Open Access

A prognostic prediction system for hepatocellular carcinoma based on gene co‑expression network

  • Authors:
    • Lianyue Guan
    • Qiang Luo
    • Na Liang
    • Hongyu Liu
  • View Affiliations

  • Published online on: April 17, 2019     https://doi.org/10.3892/etm.2019.7494
  • Pages: 4506-4516
  • Copyright: © Guan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

In the present study, gene expression data of hepatocellular carcinoma (HCC) were analyzed by using a multi‑step Bioinformatics approach to establish a novel prognostic prediction system. Gene expression profiles were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The overlapping differentially expressed genes (DEGs) between these two datasets were identified using the limma package in R. Prognostic genes were further identified by Cox regression using the survival package. The significantly co‑expressed gene pairs were selected using the R function cor to construct the co‑expression network. Functional and module analyses were also performed. Next, a prognostic prediction system was established by Bayes discriminant analysis using the discriminant.bayes function in the e1071 package, which was further validated in another independent GEO dataset. A total of 177 overlapping DEGs were identified from TCGA and the GEO dataset (GSE36376). Furthermore, 161 prognostic genes were selected and the top six were stanniocalcin 2, carbonic anhydrase 12, cell division cycle (CDC) 20, deoxyribonuclease 1 like 3, glucosylceramidase β3 and metallothionein 1G. A gene co‑expression network involving 41 upregulated and 52 downregulated genes was constructed. SPC24, endothelial cell specific molecule 1, CDC20, CDCA3, cyclin (CCN) E1 and chromatin licensing and DNA replication factor 1 were significantly associated with cell division, mitotic cell cycle and positive regulation of cell proliferation. CCNB1, CCNE1, CCNB2 and stratifin were clearly associated with the p53 signaling pathway. A prognostic prediction system containing 55 signature genes was established and then validated in the GEO dataset GSE20140. In conclusion, the present study identified a number of prognostic genes and established a prediction system to assess the prognosis of HCC patients.

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Copy and paste a formatted citation
APA
Guan, L., Luo, Q., Liang, N., & Liu, H. (2019). A prognostic prediction system for hepatocellular carcinoma based on gene co‑expression network. Experimental and Therapeutic Medicine, 17, 4506-4516. https://doi.org/10.3892/etm.2019.7494
MLA
Guan, L., Luo, Q., Liang, N., Liu, H."A prognostic prediction system for hepatocellular carcinoma based on gene co‑expression network". Experimental and Therapeutic Medicine 17.6 (2019): 4506-4516.
Chicago
Guan, L., Luo, Q., Liang, N., Liu, H."A prognostic prediction system for hepatocellular carcinoma based on gene co‑expression network". Experimental and Therapeutic Medicine 17, no. 6 (2019): 4506-4516. https://doi.org/10.3892/etm.2019.7494