Gene expression analysis of colon biopsies using high-density
oligonucleotide microarrays can contribute to the understanding
of local pathophysiological alterations and to functional
classification of adenoma (15 samples), colorectal carcinomas
(CRC) (15) and inflammatory bowel diseases (IBD) (14). Total RNA
was extracted, amplified and biotinylated from frozen colonic
biopsies. Genome-wide gene expression profile was evaluated by
HGU133plus2 microarrays and verified by RT-PCR. We applied two
independent methods for data normalization and used PAM for
feature selection. Leave one-out stepwise discriminant analysis
was performed. Top validated genes included collagenIV alpha 1,
lipocalin-2, calumenin, aquaporin-8 genes in CRC; CD44, met
proto-oncogene, chemokine ligand-12, ADAM-like decysin-1 and
ATP-binding casette-A8 genes in adenoma; and lipocalin-2,
ubiquitin D and IFITM2 genes in IBD. Best differentiating
markers between Ulcerative colitis and Crohn's disease were
cyclin-G2; tripartite motif-containing-31; TNFR shedding
aminopeptidase regulator-1 and AMICA. The discriminant analysis
was able to classify the samples in overall 96.2% using 7
discriminatory genes (indoleamine-pyrrole-2,3-dioxygenase,
ectodermal-neural cortex, TIMP3, fucosyltransferase-8, collectin
sub-family member 12, carboxypeptidase D, and transglutaminase-
2). Using routine biopsy samples we successfully performed whole
genomic microarray analysis to identify discriminative
signatures. Our results provide further insight into the
pathophysiological background of colonic diseases. The results
set up data warehouse which can be mined further
