This article reports a method for identifying groups of genes associated with tissues undergoing a particular process during mouse development. Given the Theiler stage at which each tissue starts the process, Boolean intersection analysis identifies genes expressed in some or all of these tissues both before the process starts and once it has started. This analysis is implemented in GXD-search; this tool downloads appropriate gene sets from GXD, the mouse gene expression database, and performs the calculations. Applied to mesenchyme-to-epithelium transitions (MET), GXD-search has identified Crabp1 and six transcriptional regulators (Cited1, Cited2, Meox1, Lhx1, Foxc1, and Foxc2) that are usually expressed in tissues about to undergo this process. Expression pattern analysis of these transcriptional regulators, mutations in each of which affect epithelial development, shows that this gene set is expressed in no other tissues and they are, thus, candidates for regulating MET. GXD-search is downloadable from http://www.aiai.ed.ac.uk/project/biosphere/GXD-search.html. Developmental Dynamics 237:2748–2754, 2008. © 2008 Wiley-Liss, Inc.