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

Madrigal, Pedro, Thanki, Anil S, Fexova, Silvie, Yu, Iris D, Chatzigeorgiou, Arsenios, Zucchi, Ida, Marugan Calles, Jose C, Vilmovsky, Liora, Khen, Amnon, Zhao, Lingyun, Erdos, Karoly, Kurri, Sandeep R, Selvakumar, Sandeep, Kumbham, Upendra, Prakash, Ananth, Wang, Shengbo, Green, Andrew, Ribas, Carlos Eduardo, Sweeney, Blake, Alegbe, Tobi, Suveges, Daniel, Hemrom, Anmol, Gomez Gutierrez, David E, Insua, Santiago, Jeffryes, Matt, Pearce, Matt, Basutkar, Prasad, Kaforou, Myrsini, Cunnington, Aubrey, Levin, Michael, Kumari, Sunita, Ware, Doreen, Goutte-Gattat, Damien, Röper, Katja, Brown, Nicholas H, Hu, Yanhui, Perrimon, Norbert, Papatheodorou, Irene, Brazma, Alvis, Hermjakob, Henning, Harrison, Melissa, Ocaña, David, Ochoa, David, McDonagh, Ellen M, Bateman, Alex, Keane, Thomas, Vizcaíno, Juan Antonio, Ernst, Christina (December 2025) Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration. Nucleic Acids Research (NAR). gkaf1238. ISSN 0305-1048

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URL: https://www.ncbi.nlm.nih.gov/pubmed/41370097

DOI: 10.1093/nar/gkaf1238

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.

Item Type:	Paper
Subjects:	bioinformatics
CSHL Authors:	Kumari, Sunita Ware, Doreen H.
Communities:	CSHL labs > Ware lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	10 December 2025
Date Deposited:	18 Dec 2025 14:33
Last Modified:	18 Dec 2025 14:33
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42041

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