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NEUROGENOMICS · Mouse data could help researchers understand mysteries inside the human head


January 15, 2005 | The Allen Institute for Brain Science (AIBS) has released its first set of gene-expression data in the brain for nearly 2,000 mouse genes — the first public release of the Allen Brain Atlas initiative. The institute's leadership says the data will have important relevance for the study of brain function, disease, and the role of genes in governing human behavior.

"Google for gene activity patterns in the brain" was how Genentech's Mark Tessier-Lavigne, chairman of the Allen Institute's scientific advisory board, described the initiative. "It will enable the user to identify all the nerve cells in which a gene is active, and vice versa, for each nerve cell, identify what the complement of active genes is. It will enable users to do more readily what they're already doing on a gene-by-gene basis."

Tessier-Lavigne, a world authority on neuronal migration, also noted that "having all the information in one place for 20,000 or so genes makes it possible to mine the data, to identify correlations, and make discoveries of novel markers or therapeutic targets in brain regions of interest."

BRAIN TEASER: The Atlas image viewer shows brain anatomy and gene location. 
"We wanted to embark on a project that would marry genetic information with neuroanatomic information," said Allan Jones, senior director of Atlas Operations at AIBS. "We also need to make the data fully publicly accessible."

Using in situ hybridization, the AIBS researchers and collaborators have produced expression data for 2,000 mouse genes so far, in a series of ultrathin 25-micron brain tissue sections. In aggregate, these produce a 3-D representation of the expression data for thousands of genes. The data, and tools required to analyze them, can be found at

With the Atlas data being made publicly available, the project will help scientists further research into the development and function of the human brain, which should greatly benefit studies of neurodegenerative disease, addiction disorders, depression, memory, mood, and behavior.

Some genes are already providing extraordinary markers of the "essential building blocks of the brain," said Ed Lein, AIBS director of neuroscience.

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Parkinson's disease, for example, is a disease of the striatum. "The identification of new genes and markers in dopamine-releasing neurons could have therapeutic consequences down the road," Lein said.

Caltech professor and Howard Hughes Medical Investigator David Anderson said it would take one person one to two weeks by hand to prepare and analyze the expression of one gene in 50 tissue sections. "For 2,000 genes, that would take a single person 77 years, and for all genes, about 770 years!"

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