{
  "comparison_schema": "nmd-vcell-comparison-object/1.1",
  "comparison_id": "CMP-20260726-1DF261243518",
  "key": "mixed",
  "title": "Mixed action and gap comparison",
  "payload_sha256": "1df2612435184031f398d71ed552ed8cb9afeb2934af2cab9c24eef8aab97773",
  "resource_release": "v1.0.0-database-resource",
  "schema_version": "1.1",
  "research_object_schema": "1.3",
  "evidence_freeze": "2026-07-25",
  "interface_build": "EA-20260726-13",
  "generated_at": "2026-07-26T00:00:00.000Z",
  "original_input_identifiers": [
    "ZNF133",
    "WDR4",
    "GFOD2",
    "INTS13"
  ],
  "identifier_mapping": {
    "source": {
      "licence": "CC0",
      "retrieved_at": "2026-07-25",
      "sha256": "41fe4d55110b22ac3a4c2579d281b0fcf51f18c0b622b0f88f45d49bb2c0d9fb",
      "snapshot_sha256": "272ebb642268184c6a4baeb0de9ffc6a87ea1baf96f2a286fcb07d78f1dd93c5",
      "url": "https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt"
    },
    "retrieved_at": "2026-07-25"
  },
  "ranking_generated": false,
  "lifecycle": {
    "state": "RELEASED",
    "revision": 1,
    "immutable": true,
    "registered_at": "2026-07-26T00:00:00.000Z",
    "supersedes": null
  },
  "rows": [
    {
      "input_identifiers": [
        "ZNF133"
      ],
      "normalized_symbol": "ZNF133",
      "mapping_status": "approved_symbol",
      "mapping_source": "HGNC HGNC:12917",
      "mapping_candidates": [
        "ZNF133"
      ],
      "gene": "ZNF133",
      "record": {
        "gene": "ZNF133",
        "identifiers": {
          "hgnc_id": "HGNC:12917",
          "ensembl_gene_id": "ENSG00000125846",
          "ncbi_gene_id": 7692
        },
        "decision": {
          "current_action": "muscle_assay",
          "current_display_label": "Muscle-context assay",
          "formal_deprioritization": false
        },
        "highest_supported_level": "L2_observed_same_context_perturbation",
        "highest_assessed_level": "L3a_external_context_screen",
        "dmd_context": {
          "integrated_prior_direction": "up",
          "source_direction_state": "conflicted",
          "source_direction_agreement": {
            "agreeing_sources": 3,
            "assessed_sources": 4,
            "directional_sources": 4,
            "proportion": 0.75
          },
          "variant_stability_state": "sign_varied_across_variants",
          "variant_count": 9,
          "evidence_module_memberships": [
            "direction_conflicted"
          ],
          "statistical_support_state": "direction_only_no_significant_context_rows",
          "coverage_state": "4_of_4_sources",
          "integration_method": "median signed score across significant context rows when present, otherwise across all available context rows; source-level directions are audited separately",
          "uncertainty_state": "direction_conflict_retained",
          "conflict_reason": "3 source(s) positive and 1 source(s) negative",
          "integrated_direction_is_prior_not_ground_truth": true,
          "consensus_direction": "up_in_dmd",
          "consensus_direction_deprecation": {
            "deprecated": true,
            "replacement": "integrated_prior_direction",
            "policy": "retained for one schema cycle; do not interpret as study consensus"
          }
        },
        "evidence_status": {
          "resource_record": {
            "assessment_status": "assessed",
            "support_status": "supported"
          },
          "observed_hepg2_perturbation": {
            "assessment_status": "assessed",
            "support_status": "supported",
            "observed_cells": 84
          },
          "internal_model_support": {
            "assessment_status": "assessed",
            "support_status": "supported_with_limits",
            "target_specific_predictive_support": "not_supported",
            "ood_status": "not_assessed",
            "context": "same_processed_hepg2_dataset"
          },
          "external_context_screen": {
            "assessment_status": "assessed",
            "support_status": "context_evidence_present",
            "hit": false,
            "effect_size": -0.003533,
            "fdr": 0.999999,
            "context": "GSE293514_myoblast_fusion_screen",
            "interpretation": "assessed_no_current_hit"
          },
          "independent_perturbation_replication": {
            "assessment_status": "not_assessed"
          },
          "dmd_muscle_validation": {
            "assessment_status": "not_assessed"
          },
          "functional_validation": {
            "assessment_status": "not_assessed"
          },
          "therapeutic_utility": {
            "assessment_status": "not_assessed"
          }
        },
        "context_metrics": {
          "skeletal_muscle_median_tpm": 4.55781,
          "moderate_dependency_flag": false
        },
        "evidence_gaps": {
          "decision_blocking_gap": {
            "code": "GAP-02",
            "label": "Independent muscle-context perturbation is absent"
          },
          "highest_missing_evidence_layer": "L4_dmd_functional_validation",
          "secondary_gaps": [
            "GAP-03 DMD-relevant functional validation",
            "GAP-07 independent replication"
          ]
        },
        "has_detailed_audit_record": true
      }
    },
    {
      "input_identifiers": [
        "WDR4"
      ],
      "normalized_symbol": "WDR4",
      "mapping_status": "approved_symbol",
      "mapping_source": "HGNC HGNC:12756",
      "mapping_candidates": [
        "WDR4"
      ],
      "gene": "WDR4",
      "record": {
        "gene": "WDR4",
        "identifiers": {
          "hgnc_id": "HGNC:12756",
          "ensembl_gene_id": "ENSG00000160193",
          "ncbi_gene_id": 10785
        },
        "decision": {
          "current_action": "risk_review",
          "current_display_label": "Risk/context review",
          "formal_deprioritization": false
        },
        "highest_supported_level": "L2_observed_same_context_perturbation",
        "highest_assessed_level": "L3a_external_context_screen",
        "dmd_context": {
          "integrated_prior_direction": "up",
          "source_direction_state": "consistent_up",
          "source_direction_agreement": {
            "agreeing_sources": 4,
            "assessed_sources": 4,
            "directional_sources": 4,
            "proportion": 1
          },
          "variant_stability_state": "sign_varied_across_variants",
          "variant_count": 9,
          "evidence_module_memberships": [
            "exploratory_multisource_core"
          ],
          "statistical_support_state": "direction_only_no_significant_context_rows",
          "coverage_state": "4_of_4_sources",
          "integration_method": "median signed score across significant context rows when present, otherwise across all available context rows; source-level directions are audited separately",
          "uncertainty_state": "direction_consistent_not_formal_meta_analysis",
          "conflict_reason": null,
          "integrated_direction_is_prior_not_ground_truth": true,
          "consensus_direction": "up_in_dmd",
          "consensus_direction_deprecation": {
            "deprecated": true,
            "replacement": "integrated_prior_direction",
            "policy": "retained for one schema cycle; do not interpret as study consensus"
          }
        },
        "evidence_status": {
          "resource_record": {
            "assessment_status": "assessed",
            "support_status": "supported"
          },
          "observed_hepg2_perturbation": {
            "assessment_status": "assessed",
            "support_status": "supported",
            "observed_cells": 108
          },
          "internal_model_support": {
            "assessment_status": "assessed",
            "support_status": "supported_with_limits",
            "target_specific_predictive_support": "not_supported",
            "ood_status": "not_assessed",
            "context": "same_processed_hepg2_dataset"
          },
          "external_context_screen": {
            "assessment_status": "assessed",
            "support_status": "context_evidence_present",
            "hit": false,
            "effect_size": -0.010262,
            "fdr": 0.999999,
            "context": "GSE293514_myoblast_fusion_screen",
            "interpretation": "assessed_no_current_hit"
          },
          "independent_perturbation_replication": {
            "assessment_status": "not_assessed"
          },
          "dmd_muscle_validation": {
            "assessment_status": "not_assessed"
          },
          "functional_validation": {
            "assessment_status": "not_assessed"
          },
          "therapeutic_utility": {
            "assessment_status": "not_assessed"
          }
        },
        "context_metrics": {
          "skeletal_muscle_median_tpm": 4.15911,
          "moderate_dependency_flag": true
        },
        "evidence_gaps": {
          "decision_blocking_gap": {
            "code": "GAP-08",
            "label": "Safety and dependency context blocks escalation"
          },
          "highest_missing_evidence_layer": "L4_dmd_functional_validation",
          "secondary_gaps": [
            "GAP-02 independent muscle-context perturbation",
            "GAP-03 DMD-relevant functional validation",
            "GAP-07 independent replication"
          ]
        },
        "has_detailed_audit_record": true
      }
    },
    {
      "input_identifiers": [
        "GFOD2"
      ],
      "normalized_symbol": "GFOD2",
      "mapping_status": "approved_symbol",
      "mapping_source": "HGNC HGNC:28159",
      "mapping_candidates": [
        "GFOD2"
      ],
      "gene": "GFOD2",
      "record": {
        "gene": "GFOD2",
        "identifiers": {
          "hgnc_id": "HGNC:28159",
          "ensembl_gene_id": "ENSG00000141098",
          "ncbi_gene_id": 81577
        },
        "decision": {
          "current_action": "hold_pending_external_audit",
          "current_display_label": "Provisional hold · external report not yet audited",
          "formal_deprioritization": false
        },
        "highest_supported_level": "L2_observed_same_context_perturbation",
        "highest_assessed_level": "L2_observed_same_context_perturbation",
        "dmd_context": {
          "integrated_prior_direction": "up",
          "source_direction_state": "conflicted",
          "source_direction_agreement": {
            "agreeing_sources": 2,
            "assessed_sources": 4,
            "directional_sources": 4,
            "proportion": 0.5
          },
          "variant_stability_state": "sign_varied_across_variants",
          "variant_count": 9,
          "evidence_module_memberships": [
            "direction_conflicted"
          ],
          "statistical_support_state": "direction_only_no_significant_context_rows",
          "coverage_state": "4_of_4_sources",
          "integration_method": "median signed score across significant context rows when present, otherwise across all available context rows; source-level directions are audited separately",
          "uncertainty_state": "direction_conflict_retained",
          "conflict_reason": "2 source(s) positive and 2 source(s) negative",
          "integrated_direction_is_prior_not_ground_truth": true,
          "consensus_direction": "up_in_dmd",
          "consensus_direction_deprecation": {
            "deprecated": true,
            "replacement": "integrated_prior_direction",
            "policy": "retained for one schema cycle; do not interpret as study consensus"
          }
        },
        "evidence_status": {
          "resource_record": {
            "assessment_status": "assessed",
            "support_status": "supported"
          },
          "observed_hepg2_perturbation": {
            "assessment_status": "assessed",
            "support_status": "supported",
            "observed_cells": 127
          },
          "internal_model_support": {
            "assessment_status": "assessed",
            "support_status": "supported_with_limits",
            "target_specific_predictive_support": "not_supported",
            "ood_status": "not_assessed",
            "context": "same_processed_hepg2_dataset"
          },
          "external_context_screen": {
            "assessment_status": "not_assessed",
            "hit": null
          },
          "independent_perturbation_replication": {
            "assessment_status": "not_assessed"
          },
          "dmd_muscle_validation": {
            "assessment_status": "not_assessed"
          },
          "functional_validation": {
            "assessment_status": "not_assessed"
          },
          "therapeutic_utility": {
            "assessment_status": "not_assessed"
          }
        },
        "context_metrics": {
          "skeletal_muscle_median_tpm": 2.94732,
          "moderate_dependency_flag": false
        },
        "evidence_gaps": {
          "decision_blocking_gap": {
            "code": "GAP-09",
            "label": "External quantitative evidence has not been imported and audited"
          },
          "highest_missing_evidence_layer": "L4_dmd_functional_validation",
          "secondary_gaps": [
            "GAP-02 independent muscle-context perturbation",
            "GAP-03 DMD-relevant functional validation",
            "GAP-07 independent replication"
          ]
        },
        "has_detailed_audit_record": true
      }
    },
    {
      "input_identifiers": [
        "INTS13"
      ],
      "normalized_symbol": "INTS13",
      "mapping_status": "approved_symbol",
      "mapping_source": "HGNC HGNC:20174",
      "mapping_candidates": [
        "INTS13"
      ],
      "gene": "INTS13",
      "record": {
        "gene": "INTS13",
        "identifiers": {
          "hgnc_id": "HGNC:20174",
          "ensembl_gene_id": "ENSG00000064102",
          "ncbi_gene_id": 55726
        },
        "decision": {
          "current_action": "risk_review",
          "current_display_label": "Risk/context review",
          "formal_deprioritization": false
        },
        "highest_supported_level": "L2_observed_same_context_perturbation",
        "highest_assessed_level": "L2_observed_same_context_perturbation",
        "dmd_context": {
          "integrated_prior_direction": "up",
          "source_direction_state": "consistent_up",
          "source_direction_agreement": {
            "agreeing_sources": 4,
            "assessed_sources": 4,
            "directional_sources": 4,
            "proportion": 1
          },
          "variant_stability_state": "sign_varied_across_variants",
          "variant_count": 9,
          "evidence_module_memberships": [
            "exploratory_multisource_core"
          ],
          "statistical_support_state": "direction_only_no_significant_context_rows",
          "coverage_state": "4_of_4_sources",
          "integration_method": "median signed score across significant context rows when present, otherwise across all available context rows; source-level directions are audited separately",
          "uncertainty_state": "direction_consistent_not_formal_meta_analysis",
          "conflict_reason": null,
          "integrated_direction_is_prior_not_ground_truth": true,
          "consensus_direction": "up_in_dmd",
          "consensus_direction_deprecation": {
            "deprecated": true,
            "replacement": "integrated_prior_direction",
            "policy": "retained for one schema cycle; do not interpret as study consensus"
          }
        },
        "evidence_status": {
          "resource_record": {
            "assessment_status": "assessed",
            "support_status": "supported"
          },
          "observed_hepg2_perturbation": {
            "assessment_status": "assessed",
            "support_status": "supported",
            "observed_cells": 157
          },
          "internal_model_support": {
            "assessment_status": "assessed",
            "support_status": "supported_with_limits",
            "target_specific_predictive_support": "not_supported",
            "ood_status": "not_assessed",
            "context": "same_processed_hepg2_dataset"
          },
          "external_context_screen": {
            "assessment_status": "not_assessed",
            "hit": null
          },
          "independent_perturbation_replication": {
            "assessment_status": "not_assessed"
          },
          "dmd_muscle_validation": {
            "assessment_status": "not_assessed"
          },
          "functional_validation": {
            "assessment_status": "not_assessed"
          },
          "therapeutic_utility": {
            "assessment_status": "not_assessed"
          }
        },
        "context_metrics": {
          "skeletal_muscle_median_tpm": 10.9911,
          "moderate_dependency_flag": true
        },
        "evidence_gaps": {
          "decision_blocking_gap": {
            "code": "GAP-08",
            "label": "Safety and dependency context blocks escalation"
          },
          "highest_missing_evidence_layer": "L4_dmd_functional_validation",
          "secondary_gaps": [
            "GAP-02 independent muscle-context perturbation",
            "GAP-03 DMD-relevant functional validation",
            "GAP-07 independent replication"
          ]
        },
        "has_detailed_audit_record": true
      }
    }
  ],
  "claim_boundary": "This comparison preserves evidence dimensions and missingness. It does not create a composite score, ranking, causal claim or therapeutic recommendation.",
  "stable_url": "comparison/CMP-20260726-1DF261243518/"
}
