title: Identification of prognostic genes in kidney renal clear cell carcinoma by RNA‑seq data analysis.
abstract: The present study aimed to analyze RNA-seq data of kidney renal clear cell carcinoma (KIRC) to identify prognostic genes. RNA‑seq data were downloaded from The Cancer Genome Atlas. Feature genes with a coefficient of variation (CV) >0.5 were selected using the genefilter package in R. Gene co‑expression networks were constructed with the WGCNA package. Cox regression analysis was performed using the survive package. Furthermore, a functional enrichment analysis was conducted using Database for Annotation, Visualization and Integrated Discovery tools. A total of 533 KIRC samples were collected, from which 6,758 feature genes with a CV >0.5 were obtained for further analysis. The KIRC samples were divided into two sets: The training set (n=319 samples) and the validation set (n=214 samples). Subsequently, gene co‑expression networks were constructed for the two sets. A total of 12 modules were identified, and the green module was significantly associated with survival time. Genes from the green module were revealed to be implicated in the cell cycle and p53 signaling pathway. In addition, a total of 11 hub genes were revealed, and 10 of them (CCNA2, CDC20, CDCA8, GTSE1, KIF23, KIF2C, KIF4A, MELK, TOP2A and TPX2) were validated as possessing prognostic value, as determined by conducting a survival analysis on another gene expression dataset. In conclusion, a total of 10 prognostic genes were identified in KIRC. These findings may help to advance the understanding of this disease, and may also provide potential biomarkers for therapeutic development.
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Yanqin
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Linfeng
authors.initials: L
authors.lastname: Lu
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Wu
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.affiliation: Department of Urology, The First Hospital of Jiaxing, Jiaxing, Zhejiang 314001, P.R. China.
authors.forename: Yi
authors.initials: Y
authors.lastname: He
mesh_terms: D002292:Carcinoma, Renal Cell / Q000235:genetics*; D016000:Cluster Analysis; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D052138:Genes, Neoplasm; D006801:Humans; D053208:Kaplan-Meier Estimate; D007680:Kidney Neoplasms / Q000235:genetics*; D011379:Prognosis; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013223:Statistics as Topic