title: An integrated analysis of cancer genes in clear cell renal cell carcinoma.
abstract: OBJECTIVE
  This study was performed to detect driver genes and implement integrated analyses on these drivers in clear cell renal cell carcinoma (ccRCC).
  
  
  METHODS
  Driver genes and pathways were predicted by OncodriveFM and Dendrix using 39,636 somatic mutations from The Cancer Genome Atlas, followed by DNA methylation, copy number variation, differential expression and survival analyses.
  
  
  RESULTS
  Overall, 342 driver genes and 106 pathways were determined by OncodriveFM, two driver genes by Dendrix. 28 driver genes were found hypomethylated, overexpressed and associated to a poor prognosis. By contrast, 17 driver genes showed decreased expression, hypermethylation and indicated a better outcome in ccRCC.
  
  
  CONCLUSIONS
  The set of new cancer genes and pathways opens the avenue for developing potential therapeutic targets and prognostic biomarkers in ccRCC.
authors.affiliation: Department of Geriatrics, The Shanghai tenth People's Hospital Affiliated to Tongji University, Shanghai, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Nephrology, The Shanghai ninth People's Hospital, Shanghai, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Guo
authors.affiliation: Department of Medical Statistics, School of Medicine, Tongji University, 1239 Siping Road, Yangpu District, Shanghai 200092, China.
authors.forename: Zisheng
authors.initials: Z
authors.lastname: Ai
mesh_terms: D014408:Biomarkers, Tumor; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D002471:Cell Transformation, Neoplastic / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D020869:Gene Expression Profiling; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D009154:Mutation; D009857:Oncogenes; D011379:Prognosis; D015398:Signal Transduction; D016019:Survival Analysis
chemical_list: D014408:Biomarkers, Tumor
keywords: biomarkers/oncogenes/molecular oncology; genetics; molecular oncology