The Allen Brain Atlas, which has been referred to as the “Google of gene activity in the brain”, is freely accessible to the general public. It was produced by researchers at the Seattle-based Allen Institute for Brain Science, which was funded to the tune of $100 million by billionaire software tycoon and philanthropist Paul Allen, who, in 1976, co-founded Microsoft with Bill Gates. The institute’s advisors include Steven Pinker and James Watson.
“We’re trying to advance science worldwide, [by] allow[ing] unfettered access to the data for scientists,” said Allen. “Hopefully that will jump-start or accelerate their research.”
The atlas cost $41 million to produce and took three years to complete. It is intended for use primarily by neuroscientists and physicians. The website already gets 4 million hits every month, with about 250 scientists or doctors accessing it every day.
“As gene hunters find genes that are implicated in, for example, schizophrenia or depression, the genes can immediately be looked up in the atlas to see where they’re turned on,” says David Anderson, a biologist at the California Institute of Technology who is on the Allen Institute’s scientific advisory board.
Because we share 90% of our genes with mice, the atlas can also be used by physicians to obtain data about expression patterns of human genes, such as those implicated in brain tumours and neurological disorders.
“We use it every day [and] can’t imagine life without this tool anymore,” says Ben Barres, a professor of neurology at Stanford University. “I hope they have enough bandwidth when everyone starts using it.”
The atlas comprises an interactive database of neuroanatomical data and gene expression patterns. Expression data are available for more than 21,000 mouse genes, which have been mapped down to the resolution of single cells. Much of the data has been rendered in three-dimensions; a 21 Mb application called 3D Brain Explorer is needed to view the 3D data in the atlas.
The screenshot below is from the sample data sets available on the website. It is the first of a series of coronal sections showing expression of the dopamine receptor D2.
According to the Allen Institute website, “the completed project contains more than 600 terabytes of data, enough to fill up about 20,000 iPods of the 30 gigabyte variety”. (1 terabyte = 1,000 Gigabytes.) Researchers at the institute claim that high-throughput methods enable them to analyze the expression patterns of 4,000 genes per month, and these data will be added to the atlas as they become available. Software for analysing the data is being developed and will be incorporated into the atlas.
Allan Jones, the Allen Institute’s chief scientific officer, says that the next project will involve producing a similar map of the human neocortex. This should be available “within the next couple of years”.