title: Transcriptome network analysis reveals candidate genes for renal cell carcinoma.
abstract: BACKGROUND
  Renal cell carcinoma (RCC) is a kidney cancer that originates in renal parenchyma and it is the most common type of kidney cancer with approximately 80% lethal cases.
  
  
  OBJECTIVE
  To interpret the mechanism, explore the regulation of TF-target genes and TF-pathway, and identify the potential key genes of renal cell carcinoma.
  
  
  METHODS
  After constructing a regulation network from differently expressed genes and transcription factors, pathway regulation network and gene ontology (GO) enrichment analysis were made.
  
  
  METHODS
  The gene expression profile set GSE6344, a renal cell carcinoma sample set, was collected from NCBI, pathway data from KEGG, and regulationship data from database TRANSFAC and TRED.
  
  
  METHODS
  Besides different expressed genes obtained by limma, impact analysis method and GO enrichment were applied to find the significant expressed pathways.
  
  
  RESULTS
  Finally, we constructed a TF-target gene and TF-pathway regulation network of renal cell carcinoma. And some genes proved to be highly related to renal cell carcinoma were identified.
  
  
  CONCLUSIONS
  This study illustrated that by incorporating significantly expressed pathway into a regulation network based analysis, one can derive greater insights into the underlying mechanisms of renal cell carcinoma.
authors.affiliation: Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhai
authors.forename: Yun-Fei
authors.initials: YF
authors.lastname: Xu
authors.forename: Min
authors.initials: M
authors.lastname: Liu
authors.forename: Jun-Hua
authors.initials: JH
authors.lastname: Zheng
mesh_terms: D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000473:pathology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000473:pathology; D058977:Molecular Sequence Annotation; D009367:Neoplasm Staging; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014157:Transcription Factors