Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis

  • Authors:
    • Xiaojie Lu
    • Kun Ye
    • Kailin Zou
    • Jinlian Chen
  • View Affiliations

  • Published online on: August 20, 2014     https://doi.org/10.3892/or.2014.3425
  • Pages: 1845-1852
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Abstract

To screen out copy number variation (CNV)-driven differentially expressed genes (DEGs) in liver cancer and advance our understanding of the pathogenesis, an integrated analysis of liver cancer-related CNV data from The Cancer Genome Atlas (TCGA) and gene expression data from EBI Array Express database were performed. The DEGs were identified by package limma based on the cut-off of |log2 (fold-change)| >0.585 and adjusted p-value <0.05. Using hg19 annotation information provided by UCSC, liver cancer-related CNVs were then screened out. TF-target gene interactions were also predicted with information from UCSC using DAVID online tools. As a result, 25 CNV-driven genes were obtained, including tripartite motif containing 28 (TRIM28) and RanBP-type and C3HC4-type zinc finger containing 1 (RBCK1). In the transcriptional regulatory network, 8 known cancer-related transcription factors (TFs) interacted with 21 CNV-driven genes, suggesting that the other 8 TFs may be involved in liver cancer. These genes may be potential biomarkers for early detection and prevention of liver cancer. These findings may improve our knowledge of the pathogenesis of liver cancer. Nevertheless, further experiments are still needed to confirm our findings.
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November-2014
Volume 32 Issue 5

Print ISSN: 1021-335X
Online ISSN:1791-2431

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Copy and paste a formatted citation
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Spandidos Publications style
Lu X, Ye K, Zou K and Chen J: Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis. Oncol Rep 32: 1845-1852, 2014.
APA
Lu, X., Ye, K., Zou, K., & Chen, J. (2014). Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis. Oncology Reports, 32, 1845-1852. https://doi.org/10.3892/or.2014.3425
MLA
Lu, X., Ye, K., Zou, K., Chen, J."Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis". Oncology Reports 32.5 (2014): 1845-1852.
Chicago
Lu, X., Ye, K., Zou, K., Chen, J."Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis". Oncology Reports 32, no. 5 (2014): 1845-1852. https://doi.org/10.3892/or.2014.3425