title: eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome.
abstract: eMouseAtlas (www.emouseatlas.org) is a comprehensive online resource to visualise mouse development and investigate gene expression in the mouse embryo. We have recently deployed a completely redesigned Mouse Anatomy Atlas website (www.emouseatlas.org/emap/ema) that allows users to view 3D embryo reconstructions, delineated anatomy, and high-resolution histological sections. A new feature of the website is the IIP3D web tool that allows a user to view arbitrary sections of 3D embryo reconstructions using a web browser. This feature provides interactive access to very high-volume 3D images via a tiled pan-and-zoom style interface and circumvents the need to download large image files for visualisation. eMouseAtlas additionally includes EMAGE (Edinburgh Mouse Atlas of Gene Expression) (www.emouseatlas.org/emage), a freely available, curated online database of in situ gene expression patterns, where gene expression domains extracted from raw data images are spatially mapped into atlas embryo models. In this way, EMAGE introduces a spatial dimension to transcriptome data and allows exploration of the spatial similarity between gene expression patterns. New features of the EMAGE interface allow complex queries to be built, and users can view and compare multiple gene expression patterns. EMAGE now includes mapping of 3D gene expression domains captured using the imaging technique optical projection tomography. 3D mapping uses WlzWarp, an open-source software tool developed by eMouseAtlas.
authors: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK. Chris.Armit@igmm.ed.ac.uk
authors: Chris
authors: C
authors: Armit
authors: Shanmugasundaram
authors: S
authors: Venkataraman
authors: Lorna
authors: L
authors: Richardson
authors: Peter
authors: P
authors: Stevenson
authors: Julie
authors: J
authors: Moss
authors: Liz
authors: L
authors: Graham
authors: Allyson
authors: A
authors: Ross
authors: Yiya
authors: Y
authors: Yang
authors: Nicholas
authors: N
authors: Burton
authors: Jianguo
authors: J
authors: Rao
authors: Bill
authors: B
authors: Hill
authors: Dominic
authors: D
authors: Rannie
authors: Mike
authors: M
authors: Wicks
authors: Duncan
authors: D
authors: Davidson
authors: Richard
authors: R
authors: Baldock
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D051379:Mice / Q000235:genetics*; D059467:Transcriptome