@Article{096504020X15791676105394,
AUTHOR = {Xingliang Feng, Meng Zhang, Jialin Meng, Yongqiang Wang, Yi Liu, Chaozhao Liang, Song Fan},
TITLE = {Correlating Transcriptional Networks to Papillary Renal Cell  Carcinoma Survival: A Large-Scale Coexpression Analysis  and Clinical Validation},
JOURNAL = {Oncology Research},
VOLUME = {28},
YEAR = {2020},
NUMBER = {3},
PAGES = {285--297},
URL = {http://www.techscience.com/or/v28n3/48532},
ISSN = {1555-3906},
ABSTRACT = {We aimed to investigate the potential mechanisms of progression and identify novel prognosis-related biomarkers for papillary renal cell carcinoma (PRCC) patients. The related data were derived from The Cancer Genome 
Atlas (TCGA) and then analyzed by weighted gene coexpression network analysis (WGCNA). The correlation 
between each module and the clinical traits were analyzed by Pearson’s correlation analysis. Pathway analysis 
was conducted to reveal potential mechanisms. Hub genes within each module were screened by intramodule analysis, and visualized by Cytoscape software. Furthermore, important hub genes were validated in an 
external dataset and clinical samples. A total of 5,839 differentially expressed genes were identified. By using 
WGCNA, we identified 21 coregulatory gene clusters based on 289 PRCC samples. We found many modules 
were significantly associated with clinicopathological characteristics. The gray, pink, light yellow, and salmon 
modules served as prognosis indicators for PRCC patients. Pathway enrichment analyses found that the hub 
genes were significantly enriched in the cancer-related pathways. With the external Gene Expression Omnibus 
(GEO) validation dataset, we found that PCDH12, GPR4, and KIF18A in the pink and yellow modules were 
continually associated with the survival status of PRCC, and their expressions were positively correlated with 
pathological grade. Notably, we randomly chose PCDH12 for validation, and the results suggested that the 
PRCC patients with higher pathological grades (II + III) mostly had higher PCDH12 protein expression levels 
compared with those patients in grade I. These validated hub genes play critical roles in the prognosis prediction of PRCC and serve as potential biomarkers for future personalized treatment.},
DOI = {10.3727/096504020X15791676105394}
}