eMouseAtlas:an atlas-based resource for understanding mammalian embryogenesis

Abstract The eMouseAtlas resource is an online databaseof 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expressiondatabase with about 30K spatially mapped gene-expressionpatterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expressiondata for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression. We show how mapping of gene expressiondata onto spatial models delivers a framework for capturing gene expressionthat enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expressiondatabase as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ- omicexpression patterns. We report on recent developments of the eHistology atlas and our use of web-services to support embedding of the online ‘The Atlas of Mouse Development’ in the context of other resources such as the DMDD mouse phenotype database. In addition, we discuss new developments including a cellular-resolution placental atlas, third-party atlas models, clonal analysis data and a new interactive eLearning resource for developmental processes.