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Article Open Access

Competing endogenous RNA regulatory network in papillary thyroid carcinoma

  • Authors:
    • Shouhua Chen
    • Xiaobin Fan
    • He Gu
    • Lili Zhang
    • Wenhua Zhao
  • View Affiliations / Copyright

    Affiliations: Department of Breast and Thyroid Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China, Department of Operation Room, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China, Department of Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
    Copyright: © Chen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 695-704
    |
    Published online on: May 11, 2018
       https://doi.org/10.3892/mmr.2018.9009
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Abstract

The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis. A support vector machine (SVM) classifier was built using 15 feature genes, and its classification effect was validated using two microarray data sets that were downloaded from the Gene Expression Omnibus (GEO) database. In addition, Gene Ontology function and Kyoto Encyclopedia Genes and Genomes pathway enrichment analyses were conducted for genes identified in the ceRNA network. A total of 506 samples, including 447 tumor samples and 59 normal samples, were obtained from The Cancer Genome Atlas (TCGA); 16 DE‑lncRNAs, 917 DEGs and 30 DE‑miRNAs were screened. The miRNA‑mRNA regulatory network comprised 353 nodes and 577 interactions. From these data, 15 feature genes with high predictive precision (>95%) were extracted from the network and were used to form an SVM classifier with an accuracy of 96.05% (486/506) for PTC samples downloaded from TCGA, and accuracies of 96.81 and 98.46% for GEO downloaded data sets. The ceRNA regulatory network comprised 596 lines (or interactions) and 365 nodes. Genes in the ceRNA network were significantly enriched in ‘neuron development’, ‘differentiation’, ‘neuroactive ligand‑receptor interaction’, ‘metabolism of xenobiotics by cytochrome P450’, ‘drug metabolism’ and ‘cytokine‑cytokine receptor interaction’ pathways. Hox transcript antisense RNA, miRNA‑206 and kallikrein‑related peptidase 10 were nodes in the ceRNA regulatory network of the selected feature gene, and they may serve import roles in the development of PTC.
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Copy and paste a formatted citation
Spandidos Publications style
Chen S, Fan X, Gu H, Zhang L and Zhao W: Competing endogenous RNA regulatory network in papillary thyroid carcinoma. Mol Med Rep 18: 695-704, 2018.
APA
Chen, S., Fan, X., Gu, H., Zhang, L., & Zhao, W. (2018). Competing endogenous RNA regulatory network in papillary thyroid carcinoma. Molecular Medicine Reports, 18, 695-704. https://doi.org/10.3892/mmr.2018.9009
MLA
Chen, S., Fan, X., Gu, H., Zhang, L., Zhao, W."Competing endogenous RNA regulatory network in papillary thyroid carcinoma". Molecular Medicine Reports 18.1 (2018): 695-704.
Chicago
Chen, S., Fan, X., Gu, H., Zhang, L., Zhao, W."Competing endogenous RNA regulatory network in papillary thyroid carcinoma". Molecular Medicine Reports 18, no. 1 (2018): 695-704. https://doi.org/10.3892/mmr.2018.9009
Copy and paste a formatted citation
x
Spandidos Publications style
Chen S, Fan X, Gu H, Zhang L and Zhao W: Competing endogenous RNA regulatory network in papillary thyroid carcinoma. Mol Med Rep 18: 695-704, 2018.
APA
Chen, S., Fan, X., Gu, H., Zhang, L., & Zhao, W. (2018). Competing endogenous RNA regulatory network in papillary thyroid carcinoma. Molecular Medicine Reports, 18, 695-704. https://doi.org/10.3892/mmr.2018.9009
MLA
Chen, S., Fan, X., Gu, H., Zhang, L., Zhao, W."Competing endogenous RNA regulatory network in papillary thyroid carcinoma". Molecular Medicine Reports 18.1 (2018): 695-704.
Chicago
Chen, S., Fan, X., Gu, H., Zhang, L., Zhao, W."Competing endogenous RNA regulatory network in papillary thyroid carcinoma". Molecular Medicine Reports 18, no. 1 (2018): 695-704. https://doi.org/10.3892/mmr.2018.9009
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