Stable Study Card 1.5

SC:v1.0.0-database-resource:DDX19B:1.5-DRAFTDRAFT

DDX19B

computational replication Computational replication

Does the DDX19B evidence pattern replicate in an independent dataset under a frozen analysis plan?

Registration completeness50%

Missing before registration

direction rationale
numeric minimally important effect
numeric negligible-effect margin
final powered sample size

Study Card visual summary

Frozen evidence and registration route

This multi-panel view turns the frozen Study Card fields into a visual audit of what is known, what is missing and what must be registered next.

BoundaryDescriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated.

Registration readiness 50% 4 open fields

Current supported level L2 observed same context perturbation Observed evidence ceiling in this record

Highest assessed context L3a external context screen Assessment does not imply support

Target closure layer L4 DMD functional validation required

DMD source agreement 50% 1/2 sources · conflicted

Muscle expression 7.23 TPM above 1 TPM context flag

Frozen evidence route

L1Resource recordHGNC-resolved typed research object
L2Observed HepG2 perturbation145 observed cells
L3aExternal context screenassessed no current hit
L3bIndependent perturbation replicationsame-perturbation replication absent
L4DMD muscle functional validationDMD-relevant functional validation absent
REGRegistered Study Card4 open fields before registration

Bioinformatics result snapshot

Legacy integrated DMD priorup

Source agreement50%

Skeletal-muscle TPM7.23

External screenassessed no hit

Dependency cautionnot flagged

DepMap effect-0.212

Evidence-to-experiment route

Context

At least one independent dataset with declared tissue/cell state, disease status and gene-mapping coverage.

Perturb

No new wet-lab perturbation is nominated; rerun the frozen direction, pathway and robustness analyses.

Endpoint

Predeclared gene-level direction or effect estimate in the independent dataset.

Infer

Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.

Model

Dataset-appropriate pseudobulk or aggregate model with donor/sample as the inferential unit.

Registration gap map

direction rationale
numeric minimally important effect
numeric negligible-effect margin
final powered sample size

These bars are field-state indicators only. They do not create a target score, rank, cluster or prediction claim.

Predeclared design scaffold

Biological context

At least one independent dataset with declared tissue/cell state, disease status and gene-mapping coverage.

Perturbation modality

No new wet-lab perturbation is nominated; rerun the frozen direction, pathway and robustness analyses.

Primary endpoint

Predeclared gene-level direction or effect estimate in the independent dataset.

Primary estimand

Independent-dataset gene effect and uncertainty under the frozen contrast.

Inferential unit

Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.

Planning sample size

One or more independent datasets; donor/sample adequacy must be justified from the source design rather than a generic target count.

Randomisation unit

Independent donor/sample/study unit defined by the source dataset.

Statistical model

Dataset-appropriate pseudobulk or aggregate model with donor/sample as the inferential unit.

Decision-blocking gap

GAP-07 Independent computational replication is absent

Highest missing evidence layer

L4 dmd functional validation

GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation

Perturbation-direction rationale

Current selection: unresolved requires registration

State whether the disease-associated direction is hypothesized as causal, compensatory or accompanying, and preserve the opposite-direction alternative. DMD direction and counteralignment never choose an intervention automatically.

Allowed registered hypotheses: activation; inhibition; bidirectional exploration; direction not identifiable.

Comparator and controls

Frozen null and simple baselines.
Leave-one-source-out analysis.
Negative-control genes or permuted labels.
Complete unmatched-identifier report.

Secondary endpoints

Pathway concordance.
Leave-one-source-out robustness.
Coverage and null-result diagnostics.

State-transition extension

Mechanism hypothesis and registered time axis

Scientific object: perturbation × cell state × disease context × time × phenotype

Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.

6–12 hearly molecular or signalling response

planning default requires assay calibration

24–48 hregulatory program and cell-state transition

planning default requires assay calibration

4–7 ddifferentiation and functional phenotype

planning default requires assay calibration

Cell context fields

Required before registration: healthy, DMD or isogenic corrected. Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube. Required before registration; preserve donor-specific estimates.

Cell–cell consequence

Current status: not assessed. Future levels: conditioned medium; two-cell co-culture; three-dimensional muscle model; spatial perturbation model.

Blocking factors

Study/donor.
Batch.
Cell state.
Dataset-specific covariates.

Assay QC thresholds

Minimum donor/sample coverage.
Gene detectability.
Frozen mapping and exclusion thresholds.

Minimally important effect

Required before registration; derive from assay biology or a justified pilot and store the numeric value with units.

Negligible-effect margin

Required before interpreting a null result; store a symmetric or asymmetric numeric margin with units.

Multiplicity and missing data

Frozen gene and pathway families with declared adjustment method.

Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.

Replication rules

Not applicable unless the independent dataset contains multiple perturbation reagents.

A result must persist beyond a single donor/sample and disclose leave-one-unit-out sensitivity.

Stop rules

Stop or classify as infeasible if a required numeric QC threshold fails.
Do not interpret a nonsignificant result as no material effect without a negligible-effect interval.
Do not change canonical candidate status automatically; require governed review.

Time and cost1–4 weeks after data access; planning estimate only. Institution- and assay-dependent; obtain a local itemised quote before registration.

Preregistration statusdraft requires direction rationale numeric effect margin sample size and qc thresholds

Lifecycle ruleThis draft is editable. Registration requires a timestamp and checksum; a registered revision is immutable and any correction must supersede it.

Escalation ruleEscalate from L2 to L3b only after independent context-matched perturbation replication; L4 requires replicated DMD-relevant muscle evidence.

Evidence transitionCurrent evidence state → predeclared independent test → governed evidence-level review.

Data-release planRelease the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card.

Boundary: This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation.