Computational protocol: Higher programmed cell death 1 ligand 1 (PD-L1) mRNA level in clear cell renal cell carcinomas is associated with a favorable outcome due to the active immune responses in tumor tissues

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Protocol publication

[…] Clinical, follow-up and RNA-seq data of the 536 KIRC, 291 KIRP and 66 KICH patients were obtained from TCGA by cBioportal platform and TCGA-Assembler [, ]. The patients with integrated clinical stage, T stage, overall survival information and mRNA levels in tumor were enrolled in this study. mRNA expression profiling by array of the 72 KIRC tumors in GSE53757 dataset in GEO were also included []. The data used in this study are opened to public for access without limitation and restriction. This study was performed according to the publication guidelines provided by TCGA ( [...] Gene-set enrichment analysis (GSEA) was used to identify the pathways in two different PD-L1 mRNA level groups []. RNA-seq data were processed by TCGA-Assembler, and a total of 20,486 genes were enrolled for GSEA analyses. In addition, 20,282 genes from GSE53757 dataset were used for validating the pathway analyses. In the processes of GSEA analyses, the hallmark gene sets (h.all.v5.1.symbols.gmt) were used []. The p value of GSEA was computed by 1,000-gene-set two-sided permutation test. […]

Pipeline specifications

Software tools cBioPortal, TCGA-assembler, GSEA
Databases TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Carcinoma, Renal Cell, Kidney Diseases, Kidney Neoplasms, Neoplasms