The mouse Gene Expression Database (GXD): 2026 update

Abstract

The Gene Expression Database (GXD; https://www.informatics.jax.org/expression.shtml) is an extensive, well-curated community resource that provides detailed information about gene expression patterns in mouse strains and mutants, with a particular emphasis on development. For over 25 years, GXD has systematically curated the scientific literature and collaborated with large-scale expression projects to compile and integrate detailed expression data from multiple assay types, including RNA in situ hybridization, immunohistochemistry, in situ reporter (knock-in), RT-PCR, northern blot, and western blot experiments. In recent years, GXD has expanded its scope to include bulk RNA-Seq data, imported from the EMBL-EBI Expression Atlas. Since our last report in 2021, we continued to add data to GXD on a daily basis, and we implemented new search and display features. These include: (i) searches for qualitative differential gene expression and expression profiles that include both classical types of expression data and RNA-Seq data; (ii) browsing, searching, and filtering for cell-type-specific gene expression information; and (iii) an enhancement of our RNA-Seq and microarray experiment metadata index and search to allow users to quickly and reliably find bulk, single-cell, or spatial RNA-Seq data in the public repositories.