{
  "network_schema": "nmd-vcell-perturbation-cascade-network/1.1",
  "interface_build": "EA-20260730-42",
  "resource_release": "v1.0.0-database-resource",
  "evidence_freeze": "2026-07-25",
  "lifecycle_state": "BOUNDED_MECHANISTIC_HYPOTHESIS_NETWORK_NO_DMD_RESPONSE_PREDICTION",
  "network_type": "directed_perturbation_to_pathway_to_cell_state_to_endpoint_cascade",
  "layout_policy": {
    "layout": "manual_hierarchical_cascade",
    "seed": 42,
    "comparable_across_versions": true,
    "biological_interpretation": "Node position is an explanatory layout artifact; only node identity, edge direction and evidence_state carry scientific meaning."
  },
  "evidence_policy": {
    "allowed_edge_states": [
      "observed_same_assay",
      "contextual_bridge",
      "inferred_bridge",
      "hypothesis",
      "missing_validation"
    ],
    "dmd_prediction_claim": false,
    "therapeutic_claim": false,
    "confidence_policy": "No numeric confidence is emitted until matched DMD perturbation outcomes exist."
  },
  "counts": {
    "layers": 6,
    "nodes": 20,
    "edges": 21,
    "observed_same_assay_edges": 3,
    "contextual_or_inferred_edges": 8,
    "hypothesis_edges": 6,
    "missing_validation_edges": 4,
    "target_specific_propagation_scenarios": 3,
    "validated_dmd_prediction_edges": 0,
    "independent_dmd_perturbation_edges": 0
  },
  "layers": [
    {
      "layer_id": "perturbation",
      "label": "Perturbation input",
      "interpretation": "Candidate-level intervention identity; no DMD response is inferred from identity alone."
    },
    {
      "layer_id": "early_response",
      "label": "Early molecular response",
      "interpretation": "Observed same-assay or source-linked molecular response substrate."
    },
    {
      "layer_id": "regulatory_pathway",
      "label": "Regulatory and pathway modules",
      "interpretation": "Mechanism modules used to organize hypotheses across DMD source-state and target-state evidence."
    },
    {
      "layer_id": "cell_state",
      "label": "Cell-state transition",
      "interpretation": "Myogenic and disease-state compartments where a future perturbation-conditioned model would need truth."
    },
    {
      "layer_id": "functional_endpoint",
      "label": "Functional endpoint",
      "interpretation": "Assay readouts required before a disease-relevant effect can be claimed."
    },
    {
      "layer_id": "validation_gap",
      "label": "Validation gap",
      "interpretation": "Decision-blocking evidence that is still absent in the frozen release."
    }
  ],
  "nodes": [
    {
      "id": "PERT:ZNF133",
      "label": "ZNF133 CRISPRi",
      "layer_id": "perturbation",
      "node_type": "candidate_perturbation",
      "evidence_state": "contextual_observed",
      "gene": "ZNF133",
      "route": "/resource/gene/ZNF133",
      "summary": "Observed HepG2 response and human-myoblast screen context; no DMD perturbation outcome."
    },
    {
      "id": "PERT:GFOD2",
      "label": "GFOD2 CRISPRi",
      "layer_id": "perturbation",
      "node_type": "candidate_perturbation",
      "evidence_state": "contextual_observed",
      "gene": "GFOD2",
      "route": "/resource/gene/GFOD2",
      "summary": "Observed HepG2 response; external evidence remains pending audit and not DMD validation."
    },
    {
      "id": "PERT:CPEB1",
      "label": "CPEB1 perturbation",
      "layer_id": "perturbation",
      "node_type": "candidate_perturbation",
      "evidence_state": "contextual_observed",
      "gene": "CPEB1",
      "route": "/resource/gene/CPEB1",
      "summary": "Candidate-level evidence can seed a cascade hypothesis but not a calibrated disease response."
    },
    {
      "id": "ASSAY:HEPG2_CRISPRI",
      "label": "HepG2 CRISPRi response",
      "layer_id": "early_response",
      "node_type": "observed_assay_substrate",
      "evidence_state": "observed_same_assay",
      "summary": "Processed same-assay perturbation response vectors for 21 candidates."
    },
    {
      "id": "ASSAY:MYOBLAST_CONTEXT_SCREEN",
      "label": "Human-myoblast fusion screen",
      "layer_id": "early_response",
      "node_type": "context_screen",
      "evidence_state": "external_context",
      "summary": "A related myogenic screen supplies context for 9/21 candidates but is not DMD replication."
    },
    {
      "id": "PROGRAM:DMD_SOURCE_STATE",
      "label": "DMD source-state programs",
      "layer_id": "regulatory_pathway",
      "node_type": "disease_program",
      "evidence_state": "source_linked_observed",
      "summary": "Frozen DMD single-cell and DE evidence layers define source-linked disease context."
    },
    {
      "id": "PROGRAM:NICHENET_TARGET_STATE",
      "label": "NicheNet target-state prior",
      "layer_id": "regulatory_pathway",
      "node_type": "regulatory_prior",
      "evidence_state": "regulatory_inference",
      "summary": "Target-state regulatory evidence is an inferred bridge, not perturbation validation."
    },
    {
      "id": "PATHWAY:MYOGENIC_DIFFERENTIATION",
      "label": "Myogenic differentiation",
      "layer_id": "regulatory_pathway",
      "node_type": "pathway_module",
      "evidence_state": "measured_reference",
      "summary": "Unperturbed 0/24/48/72 h myogenic reference supplies the trajectory axis."
    },
    {
      "id": "PATHWAY:ECM_FIBROSIS",
      "label": "ECM and fibrosis module",
      "layer_id": "regulatory_pathway",
      "node_type": "pathway_module",
      "evidence_state": "hypothesis_module",
      "summary": "A disease-context module requiring matched perturbation readouts before interpretation."
    },
    {
      "id": "PATHWAY:IMMUNE_CROSSTALK",
      "label": "Immune crosstalk module",
      "layer_id": "regulatory_pathway",
      "node_type": "pathway_module",
      "evidence_state": "hypothesis_module",
      "summary": "Cross-cell consequences are tracked as hypothesis edges until causal outcome data exist."
    },
    {
      "id": "PATHWAY:MITO_ENERGY",
      "label": "Mitochondrial energy module",
      "layer_id": "regulatory_pathway",
      "node_type": "pathway_module",
      "evidence_state": "hypothesis_module",
      "summary": "Energetic remodeling is represented as a testable module, not a predicted effect."
    },
    {
      "id": "STATE:PROLIFERATING_MYOBLAST",
      "label": "Proliferating myoblast",
      "layer_id": "cell_state",
      "node_type": "cell_state",
      "evidence_state": "measured_reference",
      "summary": "Human-myogenic reference start state; no candidate DMD perturbation truth yet."
    },
    {
      "id": "STATE:FUSING_MYOCYTE",
      "label": "Fusing myocyte",
      "layer_id": "cell_state",
      "node_type": "cell_state",
      "evidence_state": "partial_context",
      "summary": "Fusion context exists for selected candidates but is not disease-conditioned validation."
    },
    {
      "id": "STATE:MATURING_MYOTUBE",
      "label": "Maturing myotube",
      "layer_id": "cell_state",
      "node_type": "cell_state",
      "evidence_state": "measured_reference",
      "summary": "Unperturbed late reference state; candidate functional perturbation response is locked."
    },
    {
      "id": "FUNCTION:FUSION_INDEX",
      "label": "Fusion index",
      "layer_id": "functional_endpoint",
      "node_type": "functional_endpoint",
      "evidence_state": "required_endpoint",
      "summary": "Primary myogenic endpoint candidate for a future matched DMD/control assay."
    },
    {
      "id": "FUNCTION:MEMBRANE_INTEGRITY",
      "label": "Membrane integrity",
      "layer_id": "functional_endpoint",
      "node_type": "functional_endpoint",
      "evidence_state": "required_endpoint",
      "summary": "Disease-relevant functional readout; not measured for current candidate perturbations."
    },
    {
      "id": "FUNCTION:CALCIUM_CONTRACTION",
      "label": "Calcium and contraction",
      "layer_id": "functional_endpoint",
      "node_type": "functional_endpoint",
      "evidence_state": "required_endpoint",
      "summary": "Late muscle-function endpoint required for disease-relevant prediction claims."
    },
    {
      "id": "FUNCTION:VIABILITY_TOXICITY",
      "label": "Viability and toxicity",
      "layer_id": "functional_endpoint",
      "node_type": "safety_endpoint",
      "evidence_state": "required_endpoint",
      "summary": "Safety gate that can stop a perturbation regardless of molecular direction."
    },
    {
      "id": "GAP:DMD_PERTURBATION_TRUTH",
      "label": "Independent DMD perturbation truth",
      "layer_id": "validation_gap",
      "node_type": "decision_blocking_gap",
      "evidence_state": "missing",
      "summary": "No matched DMD candidate-perturbation outcome is released."
    },
    {
      "id": "GAP:PROSPECTIVE_REPLICATION",
      "label": "Prospective replication",
      "layer_id": "validation_gap",
      "node_type": "decision_blocking_gap",
      "evidence_state": "missing",
      "summary": "No preregistered prediction, outcome or independent replication exists yet."
    }
  ],
  "edges": [
    {
      "id": "E01",
      "source": "PERT:ZNF133",
      "target": "ASSAY:HEPG2_CRISPRI",
      "label": "observed response substrate",
      "direction": "directed",
      "evidence_state": "observed_same_assay",
      "evidence_basis": "Processed HepG2 CRISPRi response vector exists for ZNF133.",
      "edge_semantics": "observed_context_response",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "None for same-assay evidence; DMD transfer still locked."
    },
    {
      "id": "E02",
      "source": "PERT:GFOD2",
      "target": "ASSAY:HEPG2_CRISPRI",
      "label": "observed response substrate",
      "direction": "directed",
      "evidence_state": "observed_same_assay",
      "evidence_basis": "Processed HepG2 CRISPRi response vector exists for GFOD2.",
      "edge_semantics": "observed_context_response",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Audit pending external evidence before changing candidate status."
    },
    {
      "id": "E03",
      "source": "PERT:CPEB1",
      "target": "ASSAY:HEPG2_CRISPRI",
      "label": "observed response substrate",
      "direction": "directed",
      "evidence_state": "observed_same_assay",
      "evidence_basis": "Processed same-assay response can seed a candidate hypothesis.",
      "edge_semantics": "observed_context_response",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Run matched DMD/control myogenic perturbation before disease interpretation."
    },
    {
      "id": "E04",
      "source": "PERT:ZNF133",
      "target": "ASSAY:MYOBLAST_CONTEXT_SCREEN",
      "label": "related myogenic context",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "Human-myoblast screen context exists but is not DMD replication.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Repeat in matched DMD/control myogenic cells with prespecified endpoint."
    },
    {
      "id": "E05",
      "source": "ASSAY:HEPG2_CRISPRI",
      "target": "PROGRAM:DMD_SOURCE_STATE",
      "label": "cross-context comparison",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "Same-assay response is compared against DMD source-linked programs only as context.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Establish transfer on a disease-relevant perturbation holdout."
    },
    {
      "id": "E06",
      "source": "PROGRAM:DMD_SOURCE_STATE",
      "target": "PROGRAM:NICHENET_TARGET_STATE",
      "label": "regulatory target-state bridge",
      "direction": "directed",
      "evidence_state": "inferred_bridge",
      "evidence_basis": "NicheNet target-state evidence supplies regulatory context.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Validate ligand-target or regulator-target mechanism in the declared cell context."
    },
    {
      "id": "E07",
      "source": "PROGRAM:DMD_SOURCE_STATE",
      "target": "PATHWAY:ECM_FIBROSIS",
      "label": "disease module placement",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "DMD source-state evidence motivates an ECM/fibrosis module.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Measure ECM or fibrosis readouts after candidate perturbation in DMD-relevant cells."
    },
    {
      "id": "E08",
      "source": "PROGRAM:NICHENET_TARGET_STATE",
      "target": "PATHWAY:IMMUNE_CROSSTALK",
      "label": "cross-cell regulatory hypothesis",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "Regulatory context motivates a cell-cell consequence module.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Test causal cross-cell outcome or coculture readout."
    },
    {
      "id": "E09",
      "source": "ASSAY:MYOBLAST_CONTEXT_SCREEN",
      "target": "PATHWAY:MYOGENIC_DIFFERENTIATION",
      "label": "myogenic bridge",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "Fusion-screen context links candidate selection to myogenic biology.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Repeat with disease and matched-control perturbation truth."
    },
    {
      "id": "E10",
      "source": "PATHWAY:MYOGENIC_DIFFERENTIATION",
      "target": "STATE:PROLIFERATING_MYOBLAST",
      "label": "reference start state",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "Unperturbed human-myogenic trajectory anchors the starting compartment.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Add perturbation-conditioned cells at 0 h and early response times."
    },
    {
      "id": "E11",
      "source": "PATHWAY:MYOGENIC_DIFFERENTIATION",
      "target": "STATE:FUSING_MYOCYTE",
      "label": "transition context",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "The platform can place a question on the myoblast-to-fusion axis.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Measure candidate-specific state transition in DMD and control cells."
    },
    {
      "id": "E12",
      "source": "PATHWAY:MYOGENIC_DIFFERENTIATION",
      "target": "STATE:MATURING_MYOTUBE",
      "label": "late state context",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "The unperturbed trajectory includes a late reference state.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Add perturbation-conditioned myotube maturation outcomes."
    },
    {
      "id": "E13",
      "source": "PATHWAY:MITO_ENERGY",
      "target": "FUNCTION:CALCIUM_CONTRACTION",
      "label": "function-coupled hypothesis",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "Energy-state changes would need to be tied to contractile readouts.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Measure calcium handling and contraction under candidate perturbation."
    },
    {
      "id": "E14",
      "source": "PATHWAY:ECM_FIBROSIS",
      "target": "FUNCTION:MEMBRANE_INTEGRITY",
      "label": "matrix-function hypothesis",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "ECM remodeling could matter only if functional readouts change.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Measure membrane injury or repair endpoint in the same experiment."
    },
    {
      "id": "E15",
      "source": "STATE:FUSING_MYOCYTE",
      "target": "FUNCTION:FUSION_INDEX",
      "label": "state-to-endpoint mapping",
      "direction": "directed",
      "evidence_state": "contextual_bridge",
      "evidence_basis": "Fusion index is an interpretable endpoint for a myogenic transition.",
      "edge_semantics": "context_bridge_not_transfer_claim",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Freeze endpoint, effect margin and analysis before outcomes are visible."
    },
    {
      "id": "E16",
      "source": "STATE:MATURING_MYOTUBE",
      "target": "FUNCTION:CALCIUM_CONTRACTION",
      "label": "late functional endpoint",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "Mature myotube state needs functional measurement before disease interpretation.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Run late myotube function assay with viability co-readout."
    },
    {
      "id": "E17",
      "source": "STATE:PROLIFERATING_MYOBLAST",
      "target": "FUNCTION:VIABILITY_TOXICITY",
      "label": "early safety gate",
      "direction": "directed",
      "evidence_state": "hypothesis",
      "evidence_basis": "Any apparent mechanism is uninterpretable without viability/toxicity checks.",
      "edge_semantics": "hypothesis_edge",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Include toxicity controls and reagent concordance in the pilot."
    },
    {
      "id": "E18",
      "source": "FUNCTION:FUSION_INDEX",
      "target": "GAP:DMD_PERTURBATION_TRUTH",
      "label": "requires DMD truth",
      "direction": "directed",
      "evidence_state": "missing_validation",
      "evidence_basis": "No candidate perturbation fusion outcome exists in matched DMD/control cells.",
      "edge_semantics": "decision_blocking_gap",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Generate a registered DMD/control myogenic perturbation outcome."
    },
    {
      "id": "E19",
      "source": "FUNCTION:MEMBRANE_INTEGRITY",
      "target": "GAP:DMD_PERTURBATION_TRUTH",
      "label": "requires disease functional truth",
      "direction": "directed",
      "evidence_state": "missing_validation",
      "evidence_basis": "No membrane integrity endpoint is measured for current candidate perturbations.",
      "edge_semantics": "decision_blocking_gap",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Add disease-relevant functional endpoint and analysis threshold."
    },
    {
      "id": "E20",
      "source": "FUNCTION:CALCIUM_CONTRACTION",
      "target": "GAP:DMD_PERTURBATION_TRUTH",
      "label": "requires muscle function truth",
      "direction": "directed",
      "evidence_state": "missing_validation",
      "evidence_basis": "No calcium or contraction outcome exists for the candidate perturbations.",
      "edge_semantics": "decision_blocking_gap",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Measure late function in a matched, preregistered assay."
    },
    {
      "id": "E21",
      "source": "GAP:DMD_PERTURBATION_TRUTH",
      "target": "GAP:PROSPECTIVE_REPLICATION",
      "label": "must replicate before claim",
      "direction": "directed",
      "evidence_state": "missing_validation",
      "evidence_basis": "The release has zero prospective predictions and zero returned outcomes.",
      "edge_semantics": "decision_blocking_gap",
      "supports_dmd_prediction": false,
      "confidence_policy": "no_numeric_confidence_current_release",
      "unlock_condition": "Register prediction, run blinded outcome, then replicate independently."
    }
  ],
  "focal_cascades": [
    {
      "cascade_id": "CASCADE:ZNF133:MYOGENIC-FUSION",
      "perturbation": "ZNF133",
      "path": [
        "PERT:ZNF133",
        "ASSAY:MYOBLAST_CONTEXT_SCREEN",
        "PATHWAY:MYOGENIC_DIFFERENTIATION",
        "STATE:FUSING_MYOCYTE",
        "FUNCTION:FUSION_INDEX",
        "GAP:DMD_PERTURBATION_TRUTH"
      ],
      "current_state": "Best current use is experiment design for a matched DMD/control myogenic fusion endpoint.",
      "claim_boundary": "This path is a prioritized testable cascade, not a predicted therapeutic effect."
    },
    {
      "cascade_id": "CASCADE:GFOD2:ENERGY-FUNCTION",
      "perturbation": "GFOD2",
      "path": [
        "PERT:GFOD2",
        "ASSAY:HEPG2_CRISPRI",
        "PROGRAM:DMD_SOURCE_STATE",
        "PATHWAY:MITO_ENERGY",
        "FUNCTION:CALCIUM_CONTRACTION",
        "GAP:DMD_PERTURBATION_TRUTH"
      ],
      "current_state": "Mechanism module remains audit pending and requires late functional truth.",
      "claim_boundary": "External or contextual evidence cannot create a DMD function prediction."
    },
    {
      "cascade_id": "CASCADE:CPEB1:CELL-STATE-SAFETY",
      "perturbation": "CPEB1",
      "path": [
        "PERT:CPEB1",
        "ASSAY:HEPG2_CRISPRI",
        "PROGRAM:NICHENET_TARGET_STATE",
        "STATE:PROLIFERATING_MYOBLAST",
        "FUNCTION:VIABILITY_TOXICITY",
        "GAP:PROSPECTIVE_REPLICATION"
      ],
      "current_state": "Safety and state-transition endpoints must be measured before interpreting mechanism.",
      "claim_boundary": "The cascade records what would need to move together; it does not say that it will."
    }
  ],
  "propagation_scenarios": [
    {
      "scenario_id": "PROPAGATION:ZNF133:MYOGENIC-FUSION:V92",
      "target": "ZNF133",
      "perturbation_node": "PERT:ZNF133",
      "cascade_id": "CASCADE:ZNF133:MYOGENIC-FUSION",
      "lifecycle_state": "TARGET_SPECIFIC_PROPAGATION_HYPOTHESIS_NO_DMD_MODEL_INFERENCE",
      "selected_nodes": [
        "PERT:ZNF133",
        "ASSAY:HEPG2_CRISPRI",
        "ASSAY:MYOBLAST_CONTEXT_SCREEN",
        "PATHWAY:MYOGENIC_DIFFERENTIATION",
        "STATE:FUSING_MYOCYTE",
        "FUNCTION:FUSION_INDEX",
        "FUNCTION:VIABILITY_TOXICITY",
        "GAP:DMD_PERTURBATION_TRUTH"
      ],
      "selected_edge_ids": [
        "E01",
        "E04",
        "E09",
        "E11",
        "E15",
        "E17",
        "E18"
      ],
      "module_couplings": [
        {
          "module_id": "PATHWAY:MYOGENIC_DIFFERENTIATION",
          "module_label": "Myogenic differentiation",
          "evidence_state": "contextual_bridge",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "fusion_index",
            "myotube_marker_panel",
            "viability"
          ],
          "unlock_condition": "Matched DMD/control myogenic perturbation with prespecified fusion and toxicity endpoints."
        },
        {
          "module_id": "FUNCTION:FUSION_INDEX",
          "module_label": "Fusion index",
          "evidence_state": "required_endpoint",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "myotube_area",
            "nuclei_per_myotube",
            "cell_survival"
          ],
          "unlock_condition": "Prospective effect margin and null/toxic interpretation frozen before outcomes are visible."
        }
      ],
      "propagation_contract": {
        "pathway_delta_emitted": false,
        "cell_state_delta_emitted": false,
        "functional_effect_emitted": false,
        "calibrated_probability_emitted": false,
        "direction_policy": "direction_not_predicted_current_release",
        "interpretation": "Propagation scenarios define which modules and readouts should be measured together after a perturbation. They do not predict up/down pathway change, responder fraction, cell-state shift or therapeutic effect."
      },
      "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."
    },
    {
      "scenario_id": "PROPAGATION:GFOD2:ENERGY-FUNCTION:V92",
      "target": "GFOD2",
      "perturbation_node": "PERT:GFOD2",
      "cascade_id": "CASCADE:GFOD2:ENERGY-FUNCTION",
      "lifecycle_state": "TARGET_SPECIFIC_PROPAGATION_HYPOTHESIS_EXTERNAL_AUDIT_PENDING",
      "selected_nodes": [
        "PERT:GFOD2",
        "ASSAY:HEPG2_CRISPRI",
        "PROGRAM:DMD_SOURCE_STATE",
        "PATHWAY:MITO_ENERGY",
        "STATE:MATURING_MYOTUBE",
        "FUNCTION:CALCIUM_CONTRACTION",
        "FUNCTION:VIABILITY_TOXICITY",
        "GAP:DMD_PERTURBATION_TRUTH"
      ],
      "selected_edge_ids": [
        "E02",
        "E05",
        "E13",
        "E16",
        "E17",
        "E20"
      ],
      "module_couplings": [
        {
          "module_id": "PATHWAY:MITO_ENERGY",
          "module_label": "Mitochondrial energy module",
          "evidence_state": "hypothesis",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "oxygen_consumption",
            "atp_proxy",
            "calcium_handling"
          ],
          "unlock_condition": "Audit external evidence, then measure energy and calcium endpoints in the same DMD/control perturbation study."
        },
        {
          "module_id": "FUNCTION:CALCIUM_CONTRACTION",
          "module_label": "Calcium and contraction",
          "evidence_state": "required_endpoint",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "calcium_transient",
            "contractile_force",
            "viability"
          ],
          "unlock_condition": "Late myotube function assay with toxicity gate and independent replication."
        }
      ],
      "propagation_contract": {
        "pathway_delta_emitted": false,
        "cell_state_delta_emitted": false,
        "functional_effect_emitted": false,
        "calibrated_probability_emitted": false,
        "direction_policy": "direction_not_predicted_current_release",
        "interpretation": "Propagation scenarios define which modules and readouts should be measured together after a perturbation. They do not predict up/down pathway change, responder fraction, cell-state shift or therapeutic effect."
      },
      "current_interpretation": "GFOD2 is represented as an energy-function propagation hypothesis, but external evidence is still audit-pending and no function truth exists.",
      "next_experiment": "Resolve the evidence audit first, then pair energy-state and calcium/contractile readouts in a registered DMD myotube study."
    },
    {
      "scenario_id": "PROPAGATION:CPEB1:CELL-STATE-SAFETY:V92",
      "target": "CPEB1",
      "perturbation_node": "PERT:CPEB1",
      "cascade_id": "CASCADE:CPEB1:CELL-STATE-SAFETY",
      "lifecycle_state": "TARGET_SPECIFIC_PROPAGATION_HYPOTHESIS_SAFETY_FIRST",
      "selected_nodes": [
        "PERT:CPEB1",
        "ASSAY:HEPG2_CRISPRI",
        "PROGRAM:NICHENET_TARGET_STATE",
        "STATE:PROLIFERATING_MYOBLAST",
        "FUNCTION:VIABILITY_TOXICITY",
        "PATHWAY:IMMUNE_CROSSTALK",
        "GAP:PROSPECTIVE_REPLICATION"
      ],
      "selected_edge_ids": [
        "E03",
        "E06",
        "E08",
        "E17",
        "E21"
      ],
      "module_couplings": [
        {
          "module_id": "PROGRAM:NICHENET_TARGET_STATE",
          "module_label": "NicheNet target-state prior",
          "evidence_state": "inferred_bridge",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "early_transcriptome",
            "target_engagement",
            "state_marker_panel"
          ],
          "unlock_condition": "Validate regulator-target bridge in the declared myogenic cell state."
        },
        {
          "module_id": "FUNCTION:VIABILITY_TOXICITY",
          "module_label": "Viability and toxicity",
          "evidence_state": "required_endpoint",
          "expected_change_direction": "direction_not_predicted_current_release",
          "readouts_to_measure_together": [
            "cell_survival",
            "differentiation_capacity",
            "reagent_concordance"
          ],
          "unlock_condition": "Safety-first perturbation study with two reagents before interpreting downstream state change."
        }
      ],
      "propagation_contract": {
        "pathway_delta_emitted": false,
        "cell_state_delta_emitted": false,
        "functional_effect_emitted": false,
        "calibrated_probability_emitted": false,
        "direction_policy": "direction_not_predicted_current_release",
        "interpretation": "Propagation scenarios define which modules and readouts should be measured together after a perturbation. They do not predict up/down pathway change, responder fraction, cell-state shift or therapeutic effect."
      },
      "current_interpretation": "CPEB1 is a safety-first propagation scenario: early molecular and regulatory context must be separated from toxicity or differentiation blockade.",
      "next_experiment": "Measure target engagement, early transcriptome, viability and differentiation capacity before assigning pathway meaning."
    }
  ],
  "release_boundary": "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."
}