title: A network biology approach to discover the molecular biomarker associated with hepatocellular carcinoma.
abstract: In recent years, high throughput technologies such as microarray platform have provided a new avenue for hepatocellular carcinoma (HCC) investigation. Traditionally, gene sets enrichment analysis of survival related genes is commonly used to reveal the underlying functional mechanisms. However, this approach usually produces too many candidate genes and cannot discover detailed signaling transduction cascades, which greatly limits their clinical application such as biomarker development. In this study, we have proposed a network biology approach to discover novel biomarkers from multidimensional omics data. This approach effectively combines clinical survival data with topological characteristics of human protein interaction networks and patients expression profiling data. It can produce novel network based biomarkers together with biological understanding of molecular mechanism. We have analyzed eighty HCC expression profiling arrays and identified that extracellular matrix and programmed cell death are the main themes related to HCC progression. Compared with traditional enrichment analysis, this approach can provide concrete and testable hypothesis on functional mechanism. Furthermore, the identified subnetworks can potentially be used as suitable targets for therapeutic intervention in HCC.
authors.affiliation: State Key Laboratory of Robotics and System, Bio-X Centre, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China ; Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Liwei
authors.initials: L
authors.lastname: Zhuang
authors.affiliation: Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Jiwu
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Ling
authors.affiliation: Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Liguo
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
authors.forename: Chengyan
authors.initials: C
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Robotics and System, Bio-X Centre, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Yili
authors.initials: Y
authors.lastname: Fu
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000302:isolation & purification; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D011379:Prognosis; D060066:Protein Interaction Maps / Q000235:genetics*; D016019:Survival Analysis
chemical_list: D014408:Biomarkers, Tumor