Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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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. We also wish to thank key Institute advisors, K. Dooley and S. Coliton, as well as the Scientific Advisory Board for the Atlas project, M. Tessier-Lavigne, D. Anderson, C. Dulac, R. Gibbs, S. Paul, G. Schuler, A. W. Toga and J. Takahashi, for their scientific guidance and dedication to the successful execution of the Atlas project. We would particularly like to acknowledge D. Anderson for his role in the conceptual genesis and continual refinement of Atlas goals, as well as M. Tessier-Lavigne for key scientific and organizational leadership throughout the project. We also thank C. Jennings for his critical reading of the manuscript.
Author Contributions Neuroscience Group: E.S.L. (group leader), A.B., L.C., M.P.H., M.T.M, C.L.T., T.A.Z. Informatics Group: M.J.H. (group leader), C.L.K., C.L., L.L.N., S.D.P. Production Groups: Allen Institute for Brain Science: P.E.W. (group leader), S.M.S. (group leader), R.A.J. (group leader), M.A., A.F.B., E.J.B., S.D., N.R.D., A.L.D., T.D., E.D., M.J.D., J.G.D., A.J.E., L.K.E., S.R.F., S.N.G., K.J.G., K.R.H., M.R.H., J.M.K., R.H.K., J.H.L., T.A.L., L.T.L., R.J.M., N.F.M., R.N., G.J.O., T.H.P., S.E.P., O.C.P., R.B.P., Z.L.R., H.R.R., S.A.R., J.J.R., N.R.S., K.S., N.V.S., T.S., C.R.S., S.C.S., K.A.S., N.N.S., K.-R.S., L.R.V., R.M.W., C.K.W., V.Y.W., X.F.Y.; Baylor College of Medicine: C.T. (group leader), N.A., L.C. (Li Chen), T.-M.C., A.C., R.F., A.J.L., Y.L., M.J.R., A.T., M.W., M.B.Y., B.Z.; Max Planck Institute: G.E. (group leader), A.V. Technology Group: C.N.D. (group leader), C.D.T. (group leader), A.B. (Amy Bensinger), K.S.B., M.C.C., J.C., B.E.C., T.A.D., B.J.D., T.P.F., C.F. (Cliff Frensley), D.P.J., P.T.K., R.K., A.R.L., K.D.L., J.M., B.I.S., A.J.S., M.S., R.C.Y., B.L.Y. Other: H.-W.D., B.A.F., C.F. and J.J.M., Allen Reference Atlas generation; J.G.H., data annotation; C.C.O., critical review and manuscript preparation; M.S.B., overall project leadership 2003–2004; A.R.J., overall project leadership 2004–present.
Disclaimer The Nature Publishing Group has a business collaboration with the Allen Institute for the creation and maintenance of the Neuroscience gateway (http://www.brainatlas.org), but has no role in generating or curating the Allen Brain Atlas database content. As always, Nature Editors have been fully independent and solely responsible for the editorial content and peer review of this research article.
Genome-wide analysis of expression level vs. percentage of expressing cells in 12 major brain regions
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Scientific Reports (2018)