title: Identification of genes involved in Epstein-Barr virus-associated nasopharyngeal carcinoma.
abstract: Nasopharyngeal carcinoma (NPC) is the most common cancer originating from the nasopharynx, and can be induced by infection with Epstein-Barr virus (EBV). To study the mechanisms of EBV-associated NPC, a microarray of the GSE12452 dataset was analyzed. GSE12452 was downloaded from Gene Expression Omnibus and consisted of 31 NPC samples and 10 normal healthy nasopharyngeal tissue samples. The differentially-expressed genes (DEGs) were screened using the linear models for microarray data package in R. Using Database for Annotation, Visualization and Integrated Discovery software, potential functions of the DEGs were predicted by Gene Ontology and pathway enrichment analyses. With the information from the Search Tool for the Retrieval of Interacting Genes/Proteins database, the protein-protein interaction (PPI) network was visualized by Cytoscape. Furthermore, modules of the PPI network were searched using ClusterONE in Cytoscape. A total of 951 DEGs were screened in the NPC samples compared with the normal healthy nasopharyngeal tissue samples. Function enrichment indicated that the upregulated genes were associated with the cell cycle, cytoskeleton organization and DNA metabolism. Meanwhile, the downregulated genes were mainly associated with cell differentiation, hormone metabolism, inflammatory response and immune response. PPI networks for the DEGs suggested that upregulated mitotic arrest deficient 2-like 1 (MAD2L1; degree=133), proliferating cell nuclear antigen (PCNA; degree=125) and cyclin B1 (CCNB1; degree=115), and downregulated member A1 of aldehyde dehydrogenase 1 (ALDH1A1; degree=15) may be of great importance as they exhibited higher degrees on interaction. Mucin 1 (MUC1) was a key node of module 4. Overall, the study indicated thatMAD2L1,CCNB1,PCNA,ALDH1A1andMUC1may have a correlation with EBV-associated NPC.
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China; Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, Jiangsu 210008, P.R. China.
authors.forename: Junguo
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Ophthalmology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China.
authors.forename: Fang
authors.initials: F
authors.lastname: Mei
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China; Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, Jiangsu 210008, P.R. China.
authors.forename: Xia
authors.initials: X
authors.lastname: Gao
authors.affiliation: Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China; State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China.
authors.forename: Shoulin
authors.initials: S
authors.lastname: Wang
keywords: Epstein-Barr virus; differentially-expressed genes; module analysis; nasopharyngeal carcinoma; protein-protein interaction network