title: Analysis of hepatocellular carcinoma and metastatic hepatic carcinoma via functional modules in a protein-protein interaction network.
abstract: BACKGROUND
  This study aims to identify protein clusters with potential functional relevance in the pathogenesis of hepatocellular carcinoma (HCC) and metastatic hepatic carcinoma using network analysis.
  
  
  METHODS
  We used human protein interaction data to build a protein-protein interaction network with Cytoscape and then derived functional clusters using MCODE. Combining the gene expression profiles, we calculated the functional scores for the clusters and selected statistically significant clusters. Meanwhile, Gene Ontology was used to assess the functionality of these clusters. Finally, a support vector machine was trained on the gold standard data sets.
  
  
  RESULTS
  The differentially expressed genes of HCC were mainly involved in metabolic and signaling processes. We acquired 13 significant modules from the gene expression profiles. The area under the curve value based on the differentially expressed modules were 98.31%, which outweighed the classification with DEGs.
  
  
  CONCLUSIONS
  Differentially expressed modules are valuable to screen biomarkers combined with functional modules.
authors.forename: Jun
authors.initials: J
authors.lastname: Pan
authors.forename: Zhijie
authors.initials: Z
authors.lastname: Cong
authors.forename: Ming
authors.initials: M
authors.lastname: Zhong
authors.affiliation: Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China.
authors.forename: Yihui
authors.initials: Y
authors.lastname: Sun
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D009362:Neoplasm Metastasis / Q000235:genetics*; D060066:Protein Interaction Maps / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor