title: Comprehensive network analysis of genes expressed in human oropharyngeal cancer.
abstract: OBJECTIVE
  Oropharyngeal cancer (OPC) is the eighth most common cancer worldwide, however the genes involved in the development of OPC have been reported few. We constructed a co-expression network to extend knowledge of the molecular biomarkers in OPC development.
  
  
  METHODS
  Microarray data of HPV-active, -inactive, -negative OPC and normal benign tissue (uvula, tonsil) (Series GSE55550) were retrieved from NCBI GEO DataSets. We performed co-expression analysis of OPC transcriptome data by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off using 13 guide genes.
  
  
  RESULTS
  The OPC subnetwork contained three clusters: cell cycle (62 node genes and 125 edge genes), immune system (44 node genes and 70 edge genes) and organ morphogenesis (128 node gene and 215 edge genes) process separately.
  
  
  CONCLUSIONS
  Our co-expression analysis includes separated transcriptomes of OPC, which is a useful resource for OPC researchers to elucidate important and complex biological events, to prevent and to predict cancer.
authors.affiliation: Department of Periodontology, The Stomatology Affiliated Hospital of Harbin Medical University, 143 Yiman Street, Nangang District, Harbin, Heilongjiang, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Periodontology, The Stomatology Affiliated Hospital of Harbin Medical University, 143 Yiman Street, Nangang District, Harbin, Heilongjiang, China.
authors.forename: Simin
authors.initials: S
authors.lastname: Li
authors.affiliation: Center for Endemic Disease Control, The China Center for Disease Control and Prevention and Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang, China.
authors.forename: Han
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Stomatology, The Fourth Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Nangang District, Harbin, Heilongjiang, China. Electronic address: liangjia_bi@126.com.
authors.forename: Liangjia
authors.initials: L
authors.lastname: Bi
mesh_terms: D015331:Cohort Studies; D004279:DNA, Viral / Q000235:genetics; D016208:Databases, Factual; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D009959:Oropharyngeal Neoplasms / Q000453:epidemiology / Q000235:genetics* / Q000821:virology; D027383:Papillomaviridae / Q000235:genetics
chemical_list: D004279:DNA, Viral