Open Access

Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma

  • Authors:
    • Meng‑Hui Zhang
    • Qin‑Hai Shen
    • Zhao‑Min Qin
    • Qiao‑Ling Wang
    • Xi Chen
  • View Affiliations

  • Published online on: August 23, 2016     https://doi.org/10.3892/ol.2016.5039
  • Pages: 3285-3295
  • Copyright: © Zhang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The objective of the present study is to identify significant genes and pathways associated with hepatocellular carcinoma (HCC) by systematically tracking the dysregulated modules of re‑weighted protein‑protein interaction (PPI) networks. Firstly, normal and HCC PPI networks were inferred and re‑weighted based on Pearson correlation coefficient. Next, modules in the PPI networks were explored by a clique‑merging algorithm, and disrupted modules were identified utilizing a maximum weight bipartite matching in non‑increasing order. Then, the gene compositions of the disrupted modules were studied and compared with differentially expressed (DE) genes, and pathway enrichment analysis for these genes was performed based on Expression Analysis Systematic Explorer. Finally, validations of significant genes in HCC were conducted using reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) analysis. The present study evaluated 394 disrupted module pairs, which comprised 236 dysregulated genes. When the dysregulated genes were compared with 211 DE genes, a total of 26 common genes [including phospholipase C beta 1, cytochrome P450 (CYP) 2C8 and CYP2B6] were obtained. Furthermore, 6 of these 26 common genes were validated by RT‑qPCR. Pathway enrichment analysis of dysregulated genes demonstrated that neuroactive ligand‑receptor interaction, purine and drug metabolism, and metabolism of xenobiotics mediated by CYP were significantly disrupted pathways. In conclusion, the present study greatly improved the understanding of HCC in a systematic manner and provided potential biomarkers for early detection and novel therapeutic methods.
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November-2016
Volume 12 Issue 5

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Copy and paste a formatted citation
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Spandidos Publications style
Zhang MH, Shen QH, Qin ZM, Wang QL and Chen X: Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma. Oncol Lett 12: 3285-3295, 2016
APA
Zhang, M., Shen, Q., Qin, Z., Wang, Q., & Chen, X. (2016). Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma. Oncology Letters, 12, 3285-3295. https://doi.org/10.3892/ol.2016.5039
MLA
Zhang, M., Shen, Q., Qin, Z., Wang, Q., Chen, X."Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma". Oncology Letters 12.5 (2016): 3285-3295.
Chicago
Zhang, M., Shen, Q., Qin, Z., Wang, Q., Chen, X."Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma". Oncology Letters 12, no. 5 (2016): 3285-3295. https://doi.org/10.3892/ol.2016.5039