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Expression Atlas update: insights from sequencing data at both bulk and single cell level

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Fexova, Silvie 
Fuentes, Alfonso Munoz 
Madrigal, Pedro 
Bi, Yalan 


Expression Atlas ( and its newest counterpart the Single Cell Expression Atlas ( are EMBL-EBI’s knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users’ understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.


Acknowledgements: We would like to thank Olamidipupo Ajigboye and Helen Parkinson for their contributions in enriching EFO in terms needed to describe samples studied in Atlas; Awais Athar, Ahmed Ali, Ugis Sarkans for their help with the BioStudies interface and assistance in submissions of new functional genomics studies to BioStudies. We would like to thank the Bioconda community, the Galaxy community for assistance with Bioconda and Galaxy. We would like to thank the data wranglers, past and present of the Human Cell Atlas Data Coordination Platform for their assistance collating HCA data for the Single Cell Expression Atlas. Finally, we thank the Expression Atlas SAB members, Jurg Bahler (University College London), Angela Brookes (University of California Santa Cruz), Roderic Guigó (Center for Genomic Regulation, chair), Kathryn Lilley (Cambridge University) and Zemin Zhang (Peking University).

Funder: European Molecular Biology Laboratory; DOI:


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Nucleic Acids Research

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Oxford University Press
Wellcome Trust (108437/Z/15/Z, 221401/Z/20/Z, 223745/Z/21/Z)
BBSRC (BB/X001911/1, BB/T019670/1)
Fly Cell Atlas (BB/T014563/1)
Gramene (USDA-ARS-8062-21000-041-00D)