The Allen Mouse Brain Atlas is a three-dimensional atlas of gene expression throughout the adult mouse brain. The atlas is separated into four key features:

• In Situ Hybridization (ISH) Data includes image data with cellular level resolution. To find gene expression data, search can be performed using Gene Search, Differential Search, Fine Structure Search, Bulk Search, and Human Differential Search.
• Reference Atlas contains a high-resolution anatomic reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. The atlas illustrates the adult mouse brain in coronal and sagittal planes of section, and it includes the Coronal Atlas and the Sagittal Atlas.
• Anatomic Gene Expression Atlas (AGEA) explores transcriptome-based brain architecture and gene discovery. The AGEA includes three discovery tools to explore the genetic architecture of the brain: Correlation mode, Find Genes, and Clusters mode.
• Brain Explorer is an application for viewing brain anatomy and gene expression data in three dimensions in the framework of the Reference Atlas. It is a fully interactive version of the Reference Atlas in 3-D.

The atlas also contains two search related studies for gene expression: Sleep Study and Mouse Strains Study. The Sleep Study includes gene expression data in the mouse brain. It examines the effects of sleep deprivation and sleep state in mice. The Mouse Strains Study provides gene expression data from a select number of genes across seven different mouse strains and in adult female C57BL/6J mice.