Expression Atlas

Expression Atlas
Name	Expression Atlas
Producer	EMBL-EBI
Country	Cambridge, United Kingdom
Language	English
Cost	Free
Disciplines	Genomics, Transcriptomics, Proteomics

Expression Atlas Expression Atlas is a curated, searchable repository of gene and protein expression data hosted by a major European life-science institute. It aggregates high-throughput datasets from projects and organizations such as European Bioinformatics Institute, ArrayExpress, European Nucleotide Archive, Human Genome Project, ENCODE Project, and individual laboratories to enable cross-study queries across species, tissues, cell lines, and conditions. The resource supports researchers working with resources like Ensembl, UniProt, Gene Ontology Consortium, Reactome, and NCBI for integrative analyses.

Overview

Expression Atlas provides baseline and differential expression profiles spanning multiple taxa and experimental designs drawn from consortia and initiatives including GTEx Consortium, The Cancer Genome Atlas, 1000 Genomes Project, and organism-focused efforts such as Mouse Genome Informatics and Zebrafish Information Network. It curates data linked to nomenclature authorities like HGNC, MGI, WormBase, FlyBase, and TAIR to maintain consistent identifiers across resources such as UniProtKB and Ensembl Genomes. The platform complements reference resources like PDBe, KEGG, Reactome Pathway Database, and ClinVar by providing expression context for genes and proteins.

Data Content and Scope

The repository hosts RNA-seq, microarray, proteomics, and single-cell datasets submitted by projects like Human Cell Atlas, International Cancer Genome Consortium, Proteomics Identifications Database, and laboratories contributing via ArrayExpress and ENA. Expression Atlas includes baseline expression across tissues from GTEx Consortium and differential contrasts from disease studies such as The Cancer Genome Atlas and functional perturbation experiments from groups associated with Wellcome Sanger Institute and European Molecular Biology Laboratory. Taxonomic coverage ranges from model organisms catalogued by FlyBase, WormBase, MGI, and ZFIN to agricultural species referenced in Ensembl Plants and Ensembl Metazoa.

Data Acquisition and Processing

Raw and processed data are ingested from submission platforms including ArrayExpress and European Nucleotide Archive and harmonized using pipelines influenced by standards from FAIR principles advocates and infrastructures like ELIXIR. Expression quantification follows community tools and references such as STAR aligner, Salmon (software), Kallisto, and normalization approaches used in packages like DESeq2 and limma. Metadata curation aligns with ontologies and standards driven by Gene Ontology Consortium, Experimental Factor Ontology, and initiatives like MIAME to ensure compatibility with annotation resources such as UniProt and Ensembl.

User Interface and Tools

The web interface integrates visualization components and APIs compatible with ecosystems including Ensembl, UniProtKB, and Reactome to facilitate programmatic access via services similar to those of EBI Search and Europe PMC. Interactive plots, download tools, and programmatic endpoints support workflows commonly used with software from Bioconductor, Galaxy (platform), Cytoscape, and Jupyter Notebook environments. Search and browse functionality leverages vocabularies from Experimental Factor Ontology and mappings to identifier authorities like HGNC and MGI for consistent retrieval across portals such as EBI Search and partner archives.

Integration with Other Resources

Expression Atlas links expression evidence to genome assemblies and annotations from Ensembl, RefSeq, and GENCODE, and cross-references protein knowledge in UniProtKB and pathway context in Reactome and KEGG. It interoperates with data-sharing frameworks and infrastructures such as ELIXIR, European Bioinformatics Institute, and community resources including Gene Expression Omnibus and ArrayExpress. Cross-resource linking supports translational research using clinical variation catalogs like ClinVar and cancer annotation projects like COSMIC through shared identifiers and standardized metadata.

Applications and Impact

Researchers use the resource in studies tied to consortia like Human Cell Atlas, GTEx Consortium, and The Cancer Genome Atlas for biomarker discovery, tissue-specific expression profiling, and single-cell atlasing. Biomedical applications include target validation referenced against UniProtKB annotations and pathway analysis in Reactome, while agricultural and evolutionary studies leverage data linked to Ensembl Plants and comparative resources such as OrthoDB. The resource has influenced reproducibility efforts championed by organizations like ELIXIR and standards promoted by the Gene Ontology Consortium through its role in centralizing curated expression evidence.

History and Development

The platform evolved within institutions such as European Bioinformatics Institute and collaborations with projects like ArrayExpress, expanding from microarray-era archives tied to MIAME standards to modern RNA-seq and single-cell support influenced by initiatives including Human Cell Atlas and ENCODE Project. Development has paralleled advances in analysis tools exemplified by DESeq2, limma, and alignment software like STAR aligner and Salmon (software), and has integrated community-driven ontologies from Gene Ontology Consortium and Experimental Factor Ontology to improve metadata interoperability.

Category:Bioinformatics databases