The mouse Gene Expression Database (GXD): 2021 update

Area of Science:

• Developmental Biology
• Genomics
• Bioinformatics

Background:

• The Gene Expression Database (GXD) is a vital resource for mouse developmental gene expression data.
• GXD has historically integrated data from various experimental techniques like in situ hybridization and RT-PCR.
• Previous updates focused on curating literature and collaborating with large-scale expression projects.

Purpose of the Study:

• To expand the Gene Expression Database (GXD) to include RNA-Seq data.
• To enhance searchability and analysis capabilities for mouse gene expression studies.
• To integrate diverse expression data with genetic, functional, phenotypic, and disease information.

Main Methods:

• Curating RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot data.
• Developing a searchable index for RNA-Seq and microarray experiments in ArrayExpress and GEO.
• Importing uniformly processed RNA-Seq data from EBI Expression Atlas.
• Integrating RNA-Seq data with existing GXD data and Mouse Genome Informatics (MGI) resources.
• Embedding the Morpheus heat map utility for advanced data visualization and analysis.

Main Results:

• GXD now includes a searchable index for RNA-Seq and microarray studies.
• RNA-Seq data is integrated into GXD, accessible through enhanced search and filtering.
• The Morpheus utility provides advanced visualization and analysis tools for RNA-Seq data.
• Integration facilitates access to gene expression data alongside genetic, functional, and disease information.

Conclusions:

• The integration of RNA-Seq data significantly enhances the GXD resource.
• Improved search and analysis tools empower researchers studying mouse development and disease.
• GXD continues to be a comprehensive and evolving platform for gene expression information.