title: Transcriptome sequencing identified hub genes for hepatocellular carcinoma by weighted-gene co-expression analysis.
abstract: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and it remains a challenge to understand the genetic mechanisms underlying hepatocarcinogenesis. A global gene network of differential expression profiles in HCC has yet to be fully characterized. In the present study, we performed transcriptome sequencing (mRNA and lncRNA) in liver cancer and cirrhotic tissues of nine HCC patients. We identified differentially expressed genes (DEGs) and constructed a weighted gene co-expression network for the DEGs. In total, 755 DEGs (747 mRNA and eight lncRNA) were identified, and several co-expression modules were significantly associated with HCC clinical traits, including tumor location, tumor grade, and the α-fetoprotein (AFP) level. Of note, we identified 15 hub genes in the module associated with AFP level, and three (SPX, AFP and ADGRE1) of four hub genes were validated in an independent HCC cohort (n=78). Identification of hub genes for HCC clinical traits has implications for further understanding of the molecular genetic basis of HCC.
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Pan
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Xianli
authors.initials: X
authors.lastname: Long
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Liting
authors.initials: L
authors.lastname: Song
authors.affiliation: Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China.
authors.forename: Dachun
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China.
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Dewei
authors.initials: D
authors.lastname: Li
authors.affiliation: Department of Hepatobiliary Surgery, Suining Central Hospital, Suining, Sichuan Province, P. R. China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Hepatobiliary Surgery, Henan Tumor Hospital, Zhenzhou, Henan Province, P.R. China.
authors.forename: Jiahua
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Xia
authors.initials: X
authors.lastname: Tang
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ren
authors.affiliation: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China.
authors.forename: Keyue
authors.initials: K
authors.lastname: Ding
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding
keywords: hepatocellular carcinoma; hub gene; transcriptome sequencing; weighted gene co-expression network