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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

EMAGE mouse embryo spatial gene expression database: 2014 update.

Lorna Richardson¹, Shanmugasundaram Venkataraman, Peter Stevenson

¹MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital EH4 2XU, UK.

Nucleic Acids Research

|November 23, 2013

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The EMAGE database now offers spatial mapping of 3D mouse embryo images using optical projection tomography. This enhances gene expression pattern queries with integrated anatomical atlases and new web interface features.

Area of Science:

Developmental Biology
Bioinformatics
Genomics

Background:

The EMAGE database provides in situ gene expression patterns for mouse development.
Current limitations include the need for enhanced spatial querying and data integration.

Purpose of the Study:

To report progress in spatial mapping and data integration for the EMAGE database.
To enhance querying capabilities for mouse developmental gene expression patterns.

Main Methods:

Spatially mapping 3D embryo images using optical projection tomography.
Developing an IIP3D viewer for web-based visualization of 3D image data.
Integrating the eMouseAtlas anatomical atlas and EMBRYS whole mount in situ hybridization data.

Main Results:

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EMAGE now includes spatially mapped enhancer data from transgenic reporter mice.
Users can perform spatial queries alongside text-based queries.
Web interface improvements offer new query and analysis functionalities.

Conclusions:

EMAGE advancements facilitate sophisticated spatial and text-based queries of mouse gene expression.
The integrated database and visualization tools improve accessibility and analytical power.
Ongoing development enhances the utility of EMAGE for developmental biology research.