Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn´s disease and Ulcerative Colitis and control patients, respectively. All diagnoses of IBD patients were based on classical clinical features, radiological, endoscopic and laboratory findings. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected and sampled by a specialized gastroenterologist. To preserve the transcriptional profile of tissue specimens, biopsies were immediately stabilized in RNAlater solution and kept at –80°C until isolation of RNA. Total RNA was extracted from the tissue biopsies according to the manufacturer´s instructions using the RNeasy Protect Midi Kit (Qiagen). To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling to generate cRNA. Gene expression profiles were determined using Affymetrix HG-U133A and HG-U133B Gene Chips. Array scanning and expression analysis was performed using Microarray Analysis Suite 5.0 software. Each array was scaled to a target intensity of 100 (scaling to all probesets). Lot batch =
