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

Abstract

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.

Keywords

Affiliated Institutions

• Bioinformatics Institute RU
• Imperial College London GB
• European Bioinformatics Institute GB
• Harvard University US
• Cold Spring Harbor Laboratory US
• University of Cambridge GB
• Open Targets GB
• Royal College of Paediatrics and Child Health GB
• Cambridge School PT

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