title: Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain.
abstract: 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 microm3, 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.
  
  
  CONCLUSIONS
  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.
authors: Allen Institute for Brain Science, Seattle, WA, USA. chrisl@alleninstitute.org
authors: Christopher
authors: C
authors: Lau
authors: Lydia
authors: L
authors: Ng
authors: Carol
authors: C
authors: Thompson
authors: Sayan
authors: S
authors: Pathak
authors: Leonard
authors: L
authors: Kuan
authors: Allan
authors: A
authors: Jones
authors: Mike
authors: M
authors: Hawrylycz
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology* / Q000378:metabolism*; D003196:Computer Graphics; D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods; D051379:Mice; D008810:Mice, Inbred C57BL; D008953:Models, Anatomic; D008954:Models, Biological; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014018:Tissue Distribution; D014584:User-Computer Interface
chemical_list: D009419:Nerve Tissue Proteins