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A Genomic Map of the Mouse Brain

Neuroskeptic iconNeuroskepticBy NeuroskepticFebruary 25, 2009 7:58 AM


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Nature Neuroscience has a nice little report about a new resource that should prove useful for neuroscientists - an anatomic gene expression atlas of the adult mouse brain.

The atlas is freely available at, courtesy of the Allen Foundation. It's a map of the entire adult mouse brain including data on the expression levels of 4,376 genes. You can click on a point in the brain and see which areas have a similar pattern of gene expression:


The hotter the colour, the more correlated is the gene expression profile in that point vs. your selected region. This allows one to see the different regions of the brain defined not just anatomically, but genomically - fancy. Here I've clicked on a point in the cortex and this shows that other points in the cortex tend to have the same pattern of gene expression. That's hardly surprising, of course.

This is the kind of thing that will be invaluable for some neuroscientists, and not much use to most others, but it's a source of pretty pictures for everyone - and it's an example of the power of this kind of database. The genomic atlas is derived from the Allen Brain Atlas which allows you to see where in the brain any given gene is expressed. See also for a modest attempt to do the same thing for functional neuroimaging.


Lydia Ng, Amy Bernard, Chris Lau, Caroline C Overly, Hong-Wei Dong, Chihchau Kuan, Sayan Pathak, Susan M Sunkin, Chinh Dang, Jason W Bohland, Hemant Bokil, Partha P Mitra, Luis Puelles, John Hohmann, David J Anderson, Ed S Lein, Allan R Jones, Michael Hawrylycz (2009). An anatomic gene expression atlas of the adult mouse brain Nature Neuroscience, 12 (3), 356-362 DOI: 10.1038/nn.2281

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