title: EMAGE mouse embryo spatial gene expression database: 2014 update.
abstract: EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities.
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital EH4 2XU, UK.
authors.forename: Lorna
authors.initials: L
authors.lastname: Richardson
authors.forename: Shanmugasundaram
authors.initials: S
authors.lastname: Venkataraman
authors.forename: Peter
authors.initials: P
authors.lastname: Stevenson
authors.forename: Yiya
authors.initials: Y
authors.lastname: Yang
authors.forename: Julie
authors.initials: J
authors.lastname: Moss
authors.forename: Liz
authors.initials: L
authors.lastname: Graham
authors.forename: Nicholas
authors.initials: N
authors.lastname: Burton
authors.forename: Bill
authors.initials: B
authors.lastname: Hill
authors.forename: Jianguo
authors.initials: J
authors.lastname: Rao
authors.forename: Richard A
authors.initials: RA
authors.lastname: Baldock
authors.forename: Chris
authors.initials: C
authors.lastname: Armit
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030541:Databases, Genetic; D004622:Embryo, Mammalian / Q000378:metabolism*; D015870:Gene Expression; D021621:Imaging, Three-Dimensional; D020407:Internet; D051379:Mice / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D023421:Models, Animal; D014054:Tomography / Q000379:methods