ProFun

ProFun performs functional enrichment analysis of parasitic protozoan genes to support comparative multi-omics research.

Key Features:

• Analytical modules: Provides Gene Overlaps, Over-representation Analysis (ORA), and Gene Set Enrichment Analysis (GSEA) for enrichment and overlap analyses.
• Custom annotation packages: Includes custom-made annotation packages for 40 protozoan species.
• Customizable analysis parameters: Allows customization of enrichment parameters for tailored analyses.
• Comparison across experimental designs: Supports comparison of enrichment results across complex experimental designs.
• Visual analytics: Integrates visual analytic functions to generate publication-ready charts for result interpretation.
• Deployment infrastructure: Deployed using Docker container technology, ShinyProxy, and R Shiny with containerization and load-balancing.

Scientific Applications:

• Functional interpretation of differentially expressed genes: Performs FEA on parasitic protozoan gene lists to interpret biological functions and pathways.
• Therapeutic target identification: Facilitates identification of candidate therapeutic targets in parasitic protozoans.
• Host–pathogen interaction analysis: Aids analysis of pathways and biological processes involved in host–pathogen interactions and disease mechanisms.
• Comparative multi-omics studies: Enables comparative enrichment analyses across multi-omics datasets in parasitic protozoans.

Methodology:

Implements ORA, GSEA, and gene overlap analyses using custom annotation packages for 40 protozoan species, custom scripts, and visual analytic functions; deployed via Docker containers managed by ShinyProxy and executed with R Shiny with load-balancing.