Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell

Background: Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. Results: The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans-Jürgen Thiesen, Stefan Wölfl, Raimund W. Kinne
• Keywords: BMCBI 2006, Cell Fractions, Expression Profiles, MRNA Proportions