Statistical analyses were performed using R software (version 3.6.1) with relevant packages. In brief, the differential expressed mRNAs were extracted from microarray data sets using Limma package. The differential expressed mRNAs, microRNA and lncRNA of TCGA‐LIHC were identified using Linnorm packages. The difference between the two groups was compared using an independent t test or Wilcox test. Adjusted P‐value was obtained using FDR (False Discovery Rate) method. Coefficients were calculated using Pearson or Spearman correlation analysis. A chi‐squared test was used to determine the significant difference between the frequencies. Survival analysis was performed using Univariate Cox/multivariate analysis hazard analysis or Kaplan‐Meier survival estimate using a survival package. The forest‐plot R package was employed to visualize the hazard rate obtained from survival analysis. The Kaplan‐Meier survival curves were created using survminer package with Log‐rank test. A prognostic model based on hypoxia score was established using Lasso (least absolute shrinkage and selection operator)‐cox Regression method. The model was visualized and validated using Hdnom package. In the present study, statistical significance was set at a probability value of P < .05.

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