review-zoom-v7-gene-enrichment-report-backed

Metadata

Status	done
Assigned	`agent-1120`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-07T19:43:17.024483929+00:00
Started	2026-05-07T19:46:01.161467274+00:00
Completed	2026-05-07T19:57:45.416914056+00:00
Tags	`review-zoom`, `review-zoom-v7`, `gene-enrichment`, `go`, `copy-number`, `eval-scheduled`
Eval score	0.94
└ blocking impact	0.96
└ completeness	0.94
└ constraint fidelity	0.70
└ coordination overhead	0.96
└ correctness	0.93
└ downstream usability	0.95
└ efficiency	0.92
└ intent fidelity	0.89
└ style adherence	0.94

Description

Build report-backed gene enrichment/GO slide material for v7. Erik is right that the draft currently underuses the strong methods/results report. The task is to say what we can say, cleanly, without overstating p-values.\n\nGoal:\n- Make 1-3 slide-ready assets/text blocks that reference the actual reports and tables, especially end-to-end-report/report/03_gene_enrichment.md and subtelomeric_analysis_report.md section 9.\n- Explain why we should not say 'BH-significant GO enrichment proves X' from the current canonical HPRCv2 family tests, while still saying useful biology: OR4F/olfactory receptor architecture, D4Z4/DUX4L, C5 DDX11L/WASH/FAM138/IQSEC3, C15 PAR1/SHOX/GTPBP6/P2RY8, C7 acrocentric MTCO pseudogenes, pseudogene/ncRNA-rich subtelomeric gene content.\n- Include a compact table or plot of GO/functional classes from older standard/coding-only ORA outputs, clearly labeled as standard/deduplicated or exploratory copy-weighted when applicable.\n\nRequired interpretation constraints:\n- Canonical HPRCv2 community-family Fisher screen: 116 rows, no BH-significant rows; C3 OR and C7 MTCO are near-miss/candidate presence patterns, not definitive enriched classes.\n- Standard GO/ORA tables collapse copy number and are historical/brainstorming unless revalidated; they can be shown as context/method contrast if labeled.\n- Copy-weighted ORA outputs are exploratory and statistically caveated unless the task can validate/recompute them rigorously.\n- The slide should not hide the biology just because q-values are conservative. Use wording like 'recurrent gene-family architecture' and 'copy-aware candidate signal' where appropriate.\n\nDeliverables:\n- README summarizing exactly what can/cannot be claimed and citing source rows/files.\n- A slide-ready gene-family/function table and/or compact plot under slides/v2-review-zoom/_revision_assets/v7/gene_enrichment_report_backed/.\n- SLIDE_PATCH.md recommending the new v7 gene-enrichment slides and speaker-note language.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

Build report-backed gene enrichment/GO slide material for v7. Erik is right that the draft currently underuses the strong methods/results report. The task is to say what we can say, cleanly, without overstating p-values.\n\nGoal:\n- Make 1-3 slide-ready assets/text blocks that reference the actual reports and tables, especially end-to-end-report/report/03_gene_enrichment.md and subtelomeric_analysis_report.md section 9.\n- Explain why we should not say 'BH-significant GO enrichment proves X' from the current canonical HPRCv2 family tests, while still saying useful biology: OR4F/olfactory receptor architecture, D4Z4/DUX4L, C5 DDX11L/WASH/FAM138/IQSEC3, C15 PAR1/SHOX/GTPBP6/P2RY8, C7 acrocentric MTCO pseudogenes, pseudogene/ncRNA-rich subtelomeric gene content.\n- Include a compact table or plot of GO/functional classes from older standard/coding-only ORA outputs, clearly labeled as standard/deduplicated or exploratory copy-weighted when applicable.\n\nRequired interpretation constraints:\n- Canonical HPRCv2 community-family Fisher screen: 116 rows, no BH-significant rows; C3 OR and C7 MTCO are near-miss/candidate presence patterns, not definitive enriched classes.\n- Standard GO/ORA tables collapse copy number and are historical/brainstorming unless revalidated; they can be shown as context/method contrast if labeled.\n- Copy-weighted ORA outputs are exploratory and statistically caveated unless the task can validate/recompute them rigorously.\n- The slide should not hide the biology just because q-values are conservative. Use wording like 'recurrent gene-family architecture' and 'copy-aware candidate signal' where appropriate.\n\nDeliverables:\n- README summarizing exactly what can/cannot be claimed and citing source rows/files.\n- A slide-ready gene-family/function table and/or compact plot under slides/v2-review-zoom/_revision_assets/v7/gene_enrichment_report_backed/.\n- SLIDE_PATCH.md recommending the new v7 gene-enrichment slides and speaker-note language.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

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Required by

Log

2026-05-07T19:43:16.997303365+00:00 Task paused
2026-05-07T19:43:48.924916504+00:00 Task published
2026-05-07T19:46:01.161471362+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T19:46:18.997294997+00:00 Starting report-backed gene enrichment slide asset/documentation work
2026-05-07T19:48:49.594586002+00:00 Inspected report section 9, end-to-end gene-enrichment report, HPRCv2 enrichment TSVs, and parked GO/ORA tables; drafting v7 revision assets next
2026-05-07T19:55:13.943581769+00:00 Validated: deliverables added under slides/v2-review-zoom/_revision_assets/v7/gene_enrichment_report_backed; README and SLIDE_PATCH cover claim boundaries, source rows, canonical Fisher null, and GO/ORA caveats
2026-05-07T19:55:56.284633804+00:00 Validated: TSV field counts pass, SVG parses via xml.etree.ElementTree, ASCII check passes, and git diff --cached --check passes; no deck integration changes made
2026-05-07T19:56:51.434792445+00:00 Committed: cf3c531 — pushed to remote branch wg/agent-1120/review-zoom-v7-gene-enrichment-report-backed
2026-05-07T19:57:45.416922803+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T20:00:52.404237806+00:00 PendingEval → Done (evaluator passed; downstream unblocks)