Identification of significant biomarkers and pathways associated with gastric carcinogenesis by whole genome-wide expression profiling analysis

  • Authors:
    • Hong-Jun Fei
    • Song-Chang Chen
    • Jun-Yu Zhang
    • Shu-Yuan Li
    • Lan-Lan Zhang
    • Yi-Yao Chen
    • Chun-Xin Chang
    • Chen-Ming Xu
  • View Affiliations

  • Published online on: January 11, 2018     https://doi.org/10.3892/ijo.2018.4243
  • Pages:955-966
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Abstract

The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues. GSE13911, GSE19826 and GSE79973 were based on the GPL570 platform, and GSE29272 was based on the GPL96 platform. We screened out the DEGs from the two platforms and by selecting the intersection of these two platforms, we identified the common DEGs in the sequencing data from different laboratories. Finally, we obtained 3 upregulated and 34 downregulated DEGs in GC from 384 samples. As the number of downregulated DEGs was greater than that of the upregulated DEGs, functional analysis and pathway enrichment analysis were performed on the downregulated DEGs. Through our analysis, we identified the most significant genes associated with GC, such as secreted phosphoprotein 1 (SPP1), sulfatase 1 (SULF1), thrombospondin 2 (THBS2), ATPase H+/K+ transporting beta subunit (ATP4B), gastric intrinsic factor (GIF) and gastrokine 1 (GKN1). The prognostic power of these genes was corroborated in the Oncomine database and by Kaplan-Meier plotter (KM-plotter) analysis. Moreover, gastric acid secretion, collecting duct acid secretion, nitrogen metabolism and drug metabolism were significantly related to GC. Thus, these genes and pathways may be potential targets for improving the diagnosis and clinical effects in patients with GC.

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March 2018
Volume 52 Issue 3

Print ISSN: 1019-6439
Online ISSN:1791-2423

2016 Impact Factor: 3.079
Ranked #33/217 Oncology
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APA
Fei, H., Chen, S., Zhang, J., Li, S., Zhang, L., Chen, Y. ... Xu, C. (2018). Identification of significant biomarkers and pathways associated with gastric carcinogenesis by whole genome-wide expression profiling analysis. International Journal of Oncology, 52, 955-966. https://doi.org/10.3892/ijo.2018.4243
MLA
Fei, H., Chen, S., Zhang, J., Li, S., Zhang, L., Chen, Y., Chang, C., Xu, C."Identification of significant biomarkers and pathways associated with gastric carcinogenesis by whole genome-wide expression profiling analysis". International Journal of Oncology 52.3 (2018): 955-966.
Chicago
Fei, H., Chen, S., Zhang, J., Li, S., Zhang, L., Chen, Y., Chang, C., Xu, C."Identification of significant biomarkers and pathways associated with gastric carcinogenesis by whole genome-wide expression profiling analysis". International Journal of Oncology 52, no. 3 (2018): 955-966. https://doi.org/10.3892/ijo.2018.4243