TCGA dataset‑based construction and integrated analysis of aberrantly expressed long non‑coding RNA mediated competing endogenous RNA network in gastric cancer

  • Authors:
    • Wenting He
    • Dachuan Zhang
    • Xiaodong Li
    • Jun Wu
    • Xuanxuan Yang
    • Qi Wang
    • Wenbin Lu
    • Jingting Jiang
    • Changping Wu
  • View Affiliations

  • Published online on: September 21, 2018     https://doi.org/10.3892/or.2018.6720
  • Pages: 3511-3522
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Abstract

The aberrant expression of long non‑coding RNAs (lncRNAs) has been confirmed to play a pivotal role in tumor initiation and development. LncRNAs can interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate the expression of target genes in various cancers. In the present study, the authors investigated the functions of lncRNAs as ceRNAs in gastric cancer (GC) and their implications for the prognosis. The RNA sequencing profiles of 372 tumor samples and 32 adjacent non‑tumor gastric samples were downloaded from The Cancer Genome Atlas (TCGA) database. The differential expression of RNAs was identified using the ʻedgeRʼ package in R language software. Survival analysis was estimated based on Kaplan‑Meier curves. The Gene Ontology biological processes and the Kyoto Encyclopedia of Genes and Genomes pathways were analyzed for differentially expressed mRNAs. Finally, a total of 999 lncRNAs, 137 miRNAs and 1629 mRNAs were identified as differentially expressed (DE) in GC with log fold change (FC) thresholds >2 and adjusted P‑values <0.01. A ceRNA network was constructed with 65 DElncRNAs, nine DEmiRNAs and 24 DEmRNAs. Of the 65 DElncRNAs in the ceRNA network, nine were identified to be significantly associated with overall survival (P<0.05). A total of four DElncRNAs from the ceRNA network were validated by reverse transcription‑quantitative polymerase chain reaction and revealed to be associated with tumorigenesis and/or progression. In conclusion, the results of the present study provide information on the role of the ceRNA network in GC. These identified novel lncRNAs are potential candidate biomarkers and require further studies.

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December 2018
Volume 40 Issue 6

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Copy and paste a formatted citation
APA
He, W., Zhang, D., Li, X., Wu, J., Yang, X., Wang, Q. ... Wu, C. (2018). TCGA dataset‑based construction and integrated analysis of aberrantly expressed long non‑coding RNA mediated competing endogenous RNA network in gastric cancer. Oncology Reports, 40, 3511-3522. https://doi.org/10.3892/or.2018.6720
MLA
He, W., Zhang, D., Li, X., Wu, J., Yang, X., Wang, Q., Lu, W., Jiang, J., Wu, C."TCGA dataset‑based construction and integrated analysis of aberrantly expressed long non‑coding RNA mediated competing endogenous RNA network in gastric cancer". Oncology Reports 40.6 (2018): 3511-3522.
Chicago
He, W., Zhang, D., Li, X., Wu, J., Yang, X., Wang, Q., Lu, W., Jiang, J., Wu, C."TCGA dataset‑based construction and integrated analysis of aberrantly expressed long non‑coding RNA mediated competing endogenous RNA network in gastric cancer". Oncology Reports 40, no. 6 (2018): 3511-3522. https://doi.org/10.3892/or.2018.6720