title: Aberrant expression of cell cycle and material metabolism related genes contributes to hepatocellular carcinoma occurrence.
abstract: This study aims to deepen our understanding of the molecular mechanism underlying the occurrence of hepatocellular carcinoma (HCC). We first downloaded a gene expression profile dataset GSE29721 (10 HCC and 10 control samples) from Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/). Differentially expressed genes (DEGs) were identified by the paired t-test using limma package. Pathway and functional enrichment analyses were performed with DAVID tools. Transcription factors were annotated with TRANSFAC database and tumor associated genes (TAGs) were annotated with TAG and TSGene databases. Protein-protein interaction (PPI) network was conducted using STRING online tool and function module was further identified with BioNet package. Totally, 527 up-regulated DEGs and 587 down-regulated DEGs were identified. GO functional and KEGG pathway enrichment analyses showed that the up-regulated DEGs were mainly related to cell division and cell cycle, while the down-regulated DEGs were largely related to material metabolism, especially secondary metabolism. Proteins encoded by DEGs CDK1, BUB1, CDC20, NCAPG, NDC80, CDCA8, MAD2L1, CCNB1, CCNA2 and BIRC5 were hub genes with high degrees in the PPI network; further module analysis detected a subnetwork consisting of 55 proteins, such as CYP2B6, ACAA1, BHMT and ALDH2. Taken together, aberrant expression of cell cycle related genes (e.g., CDK1, CCNA2, CCNB1, BUB1, MAD2L1 and CDC20) and material metabolism related genes (e.g., CYP2B6, ACAA1, BHMT and ALDH2) may contribute to HCC occurrence.
authors.affiliation: Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China. Electronic address: yanhxianh@163.com.
authors.forename: Hongxian
authors.initials: H
authors.lastname: Yan
authors.affiliation: Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471003, PR China.
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China.
authors.forename: Quan
authors.initials: Q
authors.lastname: Shen
authors.affiliation: Department of Hepatobiliary Surgery, Henan Cancer Hospital, Zhengzhou, Henan 650000, PR China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Tian
authors.affiliation: Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China.
authors.forename: Qingfeng
authors.initials: Q
authors.lastname: Jiang
authors.affiliation: Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China.
authors.forename: Linbo
authors.initials: L
authors.lastname: Gao
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002453:Cell Cycle; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D059467:Transcriptome
keywords: Differentially expressed genes; Functional enrichment analysis; Hepatocellular carcinoma; Pathway enrichment analysis; Protein-protein interaction