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pmid:32848739
Construction and Analysis of the Tumor-Specific mRNA-miRNA-lncRNA Network in Gastric Cancer.
Xiaohao Zheng · Xiaohui Wang · Li Zheng · Hao Zhao · Wenbin Li · Bingzhi Wang · Liyan Xue · Yantao Tian · Yibin Xie
Frontiers in pharmacology · 2020 doi:10.3389/fphar.2020.01112
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Experiment
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Complete file
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Competing endogenous RNA (ceRNA) is commonly involved in the cancer gene expression regulation mechanism. Some ceRNA networks are recognized in gastric cancer; however, the prognosis-associated ceRNA network has not been fully identified using WGCNA. We performed WGCNA using datasets from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) to identify cancer-associated modules. The criteria of differentially expressed RNAs between normal stomach samples and gastric cancer samples were set at the false discovery rate (FDR) < 0.01 and |fold change (FC)| > 1.3. The ceRNA relationships obtained from the RNAinter database were examined by both the Pearson correlation test and hypergeometric test to confirm the mRNA-lncRNA regulation. Overlapped genes were recognized at the intersections of genes predicted by ceRNA relationships, differentially expressed genes, and genes in cancer-specific modules. These were then used for univariate and multivariate Cox analyses to construct a risk score model. The ceRNA network was constructed based on the genes in this model. WGCNA-uncovered genes in the green and turquoise modules are those most associated with gastric cancer. Eighty differentially expressed genes were observed to have potential prognostic value, which led to the identification of 12 prognosis-related mRNAs (KIF15, FEN1, ZFP69B, SP6, SPARC, TTF2, MSI2, KYNU, ACLY, KIF21B, SLC12A7, and ZNF823) to construct a risk score model. The risk genes were validated using the GSE62254 and GSE84433 datasets, with 0.82 as the universal cutoff value. 12 genes, 12 lncRNAs, and 35 miRNAs were used to build a ceRNA network with 86 dysregulated lncRNA-mRNA ceRNA pairs. Finally, we developed a 12-gene signature from both prognosis-related and tumor-specific genes, and then constructed a ceRNA network in gastric cancer. 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competing endogenous RNA pairs.", "rows": [["Genes", "lncRNAs", "miRNAs", "hyperPValue", "Correlation", "corPValue"], ["SPARC", "OIP5-AS1", "hsa-miR-367-3p,hsa-miR-424-5p,hsa-miR-143-3p", "3.24E-04", "1.23E-01", "4.58E-03"], ["SLC12A7", "MCF2L-AS1", "hsa-miR-105-5p", "3.85E-02", "2.67E-01", "4.97E-09"], ["SLC12A7", "TMPO-AS1", "hsa-let-7c-5p,hsa-let-7b-5p,hsa-let-7a-5p,hsa-let-7f-5p,hsa-let-7d-5p,hsa-let-7i-5p,hsa-let-7e-5p,hsa-let-7g-5p", "3.17E-11", "1.07E-01", "1.21E-02"], ["KYNU", "HCP5", "hsa-miR-106b-5p,hsa-miR-106a-5p", "2.96E-04", "2.33E-01", "3.11E-07"], ["TTF2", "DLEU1", "hsa-miR-106b-5p,hsa-miR-124-3p,hsa-miR-1224-5p,hsa-miR-3934-5p", "2.61E-02", "4.08E-01", "1.31E-19"], ["TTF2", "HCP5", "hsa-miR-106b-5p,hsa-miR-1-3p,hsa-miR-101-3p,hsa-miR-106a-5p", "4.91E-04", "1.35E-01", "2.18E-03"], ["TTF2", "PPP1R26-AS1", "hsa-miR-122-5p", "3.38E-02", "2.94E-01", "1.24E-10"], ["TTF2", "CCDC18-AS1", "hsa-miR-124-3p,hsa-miR-1-3p", "3.32E-03", "1.47E-01", "9.55E-04"], ["TTF2", "MCF2L-AS1", "hsa-miR-105-5p", "3.38E-02", "1.78E-01", "7.73E-05"], ["KIF21B", "TMPO-AS1", "hsa-let-7f-5p,hsa-let-7i-5p", "1.44E-03", "9.07E-02", "2.78E-02"], ["KIF21B", "TRG-AS1", "hsa-let-7f-5p,hsa-let-7i-5p", "1.44E-03", "2.88E-01", "3.04E-10"], ["ACLY", "PPP1R26-AS1", "hsa-miR-122-5p", "1.75E-02", "1.79E-01", "6.98E-05"], ["ACLY", "DLEU1", "hsa-miR-124-3p,hsa-miR-1224-5p,hsa-miR-940", "2.05E-02", "1.05E-01", "1.32E-02"], ["ACLY", "TMPO-AS1", "hsa-let-7c-5p,hsa-let-7b-5p,hsa-let-7a-5p,hsa-let-7f-5p,hsa-let-7d-5p,hsa-let-7i-5p,hsa-let-7e-5p,hsa-let-7g-5p", "4.06E-14", "1.47E-01", "9.60E-04"], ["MSI2", "MCF2L-AS1", "hsa-miR-105-5p", "1.55E-02", "1.77E-01", "8.64E-05"], ["MSI2", "CCDC18-AS1", "hsa-miR-1-3p", "4.59E-02", "1.32E-01", "2.68E-03"], ["MSI2", "SH3BP5-AS1", "hsa-miR-1193", "1.55E-02", "8.47E-02", "3.70E-02"], ["MSI2", "OIP5-AS1", "hsa-let-7a-5p,hsa-miR-105-5p,hsa-miR-1179,hsa-miR-1197,hsa-miR-143-3p", "5.14E-07", "9.54E-02", "2.20E-02"], ["MSI2", "TTC28-AS1", "hsa-miR-103a-3p,hsa-miR-106a-5p", "1.39E-03", "1.11E-01", "9.48E-03"], ["MSI2", "TMPO-AS1", "hsa-let-7c-5p,hsa-let-7b-5p,hsa-let-7a-5p,hsa-let-7f-5p,hsa-let-7d-5p,hsa-let-7i-5p,hsa-let-7e-5p,hsa-let-7g-5p,hsa-miR-1179", "2.04E-17", "1.26E-01", "3.86E-03"], ["KIF15", "DLEU2", "hsa-miR-193b-3p", "7.75E-03", "6.38E-01", "1.08E-52"], ["KIF15", "HCP5", "hsa-miR-1-3p", "1.85E-02", "2.13E-01", "2.96E-06"], ["FEN1", "TMPO-AS1", "hsa-let-7b-5p", "3.45E-02", "6.20E-01", "4.29E-49"], ["ZFP69B", "DLEU1", "hsa-miR-3714,hsa-miR-125a-3p,hsa-miR-124-3p,hsa-miR-506-3p,hsa-miR-764,hsa-miR-3934-5p,hsa-miR-6893-5p,hsa-miR-3910,hsa-miR-940,hsa-miR-6808-5p", "3.02E-08", "2.33E-01", "3.19E-07"], ["SP6", "HCP5", "hsa-miR-20b-5p,hsa-miR-17-5p", "1.51E-03", "1.02E-01", "1.58E-02"], ["ZNF823", "TMPO-AS1", "hsa-let-7c-5p,hsa-let-7b-5p,hsa-let-7a-5p,hsa-let-7f-5p,hsa-let-7d-5p,hsa-let-7i-5p,hsa-let-7e-5p,hsa-let-7g-5p", "1.45E-14", "3.04E-01", "2.57E-11"], ["ZNF823", "ZFAS1", "hsa-miR-106a-5p,hsa-miR-143-3p", 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