Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

Background: Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL\6J adult mouse brain. Results: Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 m3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to f...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Christopher Lau, Lydia Ng, Carol Thompson, Sayan D. Pathak, Leonard Kuan, Allan Jones, Michael Hawrylycz
• Keywords: BMCBI 2008, Brain Explorer, Expression Patterns, Gene Expression