Dark Gene Prioritization Tables

Reusable Object

These tables are ranked candidate lists for unknown or poorly annotated genes. They compress multi-source evidence into reusable priorities for characterization, module interpretation, and experiment design.

Review Brief

What changed: this product is a promoted review queue for unknown biology rather than just a ranked table.

Why review matters: a high dark-gene rank should trigger characterization, not imply function. Reviewers should confirm that each candidate carries enough evidence components and caveats to support action.

Evidence to inspect:

• functional_dark_matter for integrated prioritization.
• truly_dark_genes for separating annotation lag from genuine unknowns.
• fitness_modules for module and neighborhood context.
• Dark Gene Structure Prioritization for next-step review packets.

Questions for reviewers:

• Are score components transparent enough to explain why each candidate is ranked?
• Which candidates are likely annotation lag and need curation rather than experiments?
• Should structural priors, module membership, or ecological recurrence be required before promotion?
• What ownership route should review candidate updates as annotations improve?

Why It Is High Value

The product lets later projects start from a reviewed candidate universe instead of repeating raw extraction and scoring. It also carries caveats about annotation lag, ortholog coverage, fitness artifacts, and taxonomic breadth.

High-Value Joins

• Join candidates to Bakta and UniProt updates to detect annotation repair.
• Join candidates to ICA modules and cofitness neighbors to move from genes to systems.
• Join candidate carrier taxa to environment labels to test ecological relevance.

Caveats

Prioritization is not functional validation. Reuse should preserve the score components and avoid treating a high rank as a discovered mechanism.