Mouse Brain Gene Map

October 20, 2006 1:09 PM

The Allen Institute for Brain Science has made the Allen Brain Atlas available online for public searches. It contains maps of gene expressions in a mouse brain, searchable by gene, anatomy, or with boolean syntax. They also offer Brain Explorer, a 3-D program that lets you highlight particular genes, and rotate the model in any direction. Via
posted by owhydididoit (14 comments total)

If you download Brain Explorer, I highly recommend the tutorial, available on the Help menu. The program doesn't start off very intuitively.
posted by owhydididoit at 1:12 PM on October 20, 2006

Get a brain, morans!
Download stuck. Progress not move. Why brain not come?
posted by hal9k at 1:25 PM on October 20, 2006

Nevermind. Just got it and installed. Very cool.
Hey! I can see your mouse from here!
posted by hal9k at 1:30 PM on October 20, 2006

two comments from hal9k and no "I can feel my mind coming" crack? *tsk*
posted by boo_radley at 1:46 PM on October 20, 2006 [1 favorite]

Wow, this would be really exciting if I was a mouse!
posted by delmoi at 1:50 PM on October 20, 2006

posted by empath at 1:55 PM on October 20, 2006

Actually the genetic analysis of neurons is really fascinating. I've taken a few classes on neurobiology, and it was almost completely free of the mention of genetics in the functioning in the brain. It's looked at almost entirely on an electrical/chemical system, but genetics allows for neurons to have long term state rather then being a simple electrical component. Thinking of each neuron as an entire genetic computer on it's own massively ups the complexity of the brain. I'm really curious to find out what is figured out.

Another thing we really need to figure out is how the brain actually figures out how to connect all the neurons with each other. I mean, nerves from the eyes reach all the way to the back of the brain, and into the visual cortex. Genetics, obviously, plays a role in how that's done, but how? If we can figure that out, we may actually be able to repair the brain.
posted by delmoi at 1:57 PM on October 20, 2006

delmoi - gradients of many different neurotropic factors present at the right time during development. Some secreted by specific cells (as in the retina) or some secreted by "pioneer" neurons that first strike out on the pathway, and others follow by crawling along the growing axon highway. Some extracellular proteins, present only at specific stages, act as a surface signal for the optic nerves as they grow. Some cross over, some split off into the hypothalamus and thalamus, most continue onward to the superior colliculi and optic cortex.

It's cool stuff. For more details, try a developmental course - you'll get a good background in the different factors that promote or inhibit nerve growth (because inhibition is as important as promotion in many cases!)
posted by caution live frogs at 2:04 PM on October 20, 2006

You can also go there via the neuroscience gateway (run in conjunction with Nature), which also has commentaries on hot new papers.

my friend works for Nature on this
posted by gaspode at 2:05 PM on October 20, 2006 [1 favorite]

A few years ago, I actually interviewed at Vulcan here in Seattle for the job of being the flash developer in charge of making the brain atlas's xml datasets accessible via a neat-o animated interface. Call me a bleeding heart ELFer, but I turned the job down when I found out upwards of 25,000 mice would be killed for the project.
posted by peptide at 3:08 PM on October 20, 2006

Peptide: fair enough, but please keep in mind that lab mice are extremely well treated--well fed, lots of sex (sometimes), and painlessly euthanized when the time comes. Okay, that statement is pretty stupid, as I can't put myself in the mind of a mouse, and maybe foraging for food in the wild and running the chance of getting snatched up by an owl would be more fulfilling. But there are, in my opinion, more deserving candidates for your sympathy than lab mice!

/Ph.D. in developmental neuroscience; have killed thousands of mice with my bare hands.
posted by Turtles all the way down at 4:22 PM on October 20, 2006

(How can you use the name "peptide" without realizing that we'd know nothing about peptides without killing things?)

/Ph.D. in behavioral neuroscience, once personally guillotined 48 rats in a single sitting.
posted by caution live frogs at 9:30 AM on October 21, 2006

Well, OK technically it's "Zoology/Ecology, Evolutionary Biology and Behavior" but all my dissertation work was done in a behavioral neuroscience lab, slicing brains.
posted by caution live frogs at 9:31 AM on October 21, 2006

It wasn't so much that they were experimenting on animals that stuck in my craw; it was more the volume, which I still find astounding, which is why I posted. I mean, that's a lot of mice, right? Maybe it's not, I'm not experienced in medical research, but it seemed like a lot to me.
posted by peptide at 2:36 PM on October 21, 2006