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Updated: Jul 10, 2025
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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
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Expression Atlas update: insights from sequencing data at both bulk and single cell level.
Nancy George1, Silvie Fexova1, Alfonso Munoz Fuentes1
1European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK.
Nucleic Acids Research
|November 22, 2023
Summary
The Expression Atlas and Single Cell Expression Atlas provide comprehensive gene and protein expression data for baseline and differential expression studies across species. These EMBL-EBI knowledgebases offer advanced search and visualization tools for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) hosts the Expression Atlas and Single Cell Expression Atlas.
- These knowledgebases provide access to gene and protein expression and localization data at both bulk and single-cell levels.
- The data covers normal tissue (baseline) and responses to perturbations like disease or genetic changes (differential).
Purpose of the Study:
- To offer users a standardized interface for searching gene and protein expression data across species and biological conditions.
- To introduce new features in the Single Cell Expression Atlas, including a cell type wheel search for metadata querying.
- To facilitate the exploration and understanding of complex expression data through advanced visualization techniques.
Main Methods:
- Utilizing standardized interfaces for searching genes and metadata terms across multiple species and biological conditions.
- Implementing dimensionality reduction plots such as t-distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP) for data exploration.
- Generating marker gene heatmaps, interactive cell-level anatomograms, and cell type-specific gene expression heatmaps for data visualization.
Main Results:
- The Expression Atlas and Single Cell Expression Atlas provide searchable, species-wide gene and protein expression data.
- New visualization tools, including a cell type wheel, t-SNE, UMAP plots, and heatmaps, enhance data interpretation.
- Users can investigate gene expression in normal tissues and in response to various biological perturbations.
Conclusions:
- The Expression Atlas and Single Cell Expression Atlas are valuable resources for researchers studying gene and protein expression.
- Advanced search and visualization functionalities empower users to explore complex biological data effectively.
- These platforms support a wide range of research questions in genomics, transcriptomics, and systems biology.
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