BgeeDB

BgeeDB provides import, annotation, and analysis of re-annotated, quality-controlled gene expression datasets (including RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations) across multiple animal species for comparative and spatial expression studies.

Key Features:

• Data Integration: Imports re-annotated gene expression data into R and enables compatibility with Bioconductor packages for downstream analyses.
• Quality Control: Supplies curated, reprocessed expression datasets derived from wild-type healthy samples to enhance reliability of analyses.
• TopAnat Analysis: Implements the TopAnat gene set enrichment test to map gene lists to anatomical structures and assess preferred localization of expression complementary to GO enrichment.

Scientific Applications:

• Developmental biology: Analyze spatial localization of gene expression across anatomical structures to study developmental processes.
• Comparative genomics: Compare expression patterns across multiple animal species using standardized, reprocessed datasets.
• Evolutionary biology: Investigate evolutionary changes in tissue-specific expression and gene localization patterns.

Methodology:

Import curated expression data into R and process using Bioconductor packages; map genes to anatomical structures with the TopAnat gene set enrichment test based on expression patterns.