NIF Data Spotlight: Allen Brain Atlas

The Allen Mouse Brain Atlas is an interactive, genome-wide image database of gene expression. The Neuroscience Information Framework returns quantitative expression values on a gene by brain region basis.

We can begin searching for a gene by typing - "htrb" into NIF.



Using the NIFSTD ontology, our search for the serotonin receptor B is expanded to all known synonyms for this receptor.

Found under Nervous System Level >Genes and Data Type > Images, we have returned 51 records from the Allen Brain Atlas.

The results are organized by gene symbol and include organism and structure data, when available. Expression data are give as two values, both are normalized to 100%. To find out more information about the methods used to obtain expression values please refer to the Allen Brain site documentation.

Clicking on any Gene Symbol will open the record detail on the Allen Brain Atlas site. Here you have many options to switch between ISH, Expression Mask or Composite views of associated image. For more information please visit our Allen Brain Atlas tutorial.