An anatomic gene expression atlas of the adult mouse brain

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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 (

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Figure 1: Construction and representation of the Anatomic Gene Expression Atlas (AGEA).
Figure 2: The ventral posterior complex (VP) of the thalamus.
Figure 3: The parafascicular nucleus of the thalamus.
Figure 4: Genetic organization of the striatum.
Figure 5: Anatomic gene markers for the dorsal-ventral striatum.
Figure 6: AGEA and cortical topography.


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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.

Author information

L.N., CL. and C.D. built the AGEA application; LN., A.B, J.W.B., H.B., P.P.M. and M.H. performed the analyses; H.-W.D., L.P. and J.H. interpreted neuroanatomy; L.K. and S.P. provided informatics support; E.S.L., D.J.A., A.J.R., M.H. provided overall guidance; and L.N., C.C.O., A.B., S.M.S. and M.H. wrote the manuscript.

Correspondence to Michael Hawrylycz.

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Supplementary Methods (including Supplementary Figures 1–4) and Supplementary Results (including Supplementary Figures 5–10 and Supplementary Tables 1–7) (PDF 5131 kb)

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