expressionatlas

is an Aggregator.

Expression Atlas is EMBL-EBI's open science resource that provides information about gene and protein expression across species and biological conditions. It aggregates, processes, and visualizes gene expression data from thousands of manually curated experiments spanning multiple species, tissue types, developmental stages, diseases, and experimental perturbations. Both bulk RNA-sequencing and single-cell RNA-sequencing datasets are supported, offering baseline expression profiles and differential gene expression analysis results through standardized processing pipelines.

Domains

genomics, biological systems, organisms

Infores ID

Unknown

FAIRsharing ID

Unknown

Product Summary

Contacts

European Bioinformatics Institute (EMBL-EBI)

Email: atlas-help@ebi.ac.uk

URL: https://www.ebi.ac.uk/about/contact

Irene Papatheodorou

: Lead, Gene Expression Team, EMBL-EBI

Publications

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

Expression Atlas update: from tissues to single cells

Products

From this Resource

ID	Name	URL	Category	Format	Description
expressionatlas.portal	Expression Atlas Portal	home	GraphicalInterface	http	Main web portal for searching and exp...
expressionatlas.single-cell	Single Cell Expression Atlas	sc	GraphicalInterface	http	Single Cell Expression Atlas portal f...
expressionatlas.api	Expression Atlas REST API	api.html	ProgrammingInterface	http	REST API for programmatic access to e...
expressionatlas.ftp-bulk	Expression Atlas FTP (Bulk Data)	experiments	Product	http	FTP archive containing processed expr...
expressionatlas.experiment-downloads	Expression Atlas Experiment Downloads	download	Product	tsv	Individual experiment data downloads ...
expressionatlas.r-objects ⚠	Expression Atlas R Data Objects	r-data-objects.html	Product	mixed	Normalized gene expression data and r...
expressionatlas.baseline-summary	Expression Atlas Baseline Summary	experiments	Product	tsv	Baseline expression summary data acro...
expressionatlas.differential-results	Expression Atlas Differential Results	experiments?experimentType=differential	Product	tsv	Differential gene expression results ...
expressionatlas.documentation	Expression Atlas Help Documentation	index.html	DocumentationProduct	http	Comprehensive help documentation cove...

From other Resources

ID	Name	URL	Category	Format	Description
rnacentral.portal	RNAcentral Portal	rnacentral.org	GraphicalInterface	http	Web portal for searching and browsing...
rnacentral.api	RNAcentral REST API	api	ProgrammingInterface	http	REST API for programmatic access to R...
rnacentral.ftp	RNAcentral FTP Archive	RNAcentral	Product	http	FTP archive with current and archived...
rnacentral.public-db	RNAcentral Public Postgres Database	public-database	DataModelProduct	postgres	Public PostgreSQL database for direct...

Details

Expression Atlas

Expression Atlas is EMBL-EBI’s comprehensive knowledgebase for gene and protein expression data, serving as a major aggregator of transcriptomic information across the tree of life. The resource provides curated, standardized, and re-analyzed gene expression data from thousands of experiments covering multiple species, developmental stages, tissues, cell types, diseases, and experimental perturbations.

Key Features

Multi-Species Coverage

Expression Atlas covers over 40 different organisms including human, mouse, rat, and various plant species, with data from more than 4,500 studies encompassing over 160,000 assays.

Dual Analysis Platforms

Bulk Expression Atlas: Traditional RNA-seq and microarray data analysis with baseline and differential expression results
Single Cell Expression Atlas: Single-cell RNA-seq data with advanced clustering, dimensionality reduction, and cell type annotation

Standardized Processing

All data undergo consistent reanalysis using standardized pipelines including:

RNA-seq processing with tools like Alevin, kallisto, and STARsolo
Quality control and batch effect correction
Statistical analysis for differential gene expression
Integration with ontologies for consistent metadata annotation

Interactive Visualizations

Gene expression heatmaps with hierarchical clustering
t-SNE and UMAP plots for single-cell data exploration
Interactive anatomograms for tissue-specific expression
Cell type wheel search interface for single-cell datasets

The resource enables researchers to investigate baseline gene expression patterns, discover differentially expressed genes across conditions, and explore expression at single-cell resolution through an intuitive web interface and programmatic API access.