title: An anatomic gene expression atlas of the adult mouse brain.
abstract: Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three-dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea).
authors.affiliation: Allen Institute for Brain Science, Seattle, Washington 98103, USA.
authors.forename: Lydia
authors.initials: L
authors.lastname: Ng
authors.forename: Amy
authors.initials: A
authors.lastname: Bernard
authors.forename: Chris
authors.initials: C
authors.lastname: Lau
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Overly
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Dong
authors.forename: Chihchau
authors.initials: C
authors.lastname: Kuan
authors.forename: Sayan
authors.initials: S
authors.lastname: Pathak
authors.forename: Susan M
authors.initials: SM
authors.lastname: Sunkin
authors.forename: Chinh
authors.initials: C
authors.lastname: Dang
authors.forename: Jason W
authors.initials: JW
authors.lastname: Bohland
authors.forename: Hemant
authors.initials: H
authors.lastname: Bokil
authors.forename: Partha P
authors.initials: PP
authors.lastname: Mitra
authors.forename: Luis
authors.initials: L
authors.lastname: Puelles
authors.forename: John
authors.initials: J
authors.lastname: Hohmann
authors.forename: David J
authors.initials: DJ
authors.lastname: Anderson
authors.forename: Ed S
authors.initials: ES
authors.lastname: Lein
authors.forename: Allan R
authors.initials: AR
authors.lastname: Jones
authors.forename: Michael
authors.initials: M
authors.lastname: Hawrylycz
mesh_terms: D000367:Age Factors; D000818:Animals; D001921:Brain / Q000033:anatomy & histology* / Q000502:physiology*; D001923:Brain Chemistry / Q000235:genetics*; D001931:Brain Mapping / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000502:physiology*; D016678:Genome / Q000502:physiology; D007091:Image Processing, Computer-Assisted / Q000379:methods; D051379:Mice; D008810:Mice, Inbred C57BL; D005810:Multigene Family