GXA

GXA provides a curated compendium of differential gene expression across cell types, organism parts, developmental stages, disease states, sample treatments, and other experimental conditions to support comparative and functional genomics.

Key Features:

• Curated and re-annotated data: Datasets are curated and re-annotated from selected studies in the ArrayExpress Archive of Functional Genomics Data.
• Statistical analysis and ranking: Results are ranked using statistical measures and by the number of independent studies that corroborate specific gene–condition associations.
• Content scope: Coverage includes information on over 200,000 genes across nine species, derived from more than 30,000 assays in over 1,000 independent studies covering nearly 4,500 biological conditions.
• Query capabilities: Searches can be performed by gene name or attributes such as Gene Ontology terms, by biological conditions including diseases, organism parts, or cell types, and by combined queries.
• Differential expression data: Provides aggregated differential gene expression results across assays and studies for specified genes and conditions.

Scientific Applications:

• Comparative and functional genomics: Enables comparison of gene expression patterns across conditions and species to infer gene function and regulation.
• Identification of gene–condition associations: Facilitates discovery of genes associated with specific diseases, tissues, cell types, developmental stages, or treatments, with evidence weighting by study support.
• Target selection and prioritization: Assists selection of robust candidate genes for experimental follow-up based on ranked statistical evidence and independent-study support.
• Cross-study integration: Supports integration of results across multiple assays and independent studies to identify reproducible expression patterns.

Methodology:

Selected ArrayExpress datasets undergo curation, re-annotation, and statistical analysis, and results are ranked by statistical measures and by the number of independent studies supporting each gene–condition association.