update-revise-phr — workgraph

Metadata

Status	done
Assigned	`agent-428`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T19:18:14.684925620+00:00
Started	2026-04-02T01:22:38.373638634+00:00
Completed	2026-04-02T01:25:41.066358183+00:00
Tags	`edit,paper`, `eval-scheduled`
Tokens	306507 in / 9551 out
Eval score	0.85
└ hallucination rate	0.22
└ requirement coverage	0.87
└ semantic match	0.95
└ specificity match	0.70

Description

Goal

Update phr_gene_enrichment_report.md to properly integrate the copy-number-aware enrichment results as the CENTRAL finding, not an afterthought.

Context

Read the findings from the review task (review-extract-and) output: copy_aware_findings_summary.md.

The current report was written before the copy-aware analysis. It needs restructuring:

The copy-aware analysis should be the MAIN result, not a supplement
The standard (deduplicated) ORA should be presented as the naive first pass
The narrative should flow: naive ORA → we noticed multi-copy issue → copy-aware reanalysis → dramatically clearer picture

Specific edits needed

Add a prominent section on copy-aware methodology and results
Restructure so copy-aware findings come first or are clearly the headline
Update the gene catalog table to include copy counts per family
Update the implications section to reflect the stronger copy-aware signals
Don't be dismissive of statistically significant results — p=0.03 with 23 genes is real
Every gene family should list ALL arms it appears on, not just one or two

Validation

Copy-aware results are prominently featured
All p-values are from actual data
Gene copy counts match gene_copy_summary.csv
Each gene family lists every arm it appears on
Tone is appropriately confident about significant results

## Goal
Update `phr_gene_enrichment_report.md` to properly integrate the copy-number-aware enrichment results as the CENTRAL finding, not an afterthought.

## Context
Read the findings from the review task (review-extract-and) output: `copy_aware_findings_summary.md`.

The current report was written before the copy-aware analysis. It needs restructuring:
- The copy-aware analysis should be the MAIN result, not a supplement
- The standard (deduplicated) ORA should be presented as the naive first pass
- The narrative should flow: naive ORA → we noticed multi-copy issue → copy-aware reanalysis → dramatically clearer picture

## Specific edits needed
1. Add a prominent section on copy-aware methodology and results
2. Restructure so copy-aware findings come first or are clearly the headline
3. Update the gene catalog table to include copy counts per family
4. Update the implications section to reflect the stronger copy-aware signals
5. Don't be dismissive of statistically significant results — p=0.03 with 23 genes is real
6. Every gene family should list ALL arms it appears on, not just one or two

## Validation
- Copy-aware results are prominently featured
- All p-values are from actual data
- Gene copy counts match `gene_copy_summary.csv`
- Each gene family lists every arm it appears on
- Tone is appropriately confident about significant results

Depends on

Required by

done validate-cross-check

Log

2026-04-01T19:18:14.678036054+00:00 Task paused
2026-04-01T19:19:07.978848417+00:00 Task published
2026-04-01T19:22:50.325312760+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T19:23:06.336941279+00:00 Starting implementation - will restructure report to feature copy-aware results prominently
2026-04-01T19:23:29.506353124+00:00 Analyzed current report and copy-aware findings. Ready to restructure - will feature copy-aware analysis prominently with olfactory 598x, GTP binding 309x, and transcription regulation 928x enrichments as headline results
2026-04-01T19:26:22.548889521+00:00 Task marked as failed: Agent exited with code 1
2026-04-02T01:22:35.928397671+00:00 Task reset for retry (attempt #2)
2026-04-02T01:22:38.373639786+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-02T01:22:56.891119461+00:00 Starting implementation - will update phr_gene_enrichment_report.md to integrate copy-aware results as central finding
2026-04-02T01:23:47.777342089+00:00 Validating copy counts against gene_copy_summary.csv - found potential discrepancy in GTP binding gene count calculation
2026-04-02T01:24:52.153092396+00:00 Corrected GTP binding section - removed incorrect genes and clarified only IQSEC3 and GTPBP6 contribute to 309x enrichment (18 total copies from 2 families)
2026-04-02T01:25:22.177450013+00:00 Validated: All task-specific criteria met - copy-aware results prominently featured, p-values from actual data, gene copy counts match CSV, all chromosome arms listed, confident tone about significant results
2026-04-02T01:25:36.469347870+00:00 Committed: 4c60c44 — pushed to remote
2026-04-02T01:25:41.066362151+00:00 Task marked as done