Open Access

Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy

  • Authors:
    • Jun Liu
    • Ping Hua
    • Li Hui
    • Li‑Li Zhang
    • Zhen Hu
    • Ying‑Wei Zhu
  • View Affiliations

  • Published online on: August 12, 2016     https://doi.org/10.3892/etm.2016.3599
  • Pages: 2109-2119
  • Copyright: © Liu et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )


Abstract

The objective of this study was to identify hub genes and pathways associated with hepatocellular carcinoma (HCC) by centrality analysis of a co‑expression network. A co‑expression network based on differentially expressed (DE) genes of HCC was constructed using the Differentially Co‑expressed Genes and Links (DCGL) package. Centrality analyses, for centrality of degree, clustering coefficient, closeness, stress and betweenness for the co‑expression network were performed to identify hub genes, and the hub genes were combined together to overcome inconsistent results. Enrichment analyses were conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, validation of hub genes was conducted utilizing reverse transcription‑polymerase chain reaction (RT‑PCR) analysis. In total, 260 DE genes between normal controls and HCC patients were obtained and a co‑expression network with 154 nodes and 326 edges was constructed. From this, 13 hub genes were identified according to degree, clustering coefficient, closeness, stress and betweenness centrality analysis. It was found that reelin (RELN), potassium voltage‑gated channel subfamily J member 10 (KCNJ10) and neural cell adhesion molecule 1 (NCAM1) were common hub genes across the five centralities, and the results of RT‑PCR analysis for RELN, KCNJ10 and NCAM1 were consistent with the centrality analyses. Pathway enrichment analysis of DE genes showed that cell cycle, metabolism of xenobiotics by cytochrome P450 and p53 signaling pathway were the most significant pathways. This study may contribute to understanding the molecular pathogenesis of HCC and provide potential biomarkers for its early detection and effective therapies.

Related Articles

Journal Cover

October-2016
Volume 12 Issue 4

Print ISSN: 1792-0981
Online ISSN:1792-1015

Sign up for eToc alerts

Recommend to Library

Copy and paste a formatted citation
x
Spandidos Publications style
Liu J, Hua P, Hui L, Zhang LL, Hu Z and Zhu YW: Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Exp Ther Med 12: 2109-2119, 2016
APA
Liu, J., Hua, P., Hui, L., Zhang, L., Hu, Z., & Zhu, Y. (2016). Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Experimental and Therapeutic Medicine, 12, 2109-2119. https://doi.org/10.3892/etm.2016.3599
MLA
Liu, J., Hua, P., Hui, L., Zhang, L., Hu, Z., Zhu, Y."Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy". Experimental and Therapeutic Medicine 12.4 (2016): 2109-2119.
Chicago
Liu, J., Hua, P., Hui, L., Zhang, L., Hu, Z., Zhu, Y."Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy". Experimental and Therapeutic Medicine 12, no. 4 (2016): 2109-2119. https://doi.org/10.3892/etm.2016.3599