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Anatomic Gene Expression Atlas (AGEA)

What is AGEA?

The Allen Institute has built a data-driven three-dimensional atlas of the adult C57Bl/6J mouse brain based on the ISH gene expression images of the Allen Mouse Brain Atlas. The project is called AGEA which stands for Anatomic Gene Expression Atlas. Essentially, AGEA characterizes the multi-scale spatial relationship in the mouse brain as derived from gene expression data without a prior knowledge of classical anatomy. In the AGEA online application, you can:

  • View and navigate 3D spatial relationship maps (Correlation mode);
  • Explore a transcriptome based spatial organization of the brain (Clusters mode) and,
  • Search for genes with local regionality as defined by AGEA (Gene Finder mode).

The application

The upper panels of images in Figure 1 are orthogonal views of a 3D Nissl reference atlas volume.

Correlation Mode

In Correlation mode, the lower panels show orthogonal views of the selected spatial
relationship map. The AGEA spatial relationship maps are computed from spatially mapping
4,376 coronal images series of the ABA. This initial gene set was chosen from the ABA because
it contains many of the genes of known neuroscientific interest as well as genes exhibiting
marked or unique expression patterns.

Clusters Mode

Gene Finder Mode

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