title: Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis.
abstract: We performed weighted gene coexpression network analysis (WGCNA) to gain insights into the molecular aspects of hepatocellular carcinoma (HCC). Raw microarray datasets (including 488 samples) were downloaded from the Gene Expression Omnibus (GEO) website. Data were normalized using the RMA algorithm. We utilized the WGCNA to identify the coexpressed genes (modules) after non-specific filtering. Correlation and survival analyses were conducted using the modules, and gene ontology (GO) enrichment was applied to explore the possible mechanisms. Eight distinct modules were identified by the WGCNA. Pink and red modules were associated with liver function, whereas turquoise and black modules were inversely correlated with tumor staging. Poor outcomes were found in the low expression group in the turquoise module and in the high expression group in the red module. In addition, GO enrichment analysis suggested that inflammation, immune, virus-related, and interferon-mediated pathways were enriched in the turquoise module. Several potential biomarkers, such as cyclin-dependent kinase 1 (CDK1), topoisomerase 2α (TOP2A), and serpin peptidase inhibitor clade C (antithrombin) member 1 (SERPINC1), were also identified. In conclusion, gene signatures identified from the genome-based assays could contribute to HCC stratification. WGCNA was able to identify significant groups of genes associated with cancer prognosis.
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Xinsen
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Runchen
authors.initials: R
authors.lastname: Miao
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Qu
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Pang
authors.affiliation: Department of Hepatobiliary Surgery, the First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xian, 710061, China. liuchangdoctor@163.com.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D012044:Regression Analysis
keywords: coexpression; hepatocellular carcinoma; microarray; module; prognosis