Openness vs Functional Composition
In Progress
Project:
Openness Functional Composition
Plan
Justin Reese 
Research Question
Do species with open pangenomes show different COG functional enrichment patterns than species with closed pangenomes?
Research Plan
Hypothesis
- H0: COG enrichment patterns are independent of pangenome openness
- H1: Open pangenomes show HIGHER L (mobile element) and V (defense) enrichment in novel genes
- H2: Closed pangenomes show HIGHER metabolic diversity in core (E, C, G categories)
- H3: The universal "two-speed genome" pattern intensifies with openness
Revision History
- v1 (2026-02-19): Initial plan
Overview
The cog_analysis project found a universal "two-speed genome" pattern: novel genes are enriched in mobile elements (L: +10.88%) and defense (V: +2.83%). This project tests whether that enrichment scales with pangenome openness -- do species that acquire more novel genes also show stronger L/V enrichment? This would link genome fluidity to functional specialization of the accessory genome.
Data Collections
Atlas Reuse
Derived products, review objects, and tensions connected to this project in the BERIL Atlas.
Visualizations
Core Metabolic By Openness
Enrichment By Quartile Heatmap
Openness Vs Lv Enrichment