{ "network_schema": "nmd-vcell-human-myoblast-perturbation-network/1.0", "object_id": "HMPN:v1.2.0-measured-dmd-evidence:EA-20260817-57:STAGE-B0", "stage": "B0_PUBLIC_HUMAN_MYOBLAST_FUNCTIONAL_PERTURBATION_NETWORK", "resource_release": "v1.2.0-measured-dmd-evidence", "interface_build": "EA-20260817-57", "evidence_freeze": "2026-08-03", "generated": "2026-08-02", "study": { "accession": "GSE293514", "doi": "10.1038/s41467-025-67583-x", "article_url": "https://www.nature.com/articles/s41467-025-67583-x", "geo_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE293514", "biological_context": "immortalized healthy-donor human myoblast CRISPR knockout; initial split-toxin fusion screen plus orthogonal validation and grouped CROP-seq", "reported_scope": { "fusion_hits_fdr_lt_0_1": 250, "hits_in_ppi_network": 160, "protein_complexes": 23, "ppi_edges": 1286 }, "encoded_scope": { "named_complex_subset": 10, "positive_control_axes": 1, "encoded_unique_hit_genes": 31, "complete_23_complex_membership_reconstructed": false, "reason": "The article names a subset in text; a complete machine-readable 23-complex membership table is not present in the nine supplements" } }, "source_policy": { "article_licence": "CC-BY-NC-ND-4.0", "raw_workbooks_publicly_redistributed_by_nmd_vcell": false, "derivative_policy": "NMD-VCell publishes compact factual audit objects and calculated descriptive summaries with source links; raw workbooks stay external", "source_manifest": "human_myoblast_perturbation_network_source_manifest.json" }, "counts": { "library_genes": 6896, "non_targeting_guides": 900, "screen_genes": 7197, "fusion_hits": 250, "individually_validated_genes": 125, "myogenesis_signature_genes": 395, "myocyte_signature_genes": 142, "myoblast_signature_genes": 253, "current_candidates": 21, "current_candidates_assessed": 9, "current_candidate_fusion_hits": 0, "nodes": 45, "edges": 92, "encoded_modules": 11, "encoded_unique_hit_genes": 31, "observed_screen_edges": 31, "individual_validation_edges": 17, "grouped_transcriptomic_edges": 2, "candidate_level_transcriptomic_pathway_deltas": 0, "dmd_perturbation_edges": 0, "validated_dmd_prediction_edges": 0 }, "edge_semantics": { "observed_human_myoblast_screen": "gene knockout enriched among surviving fusion-defective cells; exact MAGeCK positive-selection LFC and FDR are retained", "observed_individual_validation": "gene was in the 125-gene individual validation set and the publication reports increased mononucleated-cell fraction", "published_complex_membership": "article-reported complex/pathway membership; not a measured activity delta", "observed_grouped_transcriptomic_qualitative": "published group-level MDS direction from Figure 6; no candidate-level effect estimate is emitted" }, "nodes": [ { "node_id": "STATE:EARLY_MYOGENIC_DIFFERENTIATION", "label": "Early myogenic differentiation", "layer": "cell_state", "node_type": "transcriptomic_state", "evidence_state": "observed_grouped_cropseq_reference" }, { "node_id": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "label": "Fusion-defect enrichment", "layer": "functional_endpoint", "node_type": "pooled_screen_endpoint", "evidence_state": "observed_human_myoblast_screen" }, { "node_id": "ENDPOINT:MONONUCLEATED_FRACTION", "label": "Mononucleated-cell fraction", "layer": "functional_endpoint", "node_type": "individual_imaging_endpoint", "evidence_state": "observed_individual_validation" }, { "node_id": "MODULE:MYOD_TCF12_EP300", "label": "MyoD-TCF12-p300 cofactor complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "transcriptional_control" }, { "node_id": "PERT:MYOD1:KO", "label": "MYOD1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "MYOD1" }, { "node_id": "PERT:TCF12:KO", "label": "TCF12 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "TCF12" }, { "node_id": "PERT:EP300:KO", "label": "EP300 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "EP300" }, { "node_id": "MODULE:SUMO_E1_E2", "label": "SUMO activation complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "protein_modification" }, { "node_id": "PERT:SAE1:KO", "label": "SAE1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "SAE1" }, { "node_id": "PERT:UBA2:KO", "label": "UBA2 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "UBA2" }, { "node_id": "PERT:UBE2I:KO", "label": "UBE2I knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "UBE2I" }, { "node_id": "MODULE:ISWI_CHROMATIN", "label": "ISWI chromatin remodelers", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "chromatin_remodeling" }, { "node_id": "PERT:SMARCA5:KO", "label": "SMARCA5 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "SMARCA5" }, { "node_id": "PERT:RBBP4:KO", "label": "RBBP4 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "RBBP4" }, { "node_id": "PERT:BPTF:KO", "label": "BPTF knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "BPTF" }, { "node_id": "MODULE:M6A_WRITER", "label": "m6A writer machinery", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "rna_modification" }, { "node_id": "PERT:METTL3:KO", "label": "METTL3 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "METTL3" }, { "node_id": "PERT:METTL14:KO", "label": "METTL14 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "METTL14" }, { "node_id": "PERT:WTAP:KO", "label": "WTAP knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "WTAP" }, { "node_id": "PERT:ZC3H13:KO", "label": "ZC3H13 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "ZC3H13" }, { "node_id": "MODULE:NEGATIVE_COFACTOR_2", "label": "Negative cofactor 2 complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "transcriptional_control" }, { "node_id": "PERT:DR1:KO", "label": "DR1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DR1" }, { "node_id": "PERT:DRAP1:KO", "label": "DRAP1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DRAP1" }, { "node_id": "MODULE:CCT_TCP1", "label": "Chaperonin TCP1 complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "protein_folding" }, { "node_id": "PERT:CCT3:KO", "label": "CCT3 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "CCT3" }, { "node_id": "PERT:CCT5:KO", "label": "CCT5 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "CCT5" }, { "node_id": "PERT:TCP1:KO", "label": "TCP1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "TCP1" }, { "node_id": "MODULE:HOPS", "label": "HOPS complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "vesicle_trafficking" }, { "node_id": "PERT:VPS33A:KO", "label": "VPS33A knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "VPS33A" }, { "node_id": "PERT:VPS39:KO", "label": "VPS39 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "VPS39" }, { "node_id": "MODULE:RNA_STABILITY", "label": "RNA stability regulators", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "rna_stability" }, { "node_id": "PERT:ILF3:KO", "label": "ILF3 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "ILF3" }, { "node_id": "PERT:DHX9:KO", "label": "DHX9 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DHX9" }, { "node_id": "MODULE:N_TERMINAL_ACETYLATION", "label": "N-terminal acetylation complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "protein_modification" }, { "node_id": "PERT:NAA30:KO", "label": "NAA30 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "NAA30" }, { "node_id": "PERT:NAA35:KO", "label": "NAA35 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "NAA35" }, { "node_id": "PERT:NAA38:KO", "label": "NAA38 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "NAA38" }, { "node_id": "MODULE:DYNEIN", "label": "Dynein-associated complex", "layer": "pathway_module", "node_type": "published_named_complex", "evidence_state": "published_complex_membership", "module_class": "cytoskeleton_transport" }, { "node_id": "PERT:ACTR10:KO", "label": "ACTR10 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "ACTR10" }, { "node_id": "PERT:DCTN1:KO", "label": "DCTN1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DCTN1" }, { "node_id": "PERT:DCTN5:KO", "label": "DCTN5 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DCTN5" }, { "node_id": "PERT:CAPZB:KO", "label": "CAPZB knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "CAPZB" }, { "node_id": "PERT:DYNLRB1:KO", "label": "DYNLRB1 knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "DYNLRB1" }, { "node_id": "MODULE:MYOMAKER_FUSOGEN", "label": "Myomaker fusogen reference", "layer": "pathway_module", "node_type": "positive_control_axis_not_one_of_named_complex_subset", "evidence_state": "published_complex_membership", "module_class": "fusion_machinery" }, { "node_id": "PERT:MYMK:KO", "label": "MYMK knockout", "layer": "perturbation", "node_type": "observed_human_myoblast_knockout", "evidence_state": "observed_human_myoblast_screen", "gene": "MYMK" } ], "edges": [ { "edge_id": "B0E001", "source": "PERT:MYOD1:KO", "target": "MODULE:MYOD_TCF12_EP300", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E002", "source": "PERT:MYOD1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.5203, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00055, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E003", "source": "PERT:MYOD1:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E004", "source": "PERT:TCF12:KO", "target": "MODULE:MYOD_TCF12_EP300", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E005", "source": "PERT:TCF12:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.6051, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00055, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E006", "source": "PERT:TCF12:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E007", "source": "PERT:EP300:KO", "target": "MODULE:MYOD_TCF12_EP300", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E008", "source": "PERT:EP300:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.55547, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.070185, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E009", "source": "PERT:EP300:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E010", "source": "MODULE:MYOD_TCF12_EP300", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 1.5203, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E011", "source": "MODULE:MYOD_TCF12_EP300", "target": "STATE:EARLY_MYOGENIC_DIFFERENTIATION", "edge_type": "published_grouped_cropseq_observation", "evidence_state": "observed_grouped_transcriptomic_qualitative", "effect_direction": "lowest_myogenesis_differentiation_score_group", "effect_size": null, "effect_unit": "published_group_level_MDS_direction", "fdr": null, "source_object": "article_Figure_6d_6e_and_main_text", "claim_boundary": "group-level published observation; candidate-level expression matrix attachment remains blocked", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E012", "source": "PERT:SAE1:KO", "target": "MODULE:SUMO_E1_E2", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E013", "source": "PERT:SAE1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.2817, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.020693, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E014", "source": "PERT:SAE1:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E015", "source": "PERT:UBA2:KO", "target": "MODULE:SUMO_E1_E2", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E016", "source": "PERT:UBA2:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.70418, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.093536, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E017", "source": "PERT:UBE2I:KO", "target": "MODULE:SUMO_E1_E2", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E018", "source": "PERT:UBE2I:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.48374, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.095354, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E019", "source": "MODULE:SUMO_E1_E2", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 0.70418, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E020", "source": "PERT:SMARCA5:KO", "target": "MODULE:ISWI_CHROMATIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E021", "source": "PERT:SMARCA5:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.88355, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.055718, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E022", "source": "PERT:SMARCA5:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E023", "source": "PERT:RBBP4:KO", "target": "MODULE:ISWI_CHROMATIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E024", "source": "PERT:RBBP4:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.1786, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.010091, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E025", "source": "PERT:RBBP4:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E026", "source": "PERT:BPTF:KO", "target": "MODULE:ISWI_CHROMATIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E027", "source": "PERT:BPTF:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.4655, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00055, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E028", "source": "PERT:BPTF:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E029", "source": "MODULE:ISWI_CHROMATIN", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 1.1786, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E030", "source": "PERT:METTL3:KO", "target": "MODULE:M6A_WRITER", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E031", "source": "PERT:METTL3:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 2.1589, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00055, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E032", "source": "PERT:METTL3:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E033", "source": "PERT:METTL14:KO", "target": "MODULE:M6A_WRITER", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E034", "source": "PERT:METTL14:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 2.2305, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00429, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E035", "source": "PERT:METTL14:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E036", "source": "PERT:WTAP:KO", "target": "MODULE:M6A_WRITER", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E037", "source": "PERT:WTAP:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.925, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00315, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E038", "source": "PERT:WTAP:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E039", "source": "PERT:ZC3H13:KO", "target": "MODULE:M6A_WRITER", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E040", "source": "PERT:ZC3H13:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.5217, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.019213, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E041", "source": "PERT:ZC3H13:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E042", "source": "MODULE:M6A_WRITER", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 2.04195, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E043", "source": "PERT:DR1:KO", "target": "MODULE:NEGATIVE_COFACTOR_2", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E044", "source": "PERT:DR1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.5016, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.018193, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E045", "source": "PERT:DR1:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E046", "source": "PERT:DRAP1:KO", "target": "MODULE:NEGATIVE_COFACTOR_2", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E047", "source": "PERT:DRAP1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 2.5053, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.00055, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E048", "source": "PERT:DRAP1:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E049", "source": "MODULE:NEGATIVE_COFACTOR_2", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 2.00345, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E050", "source": "PERT:CCT3:KO", "target": "MODULE:CCT_TCP1", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E051", "source": "PERT:CCT3:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.92081, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.087573, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E052", "source": "PERT:CCT5:KO", "target": "MODULE:CCT_TCP1", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E053", "source": "PERT:CCT5:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.94828, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.065993, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E054", "source": "PERT:TCP1:KO", "target": "MODULE:CCT_TCP1", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E055", "source": "PERT:TCP1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.78728, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.087573, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E056", "source": "MODULE:CCT_TCP1", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 0.92081, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E057", "source": "PERT:VPS33A:KO", "target": "MODULE:HOPS", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E058", "source": "PERT:VPS33A:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.79578, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.01739, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E059", "source": "PERT:VPS33A:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E060", "source": "PERT:VPS39:KO", "target": "MODULE:HOPS", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E061", "source": "PERT:VPS39:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.57929, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.028109, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E062", "source": "PERT:VPS39:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E063", "source": "MODULE:HOPS", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 0.687535, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E064", "source": "PERT:ILF3:KO", "target": "MODULE:RNA_STABILITY", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E065", "source": "PERT:ILF3:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.92983, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.02014, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E066", "source": "PERT:DHX9:KO", "target": "MODULE:RNA_STABILITY", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E067", "source": "PERT:DHX9:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.46381, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.072244, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E068", "source": "MODULE:RNA_STABILITY", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 0.69682, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E069", "source": "PERT:NAA30:KO", "target": "MODULE:N_TERMINAL_ACETYLATION", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E070", "source": "PERT:NAA30:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.2967, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.006876, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E071", "source": "PERT:NAA30:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E072", "source": "PERT:NAA35:KO", "target": "MODULE:N_TERMINAL_ACETYLATION", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E073", "source": "PERT:NAA35:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.6268, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.02014, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E074", "source": "PERT:NAA38:KO", "target": "MODULE:N_TERMINAL_ACETYLATION", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E075", "source": "PERT:NAA38:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.6593, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.010091, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E076", "source": "PERT:NAA38:KO", "target": "ENDPOINT:MONONUCLEATED_FRACTION", "edge_type": "observed_individual_validation", "evidence_state": "observed_individual_validation", "effect_direction": "increased_mononucleated_fraction", "effect_size": null, "effect_unit": "qualitative_direction_only", "fdr": null, "source_object": "Supplementary_Data_6_and_Figure_4g", "claim_boundary": "individual validation identity and published direction; the supplement does not provide a per-gene effect estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E077", "source": "MODULE:N_TERMINAL_ACETYLATION", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 1.6268, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E078", "source": "PERT:ACTR10:KO", "target": "MODULE:DYNEIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E079", "source": "PERT:ACTR10:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.68514, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.085143, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E080", "source": "PERT:DCTN1:KO", "target": "MODULE:DYNEIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E081", "source": "PERT:DCTN1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.71721, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.092251, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E082", "source": "PERT:DCTN5:KO", "target": "MODULE:DYNEIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E083", "source": "PERT:DCTN5:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.61791, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.065305, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E084", "source": "PERT:CAPZB:KO", "target": "MODULE:DYNEIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E085", "source": "PERT:CAPZB:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.62617, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.037836, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E086", "source": "PERT:DYNLRB1:KO", "target": "MODULE:DYNEIN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E087", "source": "PERT:DYNLRB1:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 0.55556, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.051497, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E088", "source": "MODULE:DYNEIN", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 0.62617, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E089", "source": "PERT:MYMK:KO", "target": "MODULE:MYOMAKER_FUSOGEN", "edge_type": "published_module_membership", "evidence_state": "published_complex_membership", "effect_direction": "membership_only_no_causal_direction", "effect_size": null, "effect_unit": null, "fdr": null, "source_object": "article_main_text_and_figure_5", "claim_boundary": "membership is not a pathway-activity estimate", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E090", "source": "PERT:MYMK:KO", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "observed_screen_effect", "evidence_state": "observed_human_myoblast_screen", "effect_direction": "knockout_impairs_fusion", "effect_size": 1.0763, "effect_unit": "MAGeCK_positive_selection_log_fold_change", "fdr": 0.002475, "source_object": "Supplementary_Data_5", "claim_boundary": "split-toxin survival-enrichment endpoint in healthy human myoblasts; not a DMD transcriptomic pathway delta", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E091", "source": "MODULE:MYOMAKER_FUSOGEN", "target": "ENDPOINT:SPLIT_TOXIN_FUSION_DEFECT", "edge_type": "descriptive_module_convergence", "evidence_state": "descriptive_convergence_of_observed_hits", "effect_direction": "all_encoded_members_impair_fusion_when_knocked_out", "effect_size": 1.0763, "effect_unit": "median_member_MAGeCK_positive_selection_log_fold_change", "fdr": null, "source_object": "Supplementary_Data_5_plus_published_membership", "claim_boundary": "descriptive member summary only; no new module-level statistical test or pathway-activity score was computed", "supports_dmd_prediction": false, "source_accession": "GSE293514" }, { "edge_id": "B0E092", "source": "PERT:MYMK:KO", "target": "STATE:EARLY_MYOGENIC_DIFFERENTIATION", "edge_type": "published_grouped_cropseq_observation", "evidence_state": "observed_grouped_transcriptomic_qualitative", "effect_direction": "highest_myogenesis_differentiation_score_group", "effect_size": null, "effect_unit": "published_group_level_MDS_direction", "fdr": null, "source_object": "article_Figure_6d_6e_and_main_text", "claim_boundary": "group-level published observation; candidate-level expression matrix attachment remains blocked", "supports_dmd_prediction": false, "source_accession": "GSE293514" } ], "modules": [ { "module_id": "MODULE:MYOD_TCF12_EP300", "label": "MyoD-TCF12-p300 cofactor complex", "module_class": "transcriptional_control", "module_kind": "published_named_complex_subset", "members": [ { "gene": "MYOD1", "fusion_screen_lfc": 1.5203, "fusion_screen_fdr": 0.00055, "individually_validated": true }, { "gene": "TCF12", "fusion_screen_lfc": 1.6051, "fusion_screen_fdr": 0.00055, "individually_validated": true }, { "gene": "EP300", "fusion_screen_lfc": 0.55547, "fusion_screen_fdr": 0.070185, "individually_validated": true } ], "member_count": 3, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 3, "median_fusion_screen_lfc": 1.5203, "transcriptomic_observation": "lowest_myogenesis_differentiation_score_group" }, { "module_id": "MODULE:SUMO_E1_E2", "label": "SUMO activation complex", "module_class": "protein_modification", "module_kind": "published_named_complex_subset", "members": [ { "gene": "SAE1", "fusion_screen_lfc": 1.2817, "fusion_screen_fdr": 0.020693, "individually_validated": true }, { "gene": "UBA2", "fusion_screen_lfc": 0.70418, "fusion_screen_fdr": 0.093536, "individually_validated": false }, { "gene": "UBE2I", "fusion_screen_lfc": 0.48374, "fusion_screen_fdr": 0.095354, "individually_validated": false } ], "member_count": 3, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 1, "median_fusion_screen_lfc": 0.70418, "transcriptomic_observation": null }, { "module_id": "MODULE:ISWI_CHROMATIN", "label": "ISWI chromatin remodelers", "module_class": "chromatin_remodeling", "module_kind": "published_named_complex_subset", "members": [ { "gene": "SMARCA5", "fusion_screen_lfc": 0.88355, "fusion_screen_fdr": 0.055718, "individually_validated": true }, { "gene": "RBBP4", "fusion_screen_lfc": 1.1786, "fusion_screen_fdr": 0.010091, "individually_validated": true }, { "gene": "BPTF", "fusion_screen_lfc": 1.4655, "fusion_screen_fdr": 0.00055, "individually_validated": true } ], "member_count": 3, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 3, "median_fusion_screen_lfc": 1.1786, "transcriptomic_observation": null }, { "module_id": "MODULE:M6A_WRITER", "label": "m6A writer machinery", "module_class": "rna_modification", "module_kind": "published_named_complex_subset", "members": [ { "gene": "METTL3", "fusion_screen_lfc": 2.1589, "fusion_screen_fdr": 0.00055, "individually_validated": true }, { "gene": "METTL14", "fusion_screen_lfc": 2.2305, "fusion_screen_fdr": 0.00429, "individually_validated": true }, { "gene": "WTAP", "fusion_screen_lfc": 1.925, "fusion_screen_fdr": 0.00315, "individually_validated": true }, { "gene": "ZC3H13", "fusion_screen_lfc": 1.5217, "fusion_screen_fdr": 0.019213, "individually_validated": true } ], "member_count": 4, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 4, "median_fusion_screen_lfc": 2.04195, "transcriptomic_observation": null }, { "module_id": "MODULE:NEGATIVE_COFACTOR_2", "label": "Negative cofactor 2 complex", "module_class": "transcriptional_control", "module_kind": "published_named_complex_subset", "members": [ { "gene": "DR1", "fusion_screen_lfc": 1.5016, "fusion_screen_fdr": 0.018193, "individually_validated": true }, { "gene": "DRAP1", "fusion_screen_lfc": 2.5053, "fusion_screen_fdr": 0.00055, "individually_validated": true } ], "member_count": 2, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 2, "median_fusion_screen_lfc": 2.00345, "transcriptomic_observation": null }, { "module_id": "MODULE:CCT_TCP1", "label": "Chaperonin TCP1 complex", "module_class": "protein_folding", "module_kind": "published_named_complex_subset", "members": [ { "gene": "CCT3", "fusion_screen_lfc": 0.92081, "fusion_screen_fdr": 0.087573, "individually_validated": false }, { "gene": "CCT5", "fusion_screen_lfc": 0.94828, "fusion_screen_fdr": 0.065993, "individually_validated": false }, { "gene": "TCP1", "fusion_screen_lfc": 0.78728, "fusion_screen_fdr": 0.087573, "individually_validated": false } ], "member_count": 3, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 0, "median_fusion_screen_lfc": 0.92081, "transcriptomic_observation": null }, { "module_id": "MODULE:HOPS", "label": "HOPS complex", "module_class": "vesicle_trafficking", "module_kind": "published_named_complex_subset", "members": [ { "gene": "VPS33A", "fusion_screen_lfc": 0.79578, "fusion_screen_fdr": 0.01739, "individually_validated": true }, { "gene": "VPS39", "fusion_screen_lfc": 0.57929, "fusion_screen_fdr": 0.028109, "individually_validated": true } ], "member_count": 2, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 2, "median_fusion_screen_lfc": 0.687535, "transcriptomic_observation": null }, { "module_id": "MODULE:RNA_STABILITY", "label": "RNA stability regulators", "module_class": "rna_stability", "module_kind": "published_named_complex_subset", "members": [ { "gene": "ILF3", "fusion_screen_lfc": 0.92983, "fusion_screen_fdr": 0.02014, "individually_validated": false }, { "gene": "DHX9", "fusion_screen_lfc": 0.46381, "fusion_screen_fdr": 0.072244, "individually_validated": false } ], "member_count": 2, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 0, "median_fusion_screen_lfc": 0.69682, "transcriptomic_observation": null }, { "module_id": "MODULE:N_TERMINAL_ACETYLATION", "label": "N-terminal acetylation complex", "module_class": "protein_modification", "module_kind": "published_named_complex_subset", "members": [ { "gene": "NAA30", "fusion_screen_lfc": 1.2967, "fusion_screen_fdr": 0.006876, "individually_validated": true }, { "gene": "NAA35", "fusion_screen_lfc": 1.6268, "fusion_screen_fdr": 0.02014, "individually_validated": false }, { "gene": "NAA38", "fusion_screen_lfc": 1.6593, "fusion_screen_fdr": 0.010091, "individually_validated": true } ], "member_count": 3, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 2, "median_fusion_screen_lfc": 1.6268, "transcriptomic_observation": null }, { "module_id": "MODULE:DYNEIN", "label": "Dynein-associated complex", "module_class": "cytoskeleton_transport", "module_kind": "published_named_complex_subset", "members": [ { "gene": "ACTR10", "fusion_screen_lfc": 0.68514, "fusion_screen_fdr": 0.085143, "individually_validated": false }, { "gene": "DCTN1", "fusion_screen_lfc": 0.71721, "fusion_screen_fdr": 0.092251, "individually_validated": false }, { "gene": "DCTN5", "fusion_screen_lfc": 0.61791, "fusion_screen_fdr": 0.065305, "individually_validated": false }, { "gene": "CAPZB", "fusion_screen_lfc": 0.62617, "fusion_screen_fdr": 0.037836, "individually_validated": false }, { "gene": "DYNLRB1", "fusion_screen_lfc": 0.55556, "fusion_screen_fdr": 0.051497, "individually_validated": false } ], "member_count": 5, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 0, "median_fusion_screen_lfc": 0.62617, "transcriptomic_observation": null }, { "module_id": "MODULE:MYOMAKER_FUSOGEN", "label": "Myomaker fusogen reference", "module_class": "fusion_machinery", "module_kind": "positive_control_axis_not_one_of_named_complex_subset", "members": [ { "gene": "MYMK", "fusion_screen_lfc": 1.0763, "fusion_screen_fdr": 0.002475, "individually_validated": false } ], "member_count": 1, "all_members_fusion_hits_fdr_lt_0_1": true, "individually_validated_members": 0, "median_fusion_screen_lfc": 1.0763, "transcriptomic_observation": "highest_myogenesis_differentiation_score_group" } ], "candidate_context_audit": [ { "gene": "ADAM10", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": -0.075195, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "CALR", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": -0.065853, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "CPEB1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "DDX19B", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": 0.069099, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "DNAAF3", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "DNM1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "EHMT2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "EPS8L1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "GFOD2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "INTS13", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "LMO2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "MON1A", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": -0.10707, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "MPHOSPH6", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": 0.37153, "fusion_screen_fdr": 0.77869, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "NAGLU", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": 0.061132, "fusion_screen_fdr": 0.685034, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "RAC3", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "RNASEH2C", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": 0.18037, "fusion_screen_fdr": 0.685016, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "RNF8", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "WDR4", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": -0.010262, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "ZFP69B", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "ZNF133", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_screen_lfc": -0.003533, "fusion_screen_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" }, { "gene": "ZNF236", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_screen_lfc": null, "fusion_screen_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated": false, "assessment_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "supports_dmd_prediction": false, "claim_boundary": "healthy-human-myoblast context only; absence of a fusion hit is endpoint-specific and is not evidence of no DMD effect" } ], "pathway_signatures": [ { "signature_id": "GSE293514_SEVEN_DONOR_UP_REFERENCE", "direction": "up", "gene_rows": 150, "donor_lines": 7, "consensus_core_7_of_7": 72, "top_consensus_genes": [ { "gene": "MYOG", "core_donors": 7, "median_log2_fold_change": 7.895447480133204 }, { "gene": "ACTA1", "core_donors": 7, "median_log2_fold_change": 7.856049602665251 }, { "gene": "ERBB3", "core_donors": 7, "median_log2_fold_change": 7.636460106539582 }, { "gene": "ACTN2", "core_donors": 7, "median_log2_fold_change": 7.616228325267023 }, { "gene": "SRL", "core_donors": 7, "median_log2_fold_change": 7.548890981918265 }, { "gene": "UNC45B", "core_donors": 7, "median_log2_fold_change": 7.546149035830735 }, { "gene": "APOBEC2", "core_donors": 7, "median_log2_fold_change": 7.460489329453156 }, { "gene": "CDKN1C", "core_donors": 7, "median_log2_fold_change": 7.4497890797790305 }, { "gene": "MRLN", "core_donors": 7, "median_log2_fold_change": 7.297735360478887 }, { "gene": "MYH3", "core_donors": 7, "median_log2_fold_change": 7.208969623331632 }, { "gene": "MYMK", "core_donors": 7, "median_log2_fold_change": 7.193538187849098 }, { "gene": "MYL4", "core_donors": 7, "median_log2_fold_change": 7.160115227295369 } ], "header_columns": 30, "evidence_state": "observed_unperturbed_reference_not_perturbation_delta" }, { "signature_id": "GSE293514_SEVEN_DONOR_DOWN_REFERENCE", "direction": "down", "gene_rows": 137, "donor_lines": 7, "consensus_core_7_of_7": 56, "top_consensus_genes": [ { "gene": "RRM2", "core_donors": 7, "median_log2_fold_change": -6.709083642092842 }, { "gene": "BIRC5", "core_donors": 7, "median_log2_fold_change": -6.05908754575008 }, { "gene": "CENPF", "core_donors": 7, "median_log2_fold_change": -5.860276089639976 }, { "gene": "UBE2C", "core_donors": 7, "median_log2_fold_change": -5.746158861654773 }, { "gene": "LMNB1", "core_donors": 7, "median_log2_fold_change": -5.160449912567839 }, { "gene": "ZWINT", "core_donors": 7, "median_log2_fold_change": -4.066891434867713 }, { "gene": "HMGA1", "core_donors": 7, "median_log2_fold_change": -3.532833331846263 }, { "gene": "CKS2", "core_donors": 7, "median_log2_fold_change": -3.449134275941942 }, { "gene": "SMC4", "core_donors": 7, "median_log2_fold_change": -3.2831493354575954 }, { "gene": "VIM", "core_donors": 7, "median_log2_fold_change": -3.1400727276474396 }, { "gene": "CKS1B", "core_donors": 7, "median_log2_fold_change": -3.095812884854839 }, { "gene": "ID3", "core_donors": 7, "median_log2_fold_change": -3.07341774294185 } ], "header_columns": 30, "evidence_state": "observed_unperturbed_reference_not_perturbation_delta" }, { "signature_id": "GSE293514_CROPSEQ_MYOCYTE_SIGNATURE", "direction": "myocyte_over_myoblast", "gene_rows": 142, "top_genes": [ { "gene": "CHRNG", "log2_fold_change_myocyte_vs_myoblast": 4.9009814, "adjusted_p_value": 0.0 }, { "gene": "ARPP21", "log2_fold_change_myocyte_vs_myoblast": 4.8895254, "adjusted_p_value": 0.0 }, { "gene": "ACTA1", "log2_fold_change_myocyte_vs_myoblast": 4.7680745, "adjusted_p_value": 0.0 }, { "gene": "TNNI1", "log2_fold_change_myocyte_vs_myoblast": 4.7631254, "adjusted_p_value": 0.0 }, { "gene": "CACNA1S", "log2_fold_change_myocyte_vs_myoblast": 4.750926, "adjusted_p_value": 0.0 }, { "gene": "MYBPH", "log2_fold_change_myocyte_vs_myoblast": 4.7252913, "adjusted_p_value": 0.0 }, { "gene": "CASQ2", "log2_fold_change_myocyte_vs_myoblast": 4.662538, "adjusted_p_value": 0.0 }, { "gene": "LDB3", "log2_fold_change_myocyte_vs_myoblast": 4.6623983, "adjusted_p_value": 0.0 }, { "gene": "ENSG00000289950", "log2_fold_change_myocyte_vs_myoblast": 4.646098, "adjusted_p_value": 0.0 }, { "gene": "MIR1-1HG", "log2_fold_change_myocyte_vs_myoblast": 4.6418896, "adjusted_p_value": 0.0 }, { "gene": "RYR1", "log2_fold_change_myocyte_vs_myoblast": 4.585076, "adjusted_p_value": 0.0 }, { "gene": "REEP1", "log2_fold_change_myocyte_vs_myoblast": 4.557833, "adjusted_p_value": 0.0 } ], "evidence_state": "observed_signature_definition_not_candidate_delta" }, { "signature_id": "GSE293514_CROPSEQ_MYOBLAST_SIGNATURE", "direction": "myoblast_over_myocyte", "gene_rows": 253, "top_genes": [ { "gene": "MT2A", "log2_fold_change_myocyte_vs_myoblast": -6.53197, "adjusted_p_value": 0.0 }, { "gene": "SERPINE1", "log2_fold_change_myocyte_vs_myoblast": -6.0203853, "adjusted_p_value": 0.0 }, { "gene": "NPTX2", "log2_fold_change_myocyte_vs_myoblast": -5.890263, "adjusted_p_value": 0.0 }, { "gene": "MKI67", "log2_fold_change_myocyte_vs_myoblast": -5.815296, "adjusted_p_value": 0.0 }, { "gene": "TOP2A", "log2_fold_change_myocyte_vs_myoblast": -5.5340753, "adjusted_p_value": 0.0 }, { "gene": "HMGA2", "log2_fold_change_myocyte_vs_myoblast": -5.383269, "adjusted_p_value": 0.0 }, { "gene": "CENPF", "log2_fold_change_myocyte_vs_myoblast": -5.3296504, "adjusted_p_value": 0.0 }, { "gene": "NT5E", "log2_fold_change_myocyte_vs_myoblast": -5.2090616, "adjusted_p_value": 0.0 }, { "gene": "ANPEP", "log2_fold_change_myocyte_vs_myoblast": -5.143213, "adjusted_p_value": 0.0 }, { "gene": "SRGN", "log2_fold_change_myocyte_vs_myoblast": -5.1321006, "adjusted_p_value": 0.0 }, { "gene": "DIAPH3", "log2_fold_change_myocyte_vs_myoblast": -5.098152, "adjusted_p_value": 0.0 }, { "gene": "CCBE1", "log2_fold_change_myocyte_vs_myoblast": -4.973643, "adjusted_p_value": 0.0 } ], "evidence_state": "observed_signature_definition_not_candidate_delta" } ], "quality_gates": [ { "gate": "official_source_sha256", "status": "PASS", "detail": "9/9 official supplementary workbooks match frozen SHA-256 values" }, { "gate": "published_screen_cardinality", "status": "PASS", "detail": "6,896 library genes; 7,197 screen rows; 250 hits at FDR < 0.1" }, { "gate": "individual_validation_identity", "status": "PASS", "detail": "125 unique published individually validated hit genes" }, { "gate": "myogenesis_signature_cardinality", "status": "PASS", "detail": "395 genes: 142 myocyte and 253 myoblast markers" }, { "gate": "candidate_context_audit", "status": "PASS", "detail": "9/21 assessed; 0/21 fusion hits; 12/21 not in the library" }, { "gate": "candidate_level_transcriptomic_pathway_delta", "status": "LOCKED", "detail": "The public CROP-seq matrix has 62,711 columns versus a 62,710-row recoverable public gene order; exact author column identity is unresolved" }, { "gate": "dmd_transfer", "status": "LOCKED", "detail": "No matched DMD perturbation outcome is present in GSE293514" } ], "matrix_identity_block": { "analysis_eligible": false, "matrix_columns": 62711, "recoverable_public_gene_order_rows": 62710, "missing_author_object": "ordered all_genes.csv or hash-frozen author gene_info", "consequence": "Do not attach gene symbols to the public CROP-seq matrix and do not emit candidate-level pathway deltas from it" }, "claim_boundary": "This is an observed healthy-human-myoblast functional perturbation network with a published named-module subset and qualitative grouped CROP-seq state edges. It is not a DMD perturbation network, not a candidate-level expression response atlas, and not a trained virtual-cell predictor.", "next_unlock": "Resolve exact GSE293514 expression-column identity for retrospective candidate-level transcriptomic analysis, then generate preregistered matched DMD/control perturbations for disease transfer.", "generated_by": "scripts/build_human_myoblast_perturbation_network_stage_b0.py" }