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Published February 15, 2009 | Supplemental Material
Journal Article Open

An anatomic gene expression atlas of the adult mouse brain


Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three-dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea).

Additional Information

© 2009 Nature Publishing Group. Received 6 November 2008; accepted 22 January 2009; published online 15 February. This work was sponsored by the Allen Institute for Brain Science. The authors wish to thank the Allen Institute founders, P.G. Allen and J. Patton, for their vision, encouragement and support. The authors also thank D. Haynor of the University of Washington, Department of Neuroradiology, and C. Thompson of the Allen Institute.

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