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review-zoom-v5-copy-number-enrichment-inventory

Inventory copy-number-aware gene enrichment sources for review zoom v5

Metadata

Statusdone
Assignedagent-1059
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-07T15:03:08.477337817+00:00
Started2026-05-07T15:07:21.305493013+00:00
Completed2026-05-07T15:19:58.007199180+00:00
Tagsreview-zoom, review-zoom-v5, gene-enrichment, copy-number, inventory, eval-scheduled
Eval score0.94
└ blocking impact0.95
└ completeness0.95
└ constraint fidelity0.55
└ coordination overhead0.94
└ correctness0.93
└ downstream usability0.96
└ efficiency0.94
└ intent fidelity0.93
└ style adherence0.95

Description

Audit and synthesize the repo's copy-number-aware gene enrichment analysis sources for review-zoom v5.

Goal:

  • Find the canonical copy-number-aware enrichment analysis results and distinguish them from stale brainstorm/root-level drafts.
  • Produce a concise source inventory and a ranked list of slide-worthy signals that can be rendered into the review zoom deck.

Context:

  • The current review zoom v4 deck does not explain the copy-number-aware gene enrichment work.
  • Relevant starting points include paper_prep/_brainstorming/, root-level copy_number_* / weighted_* / *enrichment* docs, paper_prep/surveys/SURVEY_03_gene_enrichment.md, paper_prep/figures/ed4/, HPRCv2 enrichment outputs under /moosefs/guarracino/HPRCv2/PHR_III/enrichment/ and /moosefs/guarracino/HPRCv2/PHR_III/sequence_level/enrichment/, and existing review-zoom asset slides/v2-review-zoom/_revision_assets/14_gene_enrichment_or4f/.
  • Important caveat from Erik: some community-assigned arms do not really have called PHR intervals in the CHM13/reference interval extract. Separate arm/community membership from called/rendered PHR intervals. Do not force every arm into a PHR-interval claim.
  • Be careful: previous copy-number ORA notes contain methodological caveats and may not all be final results. Do not present stale exploratory docs as validated truth.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_inventory/README.md
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_inventory/source_inventory.tsv
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_inventory/candidate_enrichment_signals.tsv
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_inventory/slide_recommendations.md

Include at minimum:

  • Which enrichment tables are canonical for slide use and why.
  • Which results are copy-number-aware versus standard/deduplicated ORA.
  • Which results are community-level HPRCv2 summaries versus genome-wide background analyses.
  • Which signals depend on called PHR intervals and which are broader arm/community/subtelomere signals.
  • Candidate slide signals such as OR/OR4F, GTP binding/GTPase/IQSEC3/GTPBP6, DDX11L/WASH/FAM138/RPL23A duplicon blocks, TAR1 if relevant, and any non-results/caveats that should be mentioned.
  • A short recommendation for 2-4 slides to add to v5.

Validation

  • All deliverables exist under _revision_assets/v5/gene_enrichment_inventory/.
  • source_inventory.tsv records path, status, coordinate/statistical scope, use/reject decision, and caveat for each key source.
  • candidate_enrichment_signals.tsv has enough columns to drive plots: signal/family/term, source, statistic, copy-count or support, community/arms if applicable, whether it is PHR-interval-specific, and caveat.
  • slide_recommendations.md proposes a small, talk-usable section, not an exhaustive methods dump.
  • The task explicitly flags stale/exploratory copy-weighted ORA outputs and the arms-without-called-PHR caveat.
  • git diff --check passes.

Depends on

Required by

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