title: [Identification of colorectal cancer, adenoma, and inflammatory bowel disease specific gene expression patterns using whole genomic oligonucleotide microarray system].
abstract: BACKGROUND
  Discrimination and classification of colorectal diseases (adenoma, colorectal cancer, inflammatory bowel disease) using biopsy samples and expression microarrays, has not been solved yet, nevertheless, it can contribute to the understanding of the colonic diseases.
  
  
  METHODS
  Total ribonucleic acid was extracted, amplified and biotinylated from frozen colonic biopsies of 15 patients with colorectal cancer, 15 with adenoma, 14 with inflammatory bowel disease and 8 normal controls. Genome-wide gene expression profile was evaluated by Human Genome U133 Plus 2.0 microarrays. Two independent methods were used for data normalization and "Prediction Analysis of Microarrays" was performed for feature selection. Leave one-out stepwise discriminant analysis was performed. The expression results were verified by real-time polymerase chain reaction.
  
  
  RESULTS
  Top validated genes included CD44 antigen, met proto-oncogene, chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette-A8 genes in adenoma; collagen IValpha1, lipocalin-2, calumenin, aquaporin-8 genes in colorectal cancer; and lipocalin-2, ubiquitin D and interferon induced transmembrane protein 2 genes in inflammatory bowel disease. The discriminant analysis was able to classify the samples in overall 96.2% using 7 discriminatory genes. The expression of 94% of the 52 genes measured by Taqman real-time polymerase chain reaction correlated with the results obtained using Affymetrix microarrays at a significance of p < 0.05.
  
  
  CONCLUSIONS
  We successfully performed whole genomic microarray analysis to identify discriminative signatures using routine biopsy samples. The results set up data warehouse which can be further mined.
authors.affiliation: Semmelweis Egyetem, Altalános Orvostudományi Kar II. Belgyógyászati Klinika Budapest. orsg1@yahoo.com
authors.forename: Orsolya
authors.initials: O
authors.lastname: Galamb
authors.forename: Balázs
authors.initials: B
authors.lastname: Gyorffy
authors.forename: Ferenc
authors.initials: F
authors.lastname: Sipos
authors.forename: Sándor
authors.initials: S
authors.lastname: Spisák
authors.forename: Anna Mária
authors.initials: AM
authors.lastname: Németh
authors.forename: Pál
authors.initials: P
authors.lastname: Miheller
authors.forename: Elek
authors.initials: E
authors.lastname: Dinya
authors.forename: Béla
authors.initials: B
authors.lastname: Molnár
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Tulassay
mesh_terms: D000236:Adenoma / Q000175:diagnosis* / Q000235:genetics; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001706:Biopsy; D015179:Colorectal Neoplasms / Q000175:diagnosis* / Q000235:genetics; D003937:Diagnosis, Differential; D016002:Discriminant Analysis; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000175:diagnosis* / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D000090063:Proto-Oncogene Mas; D012313:RNA / Q000032:analysis
chemical_list: C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D012313:RNA