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eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis
The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds li...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442644/ https://www.ncbi.nlm.nih.gov/pubmed/28161522 http://dx.doi.org/10.1016/j.ydbio.2017.01.023 |
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author | Armit, Chris Richardson, Lorna Venkataraman, Shanmugasundaram Graham, Liz Burton, Nicholas Hill, Bill Yang, Yiya Baldock, Richard A |
author_facet | Armit, Chris Richardson, Lorna Venkataraman, Shanmugasundaram Graham, Liz Burton, Nicholas Hill, Bill Yang, Yiya Baldock, Richard A |
author_sort | Armit, Chris |
collection | PubMed |
description | The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data 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 expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression 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. |
format | Online Article Text |
id | pubmed-5442644 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-54426442017-05-31 eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis Armit, Chris Richardson, Lorna Venkataraman, Shanmugasundaram Graham, Liz Burton, Nicholas Hill, Bill Yang, Yiya Baldock, Richard A Dev Biol Article The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data 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 expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression 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. Elsevier 2017-03-01 /pmc/articles/PMC5442644/ /pubmed/28161522 http://dx.doi.org/10.1016/j.ydbio.2017.01.023 Text en © 2017 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Armit, Chris Richardson, Lorna Venkataraman, Shanmugasundaram Graham, Liz Burton, Nicholas Hill, Bill Yang, Yiya Baldock, Richard A eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title | eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title_full | eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title_fullStr | eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title_full_unstemmed | eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title_short | eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis |
title_sort | emouseatlas: an atlas-based resource for understanding mammalian embryogenesis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442644/ https://www.ncbi.nlm.nih.gov/pubmed/28161522 http://dx.doi.org/10.1016/j.ydbio.2017.01.023 |
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