Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration

Abstract

Expression Atlas (https://www.ebi.ac.uk/gxa/home) is EMBL-EBI's comprehensive knowledgebase for gene and protein expression across tissues, cell types, conditions, and multiple species. Since our last update, Expression Atlas has expanded substantially in both content and functionality, now comprising >4500 studies from 67 species, with increased proteomics coverage and updated Genotype-Tissue Expression (GTEx) tissue profiles. The resource also includes hundreds of single-cell RNA-seq experiments spanning 21 species, among them externally analysed community datasets such as Tabula Sapiens and GTEx single-nucleus profiles, allowing exploration of curated atlases while maintaining their original analytical framework. Key methodological advances include a new marker gene analysis module for bulk baseline experiments, alongside workflow updates that improve reproducibility. Expression Atlas data are integrated into EMBL-EBI resources such as Ensembl, UniProt, and Europe PMC and disseminated through collaboration with model organism communities such as FlyBase and Gramene. The resource also supports translational research through the European Diagnostic Transcriptomic Library and integration with the Open Targets platform. Future directions include modernizing analysis pipelines, enhancing programmatic access, and delivering AI-ready data formats, strengthening Expression Atlas as a findable, accessible, interoperable, and reusable (FAIR) community-driven resource for both fundamental and translational discovery.

Graphical Abstract

Figure 1.

Heatmap visualization of GTEx V8 expression profiles showing the most specific marker genes across 40 selected human tissues (https://www.ebi.ac.uk/gxa/experiments/E-GTEX-8/). This view highlights tissue-restricted expression patterns and is representative of the new marker gene module implemented for all transcriptomic and proteomic baseline studies.

Figure 2.

The Human Cell Atlas–Data Portal collection in SCEA contains data from 81 Human Cell Atlas (HCA) studies, out of which 32 are source datasets for 12 upcoming or existing integrated atlases. Of note, some studies are used across many atlases. (A) Screenshot of the SCEA web application panel (https://www.ebi.ac.uk/gxa/sc/) displaying the HCA collection of experiments alongside other featured collections such as the Fly Cell Atlas and COVID-19 Data Portal [33]. (B) Sankey plot showing the shared studies between HCA and SCEA and the distribution of source datasets across atlases. (C) Example experiment page for the Human Lung Cell Atlas in SCEA, the first externally analysed HCA dataset included (https://www.ebi.ac.uk/gxa/sc/experiments/E-ANND-1/). These views illustrate how SCEA can integrate community atlases while preserving their original analyses.

Figure 3.

Example of Europe PMC web portal displaying embedded links to Expression Atlas datasets from the European Diagnostic Transcriptomic Library (EDTL) (https://europepmc.org/article/MED/37255317). Cross-references point to the corresponding RNA-seq data, visualized in Expression Atlas and archived in the ArrayExpress collection in BioStudies. The database links component of the Europe PMC record is accessible through the Europe PMC API at https://www.ebi.ac.uk/europepmc/webservices/rest/MED/37255317/datalinks.

Figure 4.

RNAcentral gene page showing the Expression Atlas heatmap widget for human non-coding RNA RN7SL1 (https://rnacentral.org/rna/URS00000478B7/9606).

Figure 5.

Expression Atlas differential expression evidence in the OTs Platform for human gene NOD2, a gene implicated in the development and pathogenesis of Crohn’s disease. (A) Availability of expression data visualized as a coloured circle. (B) Expanded panel displaying details of the underlying studies with direct links to Expression Atlas (https://platform.opentargets.org/target/ENSG00000167207/associations).