@article{ATM29848,
author = {Chuanjie Zhang and Yuxiao Zheng and Xiao Li and Xin Hu and Feng Qi and Jun Luo},
title = {Genome-wide mutation profiling and related risk signature for prognosis of papillary renal cell carcinoma},
journal = {Annals of Translational Medicine},
volume = {7},
number = {18},
year = {2019},
keywords = {},
abstract = {Background: The papillary renal cell carcinoma (pRCC) is a rare subtype of renal cell carcinoma with limited investigation. Our study aimed to explore a robust signature to predict the prognosis of pRCC from the perspective of mutation profiles.
Methods: In this study, we downloaded the simple nucleotide variation data of 288 pRCC samples from The Cancer Genome Atlas (TCGA) database. “GenVisR” package was utilized to visualize gene mutation profiles in pRCC. The PPI network was conducted based on the STRING database and the modification was performed via Cytoscape software (Version 3.7.1). Top 50 mutant genes were selected and Cox regression method was conducted to identify the hub prognostic mutant signature in pRCC using “survival” package. Mutation Related Signature (MRS) risk score was established by multivariate Cox regression method. Receiver Operating Characteristic (ROC) curve drawn by “timeROC” was conducted to assess the predictive accuracy of overall survival (OS) and Kaplan-Meier analysis was then performed. Relationships between mutants and expression levels were compared by Wilcox rank-sum test. Function enrichment pathway analysis for mutated genes was performed by “org.Hs.eg.db”, “clusterProfiler”, “ggplot2” and “enrichplot” packages. Gene Set Enrichment Analysis was exploited using the MRS as the phenotypes, which worked based on the JAVA platform. All statistical analyses were achieved by R software (version 3.5.2). P value },
issn = {2305-5847}, url = {https://atm.amegroups.org/article/view/29848}
}