Allen Brain Atlas Tutorial

For up to date issues or problems with this database please see the wiki.

For more information, please visit the Allen Brain Atlas.

The Allen Brain Atlas contains a vast quantity of gene expression information.  The gene expression is localized to various brain regions, which are labeled, and unlike other sources the gene expression (in situ hybridization) is numerical, not qualitative. 

To start browsing this resource we type in our favorite gene query

Gene:grm1

and get the following result:

Note, the gene:grm1 query expands to all the known synonyms of the metabotropic glutamate receptor 1.

The search brings up 17 results from the Allen Brain Atlas, which are shown below.  The results from Allen Brain Atlas can be found under the data type: images and also under Nervous system Level: genes.  Clicking on either tab will bring back the same list of results.

The results are organized by gene symbol and include the organism and structure where data are available.  Expression data are broken up into two values, and both are normalized to 100%.  To find out more about the methods that were used to obtain these values please refer to the Allen Brain site documentation page here http://mouse.brain-map.org/documentation/index.html.

If we click on the Grm1 (any of the gene symbols) the link will take the user to a detailed page in the Allen Brain Atlas site that contains more details about the particular experiment.

See below for the image series table, which shows example images and some details for each of the image series available for a particular gene. The contents of each on the columns in the table are described below:

Example Image
The example image is the thumbnail image nearest the midline for the section.

Click on the example image to launch the thumbnail viewer, which will display all of the thumbnails for the selected image series, with the option of displaying ISH, Expression mask or Composite images. The thumbnail page links to a high-resolution image viewer for each image.

Expression Level/Expression Density
This graph shows the scaled expression level above the midline and scaled expression density below the midline. Values are scaled from 0 - 100%. The colors of the graph bars are the same as those used for the corresponding structures in the Allen Reference Atlas.

Moving your mouse pointer over the expression graph updates the example image to show a slightly-higher resolution image, centered on the corresponding structure. Below is an example of what the image might look like when mousing over the Cerebellum graph bar for a coronal section:

Click on a graph bar to launch a high-resolution image viewer.

Experiment Info
Click anywhere in the Experiment Info column to see detailed information about the transcript, specimen & methodology used to produce the data for this image series.

The image control buttons on the toolbar allow you to switch between (from left to right) ISH, Expression Mask or Composite views of associated images. In some contexts a "Reset" button is available to reset the image(s) to the original state.

Below is an example of the Expression Mask image state from the gene detail page:

For more information, please visit the Allen Brain Atlas.