ABAEnrichment

ABAEnrichment performs enrichment analysis of user-defined gene sets against Allen Brain Atlas gene expression data and a brain-structure ontology to identify region- and development-specific expression patterns; it is implemented as an R package.

Key Features:

• Integration with Allen Brain Atlas: Uses Allen Brain Atlas gene expression datasets covering multiple human brain regions and developmental stages.
• Ontology-based enrichment: Employs an ontology of brain structural information to contextualize gene expression within an anatomical hierarchy.
• Core functionality - aba_enrich: The aba_enrich function averages candidate gene expression across donors and interfaces with FUNC for ontology enrichment analysis.
• Validation: Demonstrated recovery of gene sets associated with particular brain cell types and developmental stages.

Scientific Applications:

• Gene expression profiling: Assess enrichment of candidate genes across brain regions and developmental stages.
• Cell-type specific studies: Identify genes preferentially expressed in specific brain cell types.
• Developmental neuroscience: Investigate temporal gene expression dynamics during brain development.
• Neurological disorder research: Explore region-specific gene expression linked to neurological conditions.

Methodology:

Uses Allen Brain Atlas gene expression datasets and a brain-structure ontology, averages candidate gene expression across donors with aba_enrich, and performs ontology enrichment testing via FUNC to test candidate gene enrichment within expressed genes in brain regions.