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claim." }, "gates": { "source_object_opened": true, "identifiers_reconciled": true, "matrix_qc_read_only_complete": true, "normal_2_sensitivity_predeclared": true, "formal_ambient_closed": false, "independent_doublet_sensitivity_closed": true, "independent_annotation_disagreement_audit_closed": true, "inherited_labels_overwritten": false, "author_exact_reprocessing_closed": false, "disease_effect_testing_authorized": false, "model_training_labels_allowed": false, "direct_dmd_perturbation_truth": false }, "source_artifacts": { "stable_input": { "role": "stable_input", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/stable_module_context_input/gse288958_stable_module_context_input.tsv", "state": "CONTEXT_INPUT_CHECKSUMMED", "size_bytes": 10506, "sha256": "c6dfd032b994fdf0a0d17e2a257566fd563dc01e746023cd6121799e89dfc93a" }, "stable_manifest": { "role": "stable_manifest", "path": 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"43d133397142247daf8a604b1c21a24243974d97304201bb1d9450703347a250" }, "qc_sample_gate": { "role": "qc_sample_gate", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/qc_context_gate/gse288958_qc_context_gate_by_sample.tsv", "state": "CONTEXT_INPUT_CHECKSUMMED", "size_bytes": 2627, "sha256": "075b8491e1c650cf7b6356eb22e6f1068d7f93e7295bc66ae84253d4b5bde41c" } }, "reference_audit": { "audit_id": "GSE288958:REFERENCE-AUDIT:20260909:1", "supersedes_partial_audit_level": "PARTIAL_ANNOTATION_AND_SENSITIVITY_AUDIT", "api_route": "/resource/api/v1.1/gse288958_reference_audit.json", "web_route": "/resource/gse288958-audit/", "independent_doublet_candidates": 1579, "independent_doublet_fraction": 0.026662388977069334, "independent_annotation_resolved_cells": 58912, "independent_annotation_unresolved_cells": 310, "independent_annotation_concordance_fraction_resolved": 0.7588606735469854 }, "claim_boundary": "This object supports bounded descriptive, sample-aware module context with predeclared Normal_2, independent Scrublet and annotation-disagreement sensitivities. It does not support disease-effect p-values, causal inference, model-training labels, therapeutic efficacy, author-exact reprocessing, formal ambient-RNA clearance or direct DMD perturbation truth.", "next_gate": "Use the bounded context object with all three sensitivity layers. Unfiltered droplets are needed only for ambient-RNA closure, and exact author artifacts are needed only before an author-exact reprocessing claim.", "markdown": "# GSE288958 sample-aware context object\n\n- Object ID: `CONTEXT:GSE288958:SAMPLE_AWARE_MODULE:1.1`\n- Status: **CITABLE_BOUNDED_REFERENCE_CONTEXT_INDEPENDENT_AUDITS_COMPLETE**\n- Checked: 2026-08-12T18:15:46+0800\n\n## Scope\n\nDMD/BMD/control muscle sample-aware context reuse from the existing processed reference. The inferential unit is **independent biopsy/sample; cells are nested observations and not independent disease replicates**.\n\n## Denominators\n\n- Raw matrix inventory: **61,189** cells\n- Read-only broad QC gate: **59,237** cells\n- Pilot RDS: **59,222** cells\n- Raw minus pilot: **1,967** cells\n\n## Context policy\n\n- Stable modules retained: **6**\n- Unstable module excluded: `macrophage_monocyte:TLR2_NOD2_sensing`\n- Candidate context-only alignments: **ADAM10, CPEB1**\n- Normal_2 remains in all-sample summaries and is excluded only in the predeclared sensitivity rerun.\n- Donor-wise Scrublet and the independent annotation-disagreement audit are linked through `GSE288958:REFERENCE-AUDIT:20260909:1`.\n\n## Claim boundary\n\nThis object supports bounded descriptive, sample-aware module context with predeclared Normal_2, independent Scrublet and annotation-disagreement sensitivities. It does not support disease-effect p-values, causal inference, model-training labels, therapeutic efficacy, author-exact reprocessing, formal ambient-RNA clearance or direct DMD perturbation truth.\n\nDirect DMD candidate perturbation truth remains **0/21**.\n", "stable_module_tsv": "sample_id\tcondition\tcoarse_celltype\tmodule\tmodule_key\tmodule_score\tnormal2_flag\tcontext_use\ttraining_label_allowed\tdisease_effect_testing_authorized\tdirect_perturbation_truth\r\nBMD_1\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.697541609496592\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.149251596038956\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.512636713792647\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t0.0635312010319975\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.589105651010808\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t0.572345202172232\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.979079930863779\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.198052062204519\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.963292251703173\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.00795765934277582\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.840560980541787\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0359403735474511\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.421827852262449\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.159945314885268\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.447339814662442\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0649280774076423\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.41134752311047\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.120789978819349\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t1.06137129820314\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0716617937191094\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t1.30983659853778\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.160230978407706\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0867922498375757\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.153577559873763\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.151948871106479\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.153315732553065\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.231436472779371\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.146183131997565\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0663036065923441\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0166716561498669\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0561172006942313\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.234431069630272\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.321622271377184\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0188623398694717\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.308383934627271\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0328386595997632\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.278331469545741\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.249589465932999\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.525454402434192\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t-0.00628796229747893\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.299391623974486\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0510268107781476\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.470647324724108\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0122675492255476\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.419021902477222\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0791485232175506\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.120125490686228\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0153843315596294\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.154035323777924\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t-0.0236779848498501\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.341196058289937\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0769194181761811\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.171232292027875\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0140478883751588\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.269217266132525\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0205732997710225\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.227225358302042\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.75548091532344\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t-0.00509484809381969\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.140290124444811\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.175527967149447\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0237234583751645\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0881055234986414\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0166868187557854\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.236239919509336\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0253655912619156\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\n", "candidate_triage_tsv": "gene\texperimental_rank\tpriority_tier\texperimental_role\tmechanism_axis\tcandidate_context_decision\tcontext_overlay_status\tsupporting_context_modules\tcontext_celltypes\tall_samples_delta\tnormal2_excluded_delta\tdirection_stability\tstable_module_count\tstable_module_sample_rows\tstable_module_sample_count\tstable_module_flagged_samples\tqc_context_gate_state\tnormal2_sensitivity_required\ttraining_label_allowed\tdisease_effect_testing_authorized\tdirect_dmd_perturbation_truth\texperimental_rank_preserved\tcandidate_score_changed\texternal_context_evidence_scope\tcandidate_claim_ceiling\tmodel_output_changed\tmapping_rationale\texcluded_unstable_context\r\nADAM10\t1\tA\tprimary_rescue\tmembrane shedding / Notch / adhesion\tSUPPORTIVE_STABLE_MODULE_CONTEXT\tSUPPORTIVE_CONTEXT_ALIGNMENT_NOT_GENE_VALIDATED\tsatellite_myogenic:regeneration_stress\tsatellite_myogenic\tsatellite_myogenic:regeneration_stress=0.025550\tsatellite_myogenic:regeneration_stress=0.028070\tPRESERVED_AFTER_NORMAL_2_EXCLUSION\t1\t11\t11\tNormal_2\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tL2_CONTEXT_TRIAGE_ONLY\tFALSE\tExisting ranking links ADAM10 to muscle Notch/satellite-cell biology; the reference satellite regeneration-stress module is direction-stable.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nCALR\t2\tA\tprimary_rescue\tER proteostasis / calcium handling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nMPHOSPH6\t3\tA\tprimary_rescue\tnuclear RNA exosome / RNA surveillance\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZNF236\t4\tB\thigh_information_contrast\ttranscriptional phenotype / candidate ribosome-biogenesis regulator\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nCPEB1\t5\tB\tmuscle_mechanism_contrast\tcytoplasmic polyadenylation / MYOD1 translation\tSUPPORTIVE_STABLE_MODULE_CONTEXT\tSUPPORTIVE_CONTEXT_ALIGNMENT_NOT_GENE_VALIDATED\tsatellite_myogenic:regeneration_stress\tsatellite_myogenic\tsatellite_myogenic:regeneration_stress=0.025550\tsatellite_myogenic:regeneration_stress=0.028070\tPRESERVED_AFTER_NORMAL_2_EXCLUSION\t1\t11\t11\tNormal_2\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tL2_CONTEXT_TRIAGE_ONLY\tFALSE\tExisting ranking links CPEB1 to MYOD1 translation and muscle-regeneration biology; the reference satellite regeneration-stress module is direction-stable.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nEPS8L1\t6\tB\ttransfer_contrast\tRAC-linked actin remodeling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nINTS13\t7\tB\tdiscordance_contrast\tIntegrator enhancer module / lineage transcription\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRAC3\t8\tB\tcytoskeleton_contrast\tRho-family actin / adhesion signaling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDNM1\t9\tC\texploratory\tdynamin-dependent membrane fission\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nGFOD2\t10\tC\texploratory\tpoorly characterized oxidoreductase-like protein\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nMON1A\t11\tC\texploratory\tRab7 activation / endolysosomal maturation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nEHMT2\t12\tC\tmechanism_negative_control\tH3K9 methylation / chromatin repression\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDDX19B\t13\tD\tfailure_mode_calibration\tmRNA export termination / RNA remodeling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nNAGLU\t14\tD\tfailure_mode_calibration\tlysosomal heparan-sulfate degradation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nWDR4\t15\tD\tfailure_mode_calibration\tMETTL1-WDR4 tRNA m7G methylation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRNF8\t16\tD\tfailure_mode_calibration\tDNA-damage histone ubiquitylation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRNASEH2C\t17\tD\tfailure_mode_calibration\tRNase H2 / ribonucleotide and R-loop removal\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZFP69B\t18\tE\tlow_priority_calibration\tpoorly characterized zinc-finger regulation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDNAAF3\t19\tE\tlow_priority_calibration\taxonemal-dynein preassembly\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nLMO2\t20\tE\tsafety_calibration\thematopoietic / endothelial transcriptional cofactor\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZNF133\t21\tE\thistorical_negative_control\tKRAB zinc-finger transcriptional repression\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\n" }