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Related Experiment Video

Updated: Jan 10, 2026

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The mouse Gene Expression Database (GXD): 2026 update.

Constance M Smith1, Terry F Hayamizu1, Jacqueline H Finger1

  • 1The Jackson Laboratory, Bar Harbor, ME 04609, United States.

Nucleic Acids Research
|November 20, 2025
PubMed
Summary
This summary is machine-generated.

The Gene Expression Database (GXD) offers comprehensive mouse gene expression data, integrating traditional assays and RNA-Seq. Recent updates enhance searching for differential expression, cell-type specificity, and RNA-Seq data across repositories.

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Area of Science:

  • Developmental Biology
  • Genomics
  • Bioinformatics

Background:

  • The Gene Expression Database (GXD) is a long-standing resource for mouse gene expression patterns.
  • It systematically curates data from scientific literature and large-scale projects.
  • GXD integrates diverse experimental data types, including in situ hybridization, immunohistochemistry, and various blotting techniques.

Purpose of the Study:

  • To report on the continued expansion and enhancement of the Gene Expression Database (GXD).
  • To detail new search and display functionalities implemented since the last report in 2021.
  • To improve accessibility and searchability of mouse gene expression data, including RNA-Seq.

Main Methods:

  • Continued daily data curation from scientific literature and collaborative projects.
  • Integration of bulk RNA-Seq data from EMBL-EBI Expression Atlas.
  • Development of new search algorithms and user interface features for data retrieval.

Main Results:

  • Enhanced search capabilities for qualitative differential gene expression and expression profiles, combining classical data and RNA-Seq.
  • New browsing, searching, and filtering options for cell-type-specific gene expression.
  • Improved metadata index and search for RNA-Seq and microarray experiments, facilitating discovery of bulk, single-cell, and spatial data.

Conclusions:

  • GXD remains a vital, evolving resource for mouse gene expression research.
  • The implemented features significantly improve data discovery and analysis for researchers.
  • The database supports a comprehensive understanding of gene expression during development and across various conditions.