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)

The human brain online: an open resource for advancing brain research.

This community page describes the database and associated Web application that comprise the Allen Human Brain Atlas, an open online resource that integrates genomic and anatomic human brain data

The Allen Human Brain Atlas contains multimodal data integrated into a unified 3-D framework with search and visualization features allowing one to journey through the brain readily climbing up and down levels of resolution.

<p>See it in action: Check out video tutorials on the Allen Human Brain Atlas and Brain Explorer® 3-D Viewer. Key Features: An “all genes, all structures” gene expression survey in multiple adult control brains. • >62,000 gene probes per profile. • ∼500 samples per hemisphere across cerebrum, cerebellum, and brainstem. • Data mapped with histology into unified 3-D anatomic framework based on MRI. High-resolution ISH image data covering selected genes in specific brain regions. • Subcortex Study: 55 genes across subcortical regions and 10 additional genes in hypothalamus in one male and one female donor. • Cortex Study: 1,000 genes in visual and temporal cortices in multiple adult control brains. • Schizophrenia Study: 60 genes in dorsolateral prefrontal cortex of over 50 control and schizophrenia cases. • Autism Study: 25 genes in frontal, temporal and occipital cortical regions of 11 control and 11 autism cases. • Neurotransmitter Study: Selected neurotransmitter system genes in major cortical and subcortical areas in adult control brains. MRI data for brains used for all microarray and some ISH analyses. Search and viewing tools, including: • Brain Explorer® 3-D viewer. • Heatmap viewer for exploring microarray data across genes and brain regions. • Gene-based and anatomic search features. • Multiplanar MRI viewer with gene expression overlay. • Linked viewing of MRI, gene expression, histology, anatomic delineations.</p