Expression analysis of Barrett’s epithelium and normal gastrointestinal tissues

Barrett’s esophagus is a premalignant condition that arises due to chronic acid reflux in which the normal squamous epithelium of the esophagus is replaced by a metaplastic columnar epithelium. A fundamental question is the distinction between neoplastic Barrett’s epithelium and surrounding normal tissues of the upper gastrointestinal tract. For example, although it arises in the esophagus, the Barrett’s epithelium more closely resembles the epithelium of the duodenum at the histologic level. Therefore, we compared the transcriptional profile of the Barrett’s epithelium to those of normal upper gastrointestinal tissues, including gastric epithelium, squamous epithelium of the esophagus and duodenal epithelium. We found that the Barrett’s epithelium has comparable similarities to the three normal gastrointestinal tissues at the expression level. In addition, we proposed a novel approach to filter out non-tissue specific genes. We searched for tissue specific patterns, and identified many tissue specific genes. Furthermore, we developed a novel algorithm to identify genes that drive the similarity (or dissimilarity) between different tissue samples. Equal contribution to this work.