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review-zoom-v5-copy-number-enrichment-narrative

Write copy-number-aware gene enrichment narrative for review zoom v5

Metadata

Statusdone
Assignedagent-1064
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-07T15:05:39.705846810+00:00
Started2026-05-07T15:24:11.931774209+00:00
Completed2026-05-07T15:31:44.554009356+00:00
Tagsreview-zoom, review-zoom-v5, gene-enrichment, copy-number, narrative, eval-scheduled
Eval score0.91
└ blocking impact0.97
└ completeness0.85
└ constraint fidelity0.55
└ coordination overhead0.95
└ correctness0.90
└ downstream usability0.96
└ efficiency0.93
└ intent fidelity0.85
└ style adherence0.95

Description

Write the concise narrative/methodology text for the copy-number-aware gene enrichment section in review-zoom v5.

Depends on:

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

Goal:

  • Produce speaker-usable slide text that explains what the copy-number-aware enrichment analysis is, why it matters here, what the main signals are, and what caveats apply.
  • This should be a talk section, not a methods appendix.

Must cover:

  • Standard ORA treats each gene symbol once; copy-number-aware enrichment accounts for repeated gene instances/copies in PHR/subtelomeric duplicon regions.
  • The biology being tested is copy-rich and duplicated; ignoring copy number can understate expanded families.
  • Some arms are community-assigned subtelomeres but do not have called CHM13 PHR intervals in chm13.phrs.bed; language must not imply every arm has a called interval.
  • What the top candidate signals mean biologically, with brief background for OR4F/olfactory, GTP binding/GTPase/IQSEC3/GTPBP6, DDX11L/WASH/FAM138/RPL23A, TAR1 only if relevant.
  • Methodological caveats from prior copy-weighted ORA notes: exploratory status, permutation/validation needs, standard-vs-copy-weighted contrast, FDR/parameter caveats if applicable.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_narrative/README.md
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_narrative/slide_text.md
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_narrative/method_box.md
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_narrative/speaker_notes.md

Validation

  • Deliverables exist under _revision_assets/v5/gene_enrichment_narrative/.
  • slide_text.md proposes 2-4 slides with concise titles, subtitles, and 2-4 bullets each.
  • method_box.md explains copy-number-aware enrichment in plain language suitable for a slide.
  • speaker_notes.md includes caveats and avoids overclaiming stale/exploratory analyses.
  • Text explicitly handles arms with community assignment but no called CHM13 PHR interval.
  • git diff --check passes.

Depends on

Required by

Log