NMD-VCell Evidence & Experiment Workbench Audit disease-specific evidence, compare gaps, and freeze the missing test Module: Research Workbench · evidence-to-experiment workflow NMD = neuromuscular disorders
Search Data & API Current release

Current limit: disease modules compare measured states and intervention evidence, but none emits a calibrated patient-level prediction. DMD candidate validation remains prospective.

Research evidence only 21 prioritized candidate perturbation records 2,160 benchmark perturbation targets 250 observed human-myoblast fusion hits Prospective DMD candidate validation pending Boundary & release
21 Workbench candidates are surfaced for consideration, not ranked as validated targets 2,160 target-level perturbation responses form the frozen HepG2 benchmark substrate GSE293514 Stage B0 contributes 250 healthy-human-myoblast fusion hits and 125 individually validated genes No validated DMD perturbation prediction v1.2.0-measured-dmd-evidence Frozen 3 August 2026 Schema 1.1 Model ridge-safe-v2.3 Benchmark repeated-fold-v2.2 Build EA-20260804-49 DOI pending Open evidence boundary →

Disease evidence module · multidisease-evidence-v0.1.0

SMA · Spinal muscular atrophy

Human neural intervention-response evidence is separated from residual treated-muscle signals.

Open module APICompare disease axes
Spinal organoids31 samples · 3 control + 2 SMA lines
Global ASO expression reversalNot observed · ρ=+0.10
Treated muscle8 SMA II + 7 controls
KIF5A after SMN loss−1.31 / −1.32 log2FC

Primary reanalysis interpretation

Positive, null and negative axes stay separate.

R6-MO does not globally reverse bulk gene expression (rho +0.10; 16.6% consistent directional reversal among |disease LFC|≥0.5 genes). Source-reported splicing and functional rescue remains separate. OXPHOS and denervation move in expected directions in treated muscle, but all module q-values exceed 0.30 here.

Measured evidence

Patient state, causal/intervention axis and ceiling in one figure.

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SMA disease evidence module showing measured data, intervention or correction analysis, null results and the claim boundary.

Datasets

Each object has a declared biological and statistical role.

MEASURED+INTERVENTION_RESPONSEGSE290979 ↗

Human SMA type I spinal-cord organoids

31 bulk RNA-seq samples; 3 control and 2 SMA donor-derived lines

Disease and R6-MO / scramble response at line level
REGISTEREDGSE290980 ↗

Matched spinal/cerebral organoid single-cell data

8 single-cell libraries; registered as cell-resolution companion

Neural cell-state reference
MEASURED_DIRECTIONALGSE252128 ↗

Treated type II SMA paravertebral muscle

8 treated SMA vs 7 controls

Residual OXPHOS, denervation and fibrosis hypotheses; all module q>0.30 here
PERTURBEDGSE302774 ↗

Human motor and cortical neurons after SMN knockdown

3 replicates per condition in each neural context

Orthogonal KIF5A downstream mechanism evidence

Candidate establishment

Anchors, markers, endpoints and intervention nodes are typed—not pooled into one score.

ObjectRoleEvidence statePermitted interpretation
SMN1etiologic_anchorMEASUREDDisease anchor
SMN2validated_treatment_axisCORRECTED_SOURCEPositive-control treatment axis; bulk expression did not globally reverse
KIF5Adownstream_candidatePERTURBEDMechanistic candidate; source-reported functional rescue, no patient efficacy
OXPHOS_MODULEresidual_programMEASURED_DIRECTIONALCombination-therapy hypothesis space; no single target rank or significant module claim
Supports
  • human neural disease/intervention response
  • source-reported SMN2 splicing and functional rescue
  • KIF5A downstream mechanism
  • residual-muscle hypotheses
Does not support
  • global gene-expression reversal
  • significant OXPHOS/denervation/fibrosis module claim in this reanalysis
  • patient motor-outcome prediction
  • combination-therapy ranking

Machine-readable module

Summary, datasets, candidate logic and claim boundary are separate objects.

summary.json · datasets.json · candidate-logic.json · claim-boundary.json