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Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration
Pedro Madrigal1, Anil S Thanki1, Silvie Fexova1
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
Nucleic Acids Research
|December 10, 2025
Summary
Expression Atlas is a comprehensive gene and protein expression knowledgebase. It now includes over 4500 studies, single-cell RNA-seq data, and new analysis tools, enhancing biological discovery.
Area of Science:
- Bioinformatics
- Genomics
- Proteomics
Background:
- Expression Atlas is a key resource from EMBL-EBI for gene and protein expression data.
- It covers multiple species, tissues, cell types, and conditions.
Purpose of the Study:
- To detail the recent expansion and enhanced functionality of the Expression Atlas.
- To highlight new data types, analysis modules, and integration capabilities.
Main Methods:
- Data integration from >4500 studies across 67 species.
- Inclusion of hundreds of single-cell RNA-seq experiments from 21 species.
- Development of a new marker gene analysis module for bulk baseline experiments.
Main Results:
- Substantial expansion in content and functionality.
- Increased proteomics coverage and updated Genotype-Tissue Expression (GTEx) profiles.
- Integration of community datasets and enhanced reproducibility through workflow updates.
Conclusions:
- Expression Atlas is a significantly enhanced, FAIR community-driven resource.
- It supports both fundamental and translational research through expanded data and tools.
- Future developments focus on modernizing pipelines and AI-ready data formats.
