multiGSEA

multiGSEA performs gene set enrichment analysis (GSEA) on multi-omics data to identify pathway-level molecular responses across genomics, transcriptomics, proteomics, and metabolomics.

Key Features:

• Integration of Multiple Omics Layers: Facilitates combined analysis of genomics, transcriptomics, proteomics, and metabolomics data to capture cross-layer interactions and leverage GSEA robustness to control type I and type II errors.
• Pathway Enrichment Analysis: Performs pathway enrichment using the GSEA algorithm and queries eight different pathway databases covering multiple organisms.
• Composite Multi-Omics Measure: Combines individual omics-layer GSEA scores to generate a composite multi-omics pathway enrichment measure.
• Broad Organismal Support: Supports 11 different organisms and includes mapping of transcripts, proteins, and metabolite IDs for cross-layer integration.

Scientific Applications:

• Disease Mechanism Elucidation: Integrates multi-omics pathway signals to reveal complex molecular mechanisms underlying disease phenotypes.
• Treatment Response Analysis: Analyzes pathway-level responses across omics layers to assess therapeutic efficacy and resistance mechanisms.
• Biomarker Discovery: Identifies pathway-associated biomarkers across transcriptomic, proteomic, and metabolomic levels.

Methodology:

Performs GSEA on individual omics layers, queries eight pathway databases, maps transcript/protein/metabolite IDs across layers, and combines layer-specific enrichment scores into a composite multi-omics pathway score.