Resources abstract
Nature Neuroscience 12, 356 - 362 (2009)
Published online: 15 February 2009 | doi:10.1038/nn.2281
An anatomic gene expression atlas of the adult mouse brain
Lydia Ng1, Amy Bernard1, Chris Lau1, Caroline C Overly1, Hong-Wei Dong2, Chihchau Kuan1, Sayan Pathak1, Susan M Sunkin1, Chinh Dang1, Jason W Bohland3, Hemant Bokil3, Partha P Mitra3, Luis Puelles4,5, John Hohmann1, David J Anderson6, Ed S Lein1, Allan R Jones1 & Michael Hawrylycz1
Abstract
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).
- Allen Institute for Brain Science, Seattle, Washington 98103, USA.
- Laboratory for NeuroImaging, University of California Los Angeles, Los Angeles, California 90095, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
- Department of Human Anatomy and Psychobiology, University of Murcia, Murcia, Spain.
- CIBER en Enfermedades Raras, U736, Faculty of Medicine, University of Murcia, Murcia, Spain.
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
Correspondence to: Michael Hawrylycz1 e-mail: mikeh@alleninstitute.org
