Perturbation Cascade Network

Map how one perturbation could propagate through pathway, cell-state and function layers.

This V92 atomic build consistency workbench turns the current evidence into a directed “牵一发动全身” network: perturbation inputs connect to observed response substrates, regulatory modules, myogenic states, functional endpoints and the exact validation gaps that still block prediction.

Open network JSON Switch target scenario Audit every edge

V92 atomic build consistency workbench. The page lets a reader switch candidate-specific cascade scenarios and see which modules, readouts and validation gaps must move together. It still emits no pathway delta, cell-state delta, functional effect or calibrated DMD response prediction.

Cascade map

Perturbation to pathway to phenotype, with missing truth still visible.

Manual hierarchical layout · seed 42

Perturbation input3

Candidate-level intervention identity; no DMD response is inferred from identity alone.

ZNF133 CRISPRicontextual observed GFOD2 CRISPRicontextual observed CPEB1 perturbationcontextual observed

Early molecular response2

Observed same-assay or source-linked molecular response substrate.

HepG2 CRISPRi responseobserved same assay Human-myoblast fusion screenexternal context

Regulatory and pathway modules6

Mechanism modules used to organize hypotheses across DMD source-state and target-state evidence.

DMD source-state programssource linked observed NicheNet target-state priorregulatory inference Myogenic differentiationmeasured reference ECM and fibrosis modulehypothesis module Immune crosstalk modulehypothesis module Mitochondrial energy modulehypothesis module

Cell-state transition3

Myogenic and disease-state compartments where a future perturbation-conditioned model would need truth.

Proliferating myoblastmeasured reference Fusing myocytepartial context Maturing myotubemeasured reference

Functional endpoint4

Assay readouts required before a disease-relevant effect can be claimed.

Fusion indexrequired endpoint Membrane integrityrequired endpoint Calcium and contractionrequired endpoint Viability and toxicityrequired endpoint

Validation gap2

Decision-blocking evidence that is still absent in the frozen release.

Independent DMD perturbation truthmissing Prospective replicationmissing

Layout boundary: Node position is an explanatory layout artifact; only node identity, edge direction and evidence_state carry scientific meaning.

Target-specific propagation

Switch the target to see the module bundle and joint readouts.

Target scenario

What this adds: target-specific propagation scenarios show the coupled module/readout bundle for experiment design. pathway_delta_emitted, cell_state_delta_emitted and functional_effect_emitted remain false.

PROPAGATION:ZNF133:MYOGENIC-FUSION:V92

ZNF133 target-specific propagation scenario

TARGET SPECIFIC PROPAGATION HYPOTHESIS NO DMD MODEL INFERENCE

ZNF133 CRISPRicontextual observed
HepG2 CRISPRi responseobserved same assay
Human-myoblast fusion screenexternal context
Myogenic differentiationmeasured reference
Fusing myocytepartial context
Fusion indexrequired endpoint
Viability and toxicityrequired endpoint
Independent DMD perturbation truthmissing

contextual bridge

Myogenic differentiation

Direction: direction not predicted current release

Measure together: fusion index · myotube marker panel · viability

Matched DMD/control myogenic perturbation with prespecified fusion and toxicity endpoints.

required endpoint

Fusion index

Direction: direction not predicted current release

Measure together: myotube area · nuclei per myotube · cell survival

Prospective effect margin and null/toxic interpretation frozen before outcomes are visible.

Pathway delta emittedNo

Cell-state delta emittedNo

Functional effect emittedNo

Calibrated probabilityNo

Current interpretation: ZNF133 is the strongest current example of a myogenic propagation question because it links observed perturbation substrate to a contextual fusion screen, while the disease outcome remains absent.

Next experiment: Run ZNF133 perturbation in matched DMD/control human-myogenic cells and measure fusion, viability and target engagement together.

System coupling

The network makes downstream coupling explicit without inventing outcome truth.

3Observed same-assay edges

Current perturbation response evidence is real but bounded to its assay context.

8Context and inferred bridges

DMD source-state, myogenic reference and regulatory priors organize possible propagation routes.

6Hypothesis edges

ECM, immune, energy and late-function modules are testable cascade branches, not predictions.

4Validation-gap edges

These edges point to the exact assays needed before any disease-response claim.

Focal cascades

Three candidate paths are ready for experiment design, not efficacy claims.

Open 24-slot pilot →

CASCADE:ZNF133:MYOGENIC-FUSION

ZNF133 pathway-change hypothesis

ZNF133 CRISPRiperturbation
Human-myoblast fusion screenearly response
Myogenic differentiationregulatory pathway
Fusing myocytecell state
Fusion indexfunctional endpoint
Independent DMD perturbation truthvalidation gap

Best current use is experiment design for a matched DMD/control myogenic fusion endpoint.

This path is a prioritized testable cascade, not a predicted therapeutic effect.

CASCADE:GFOD2:ENERGY-FUNCTION

GFOD2 pathway-change hypothesis

GFOD2 CRISPRiperturbation
HepG2 CRISPRi responseearly response
DMD source-state programsregulatory pathway
Mitochondrial energy moduleregulatory pathway
Calcium and contractionfunctional endpoint
Independent DMD perturbation truthvalidation gap

Mechanism module remains audit pending and requires late functional truth.

External or contextual evidence cannot create a DMD function prediction.

CASCADE:CPEB1:CELL-STATE-SAFETY

CPEB1 pathway-change hypothesis

CPEB1 perturbationperturbation
HepG2 CRISPRi responseearly response
NicheNet target-state priorregulatory pathway
Proliferating myoblastcell state
Viability and toxicityfunctional endpoint
Prospective replicationvalidation gap

Safety and state-transition endpoints must be measured before interpreting mechanism.

The cascade records what would need to move together; it does not say that it will.

Edge audit

Every arrow states what evidence it has and what would unlock it.

Machine-readable network →

Arrow	Meaning	Evidence state	Basis	Unlock condition
PERT:ZNF133 → ASSAY:HEPG2_CRISPRI	observed response substrate	observed same assay	Processed HepG2 CRISPRi response vector exists for ZNF133.	None for same-assay evidence; DMD transfer still locked.
PERT:GFOD2 → ASSAY:HEPG2_CRISPRI	observed response substrate	observed same assay	Processed HepG2 CRISPRi response vector exists for GFOD2.	Audit pending external evidence before changing candidate status.
PERT:CPEB1 → ASSAY:HEPG2_CRISPRI	observed response substrate	observed same assay	Processed same-assay response can seed a candidate hypothesis.	Run matched DMD/control myogenic perturbation before disease interpretation.
PERT:ZNF133 → ASSAY:MYOBLAST_CONTEXT_SCREEN	related myogenic context	contextual bridge	Human-myoblast screen context exists but is not DMD replication.	Repeat in matched DMD/control myogenic cells with prespecified endpoint.
ASSAY:HEPG2_CRISPRI → PROGRAM:DMD_SOURCE_STATE	cross-context comparison	contextual bridge	Same-assay response is compared against DMD source-linked programs only as context.	Establish transfer on a disease-relevant perturbation holdout.
PROGRAM:DMD_SOURCE_STATE → PROGRAM:NICHENET_TARGET_STATE	regulatory target-state bridge	inferred bridge	NicheNet target-state evidence supplies regulatory context.	Validate ligand-target or regulator-target mechanism in the declared cell context.
PROGRAM:DMD_SOURCE_STATE → PATHWAY:ECM_FIBROSIS	disease module placement	hypothesis	DMD source-state evidence motivates an ECM/fibrosis module.	Measure ECM or fibrosis readouts after candidate perturbation in DMD-relevant cells.
PROGRAM:NICHENET_TARGET_STATE → PATHWAY:IMMUNE_CROSSTALK	cross-cell regulatory hypothesis	hypothesis	Regulatory context motivates a cell-cell consequence module.	Test causal cross-cell outcome or coculture readout.
ASSAY:MYOBLAST_CONTEXT_SCREEN → PATHWAY:MYOGENIC_DIFFERENTIATION	myogenic bridge	contextual bridge	Fusion-screen context links candidate selection to myogenic biology.	Repeat with disease and matched-control perturbation truth.
PATHWAY:MYOGENIC_DIFFERENTIATION → STATE:PROLIFERATING_MYOBLAST	reference start state	contextual bridge	Unperturbed human-myogenic trajectory anchors the starting compartment.	Add perturbation-conditioned cells at 0 h and early response times.
PATHWAY:MYOGENIC_DIFFERENTIATION → STATE:FUSING_MYOCYTE	transition context	contextual bridge	The platform can place a question on the myoblast-to-fusion axis.	Measure candidate-specific state transition in DMD and control cells.
PATHWAY:MYOGENIC_DIFFERENTIATION → STATE:MATURING_MYOTUBE	late state context	contextual bridge	The unperturbed trajectory includes a late reference state.	Add perturbation-conditioned myotube maturation outcomes.
PATHWAY:MITO_ENERGY → FUNCTION:CALCIUM_CONTRACTION	function-coupled hypothesis	hypothesis	Energy-state changes would need to be tied to contractile readouts.	Measure calcium handling and contraction under candidate perturbation.
PATHWAY:ECM_FIBROSIS → FUNCTION:MEMBRANE_INTEGRITY	matrix-function hypothesis	hypothesis	ECM remodeling could matter only if functional readouts change.	Measure membrane injury or repair endpoint in the same experiment.
STATE:FUSING_MYOCYTE → FUNCTION:FUSION_INDEX	state-to-endpoint mapping	contextual bridge	Fusion index is an interpretable endpoint for a myogenic transition.	Freeze endpoint, effect margin and analysis before outcomes are visible.
STATE:MATURING_MYOTUBE → FUNCTION:CALCIUM_CONTRACTION	late functional endpoint	hypothesis	Mature myotube state needs functional measurement before disease interpretation.	Run late myotube function assay with viability co-readout.
STATE:PROLIFERATING_MYOBLAST → FUNCTION:VIABILITY_TOXICITY	early safety gate	hypothesis	Any apparent mechanism is uninterpretable without viability/toxicity checks.	Include toxicity controls and reagent concordance in the pilot.
FUNCTION:FUSION_INDEX → GAP:DMD_PERTURBATION_TRUTH	requires DMD truth	missing validation	No candidate perturbation fusion outcome exists in matched DMD/control cells.	Generate a registered DMD/control myogenic perturbation outcome.
FUNCTION:MEMBRANE_INTEGRITY → GAP:DMD_PERTURBATION_TRUTH	requires disease functional truth	missing validation	No membrane integrity endpoint is measured for current candidate perturbations.	Add disease-relevant functional endpoint and analysis threshold.
FUNCTION:CALCIUM_CONTRACTION → GAP:DMD_PERTURBATION_TRUTH	requires muscle function truth	missing validation	No calcium or contraction outcome exists for the candidate perturbations.	Measure late function in a matched, preregistered assay.
GAP:DMD_PERTURBATION_TRUTH → GAP:PROSPECTIVE_REPLICATION	must replicate before claim	missing validation	The release has zero prospective predictions and zero returned outcomes.	Register prediction, run blinded outcome, then replicate independently.

Claim boundary

A network can improve the research question before it becomes a predictor.

The cascade network is an audit scaffold for perturbation-pathway experiments. It does not run a virtual-cell simulator, emit a calibrated DMD response, rank targets or recommend treatment.

{
  "network_schema": "nmd-vcell-perturbation-cascade-network/1.1",
  "lifecycle_state": "BOUNDED_MECHANISTIC_HYPOTHESIS_NETWORK_NO_DMD_RESPONSE_PREDICTION",
  "target_specific_propagation_scenarios": 3,
  "pathway_delta_emitted": false,
  "validated_dmd_prediction_edges": 0,
  "layout": "manual_hierarchical_cascade",
  "seed": 42
}