NMD-VCell Research Workbench Module: Study design · evidence-to-experiment workflow NMD = neuromuscular disorders
Search Release v1.0 candidate
Governance ▾
Scientific program No-new-wet-lab evaluation Methods Claim boundary Benchmarks v1 release gate v1 authorization Prediction gate Registry Transitions Maintenance
v1.0 candidate Frozen 25 Jul 2026 DOI pending
v1.0.0-database-resource Schema 1.1 Model ridge-safe-v2.3 Benchmark repeated-fold-v2.2 Build EA-20260729-18 v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.
Research evidence only Observed HepG2 perturbations with limited external myogenic context No validated DMD perturbation prediction Evidence boundary

Plan experiments from evidence gaps

Filter the 21 governed hypotheses

All 21 have L2-bounded target-level HepG2 evidence. This research route does not load historical ranks or scores; use the separate historical audit route when provenance fields are required.

Candidate visual dashboard

One screen for action, agreement and missing evidence

Click a bar or tile to filter the table. The tile order follows current action and gene name; it is not clustered and not ranked.

21L2 hypotheses
9L3a assessed
16Muscle TPM ≥ 1
7Dependency caution
Action queueCurrent next step; bar length is count.
Source-agreement heatmapEach tile is a candidate gene; color is source-direction agreement, not biological truth.
Conflicted Partial agreement Full agreement Muscle expression L3a assessed Dependency caution

Gene evidence card

Click any tile to inspect one candidate

The card converts the selected row into a compact evidence route, current gap and minimum next experiment. It is descriptive and reuses frozen fields only.

Showing ZNF133 as an example entry.

Gene evidence card

ZNF133

Muscle-context assay · current research action, not a target rank.

Open gene Study Card

Evidence route

  1. L2 perturbation Observed same-context perturbation
  2. Expression feasibility 4.558 TPM
  3. DMD source direction Conflicted · 3/4 sources
  4. Muscle screen Assessed · no current hit
  5. Dependency context No moderate-dependency flag
Source agreement
3/4 sources
Legacy integrated DMD prior
up
Variant stability
sign varied across variants
Observed cells
84
GAP-02

Independent muscle-context perturbation is absent Highest missing layer: L4 dmd functional validation. Secondary gaps: GAP-03 DMD-relevant functional validation; GAP-07 independent replication.

Minimum next experiment

Design a preregistered muscle-context perturbation assay with controls, QC and stop rules.

No new score or ranking is generated; this card reorganizes frozen current-status and evidence-gap fields for inspection.

Interpretation boundary: this view is a triage dashboard. It does not create a target score, rank, cluster, perturbation truth label or prediction claim.
Current action and evidence state; no historical rank or score is shown
Gene Current action Highest supported level Integrated direction Source agreement Source state Prior-variant stability Evidence modules Statistical support Muscle context External screen (L3a) Decision-blocking gap Highest missing layer Secondary gaps
CPEB1 Verify expression L2 · observed same-context perturbation up 2/3 Conflicted same sign across variants direction conflicted direction only no significant context rows 0.731 TPM · confirm expression Not assessed GAP-06 Expression feasibility is not verified in the intended model L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
DNAAF3 Verify expression L2 · observed same-context perturbation up 1/1 Direction-consistent up sign varied across variants source limited direction only no significant context rows 0.076 TPM · confirm expression Not assessed GAP-06 Expression feasibility is not verified in the intended model L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
EPS8L1 Verify expression L2 · observed same-context perturbation up 2/2 Direction-consistent up sign varied across variants multisource direction consistent direction only no significant context rows 0.236 TPM · confirm expression Not assessed GAP-06 Expression feasibility is not verified in the intended model L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
ZFP69B Verify expression L2 · observed same-context perturbation up 2/3 Conflicted sign varied across variants direction conflicted direction only no significant context rows 0.155 TPM · confirm expression Not assessed GAP-06 Expression feasibility is not verified in the intended model L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
INTS13 Risk/context review L2 · observed same-context perturbation up 4/4 Direction-consistent up sign varied across variants exploratory multisource core direction only no significant context rows 10.991 TPM Not assessed GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
NAGLU Risk/context review L2 · observed same-context perturbation up 3/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 8.664 TPM Assessed · no current hit GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
RAC3 Risk/context review L2 · observed same-context perturbation up 3/4 Conflicted same sign across variants direction conflicted direction only no significant context rows 0.339 TPM · confirm expression Not assessed GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
RNASEH2C Risk/context review L2 · observed same-context perturbation up 4/4 Direction-consistent up sign varied across variants exploratory multisource core direction only no significant context rows 9.526 TPM Assessed · no current hit GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
RNF8 Risk/context review L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 4.105 TPM Not assessed GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
WDR4 Risk/context review L2 · observed same-context perturbation up 4/4 Direction-consistent up sign varied across variants exploratory multisource core direction only no significant context rows 4.159 TPM Assessed · no current hit GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
ZNF236 Risk/context review L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 2.007 TPM Not assessed GAP-08 Safety and dependency context blocks escalation L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
MON1A Muscle-context assay L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 8.057 TPM Assessed · no current hit GAP-02 Independent muscle-context perturbation is absent L4 dmd functional validation GAP-03 DMD-relevant functional validation; GAP-07 independent replication
ZNF133 Muscle-context assay L2 · observed same-context perturbation up 3/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 4.558 TPM Assessed · no current hit GAP-02 Independent muscle-context perturbation is absent L4 dmd functional validation GAP-03 DMD-relevant functional validation; GAP-07 independent replication
ADAM10 Computational replication L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 3.116 TPM Assessed · no current hit GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
CALR Computational replication L2 · observed same-context perturbation up 3/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 88.631 TPM Assessed · no current hit GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
DDX19B Computational replication L2 · observed same-context perturbation up 1/2 Conflicted sign varied across variants direction conflicted direction only no significant context rows 7.229 TPM Assessed · no current hit GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
DNM1 Computational replication L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 1.4 TPM Not assessed GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
EHMT2 Computational replication L2 · observed same-context perturbation up 3/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 6.406 TPM Not assessed GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
LMO2 Computational replication L2 · observed same-context perturbation up 3/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 15.237 TPM Not assessed GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
MPHOSPH6 Computational replication L2 · observed same-context perturbation up 4/4 Direction-consistent up sign varied across variants exploratory multisource core direction only no significant context rows 4.946 TPM Assessed · no current hit GAP-07 Independent computational replication is absent L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation
GFOD2 Provisional hold · external report not yet audited L2 · observed same-context perturbation up 2/4 Conflicted sign varied across variants direction conflicted direction only no significant context rows 2.947 TPM Not assessed GAP-09 External quantitative evidence has not been imported and audited L4 dmd functional validation GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication
Gap ontology

GAP-01 no independent perturbation · GAP-02 no muscle-context perturbation · GAP-03 no DMD-derived model · GAP-04 no functional phenotype · GAP-05 no dose/time response · GAP-06 no protein/expression validation · GAP-07 no donor or dataset replication · GAP-08 no safety assessment · GAP-09 external evidence not imported.