Several large-scale projects are evaluating gene expression in the mouse brain, both spatially and temporally. These range from projects that cover a broad spectrum of genes and developmental stages to those with high-spatial resolution and gene coverage but for only a single developmental stage. Each project contains its own self-consistent data set and tools for analysis and mining. Preliminary efforts are under way to construct tools and an infrastructure with which the data from across these different projects can be statistically pooled and analyzed. However, many obstacles remain, and these must be addressed and overcome soon if we are to unify the data sets, otherwise the preliminary efforts will be wasted. Here, the various projects for collecting and mining this information are reviewed, some challenges in data set comparisons are discussed, and some basic proposals are made for overcoming the challenges.