Bubble GUM

Bubble GUM performs extraction of phenotype-specific molecular signatures from transcriptomic datasets and generates custom gene sets for exhaustive Gene Set Enrichment Analysis (GSEA) across multiple experimental conditions.

Key Features:

• Automatic extraction of molecular signatures: Derives phenotype-relevant gene expression signatures directly from transcriptomic data.
• Generation of custom gene sets for GSEA: Produces user-defined/home-made gene sets tailored to specific biological questions for downstream enrichment analysis.
• Exhaustive GSEA with multiple testing correction: Executes comprehensive GSEA comparisons across numerous conditions while applying multiple testing corrections.
• Integration and graphical comparison of GSEA results: Integrates multiple GSEA outputs and provides comparative graphical representations of enrichment patterns.

Scientific Applications:

• Cross-species transcriptomic fingerprinting: Generation of transcriptomic fingerprints for murine cell types and assessment of their enrichment in human cell types.
• Comparative immunocyte genomics: Identification and confirmation of homologies between mouse and human immunocytes via enrichment analysis.
• Cross-study microarray comparison: Evaluation of similarities between microarray datasets originating from different laboratories or experimental models.

Methodology:

Automatic derivation of molecular signatures from transcriptomic data, generation of custom gene sets, exhaustive GSEA with multiple testing correction, and integration plus graphical comparison of multiple GSEA outputs.