Expression Atlas update: from tissues to single cells

By I. Papatheodorou, P. Moreno, J. Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A. Fonseca, Anja Füllgrabe, M. Green, N. Huang and 15 more. Nucleic Acids Res., 2019

478 citations recorded by the source corpus.

Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/411b6e649f3713033017dbbfdb9c6f838af0189c

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In Molecular Biology

Citations in the corpus

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment (2020, background): “Large scale repositories, such as Single Cell Portal from the Broad Institute (14) and Single Cell Expression Atlas from European Bioinformatics Institute (EMBL-EBL; 15), provide greater numbers of datasets.”
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences (2021, background): “PRIDE resources have two main missions for the proteomics community: (i) support data deposition and quality assessment of submitted proteomics experiments, to help reproducible research; and (ii) promote and facilitate the reuse of public proteomics data, and disseminate high-quality proteomics evi”
The reactome pathway knowledgebase 2022 (2021, unknown): “Public datasets can be directly integrated from ExpressionAtlas and Single Cell Expression-Atlas (16).”
Large Scale Foundation Model on Single-cell Transcriptomics (2023, unknown): “The ablation studies (Supplementary Note 1) of taking downsampling strategy (Supplementary Table 8) and regression loss (Supplementary Fig.”
FlyBase: updates to the Drosophila genes and genomes database (2024, unknown): “Under the ribbon, a link allows the user to find on the SCEA website all the scRNA-seq datasets (not only the Fly Cell Atlas data-set) that contain data for the current gene.”
Open Targets Platform: supporting systematic drug–target identification and prioritisation (2020, unknown): “Many remain stable and provide constant updates for every one of our releases––such as ChEMBL (13), COSMIC (18), Reactome (19), ExpressionAtlas (20), Cancer Gene Census (21) or ePMC (22).”