GSCA

GSCA analyzes gene and gene set activity patterns across a compendium of human and mouse gene expression samples to identify biological contexts associated with those patterns.

Key Features:

• Expression compendium: Contains over 25,000 consistently normalized human and mouse gene expression samples compiled from publicly available gene expression datasets (PED) covering diverse cell types, tissues, and disease states.
• Query input: Accepts one or multiple genes or gene sets together with a specified gene set activity pattern as the query.
• Context identification: Systematically identifies biological contexts whose aggregate expression profiles correlate with the user-defined gene set activity patterns.
• Visualization and analysis: Visualizes and analyzes gene and gene set activities across the compendium to characterize pattern-associated contexts.
• Output generation: Produces publication-quality figures and tables summarizing analysis results.
• R integration: Provides traditional R functions for programmatic access and analysis.

Scientific Applications:

• Hypothesis generation and screening: Use patterns of gene set activity across PED to generate and prioritize hypotheses about biological contexts linked to those patterns.
• Functional context discovery: Reveal previously unrecognized tissues, cell types, or disease states associated with novel or experimentally derived gene sets.
• Comparative expression analysis: Compare gene set activity patterns across human and mouse samples to investigate conserved or divergent contexts.

Methodology:

Uses a compiled compendium of over 25,000 consistently normalized human and mouse gene expression samples and queries this compendium (via traditional R functions) to identify contexts whose expression profiles correlate with user-specified gene or gene-set activity patterns.