EMAGE mouse embryo spatial gene expression database: 2014 update Lorna Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, … It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwideMedical Research Council (EMAGE). These models are used as a framework to store spatial information, and we have used this strategy to collect spatially registered gene expression data. Our study fills an important gap in mammalian developmental studies by identifying functional pathways involved in this critical but previously not studied period. The nature of the spatial annotations held in EMAGE enables complex query and visualization solutions that are unique to this resource. We further identified >5000 regulated genes, most of which previously were not known to be associated with animal development. This ability to execute a query from the format of the URL makes it particularly easy to integrate EMAGE into tools and other resources.EMAGE has developed an integrated query with the Kyoto Encyclopedia of Genes and Genomes (KEGG) allowing users to use KEGG pathway descriptions as a means of querying the EMAGE database.
There are also computational access methods that do not require registration before use, such as query by Webservices, by DAS and by formattable URLs. However, it is also possible to use direct computational access to the underlying data by a number of methods.For full access to this pdf, sign in to an existing account, or purchase an annual subscription.Oxford University Press is a department of the University of Oxford. Funding to pay the Open Access publication charge: Medical Research Council.This PDF is available to Subscribers OnlyFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.Data in EMAGE are sourced from the community (primarily via the literature and mid- to large-scale screening projects) and is curated by full-time editorial staff to ensure data accuracy and consistency. New data are added regularly.
Elsevier recently implemented reciprocal links for a variety of data repository resources, including EMAGE. Clonal analysis lineage data TRACER enhancer data VISTA enhancer data EMBRYS gene expression data 3D OPT mapping now available. Similar to the gene summary, all EMAGE entries pertaining to a KEGG pathway description are condensed into a pathway summary table with each row relating to a developmental stage.
Every year, EMAGE has also been exhibited at other relevant meetings likely to attract both current and potential new users. In this study, we analyzed the gene expression variability of human embryos at different developmental stages.
Such a database should serve as a highly valuable resource for the molecular analysis of human development and pathogenesis.—Yi, H., Xue, L., Guo, M.-X. Generally, the method chosen by in situ expression databases has been for a human annotator to use a controlled anatomy vocabulary to describe the pattern of gene expression that is seen in the data images (1– 3).
EMBRYS contains the data of gene expression patterns mapped in the whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which the most striking dynamics in pattern formation and organogenesis is observed.
Then, by merely clicking a button on the gene expression data search summary, these data, including the curated sample metadata, will be rendered into an expression heat map via Morpheus, a heat map visualization and analysis tool created at the Broad Institute. A database of spatially mapped gene expression, enhancer and lineage data ... more info. Our analysis not only uncovered >5000, mostly novel, developmentally regulated genes but also revealed that maternal genes belonged to 3 groups, with many functioning only during the early cell proliferation phase (0–4 wk) of human development.
18S rRNA was analyzed as a loading control.The above analysis suggests that genes that participate in the same biological processes tend to be regulated coordinately during wk 4–9 of development.
This functionality was made possible by the inclusion of DOI as a valid query string in the EMAGE formattable URL system.Originally, the image data acquired for mapping and inclusion in the EMAGE database were sourced from the literature in a bid to provide a large base of data on which to query. Subsequently, cartilages are replaced gradually by bones throughout the embryo. In this respect, to allow navigation of the complex data available in EMAGE, we have implemented an advanced/combination query, allowing users to deliver bespoke queries across the EMAGE database. Anatomical domains were prioritized for segmentation if they were included in the text annotation of the EMBRYS whole mount ISH screen. Our study also revealed that the genes involved here are distinct from those during early embryogenesis, which include three groups of maternal genes. Furthermore, we have developed query and analysis methods that allow the research community to access this data easily using the EMAGE web interface. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwideEMAGE is a free online database resource for mouse developmental biology.