Figure 1
(a) Schematic overview of the strategy used to study pathways associated with clinically relevant lncRNAs and its potential regulated genes. LncRNA and mRNA expression profile are performed on HCC tumor tissues and adjacent non-tumor tissues. Clinical phenotypes of HCC tumor tissues are used for clinical association studies. Only differentially expressed (DE) and clinically relevant lncRNAs are included for further analysis. DEmRNAs that are correlated with clinically relevant DElncRNAs are included for further analysis. Clinical association of DEmRNAs are also identified. Two different analysis are carried out on clinically relevant lncRNAs-mRNAs pairs. Among correlated pairs, lncRNAs that are associated with only 1 clinical phenotype are selected for pathway analysis to identify potential prognostic markers. LncRNAs that are associated with more than 1 clinical phenotypes are selected for network analysis, followed by pathway analysis. Clinical association of DEmRNAs are also considered in the network analysis. Colored circles represent 5 groups of clinical phenotypes in this study: Tumor properties in orange, Tumor capsule in yellow, Tumor grade in blue, Tumor invasion in green, Patient overall survival in purple. (b) Differentially expressed lncRNAs and mRNAs between tumor (T) and non-tumor (NT) samples. Top: Workflow shows the number of lncRNAs/mRNAs at different stages of the workflow. Bottom: heatmap of the differentially expressed lncRNAs/mRNAs in T and NT samples. Each column in the heatmap represent the patient tissues samples types: red in column: T; blue in column: NT. Each row in the heatmap represents lncRNA/mRNA: red: Upregulation; green: Downregulation.
