Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
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DOI：
10.1186/1471-2105-9-153
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发表时间：
2008-03-18
影响因子：
3
通讯作者：
Hawrylycz, Mike
中科院分区：
文献类型：
--
作者：
Lau, Christopher;Ng, Lydia;Hawrylycz, Mike
背景：空间映射的大规模基因表达数据库能够对基因、解剖结构和表型之间的数据测量进行定量比较。在大多数正在进行的哺乳动物大脑基因表达研究工作中，大量资源被用于数据的映射和可视化。本文描述了Brain Explorer的实施和用途，Brain Explorer是一种3D可视化工具，用于研究艾伦脑图谱中基于原位杂交（ISH）的表达模式，艾伦脑图谱是对C57BL/6J成年小鼠大脑中21000种表达模式的全基因组调查。
结果：Brain Explorer使用户能够以100μm³的分辨率在3D模式下可视化C57BL/6J小鼠大脑的基因表达数据，允许同时展示多个实验以及179个参考神经解剖结构。Brain Explorer还允许查看从3D数据集中任何一点引用的原始ISH图像。可以从应用程序中进行解剖和空间同源性搜索，以找到在特定结构中有表达且具有相似表达模式的数据集合。后一种功能允许进行不依赖解剖结构的查询以及全基因组表达相关性研究。
结论：这些工具为获取成年小鼠大脑中的详细表达信息提供了便利途径，并能够以综合的方式对基因表达和神经解剖结构进行数据挖掘和可视化。
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 mu m(3), 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. ''Conclusion: 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.