BackgroundSince the appearance of whole genome gene expression (WGGE) analysis, it has been used to analyse mucosal IBD samples. As ulcerative colitis (UC) and Crohn's disease (CD) are clinically distinct, many efforts have been made to differentiate these at a transcriptional level. Even though several studies have shown promise in discerning UC and CD, gene expression fingerprinting has not yet reached the clinic. However, using publicly available data sets from these previous analyses enable instant cross-platform, cross-laboratory validation of local analysis. This opens for powerful analysis comparing the two diseases on both a global and focused gene expression level. We present the to date largest WGGE analysis of colonic mucosal IBD samples including samples from inflamed and uninflamed tissue from both UC and CD, as well as normal controls. Focusing on subsets of genes representing areas of particular interest in IBD, T helper (Th) cell differentiation and antimicrobial peptide (AMP)-related expression, eases the interpretation of results. A meta-analysis including all available, comparable data was used to validate and strengthen observations.
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