The gastrointestinal (GI) tract is divided into several segments that have distinct functional properties, largely absorptive. The gastric corpus is the only segment thought of as largely secretory. Microarray hybridization of the gastric corpus mucosal epithelial cells was used to compare gene expression with other segments of the columnar GI tract followed by statistical data subtraction to identify genes selectively expressed by the rat gastric corpus mucosa. This provides a means of identifying less obvious specific functions of the corpus in addition to its secretionrelated genes. For example, important properties found by this GI tract comparative transcriptome reflect the energy demand of acid secretion, a role in lipid metabolism, the large variety of resident neuroendocrine cells, responses to damaging agents and transcription factors defining differentiation of its epithelium. In terms of overlap of gastric corpus genes with the rest of the GI tract, the distal small bowel appears to express many of the gastric corpus genes in contrast to proximal small and large bowel. This differential map of gene expression by the gastric corpus epithelium will allow a more detailed description of major properties of the gastric corpus and may lead to the discovery of gastric corpus cell differentiation genes and those mis-regulated in gastric carcinomas.transcriptome; stomach THE FUNCTION OF AN ORGAN DEPENDS on the genes and protein products expressed and their regulation. Much has been learnt by classical physiological or biochemical approaches, but the complexity of biology suggests that many functions may be overlooked by conventional approaches. If a complete and specific gene expression profile were available, a more realistic understanding of a specific organ's capabilities would ensue.The gastric corpus epithelium is the most complicated region of the gastrointestinal (GI) tract in terms of secretion, endocrine function, and differentiation due to its large variety of cell types. In this article, we present the specific transcriptome of the rat gastric corpus mucosa as obtained by whole rat genome microarray hybridization compared with three other mucosal segments of the columnar GI tract (proximal and distal small bowel, and colon). This is followed by statistical data subtraction to identify genes selectively expressed by the rat gastric corpus mucosa, but not by the other segments. Genes identified with this method most likely reflect functional importance in the stomach when considered in the context of relative rather than absolute expression levels. For example, many receptors are expressed at relatively low levels but their increased expression relative to other regions of the GI tract indicates significant function in the gastric secretory epithelium. The success of this method has been previously shown during transcriptomal analysis of purified suspensions of individual cell types, such as parietal and enterochromaffin-like (ECL) cells compared with the primary mucosal digest of the gastric corpus m...