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
Visualizations
Core Metabolic By Openness
Enrichment By Quartile Heatmap
Openness Vs Lv Enrichment