected by PPIs. For this, a significantly connected mRNA set was considered to be the lncRNA-associated PPI module. Finally, the prospective functions of a lncRNA was inferred using Gene Ontology enrichment analysis on the associated module. We found that lncRNA-associated PPI modules were subtype-dependent and each subtype had unique molecular mechanisms. In addition, antisense lncRNAs and sense genes tended to be functionally associated. Our results might provide new directions for understanding lncRNA regulations in lung cancer. The analysis pipeline was implemented in a web tool, available at http://lncin.ym.edu.tw/.
authors: Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.|Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Taiwan.
authors: Chih-Hsun
authors: CH
authors: Wu
authors: Department of Life Science, National Taiwan University, Taipei 106, Taiwan.
authors: Chia-Lang
authors: CL
authors: Hsu
authors: Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Taiwan.
authors: Pei-Chun
authors: PC
authors: Lu
authors: Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.|Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
authors: Wen-Chang
authors: WC
authors: Lin
authors: Department of Life Science, National Taiwan University, Taipei 106, Taiwan.|Graduate Institute of Biomedical Electronics and Bioinformatics, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan.
authors: Hsueh-Fen
authors: HF
authors: Juan
authors: Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 112, Taiwan.
authors: Hsuan-Cheng
authors: HC
authors: Huang
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D051272:Glucose Transporter Type 1 / Q000235:genetics; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D060066:Protein Interaction Maps; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism
chemical_list: D051272:Glucose Transporter Type 1; C542359:MIRN143 microRNA, human; D035683:MicroRNAs; D016372:RNA, Antisense; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012334:RNA, Neoplasm; C495677:SLC2A1 protein, human