FUNAGE-Pro

FUNAGE-Pro performs gene set enrichment analysis for prokaryotic organisms to interpret high-throughput (meta-)transcriptomic and proteomic data.

Key Features:

• Extensive Functional Classification Database: A curated repository built from over 55,000 publicly available complete bacterial genomes that includes COG, GO, KEGG, InterPro, PFAM, eggNOG, and operon classes.
• Annotation and Classification: Rapid annotation and classification of proteins from newly sequenced bacterial genomes to enable integration into downstream analyses.
• Data-Type Support: Explicit support for analysis of (meta-)transcriptomic and proteomic gene sets.
• Versatile Analysis Capabilities: Functional analysis of single gene sets, multiple experiments, time series, clusters, and gene network modules.

Scientific Applications:

• Microbial Genomics: Interpreting functional patterns across bacterial genomes using enrichment results.
• Systems Biology: Linking gene set enrichment to interactions and regulatory mechanisms within prokaryotic systems.
• Comparative Genomics: Comparing functional profiles across species or strains using standardized classifications.
• Evolutionary Biology: Investigating functional conservation and divergence through enriched gene categories.
• Functional Genomics: Assigning biological meaning to gene expression and protein abundance changes in bacteria.

Methodology:

Constructs a database from over 55,000 complete bacterial genomes and performs gene set enrichment analysis alongside rapid protein annotation and classification across COG, GO, KEGG, InterPro, PFAM, eggNOG, and operon classes.