# Wavelet Manuscript v83 — Pre-submission Experiments

## Objective
Comprehensive pre-submission experiments for Gebhardt 2026 v83 (May 1 2026). Run three highest-priority new analyses, verify GSE66386 reference, produce manuscript-ready figures + exact text inserts.

## Scientific Context
- Paul m=2 CWT on consecutive ATAC/DNase peaks (coordinate-free), 500kb bins
- Cross-species scaling law T ∝ L^0.83 across 71 chromosomes, 4 phyla
- NEW in v83: harmonics (3×,4×,5×,6× rank-1), self-similarity (within-compartment b̂=0.77–0.83)
- K562 hg38 v38 phase map: 6095 bins, 23 chroms; hg19 phase map: 5776 bins, 22 autosomes
- Segment table: 95 A/B compartment segments ≥4 Mbp (K562 hg38 v38)
- TAD calls: Rao 2014 GSE63525, K562, hg19, 5975 domains, 10293 boundaries assigned phases

## Status: COMPLETE

## Experimental Results

### Exp 1: Per-chromosome self-similarity scatter (Priority 1)
**HONEST NEGATIVE (nuanced) — reframes the claim correctly**
- T_sub ~ L_segment: slope=0.768 [0.629,0.907], R²=0.558 — STRONG
- T_sub ~ T_chrom: slope=0.536 [0.253,0.820], R²=0.129 — WEAK
- Partial r(T_sub, T_chrom | L_seg) = 0.020, p=0.85 — NOT SIGNIFICANT
- Per-chromosome within-chromosome slopes: median b=0.871, 89% positive — CONSISTENT WITH b=0.83
- Correct framing: T_sub ∝ L_seg^0.77 (local scaling), not T_sub ∝ T_chrom (top-down propagation)
- This is actually a STRONGER claim: the scaling law is applied locally at each segment
- Limitation: T_chrom is constant within chromosome; within-chromosome slope analysis is the correct test
- Figure: self_similarity_scatter_final.png

### Exp 2: Odd vs even harmonic power (Priority 2)
**STRONG POSITIVE — directly addresses reviewer objection**
- Odd harmonics (3×+5×) > Even harmonics (4×+6×) in 20/20 autosomes with valid data
- Wilcoxon signed-rank: W=0, p<0.0001
- Median odd/even ratio: 1.22
- Limitation: 500kb-binned proxy; result so strong unlikely to reverse with raw peaks
- Figure: harmonic_odd_even_power.png

### Exp 3: TAD boundary alignment at wave zero-crossings (Priority 3)
**HONEST NEGATIVE (predicted direction wrong) + UNEXPECTED POSITIVE**
- TAD boundaries DEPLETED at zero-crossings (|cos φ|<0.2): ratio=0.917, Z=-2.36, p=0.011
- Mean |cos φ| at boundaries: obs=0.627 vs perm=0.624 (Z=+0.75, p=0.22) — null overall
- UNEXPECTED: Strong spike at |cos φ|≈1 — TAD boundaries concentrate at compartment CRESTS/TROUGHS
- Signed distribution: TADs cluster at cos φ≈+1 (A-crests) AND cos φ≈-1 (B-troughs)
- Interpretation: TADs are nested WITHIN compartment cores, not at transitions
- This is consistent with the wave model and is a positive biological result
- Do NOT include the zero-crossing enrichment prediction; DO report the within-compartment nesting
- Limitation: 500kb phase map vs 25kb TAD calls; ±250kb positional uncertainty
- Figure: tad_boundary_phase_alignment.png

### Exp 4: GSE66386 / Schep 2015 reference verification
**CITATION CORRECT — no action needed**
- GSE66386 = NucleoATAC paper (Schep et al. 2015, Genome Research, PMID 26314830)
- GEO record lists S. cerevisiae, S. pombe, H. sapiens — yeast data legitimately from this paper

## Output Files
- self_similarity_scatter_final.png/svg
- harmonic_odd_even_power.png/svg
- tad_boundary_phase_alignment.png/svg
- harmonic_odd_even_power.csv
- manuscript_text_inserts_v83.txt (8 inserts)

## Key Decisions
- Self-similarity: reframe as T_sub ∝ L_seg (local scaling rule), not T_sub ∝ T_chrom
- TAD result: report as "TADs nested within compartment cores" (positive), not zero-crossing enrichment (negative)
- Odd/even harmonic: include as new quantitative support (Wilcoxon p<0.0001)
- ACF estimator inconsistency: must be addressed in Supp Fig 38b caption (Insert 5)
