Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
<p>Abstract</p> <p>Background</p> <p>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 res...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/153 |
| _version_ | 1818835625269264384 |
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| author | Pathak Sayan Thompson Carol Ng Lydia Lau Christopher Kuan Leonard Jones Allan Hawrylycz Mike |
| author_facet | Pathak Sayan Thompson Carol Ng Lydia Lau Christopher Kuan Leonard Jones Allan Hawrylycz Mike |
| author_sort | Pathak Sayan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>in situ </it>hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL6J adult mouse brain.</p> <p>Results</p> <p>Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm<sup>3</sup>, 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 find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.</p> <p>Conclusion</p> <p>These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.</p> |
| first_indexed | 2024-12-19T02:53:41Z |
| format | Article |
| id | doaj.art-578a5c9e71224710a437e8b11c790708 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T02:53:41Z |
| publishDate | 2008-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-578a5c9e71224710a437e8b11c7907082022-12-21T20:38:27ZengBMCBMC Bioinformatics1471-21052008-03-019115310.1186/1471-2105-9-153Exploration and visualization of gene expression with neuroanatomy in the adult mouse brainPathak SayanThompson CarolNg LydiaLau ChristopherKuan LeonardJones AllanHawrylycz Mike<p>Abstract</p> <p>Background</p> <p>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 <it>in situ </it>hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL6J adult mouse brain.</p> <p>Results</p> <p>Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm<sup>3</sup>, 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 find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.</p> <p>Conclusion</p> <p>These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.</p>http://www.biomedcentral.com/1471-2105/9/153 |
| spellingShingle | Pathak Sayan Thompson Carol Ng Lydia Lau Christopher Kuan Leonard Jones Allan Hawrylycz Mike Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain BMC Bioinformatics |
| title | Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| title_full | Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| title_fullStr | Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| title_full_unstemmed | Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| title_short | Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| title_sort | exploration and visualization of gene expression with neuroanatomy in the adult mouse brain |
| url | http://www.biomedcentral.com/1471-2105/9/153 |
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