Computational protocol: Comprehensive analysis of a novel four-lncRNA signature as a prognostic biomarker for human gastric cancer

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Protocol publication

[…] The GC-specific lncRNAs were selected, and the expression level of each lncRNA was log2 transformed for further analysis. The univariate Cox proportional hazards regression model was used to analyze the GC-specific lncRNAs associated with OS. The multivariate Cox regression model was further performed to evaluate the prognostic value of these OS-related lncRNAs. The semi-supervised method that combines the gene expression profile with clinical information was used to conduct univariate Cox regression analyses [, ]. In each subgroup stratified by tumor TNM system, the OS-related lncRNAs were identified by the multivariate Cox regression model.The prognostic risk score for predicting OS was calculated: Risk score = explncRNA1*βlncRNA1 + explncRNA2*βlncRNA2 + …explncRNAn*βlncRNAn (exp: expression level; β: the regression coefficient derived from the multivariate Cox regression model) []. The median risk score was used as the cutoff point, and GC patients were divided into high- and low- groups []. Further univariate and multivariate Cox proportional hazards regression analyses were conducted to investigate the effects of various clinical features and the risk score of OS for GC patients. The hazard ratio (HR) and 95% confidence interval (CI) were assessed. The defining point set up by 5-year time-dependent receiver operating characteristic (ROC) curve analysis, was used to evaluate the predictive value of the risk score for time-dependent outcomes []. Via IBM SPSS Statistics 21 (SPSS Inc., Chicago, IL, USA), Kaplan-Meier survival curves and the log-rank test were used to assess the equality of survival distributions in different groups. The ROC was used to assess GC-specific lncRNAs for the sensitivity and specificity of GC detection. [...] The four lncRNAs expression was heterogeneous across different grade GC. To investigate the biological feature of GC with different four lncRNAs expression, we asked the genes that strongly correlated with these four lncRNAs expression (Pearson |R| > 0.5) in TCGA database []. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of co-expressed mRNAs of these lncRNAs were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/). The enriched results were restricted to KEGG pathway and GO biological process. The adjusted P-value < 0.05 was considered to be significant. Then, the co-expressed genes were performed to construct the protein-protein interaction (PPI) network via STRING (Version 10.5) (https://string-db.org/). […]

Pipeline specifications

Software tools SPSS, DAVID
Databases TCGA Data Portal KEGG KEGG PATHWAY
Applications Miscellaneous, Protein interaction analysis
Organisms Homo sapiens