AOE

AOE indexes public gene expression datasets from Gene Expression Omnibus (GEO), ArrayExpress (AE), Genomic Expression Archive (GEA), and the Sequence Read Archive (SRA) to unify microarray and RNA-seq metadata for comparative and integrative analyses.

Key Features:

• Integration across databases: Consolidates gene expression metadata and accession links from GEO, ArrayExpress (AE), and Genomic Expression Archive (GEA).
• Inclusion of RNA-seq data: Incorporates RNA-seq datasets by harvesting entries and accession information from the Sequence Read Archive (SRA) to complement microarray records.
• Indexed accession linking: Builds an index linking dataset records and accession identifiers across GEO, AE, GEA, and SRA to enable cross-repository mapping.

Scientific Applications:

• Functional interpretation of genes: Enables exploration of gene expression patterns across conditions and organisms to support functional inference.
• Comparative studies: Supports cross-study and cross-platform comparisons of expression profiles to identify conserved or differential patterns.
• Data integration and meta-analysis: Facilitates combining microarray and RNA-seq datasets for integrated analyses and meta-analyses.

Methodology:

Constructs an index that links gene expression datasets and accession metadata from GEO, ArrayExpress (AE), Genomic Expression Archive (GEA), and the Sequence Read Archive (SRA), including RNA-seq entries.