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Issue No.03 - July-September (2007 vol.4)
pp: 382-393
Large scale gene expression studies in the mammalian brain offer the promise of understanding the topology, networks and ultimately the function of its complex anatomy, opening previously unexplored avenues in neuroscience. High-throughput methods permit genome-wide searches to discover genes that are uniquely expressed in brain circuits and regions that control behavior. Previous gene expression mapping studies in model organisms have employed situ hybridization (ISH), a technique that uses labeled nucleic acid probes to bind to specific mRNA transcripts in tissue sections. A key requirement for this effort is the development of fast and robust algorithms for anatomically mapping and quantifying gene expression for ISH. We describe a neuroinformatics pipeline for automatically mapping expression profiles of ISH data and its use to produce the first genomic scale 3-D mapping of gene expression in a mammalian brain. The pipeline is fully automated and adaptable to other organisms and tissues. Our automated study of over 20,000 genes indicates that at least 78.8% are expressed at some level in the adult C56BL/6J mouse brain. In addition to providing a platform for genomic scale search, high-resolution images and visualization tools for expression analysis are available at the Allen Brain Atlas web site (
Bioinformatics (genome or protein) databases, Data mining, Registration, Segmentation, Information Visualization
Sayan Pathak, Chihchau Kuan, Chris Lau, Hong-wei Dong, Andrew Sodt, Chinh Dang, Brian Avants, Paul Yushkevich, James Gee, David Haynor, Ed Lein, Allan Jones, Mike Hawrylycz, "Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, no. 3, pp. 382-393, July-September 2007, doi:10.1109/tcbb.2007.1035
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