Flame

Flame performs functional enrichment and multi-list analysis by integrating multiple gene or protein lists and leveraging g:Profiler and aGOtool to identify enriched Gene Ontologies, pathways, regulatory motifs, domains, diseases, phenotypes, and literature associations across 197 organisms.

Key Features:

• Multi-list Integration: Supports simultaneous input of multiple gene/protein lists and uses UpSet plots to evaluate unions and intersections among lists.
• Comprehensive Enrichment Analysis: Executes functional enrichment and literature enrichment via g:Profiler and aGOtool across 197 organisms, reporting associations with Gene Ontologies, pathways, annotations, regulatory motifs, domains, diseases, and phenotypes.
• Gene Conversion and Interaction Networks: Performs gene identifier conversions and constructs protein-protein interaction networks using STRING data.
• Visualization Outputs: Produces heatmaps, barcharts, Manhattan plots, network visualizations, and tables for exploration of enrichment results and gene/protein relationships.

Scientific Applications:

• Colitis-propelled colon cancer gene expression analysis: Validated on gene expression data related to the sensitivity of the distal part of the large intestine to experimental colitis-propelled colon cancer, supporting application in oncology-focused functional studies.

Methodology:

Uses UpSet plots for multi-list set operations, performs functional enrichment via g:Profiler and literature enrichment via aGOtool across 197 organisms, conducts gene ID conversions, generates protein-protein interaction networks from STRING, and outputs heatmaps, barcharts, Manhattan plots, networks, and tables.