Blow your Brain Explorer out with the Human Allen Brain Atlas!

At the SciFoo Camp last year at the Googleplex I suggested a little unconference session (ok, there were some slides ready on my MacBook) and one participant was Chinh Dang (another was this inventor) Technology Director of the Allen Institute for Brain Science who made a little intro to the work of the Institute to the 9-10 attendees after this slide of mine:

SciFoo Brain Atlas

Paul Allen is the likable, Steven Wozniak-type co-founder of Microsoft, but I guess a bit richer (once we estimated with a friend of mine that he could buy all the Budapest condos circa 180 times or sg like that).

But instead of doing that he provided $100M – amongst others – in seed money to fund the Allen Brain Atlas.

The Allen Institute for Brain Science in Seattle, Washington, US, is today (13/03/08) launching a four-year, $55-million effort to build a three-dimensional map documenting the levels of activity of some 20,000 different genes across the human brain.

“The Human Genome Project was the ‘what’, and our project is the ‘where’,” says Allan Jones, the institute’s chief scientific officer….

However the human brain is a little more complicated than the mouse (also there is a little accessibility issue there), so just like in the Human Genome Case some initial trickery is needed:

The mouse atlas was produced using a method called “in situ hybridization”, in which thin slices of brain tissue are bathed in a solution containing molecular probes that bind to messenger RNA sequences produced by each gene. This gives a very detailed map of gene activity, down to the level of individual cells.

Trying to repeat this effort for all 20,000 genes across an organ about 2000 times larger than the mouse brain is impractical, for now. So Allen institute scientists will instead divide the human brain into between 500 and 2000 anatomical regions, and study gene activity in each by washing extracts from tissues in these regions across “gene chips” that can record which messenger RNA is present.

Once results from this initial phase of the project are in, which will take about two years, the institute’s scientists will perform in situ hybridization across the whole brain for up to 500 genes with the most interesting patterns of activity.

How to start exploring? Well for non-neuroscientists like me, I suggest the good old trial-and-error way.

Download the Brain Explorer, which is a desktop app for viewing Allen Brain Atlas (ABA) gene expression data in the framework of the Allen Reference Atlas (ARA) in 3D. You can “view gene expression data in 3D at 100 μm3 resolution, expression data from multiple genes superimposed on each other in 3D, navigate the high-resolution 2D ISH images from the ABA using the 3D model, link to associated gene metadata on the ABA website”.

Here is a little trial with the Alstrom syndrome 1 homolog (human) (Alms1)


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