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Comprehensive analysis of lncRNA biomarkers in kidney renal clear cell carcinoma by lncRNA-mediated ceRNA network

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  • Ke Gong
  • Ting Xie
  • Yong Luo
  • Hui Guo
  • Jinlan Chen
  • Zhiping Tan
  • Yifeng Yang
  • Li Xie

Abstract

Introduction: Kidney renal clear cell carcinoma (KIRC) has a high incidence globally, and its pathogenesis remains unclear. Long non-coding RNA (lncRNA), as a molecular sponge, participates in the regulation of competitive endogenous RNA (ceRNA). We aimed to construct a ceRNA network and screened out possible lncRNAs to predict KIRC prognosis. Material and methods: All KIRC data were downloaded from the TCGA database and screened to find the possible target lncRNA; a ceRNA network was designed. Next, GO functional enrichment and KEGG pathway of differentially expressed mRNA related to lncRNA were performed. We used Kaplan-Meier curve analysis to predict the survival of these RNAs. We used Cox regression analysis to construct a model to predict KIRC prognosis. Results: In the KIRC datasets, 1457 lncRNA, 54 miRNA and 2307 mRNA were screened out. The constructed ceRNA network contained 81 lncRNAs, nine miRNAs, and 17 mRNAs differentially expressed in KIRC. Survival analysis of all differentially expressed RNAs showed that 21 lncRNAs, four miRNAs, and two mRNAs were related to the overall survival rate. Cox regression analysis was performed again, and we found that eight lncRNAs were related to prognosis and used to construct predictive models. Three lnRNAs from independent samples were meaningful. Conclusion: The construction of ceRNA network was involved in the process and transfer of KIRC, and three lncRNAs may be potential targets for predicting KIRC prognosis.

Suggested Citation

  • Ke Gong & Ting Xie & Yong Luo & Hui Guo & Jinlan Chen & Zhiping Tan & Yifeng Yang & Li Xie, 2021. "Comprehensive analysis of lncRNA biomarkers in kidney renal clear cell carcinoma by lncRNA-mediated ceRNA network," PLOS ONE, Public Library of Science, vol. 16(6), pages 1-24, June.
    • Handle: RePEc:plo:pone00:0252452
    DOI: 10.1371/journal.pone.0252452
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    References listed on IDEAS

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    1. Yvonne Tay & John Rinn & Pier Paolo Pandolfi, 2014. "The multilayered complexity of ceRNA crosstalk and competition," Nature, Nature, vol. 505(7483), pages 344-352, January.
    2. Hawre Jalal & Petros Pechlivanoglou & Eline Krijkamp & Fernando Alarid-Escudero & Eva Enns & M. G. Myriam Hunink, 2017. "An Overview of R in Health Decision Sciences," Medical Decision Making, , vol. 37(7), pages 735-746, October.
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