title: Bioinformatics analysis of hepatitis C virus genotype 2a-induced human hepatocellular carcinoma in Huh7 cells.
abstract: Hepatocellular carcinoma (HCC) is a liver cancer that could be induced by hepatitis C virus genotype 2a Japanese fulminant hepatitis-1 (JFH-1) strain. The aim of this study was to investigate the molecular mechanisms of HCC. The microarray data GSE20948 includes 14 JFH-1- and 14 mock (equal volume of medium [control])-infected Huh7 samples. The data were downloaded from the Gene Expression Omnibus. After data processing, soft cluster analyses were performed to identify co-regulated genes with similar temporal expression patterns. Functional and pathway enrichment analyses, as well as functional annotation analysis, were performed. Subsequently, combined networks of protein-protein interaction network, microRNA regulatory network, and transcriptional regulatory network were constructed. Hub nodes, modules, and five clusters of co-regulated genes were also identified. In total, 173 up and 207 down co-regulated genes were separately identified in JFH-1-infected Huh7 cells compared with those of control cells. Functional enrichment analysis indicated that up co-regulated genes were related to skeletal system morphogenesis and neuron differentiation and down co-regulated genes were related to steroid/cholesterol/sterol metabolisms. Hub genes (such as IRF1, GBP1, ICAM1, Foxa1, DHCR7, HMGCS2, and MSMO1) were identified. Transcription factors IRF1 and Foxa1 were the targets of miR-130a, miR-17-5p, and miR-20a. PPARGC1A was targeted by miR-29 family, and MSMO1 was the target of miR-23 family. Hub nodes (such as IRF1, GBP1, ICAM1, Foxa1, DHCR7, HMGCS2, and MSMO1) and microRNAs might be used as candidate biomarkers of JFH-1-infected HCC.
authors.affiliation: Inspection Center, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China; Key Laboratory of TB Prevention and Cure of Suzhou City, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.affiliation: Key Laboratory of TB Prevention and Cure of Suzhou City, Suzhou, Jiangsu Province, People's Republic of China; Department of Respiratory Medicine, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Meiying
authors.initials: M
authors.lastname: Wu
authors.affiliation: Inspection Center, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China; Key Laboratory of TB Prevention and Cure of Suzhou City, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Hui
authors.initials: H
authors.lastname: Chen
authors.affiliation: Inspection Center, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China; Key Laboratory of TB Prevention and Cure of Suzhou City, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Junchi
authors.initials: J
authors.lastname: Xu
authors.affiliation: Inspection Center, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Minjuan
authors.initials: M
authors.lastname: Wu
authors.affiliation: Department of Infectious Diseases, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Infectious Diseases, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Feng
authors.initials: F
authors.lastname: Qian
authors.affiliation: Key Laboratory of TB Prevention and Cure of Suzhou City, Suzhou, Jiangsu Province, People's Republic of China; Department of Infectious Diseases, Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China.
authors.forename: Junhua
authors.initials: J
authors.lastname: Xu
keywords: co-regulated genes; combined network; microRNAs; soft cluster analysis; transcription factors
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