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Allen Institute for Brain Science launches new atlas resource and enhances others with new data and tools

Free online resources foster scientific discovery and collaboration


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The Allen Institute for Brain Science today announced the launch of a new brain atlas resource and significant additions to existing resources, all freely available online to accelerate progress by scientists worldwide toward understanding the brain in health and disease. The new brain atlas, the Allen Developing Mouse Brain Atlas, is launched with an initial installment of data detailing gene activity in the brain at multiple stages of development. In addition, a substantial amount of new data has been added to the Allen Spinal Cord Atlas and the Allen Institute’s Human Cortex Study.

“Following the completion of the Allen Brain Atlas in 2006, the Allen Institute has launched two major atlases – the mouse spinal cord and developing mouse brain – as well as several large, thematically focused studies,” said Allan Jones, Ph.D., Chief Scientific Officer at the Allen Institute for Brain Science. “As a central part of our mission to help the scientific community advance brain research, all of these resources are publicly available 24/7 for free online to enable and encourage widespread use and collaboration.”

Molecular approaches to understanding the functional organization of the brain promise new insights into the relationship between genes, brain, behavior and disease. To catalyze such insights, the Allen Institute produces large-scale resources and makes the resulting data and tools freely available to the global research community. All of these open resources are available at

First Allen Developing Mouse Brain Atlas Data Now Available

The newest atlas project of the Institute, the Allen Developing Mouse Brain Atlas builds on the inaugural Allen Brain Atlas adult mouse brain project. It provides a highly detailed map of gene activity in the brain at several time points across development. This first release includes data for approximately 160 genes across multiple stages of development, along with basic viewing, search and navigation tools.

Upon completion, the full atlas will include an extensive image database showing where several thousand genes are expressed, or “turned on,” in the mouse brain at multiple stages of development, from before birth through adulthood.

This new atlas will provide insight into how a brain develops and matures. It thus holds promise for revealing how human developmental disorders such as autism and other age-associated conditions including schizophrenia begin and unfold. It also has potential to enable discovery of new therapeutic interventions that harness the machinery normally used to build a brain in order to protect or repair brain tissue damaged by injury or disease.

New Data and Tools Added to the Allen Spinal Cord Atlas

A substantial amount of new data has been generated and added to the Allen Spinal Cord Atlas, a comprehensive map of gene activity throughout the mouse spinal cord. Launched in July 2008 with data for approximately 2,000 genes, the atlas now includes data for more than 13,000 genes in the adult and juvenile spinal cord. When completed next year, the Allen Spinal Cord Atlas will have genome-wide coverage.

The Web application for this atlas has been enhanced with new tools, including options for side-by-side viewing and comparison across data sets, colorized expression masks that highlight the areas of gene activity and the ability to download high-resolution images.

The Institute’s unique funding model, designed to transform public, private and foundation funds into high-value resources that enable breakthrough scientific discoveries, supported the creation of the Allen Spinal Cord Atlas. A dedicated consortium of public and private entities—including disease organizations, corporate entities, foundations and individual donors—provided funding for the project.

New Data Added to Human Cortex Study

Launched in late 2007, the Allen Institute’s Human Cortex Study is a growing image database detailing gene activity in the cortex, the area of the human brain responsible for sophisticated information processing and cognition. With today’s data release, a survey of gene activity for approximately 1,000 genes of wide scientific and clinical interest is now complete and available online. The 1,000-gene survey covers two areas of the cortex—the visual cortex and the temporal cortex—in multiple non-diseased subjects.

Additionally, the first installment of data has been released for a second phase of the study, which will examine the activity of a focused set of genes across many individuals in one of the most clinically interesting parts of the cortex – the dorsolateral prefrontal cortex. This brain area has been implicated in a number of neuropsychiatric disorders. In the current data release, gene activity data is available for non-diseased subjects. This second phase is a collaborative effort with Drs. Thomas M. Hyde and Joel E. Kleinman, investigators in the Section on Neuropathology, Clinical Brain Disorders Branch, Genes Cognition and Psychosis Program, Intramural Research Program, NIMH, NIH.

Science Programs at Allen Institute