title: Genetic profiling of Gleason grade 4/5 prostate cancer: which is the best prostatic control tissue?
abstract: OBJECTIVE
  We examined the variation in gene expression profiles of prostate cancer caused by zone specific genes.
  
  
  METHODS
  Ten normal central zone, 10 transition zone (benign prostatic hyperplasia) and 6 normal peripheral zone tissues from radical retropubic prostatectomies were compared to each other and to 12 peripheral zone Gleason grade 4/5 cancers. Test chips and HuGeneFL6800 (Affymetrix, Inc., Santa Clara, California) chips were used to assay the transcribed genes. Data were obtained with the Microarray Suite Version 4.0.1 (Affymetrix, Inc.) and analyzed statistically.
  
  
  RESULTS
  Substantially different gene expression profiles were found depending upon which of the 3 zonal tissues were used as a control. All 3 profiles were compared for efficiency (ability to locate genes) and for robustness (the magnitude of difference between the control and the Gleason grade 4/5 tissue). Microscopically normal appearing peripheral zone tissue at the gene level shows many characteristics of Gleason grade 4/5 cancer.
  
  
  CONCLUSIONS
  Gene expression profiles of prostate cancer are affected by the zonal location of the control tissue and the cancer.
authors.affiliation: Department of Urology, School of Medicine, Stanford University, California 94305, USA.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Stamey
authors.forename: Mitchell C
authors.initials: MC
authors.lastname: Caldwell
authors.forename: Zhenbin
authors.initials: Z
authors.lastname: Fan
authors.forename: Zhaomei
authors.initials: Z
authors.lastname: Zhang
authors.forename: John E
authors.initials: JE
authors.lastname: McNeal
authors.forename: Rosalie
authors.initials: R
authors.lastname: Nolley
authors.forename: Zuxiong
authors.initials: Z
authors.lastname: Chen
authors.forename: Mamatha
authors.initials: M
authors.lastname: Mahadevappa
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
mesh_terms: D015536:Down-Regulation; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D011467:Prostate / Q000473:pathology; D011470:Prostatic Hyperplasia / Q000235:genetics; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D015854:Up-Regulation