Three years, 21,000 genes and US$41 million after the Allen Brain Atlas was begun, it is finished. A three-dimensional map of gene expression in the mouse brain, the atlas is the most comprehensive study of its kind to date.

A personal interest in neuroscience saw Paul Allen, the billionaire philanthropist who co-founded Microsoft, establish the Allen Institute for Brain Science in Seattle, Washington, in 2001. He donated $100 million: half went on the Brain Atlas, launched in 2003 as the institute's first major project after two years of consultation.

Computergenerated cutaway of a mouse brain from Allen Brain Atlas data. Credit: ALLEN INSTITUTE FOR BRAIN SCIENCE

Researchers mapped where each of the mouse brain's 21,000 genes are expressed by staining brain sections with probes specific to each gene. The resulting atlas provides insight into the brain's function, helping researchers understand how different regions operate and interact. Allan Jones, chief scientific officer at the Allen Institute, is confident that the atlas will “dramatically propel neuroscience forwards”.

The atlas is available free of charge online in the form of a database. Users can search for particular genes, then scroll through photographs of vertical or horizontal sections to see how expression is distributed. The completed atlas contains around 85 million images and 600 terabytes of data — enough to fill more than 7,500 top-of-the-range iPods.

The mice used in the Allen Brain Atlas were all 56 days old. An alternative project, the Gene Expression Nervous System Atlas (GENSAT), launched by the US National Institutes of Health in 2003, is mapping gene expression in the mouse brain throughout development. The project has begun to publish results but is still some way from completion.

Much of the Allen Brain Atlas information was released before the project was completed, and researchers in the field already seem pleased with the resource. According to the Allen Institute for Brain Science, 250 scientists are using the atlas each day, and it is turning up in citations. “Combining the classical approaches of brain research with this new genetic approach is a breakthrough in neuroscience,” says Susumu Tonegawa, director of the Picower Center for Learning and Memory at the Massachusetts Institute of Technology. “It's an extremely powerful approach to try to understand the brain.”

“This will likely become the reference atlas for molecular and cellular neuroscientists,” adds Thomas Insel, director of the National Institute of Mental Health in Bethesda, Maryland. He says the atlas has already produced two surprising results: “First, the percentage of genes expressed in the adult brain is greater than we had expected, and second, the regional distribution is more selective than expected.”

It's fantastic that someone has invested so much money in neuroscience.

Alongside data on gene expression, the atlas provides an anatomical map of the mouse brain. Charles Watson is an expert on brain mapping, currently working with George Paxinos to produce the sixth edition of The Rat Brain in Stereotaxic Coordinates — one of the most cited texts in the field. “The project is doing a really good thing and it's fantastic that someone has invested so much money in neuroscience,” he says.

But Watson notes that the makers of the mouse atlas have chosen a different set of abbreviations from those in Paxinos' books. “We have the lingua franca and they're refusing to use it, which seems a bit silly,” he says.

Mice are an important model species in neuroscience research, due in part to their potential for genetic manipulation and drug testing not possible in humans. A corresponding atlas of the human brain is an obvious next step, however, and the Allen Institute has initiated pilot studies towards this end. “We plan to address key questions about the human brain and will be focusing our internal research efforts on understanding the cortex — the part of the brain associated with 'higher order' functions,” says Jones.