Thursday, January 11, 2007

The Allen Brain Atlas

The latest issue of Nature has a fascinating article entitled "Genome-wide atlas of gene expression in the adult mouse brain" which details the research of The Allen Brain Atlas. Here is an excerpt from the Nature article:

The mammalian central nervous system (CNS) contains an enormous variety of cell types, each with unique morphology, connectivity, physiology and function. A characterization of the full complement of neural cell types is essential to understand functional circuit properties and their relation to higher cognitive functions and behaviours. The phenotypic properties of different neuronal and non-neuronal cells are largely the product of unique combinations of expressed gene products; therefore, gene expression profiles provide an informative modality to define cellular diversity in the brain. However, histological data are typically generated for one gene at a time, and data are neither systematically produced and analysed nor consolidated in an easily accessible format. Consequently, a limited set of established cellular markers dominates the current literature, and expression patterns of many genes remain uncharacterized.

...The Allen Brain Atlas project has taken a global approach to understanding the genetic structural and cellular architecture of the mouse brain by generating a genome-scale collection of cellular resolution gene expression profiles using ISH. Highly methodical data production methods and comprehensive anatomical coverage via dense, uniformly spaced sampling facilitate data consistency and comparability across >20,000 genes. The use of an inbred mouse strain with minimal animal-to-animal variance allows one to treat the brain essentially as a complex but highly reproducible three-dimensional tissue array. Image-based informatics methods for signal detection and three-dimensional registration of ISH data to a de novo age-matched annotated reference atlas have been developed to allow automated signal quantification across the anatomical structures in the reference atlas, or its associated grid-based coordinate system. These methods enable global analysis and mining for detailed expression patterns in the brain. The entire Allen Brain Atlas data set and associated informatics tools are available through an unrestricted web-based viewing application.