Gene

Gene aggregates curated human transcriptome datasets from primary immunodeficiency (PID) patients and integrates them into GXB to enable comparative genome-wide analysis of transcriptional responses.

Key Features:

• Curated transcriptome dataset collection: A collection of public transcriptome datasets derived from human whole blood, peripheral blood mononuclear cells (PBMCs), and fibroblasts from PID patients and controls.
• Data source and integration: Eighteen datasets sourced from the NCBI Gene Expression Omnibus (GEO) are integrated into the GXB platform for consolidated analysis.
• Experimental conditions: Included samples derive from well-characterized PID patients subjected to ex vivo stimulation to assess genome-wide molecular consequences of gene defects.
• Comparative analysis: Multiple sample groupings and rank lists are generated to compare transcriptional responses between PID patients and control subjects.
• Querying and visualization: GXB provides querying and visualization of individual transcripts across integrated studies to examine molecular roles across PIDs.

Scientific Applications:

• Understanding molecular phenotypes: Enables analysis of transcriptional responses to characterize molecular, cellular, and immunological phenotypes associated with PIDs.
• Improving clinical diagnostics and management: Facilitates identification of molecular markers and pathways relevant to diagnosis and management of primary immunodeficiencies.

Methodology:

Manual curation of transcriptome datasets, integration of eighteen GEO datasets into the GXB platform, and use of interactive tools for data analysis.