{ "contract_schema": "nmd-vcell-external-perturbation-evidence/1.1", "feature_build": "EXT-PERT-20260729-02", "generated_at": "2026-07-29T06:50:25+0800", "datasets": [ { "accession": "GSE293514", "title": "Human myoblast fusion CRISPR screen and single-cell CRISPR/RNA-seq", "evidence_role": "external_human_myoblast_context_and_fusion_safety_screen", "qualification_state": "QUALIFIED_BOUNDED_CONTEXT", "direct_validation_of_current_21_candidates": false, "limitations": [ "healthy-donor myoblast context rather than DMD", "fusion endpoint does not cover all neuromuscular mechanisms", "processed single-cell guide assignment is not fully reconstructable from deposited sidecars" ], "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE293514", "selected_candidate_summary": { "candidate_count": 21, "in_myo_crispr_library": 9, "not_in_myo_crispr_library": 12, "fusion_hits_fdr_lt_0_1": 0, "individually_validated_hits": 0 } }, { "accession": "GSE272233", "title": "CRISPR correction of DMD exon duplications in patient-derived myogenic cells", "evidence_role": "orthogonal_dmd_crispr_correction_transcriptome_reference", "qualification_state": "QUALIFIED_ORTHOGONAL_REFERENCE", "sample_count": 21, "biological_replicates_per_group": 3, "mutation_contexts": [ "duplication_exon_2", "duplication_exons_2_9", "duplication_exons_8_9" ], "direct_validation_of_current_21_candidates": false, "limitations": [ "bulk RNA-seq rather than single-cell perturbation", "candidate genes were not themselves perturbed", "wild-type comparator is not isogenic", "corrected clones may retain clone-specific effects" ], "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE272233" }, { "accession": "GSE52529", "title": "Single-cell trajectory reconstruction of human skeletal myoblast differentiation", "evidence_role": "time_anchored_human_myogenic_trajectory_reference", "qualification_state": "QUALIFIED_REFERENCE_ONLY", "cell_count": 271, "physical_timepoints_hours": [0, 24, 48, 72], "direct_validation_of_current_21_candidates": false, "perturbation_conditioned_trajectory": false, "limitations": [ "unperturbed differentiation reference rather than candidate perturbation", "published pseudotime is descriptive and does not establish causal fate control", "healthy primary myoblast context rather than DMD" ], "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52529", "package_url": "https://bioconductor.org/packages/release/data/experiment/html/HSMMSingleCell.html" }, { "accession": "GSE133344", "title": "Mapping cellular behavior with combinatorial CRISPRa perturbations", "evidence_role": "cross_cell_line_crispra_and_combination_method_calibration", "qualification_state": "QUALIFIED_METHOD_CALIBRATION_ONLY", "cell_line": "K562", "reported_perturbations": 287, "reported_single_target_gene_set": 112, "direct_validation_of_current_21_candidates": false, "limitations": [ "K562 rather than muscle or DMD context", "current local compact asset contains expression features, not guide identities", "candidate feature presence does not mean the candidate was a CRISPRa target" ], "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133344", "paper_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6746554/" } ], "gse272233": { "source": { "file": "GSE272233_matrix.txt.gz", "size_bytes": 1326864, "sha256": "072e1398918140af4898cc895dcbd6c72c28beb39353834063e457f9d0161eee", "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE272nnn/GSE272233/suppl/GSE272233_matrix.txt.gz" }, "qc": { "raw_gene_rows": 62757, "aggregated_gene_symbols": 62710, "genes_retained_filter_by_expr": 22230, "sample_count": 21, "groups": { "WT": 3, "Dup2": 3, "Dup2_corrected": 3, "Dup2_9": 3, "Dup2_9_corrected": 3, "Dup8_9": 3, "Dup8_9_corrected": 3 } }, "contrast_summary": [ { "contrast": "dup2_correction", "tested_genes": 22230, "fdr_lt_0_05": 2812, "fdr_lt_0_05_abs_logfc_ge_1": 1090, "up_fdr_lt_0_05": 1125, "down_fdr_lt_0_05": 1687 }, { "contrast": "dup2_9_correction", "tested_genes": 22230, "fdr_lt_0_05": 375, "fdr_lt_0_05_abs_logfc_ge_1": 167, "up_fdr_lt_0_05": 154, "down_fdr_lt_0_05": 221 }, { "contrast": "dup8_9_correction", "tested_genes": 22230, "fdr_lt_0_05": 2736, "fdr_lt_0_05_abs_logfc_ge_1": 979, "up_fdr_lt_0_05": 1498, "down_fdr_lt_0_05": 1238 } ], "dmd_transcript_correction": [ { "contrast": "dup2_correction", "logfc": 2.00289708, "fdr": 2.5122311e-11 }, { "contrast": "dup2_9_correction", "logfc": 2.4511413, "fdr": 3.14569291e-12 }, { "contrast": "dup8_9_correction", "logfc": 1.78448901, "fdr": 1.64769557e-09 } ], "candidate_records": [ { "gene": "ADAM10", "observed_in_filtered_matrix": true, "mean_log_cpm": 8.52768073, "correction_effects": { "dup2": { "logfc": 0.34502215, "fdr": 0.02082656 }, "dup2_9": { "logfc": 0.14643984, "fdr": 0.5478339 }, "dup8_9": { "logfc": 0.16224166, "fdr": 0.32438886 } }, "significant_correction_contrasts_fdr_0_05": 1, "exploratory_reversal_contrasts_fdr_0_05": 1, "correction_direction_state": "consistent_up_when_significant", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "CALR", "observed_in_filtered_matrix": true, "mean_log_cpm": 8.19937769, "correction_effects": { "dup2": { "logfc": -0.42896174, "fdr": 0.0082007 }, "dup2_9": { "logfc": -0.01033944, "fdr": 0.98442435 }, "dup8_9": { "logfc": 0.23596725, "fdr": 0.16220968 } }, "significant_correction_contrasts_fdr_0_05": 1, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "consistent_down_when_significant", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "CPEB1", "observed_in_filtered_matrix": true, "mean_log_cpm": 1.05532863, "correction_effects": { "dup2": { "logfc": -0.94693216, "fdr": 0.01005329 }, "dup2_9": { "logfc": 0.58998749, "fdr": 0.32772329 }, "dup8_9": { "logfc": -0.22296312, "fdr": 0.66510356 } }, "significant_correction_contrasts_fdr_0_05": 1, "exploratory_reversal_contrasts_fdr_0_05": 1, "correction_direction_state": "consistent_down_when_significant", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "DDX19B", "observed_in_filtered_matrix": true, "mean_log_cpm": 4.01880946, "correction_effects": { "dup2": { "logfc": -0.16249822, "fdr": 0.40020702 }, "dup2_9": { "logfc": -0.28941549, "fdr": 0.24582336 }, "dup8_9": { "logfc": -0.19440813, "fdr": 0.30635495 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "DNAAF3", "observed_in_filtered_matrix": true, "mean_log_cpm": -1.69156951, "correction_effects": { "dup2": { "logfc": -0.23027013, "fdr": 0.78683638 }, "dup2_9": { "logfc": -0.15010408, "fdr": 0.95519715 }, "dup8_9": { "logfc": -0.8584961, "fdr": 0.35018444 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "DNM1", "observed_in_filtered_matrix": true, "mean_log_cpm": -1.54084661, "correction_effects": { "dup2": { "logfc": -0.4950344, "fdr": 0.72145172 }, "dup2_9": { "logfc": 1.19036839, "fdr": 0.49654474 }, "dup8_9": { "logfc": 0.00393384, "fdr": 0.99845066 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "EHMT2", "observed_in_filtered_matrix": true, "mean_log_cpm": 3.99795178, "correction_effects": { "dup2": { "logfc": 0.20451853, "fdr": 0.24694616 }, "dup2_9": { "logfc": -0.07007108, "fdr": 0.84707042 }, "dup8_9": { "logfc": 0.02993864, "fdr": 0.91043887 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "EPS8L1", "observed_in_filtered_matrix": true, "mean_log_cpm": -1.85154692, "correction_effects": { "dup2": { "logfc": 0.00313593, "fdr": 0.99893288 }, "dup2_9": { "logfc": -1.40379447, "fdr": 0.42667264 }, "dup8_9": { "logfc": -0.91259136, "fdr": 0.40544798 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "GFOD2", "observed_in_filtered_matrix": true, "mean_log_cpm": 3.41928109, "correction_effects": { "dup2": { "logfc": -0.26365887, "fdr": 0.1897428 }, "dup2_9": { "logfc": -0.16652531, "fdr": 0.62370287 }, "dup8_9": { "logfc": 0.00365379, "fdr": 0.98940775 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "INTS13", "observed_in_filtered_matrix": true, "mean_log_cpm": 4.676713, "correction_effects": { "dup2": { "logfc": -0.25535064, "fdr": 0.05991596 }, "dup2_9": { "logfc": -0.01431687, "fdr": 0.97068432 }, "dup8_9": { "logfc": -0.30601963, "fdr": 0.02491036 } }, "significant_correction_contrasts_fdr_0_05": 1, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "consistent_down_when_significant", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "LMO2", "observed_in_filtered_matrix": true, "mean_log_cpm": 0.27828039, "correction_effects": { "dup2": { "logfc": -0.98148905, "fdr": 0.07112593 }, "dup2_9": { "logfc": -0.80318856, "fdr": 0.4273561 }, "dup8_9": { "logfc": -1.22445994, "fdr": 0.0147092 } }, "significant_correction_contrasts_fdr_0_05": 1, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "consistent_down_when_significant", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "MON1A", "observed_in_filtered_matrix": true, "mean_log_cpm": 2.974323, "correction_effects": { "dup2": { "logfc": -0.13835549, "fdr": 0.58692601 }, "dup2_9": { "logfc": -0.20633493, "fdr": 0.56792726 }, "dup8_9": { "logfc": -0.40090832, "fdr": 0.06930161 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "MPHOSPH6", "observed_in_filtered_matrix": true, "mean_log_cpm": 3.22524103, "correction_effects": { "dup2": { "logfc": -0.00892899, "fdr": 0.98072645 }, "dup2_9": { "logfc": -0.04867437, "fdr": 0.92657792 }, "dup8_9": { "logfc": -0.30458736, "fdr": 0.15992667 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "NAGLU", "observed_in_filtered_matrix": true, "mean_log_cpm": 3.7992606, "correction_effects": { "dup2": { "logfc": -0.09252269, "fdr": 0.72054461 }, "dup2_9": { "logfc": -0.24794554, "fdr": 0.41269803 }, "dup8_9": { "logfc": 0.03135597, "fdr": 0.9216087 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "RAC3", "observed_in_filtered_matrix": true, "mean_log_cpm": -0.23989122, "correction_effects": { "dup2": { "logfc": -0.39371699, "fdr": 0.60497002 }, "dup2_9": { "logfc": -0.27518952, "fdr": 0.83521397 }, "dup8_9": { "logfc": 0.74679524, "fdr": 0.34648736 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "RNASEH2C", "observed_in_filtered_matrix": true, "mean_log_cpm": 2.16968785, "correction_effects": { "dup2": { "logfc": -0.16286848, "fdr": 0.71220965 }, "dup2_9": { "logfc": -0.38463052, "fdr": 0.50437664 }, "dup8_9": { "logfc": -0.18523044, "fdr": 0.6852228 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "RNF8", "observed_in_filtered_matrix": true, "mean_log_cpm": 1.93662715, "correction_effects": { "dup2": { "logfc": -0.10171706, "fdr": 0.80278766 }, "dup2_9": { "logfc": -0.08534453, "fdr": 0.91080538 }, "dup8_9": { "logfc": -0.00148063, "fdr": 0.99828882 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "WDR4", "observed_in_filtered_matrix": true, "mean_log_cpm": 1.69977043, "correction_effects": { "dup2": { "logfc": -0.59666178, "fdr": 0.0551182 }, "dup2_9": { "logfc": -0.42808438, "fdr": 0.43716556 }, "dup8_9": { "logfc": -0.47638268, "fdr": 0.17866594 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "ZFP69B", "observed_in_filtered_matrix": true, "mean_log_cpm": 1.56814752, "correction_effects": { "dup2": { "logfc": -0.25690467, "fdr": 0.56079923 }, "dup2_9": { "logfc": 0.057161, "fdr": 0.94372095 }, "dup8_9": { "logfc": -0.17294162, "fdr": 0.7032864 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "ZNF133", "observed_in_filtered_matrix": true, "mean_log_cpm": 2.04897248, "correction_effects": { "dup2": { "logfc": 0.13505433, "fdr": 0.69395003 }, "dup2_9": { "logfc": -0.03955329, "fdr": 0.96061378 }, "dup8_9": { "logfc": -0.0848011, "fdr": 0.83341441 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" }, { "gene": "ZNF236", "observed_in_filtered_matrix": true, "mean_log_cpm": 4.91232045, "correction_effects": { "dup2": { "logfc": 0.07980343, "fdr": 0.63453741 }, "dup2_9": { "logfc": 0.11648346, "fdr": 0.60944169 }, "dup8_9": { "logfc": 0.03624907, "fdr": 0.85618164 } }, "significant_correction_contrasts_fdr_0_05": 0, "exploratory_reversal_contrasts_fdr_0_05": 0, "correction_direction_state": "no_repair_contrast_fdr_lt_0_05", "interpretation": "candidate transcript response to DMD correction; not a perturbation effect of this candidate" } ], "program_records": [ { "program_id": "myogenic_contractile", "program_label": "Myogenic / contractile", "contrast": "dup2_correction", "panel_gene_count": 17, "measured_gene_count": 15, "median_logfc": -0.846983, "significant_gene_count_fdr_0_05": 8, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "myogenic_contractile", "program_label": "Myogenic / contractile", "contrast": "dup2_9_correction", "panel_gene_count": 17, "measured_gene_count": 15, "median_logfc": -0.41136625, "significant_gene_count_fdr_0_05": 4, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "myogenic_contractile", "program_label": "Myogenic / contractile", "contrast": "dup8_9_correction", "panel_gene_count": 17, "measured_gene_count": 15, "median_logfc": -0.6790707, "significant_gene_count_fdr_0_05": 9, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "ecm_fibrotic", "program_label": "ECM / fibrotic", "contrast": "dup2_correction", "panel_gene_count": 16, "measured_gene_count": 13, "median_logfc": -0.96301926, "significant_gene_count_fdr_0_05": 9, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "ecm_fibrotic", "program_label": "ECM / fibrotic", "contrast": "dup2_9_correction", "panel_gene_count": 16, "measured_gene_count": 13, "median_logfc": -0.10875128, "significant_gene_count_fdr_0_05": 0, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "ecm_fibrotic", "program_label": "ECM / fibrotic", "contrast": "dup8_9_correction", "panel_gene_count": 16, "measured_gene_count": 13, "median_logfc": 0.71105894, "significant_gene_count_fdr_0_05": 8, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "inflammatory_stress", "program_label": "Inflammatory / stress", "contrast": "dup2_correction", "panel_gene_count": 15, "measured_gene_count": 11, "median_logfc": -0.26263402, "significant_gene_count_fdr_0_05": 1, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "inflammatory_stress", "program_label": "Inflammatory / stress", "contrast": "dup2_9_correction", "panel_gene_count": 15, "measured_gene_count": 11, "median_logfc": 0.15829123, "significant_gene_count_fdr_0_05": 1, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "inflammatory_stress", "program_label": "Inflammatory / stress", "contrast": "dup8_9_correction", "panel_gene_count": 15, "measured_gene_count": 11, "median_logfc": 0.04342144, "significant_gene_count_fdr_0_05": 1, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "cell_cycle", "program_label": "Cell cycle / proliferation", "contrast": "dup2_correction", "panel_gene_count": 11, "measured_gene_count": 11, "median_logfc": -0.89851453, "significant_gene_count_fdr_0_05": 3, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "cell_cycle", "program_label": "Cell cycle / proliferation", "contrast": "dup2_9_correction", "panel_gene_count": 11, "measured_gene_count": 11, "median_logfc": -0.36123947, "significant_gene_count_fdr_0_05": 0, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "cell_cycle", "program_label": "Cell cycle / proliferation", "contrast": "dup8_9_correction", "panel_gene_count": 11, "measured_gene_count": 11, "median_logfc": -0.34080157, "significant_gene_count_fdr_0_05": 2, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "metabolic_secretory", "program_label": "Metabolic / secretory", "contrast": "dup2_correction", "panel_gene_count": 11, "measured_gene_count": 5, "median_logfc": -0.55787077, "significant_gene_count_fdr_0_05": 2, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "metabolic_secretory", "program_label": "Metabolic / secretory", "contrast": "dup2_9_correction", "panel_gene_count": 11, "measured_gene_count": 5, "median_logfc": -0.2552975, "significant_gene_count_fdr_0_05": 0, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "metabolic_secretory", "program_label": "Metabolic / secretory", "contrast": "dup8_9_correction", "panel_gene_count": 11, "measured_gene_count": 5, "median_logfc": -0.5209601, "significant_gene_count_fdr_0_05": 3, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "proteostasis_membrane", "program_label": "Proteostasis / membrane", "contrast": "dup2_correction", "panel_gene_count": 12, "measured_gene_count": 12, "median_logfc": -0.25367062, "significant_gene_count_fdr_0_05": 4, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "proteostasis_membrane", "program_label": "Proteostasis / membrane", "contrast": "dup2_9_correction", "panel_gene_count": 12, "measured_gene_count": 12, "median_logfc": -0.06349777, "significant_gene_count_fdr_0_05": 0, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" }, { "program_id": "proteostasis_membrane", "program_label": "Proteostasis / membrane", "contrast": "dup8_9_correction", "panel_gene_count": 12, "measured_gene_count": 12, "median_logfc": 0.00504879, "significant_gene_count_fdr_0_05": 2, "interpretation": "descriptive project-panel shift; not formal pathway enrichment" } ], "interpretation": "The reference measures transcript changes after DMD-locus CRISPR correction. It is an orthogonal disease-correction benchmark, not evidence that a displayed candidate perturbation is therapeutic or causal." }, "claim_boundary": "GSE293514 is a bounded human-myoblast fusion screen; GSE272233 is an orthogonal DMD-correction transcriptome reference; GSE52529 is an unperturbed, time-anchored myogenic trajectory reference; and GSE133344 is cross-cell-line CRISPRa/combination method calibration. None supplies direct independent DMD perturbation validation for the current 21 candidates, observed candidate-pair interactions, candidate overexpression responses in muscle, or perturbation-conditioned fate.", "gse293514": { "source_files": [ { "file": "Supplementary_Data_2_MyoCRISPR_library.xlsx", "size_bytes": 988152, "sha256": "362806fb11b2798733bb54f8f34b4454f0870aa2de4e487ce7e5aebd20d3ee82", "role": "MyoCRISPR library membership" }, { "file": "Supplementary_Data_5_fusion_hits.xlsx", "size_bytes": 774760, "sha256": "b362439cbec443265aa157c4630a9721d553d9d687fee1e7d1a5eed1374467e2", "role": "gene-level fusion screen summary" }, { "file": "Supplementary_Data_6_individual_validation.xlsx", "size_bytes": 15603, "sha256": "c3d425e8d577cf4fb7bfdf26591c74a540b98aac005a521624fe56aee4e5fea6", "role": "individual fusion-hit validation subset" } ], "selected_candidate_summary": { "candidate_count": 21, "in_myo_crispr_library": 9, "not_in_myo_crispr_library": 12, "fusion_hits_fdr_lt_0_1": 0, "individually_validated_hits": 0 }, "candidate_records": [ { "gene": "ADAM10", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": -0.075195, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "CALR", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": -0.065853, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "CPEB1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "DDX19B", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": 0.069099, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "DNAAF3", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "DNM1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "EHMT2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "EPS8L1", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "GFOD2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "INTS13", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "LMO2", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "MON1A", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": -0.10707, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "MPHOSPH6", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": 0.37153, "fusion_pos_fdr": 0.77869, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "NAGLU", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": 0.061132, "fusion_pos_fdr": 0.685034, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "RAC3", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "RNASEH2C", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": 0.18037, "fusion_pos_fdr": 0.685016, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "RNF8", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "WDR4", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": -0.010262, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "ZFP69B", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "ZNF133", "in_myo_crispr_library": true, "fusion_screen_assessed": true, "fusion_pos_lfc": -0.003533, "fusion_pos_fdr": 0.999999, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "ASSESSED_NO_FUSION_HIT_AT_FDR_0_1", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" }, { "gene": "ZNF236", "in_myo_crispr_library": false, "fusion_screen_assessed": false, "fusion_pos_lfc": null, "fusion_pos_fdr": null, "fusion_hit_fdr_lt_0_1": false, "individually_validated_hit": false, "external_context_state": "NOT_INCLUDED_IN_MYOCRISPR_LIBRARY", "interpretation": "human-myoblast fusion context only; not direct DMD candidate perturbation validation" } ], "interpretation": "The audit tests whether the 21 displayed candidates were included in the human-myoblast library and whether they met the publication's fusion-hit threshold. It does not test DMD rescue." }, "gse52529": { "source": { "package": "HSMMSingleCell_1.32.0.tar.gz", "package_size_bytes": 16875752, "package_sha256": "e9a7f53dd27bc8034cfdc34b8aac33d2c56439e0e36a95422412aa41b05f23fc", "expression_object": "HSMM_expr_matrix.rda", "annotation_object": "HSMM_gene_annotation.rda", "sample_sheet_object": "HSMM_sample_sheet.rda" }, "qc": { "feature_rows": 47192, "representative_gene_symbols": 46992, "cell_count": 271, "cells_by_physical_timepoint": { "0": 69, "24": 74, "48": 79, "72": 49 }, "cells_by_published_state": { "1": 99, "2": 129, "3": 43 }, "pseudotime_min": 0, "pseudotime_median": 45.04439887, "pseudotime_max": 76.65415946, "candidate_genes_measured": 20, "candidate_genes_total": 21 }, "candidate_records": [ { "gene": "ADAM10", "measured": true, "representative_ensembl_feature": "ENSG00000137845.10", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 265, "detected_fraction_gt_0": 0.97785978, "overall_mean_fpkm": 33.99613648, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.51360317, "pseudotime_spearman_rho": 0.10573881, "pseudotime_spearman_p": 0.08229746, "physical_time_kruskal_wallis_p": 0.01040609, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 19.79135986, "median_fpkm": 15.3611, "mean_log1p_fpkm": 2.70495072 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 42.9995621, "median_fpkm": 26.7802, "mean_log1p_fpkm": 3.13894598 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 41.50407899, "median_fpkm": 30.1722, "mean_log1p_fpkm": 3.13697187 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 28.29712898, "median_fpkm": 18.0358, "mean_log1p_fpkm": 2.87821727 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 2.79057486 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 2.72814578 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 2.72916878 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 3.35355625 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 3.18906 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 3.17212527 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 3.06039478 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 2.39226087 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 3.10458352 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 3.27644761 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.19545648, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.02824511, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "CALR", "measured": true, "representative_ensembl_feature": "ENSG00000179218.8", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 271, "detected_fraction_gt_0": 1, "overall_mean_fpkm": 137.04550756, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.57455099, "pseudotime_spearman_rho": 0.08676531, "pseudotime_spearman_p": 0.1543242, "physical_time_kruskal_wallis_p": 1.03542605e-08, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 132.54667754, "median_fpkm": 128.54, "mean_log1p_fpkm": 4.80985077 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 152.82966351, "median_fpkm": 138.737, "mean_log1p_fpkm": 4.88525422 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 156.00769494, "median_fpkm": 140.007, "mean_log1p_fpkm": 4.9117559 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 88.97160816, "median_fpkm": 72.9151, "mean_log1p_fpkm": 4.30858799 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 4.75490627 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 4.70426011 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 4.77381639 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 4.82936568 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 4.56547027 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 4.83886601 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 4.84689706 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 4.5261103 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 4.81787166 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 5.02799366 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.24434664, "physical_time_kruskal_wallis_fdr_among_21_candidates": 1.96730949e-07, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "CPEB1", "measured": true, "representative_ensembl_feature": "ENSG00000214575.5", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 16, "detected_fraction_gt_0": 0.05904059, "overall_mean_fpkm": 0.16409678, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.91154148, "pseudotime_spearman_rho": -0.02239986, "pseudotime_spearman_p": 0.71355203, "physical_time_kruskal_wallis_p": 0.20200418, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.42011116, "median_fpkm": 0, "mean_log1p_fpkm": 0.09410543 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0.0572723, "median_fpkm": 0, "mean_log1p_fpkm": 0.03005448 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0.03285971, "median_fpkm": 0, "mean_log1p_fpkm": 0.01880874 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0.17649982, "median_fpkm": 0, "mean_log1p_fpkm": 0.06432559 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.16934294 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.00295131 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.07813727 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.03041963 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.16900316 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.00570472 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.00629358 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.03161179 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.84734303, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.27414853, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "DDX19B", "measured": true, "representative_ensembl_feature": "ENSG00000157349.11", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 153, "detected_fraction_gt_0": 0.56457565, "overall_mean_fpkm": 10.93480133, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.57097177, "pseudotime_spearman_rho": -0.09632341, "pseudotime_spearman_p": 0.11364169, "physical_time_kruskal_wallis_p": 0.15012099, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 13.66222875, "median_fpkm": 3.10425, "mean_log1p_fpkm": 1.58355623 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 9.53733336, "median_fpkm": 0.093354, "mean_log1p_fpkm": 1.02743076 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 10.95984343, "median_fpkm": 0.314919, "mean_log1p_fpkm": 1.14512394 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 9.16422604, "median_fpkm": 0.886717, "mean_log1p_fpkm": 1.25504107 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 1.47202823 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 1.79839453 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 1.29458891 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 1.26655129 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 1.55392776 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.68134293 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.85428533 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 1.23034735 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 1.14573639 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 1.15116378 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.21591921, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.2592999, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "DNAAF3", "measured": true, "representative_ensembl_feature": "ENSG00000167646.9", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 1, "detected_fraction_gt_0": 0.00369004, "overall_mean_fpkm": 0.10325018, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -2.33776486, "pseudotime_spearman_rho": -0.09257407, "pseudotime_spearman_p": 0.12846488, "physical_time_kruskal_wallis_p": 0.40293313, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.40551884, "median_fpkm": 0, "mean_log1p_fpkm": 0.04879179 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.12469013 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.22189389, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.4253183, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "DNM1", "measured": true, "representative_ensembl_feature": "ENSG00000106976.14", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 26, "detected_fraction_gt_0": 0.09594096, "overall_mean_fpkm": 0.08341871, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.6269278, "pseudotime_spearman_rho": -0.00405565, "pseudotime_spearman_p": 0.94701475, "physical_time_kruskal_wallis_p": 1.03372513e-07, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.00119026, "median_fpkm": 0, "mean_log1p_fpkm": 0.00114391 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0.15888791, "median_fpkm": 0, "mean_log1p_fpkm": 0.05942777 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0.10138777, "median_fpkm": 0, "mean_log1p_fpkm": 0.05331307 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0.05626539, "median_fpkm": 0, "mean_log1p_fpkm": 0.05087618 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.01413386 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.00389097 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.00484822 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.04651083 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.12675349 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.08193478 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.02906096 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.10175461 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.00504577 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.98808617, "physical_time_kruskal_wallis_fdr_among_21_candidates": 9.82038877e-07, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "EHMT2", "measured": true, "representative_ensembl_feature": "ENSG00000204371.7", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 148, "detected_fraction_gt_0": 0.54612546, "overall_mean_fpkm": 5.39065521, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.25131168, "pseudotime_spearman_rho": -0.00091129, "pseudotime_spearman_p": 0.98808617, "physical_time_kruskal_wallis_p": 7.1685762e-06, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 5.4572273, "median_fpkm": 0.0932865, "mean_log1p_fpkm": 0.8301313 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 4.24857966, "median_fpkm": 0, "mean_log1p_fpkm": 0.62828076 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 6.91205697, "median_fpkm": 0, "mean_log1p_fpkm": 0.72740537 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 4.56880576, "median_fpkm": 1.00165, "mean_log1p_fpkm": 1.066764 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.74827804 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.67111338 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 1.01734772 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.91853953 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.96231531 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.6407299 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.73611342 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.5721616 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.69639157 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.91098406 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.98808617, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.00003405, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "EPS8L1", "measured": true, "representative_ensembl_feature": "ENSG00000131037.10", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 53, "detected_fraction_gt_0": 0.19557196, "overall_mean_fpkm": 6.00596172, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 4.22504947, "pseudotime_spearman_rho": 0.18118933, "pseudotime_spearman_p": 0.00275541, "physical_time_kruskal_wallis_p": 0.00187556, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.26173516, "median_fpkm": 0, "mean_log1p_fpkm": 0.07104243 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 7.56641135, "median_fpkm": 0, "mean_log1p_fpkm": 0.53525637 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 9.15271443, "median_fpkm": 0, "mean_log1p_fpkm": 0.75325908 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 6.66483714, "median_fpkm": 0, "mean_log1p_fpkm": 0.8360015 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.73745768 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.02044615 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.08603535 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.26725071 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.66383548 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.10972858 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.33388027 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.91375928 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 1.06067209 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 1.13463104 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.01834889, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.00712712, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "GFOD2", "measured": true, "representative_ensembl_feature": "ENSG00000141098.8", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 81, "detected_fraction_gt_0": 0.29889299, "overall_mean_fpkm": 2.53516432, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.78197837, "pseudotime_spearman_rho": -0.055672, "pseudotime_spearman_p": 0.36126948, "physical_time_kruskal_wallis_p": 2.30076625e-07, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 1.60346549, "median_fpkm": 0, "mean_log1p_fpkm": 0.39689095 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 1.45647555, "median_fpkm": 0, "mean_log1p_fpkm": 0.25593139 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 4.17703739, "median_fpkm": 0, "mean_log1p_fpkm": 0.42009395 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 2.82908709, "median_fpkm": 0.345698, "mean_log1p_fpkm": 0.66420691 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.52330282 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.5023675 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.36262099 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.56114897 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.43027109 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.09847926 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.77002485 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.49391383 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.27782881 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.12568177 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.52800924, "physical_time_kruskal_wallis_fdr_among_21_candidates": 1.45715196e-06, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "INTS13", "measured": false, "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "interpretation": "Gene symbol was not present in the curated HSMMSingleCell annotation; no trajectory reference is emitted." }, { "gene": "LMO2", "measured": true, "representative_ensembl_feature": "ENSG00000135363.7", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 1, "detected_fraction_gt_0": 0.00369004, "overall_mean_fpkm": 0.00863373, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.42125589, "pseudotime_spearman_rho": -0.09724167, "pseudotime_spearman_p": 0.11022384, "physical_time_kruskal_wallis_p": 0.40293313, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.03390928, "median_fpkm": 0, "mean_log1p_fpkm": 0.01747671 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.0446627 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.21591921, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.4253183, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "MON1A", "measured": true, "representative_ensembl_feature": "ENSG00000164077.9", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 58, "detected_fraction_gt_0": 0.21402214, "overall_mean_fpkm": 1.69594649, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.45349461, "pseudotime_spearman_rho": -0.01860229, "pseudotime_spearman_p": 0.76048561, "physical_time_kruskal_wallis_p": 0.28509957, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 2.01348628, "median_fpkm": 0, "mean_log1p_fpkm": 0.34521114 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 1.77436673, "median_fpkm": 0, "mean_log1p_fpkm": 0.16653842 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0.66400578, "median_fpkm": 0, "mean_log1p_fpkm": 0.21166557 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 2.79410918, "median_fpkm": 0, "mean_log1p_fpkm": 0.5118543 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.57502389 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.02800953 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.42735991 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.36403418 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.43967946 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.21211118 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.27034135 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.28961351 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.19199914 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.08554303 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.84995451, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.33855573, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "MPHOSPH6", "measured": true, "representative_ensembl_feature": "ENSG00000135698.5", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 191, "detected_fraction_gt_0": 0.70479705, "overall_mean_fpkm": 28.86078979, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.45542811, "pseudotime_spearman_rho": -0.12193511, "pseudotime_spearman_p": 0.04490789, "physical_time_kruskal_wallis_p": 0.18837539, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 30.82872803, "median_fpkm": 20.8343, "mean_log1p_fpkm": 2.57249316 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 33.27023207, "median_fpkm": 5.836225, "mean_log1p_fpkm": 2.07710354 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 26.98410615, "median_fpkm": 2.89955, "mean_log1p_fpkm": 1.89109175 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 22.45612735, "median_fpkm": 9.82138, "mean_log1p_fpkm": 2.08796072 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 3.08990516 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 2.73017709 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 2.15072028 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 2.21301992 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 1.81381275 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 1.35701387 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 1.6531733 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 2.25554566 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 1.71237936 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 2.5203155 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.14220831, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.27414853, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "NAGLU", "measured": true, "representative_ensembl_feature": "ENSG00000108784.5", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 42, "detected_fraction_gt_0": 0.15498155, "overall_mean_fpkm": 0.92402156, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.00488155, "pseudotime_spearman_rho": 0.02909939, "pseudotime_spearman_p": 0.63341686, "physical_time_kruskal_wallis_p": 0.60779782, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0.81778426, "median_fpkm": 0, "mean_log1p_fpkm": 0.19730024 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0.38778793, "median_fpkm": 0, "mean_log1p_fpkm": 0.14418266 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 1.58692284, "median_fpkm": 0, "mean_log1p_fpkm": 0.29375321 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0.81468406, "median_fpkm": 0, "mean_log1p_fpkm": 0.17609166 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.10701441 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.175253 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.21042623 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.20497936 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.21189825 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.17996016 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.08309807 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.33336709 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.26038593 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.30092504 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.80232802, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.60779782, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "RAC3", "measured": true, "representative_ensembl_feature": "ENSG00000169750.4", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 0, "detected_fraction_gt_0": 0, "overall_mean_fpkm": 0, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0, "pseudotime_spearman_rho": null, "pseudotime_spearman_p": null, "physical_time_kruskal_wallis_p": null, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0, "median_fpkm": 0, "mean_log1p_fpkm": 0 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": null, "physical_time_kruskal_wallis_fdr_among_21_candidates": null, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "RNASEH2C", "measured": true, "representative_ensembl_feature": "ENSG00000172922.4", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 210, "detected_fraction_gt_0": 0.77490775, "overall_mean_fpkm": 10.07903629, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.56865443, "pseudotime_spearman_rho": -0.18027603, "pseudotime_spearman_p": 0.00289719, "physical_time_kruskal_wallis_p": 0.07561696, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 8.08714705, "median_fpkm": 5.01701, "mean_log1p_fpkm": 1.57698868 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 8.23966926, "median_fpkm": 1.57829, "mean_log1p_fpkm": 1.33452089 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 12.32378143, "median_fpkm": 3.61144, "mean_log1p_fpkm": 1.6670169 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 12.04268224, "median_fpkm": 7.24647, "mean_log1p_fpkm": 1.92091938 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 2.02777114 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 1.67777341 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 1.6258745 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 1.89489535 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 1.91144567 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 1.47015683 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 1.52138533 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 1.21642213 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 1.25137317 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 1.40230416 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.01834889, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.1596358, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "RNF8", "measured": true, "representative_ensembl_feature": "ENSG00000112130.12", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 107, "detected_fraction_gt_0": 0.39483395, "overall_mean_fpkm": 4.64000889, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 0.64664912, "pseudotime_spearman_rho": -0.11048828, "pseudotime_spearman_p": 0.06936683, "physical_time_kruskal_wallis_p": 0.01029588, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 3.02748946, "median_fpkm": 0, "mean_log1p_fpkm": 0.70269726 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 7.23546712, "median_fpkm": 0, "mean_log1p_fpkm": 1.02118759 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 3.52036275, "median_fpkm": 0, "mean_log1p_fpkm": 0.49953023 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 4.79617167, "median_fpkm": 0, "mean_log1p_fpkm": 0.86698479 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.82240802 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.93221824 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.59933699 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.91792517 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.67504649 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.90690084 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.73141796 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 1.15345339 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.66605482 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.21680587 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.18828138, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.02824511, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "WDR4", "measured": true, "representative_ensembl_feature": "ENSG00000160193.7", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 66, "detected_fraction_gt_0": 0.24354244, "overall_mean_fpkm": 1.80239488, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -2.03853874, "pseudotime_spearman_rho": -0.2146744, "pseudotime_spearman_p": 0.00037193, "physical_time_kruskal_wallis_p": 0.03518274, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 3.43193523, "median_fpkm": 0, "mean_log1p_fpkm": 0.51804616 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 1.45866673, "median_fpkm": 0, "mean_log1p_fpkm": 0.2619046 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 1.34782795, "median_fpkm": 0, "mean_log1p_fpkm": 0.23362539 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 0.7597089, "median_fpkm": 0, "mean_log1p_fpkm": 0.33096841 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.30583657 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.51355218 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.55710352 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.59094019 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.54458656 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.11590032 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.25189656 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.03023102 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.30303102 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.10881711 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.00706676, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.083559, "trajectory_state": "decreases_along_published_pseudotime" }, { "gene": "ZFP69B", "measured": true, "representative_ensembl_feature": "ENSG00000187801.10", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 24, "detected_fraction_gt_0": 0.08856089, "overall_mean_fpkm": 1.52584143, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 1.77443151, "pseudotime_spearman_rho": -0.17103911, "pseudotime_spearman_p": 0.00475055, "physical_time_kruskal_wallis_p": 0.10451214, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 1.17982805, "median_fpkm": 0, "mean_log1p_fpkm": 0.25251622 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 0.10330081, "median_fpkm": 0, "mean_log1p_fpkm": 0.04926967 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 1.4533208, "median_fpkm": 0, "mean_log1p_fpkm": 0.16121097 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 4.27833245, "median_fpkm": 0, "mean_log1p_fpkm": 0.3479682 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.44459837 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.33747792 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.13886301 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.1063427 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.32434795 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.031844 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.15990657 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.04953502 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.10949298 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.17466618 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.0225651, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.19857306, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "ZNF133", "measured": true, "representative_ensembl_feature": "ENSG00000125846.11", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 70, "detected_fraction_gt_0": 0.25830258, "overall_mean_fpkm": 3.20798306, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": -0.03481638, "pseudotime_spearman_rho": -0.02935485, "pseudotime_spearman_p": 0.63043703, "physical_time_kruskal_wallis_p": 0.18364261, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 2.20353806, "median_fpkm": 0, "mean_log1p_fpkm": 0.41552225 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 2.88750254, "median_fpkm": 0, "mean_log1p_fpkm": 0.28320335 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 5.042558, "median_fpkm": 0, "mean_log1p_fpkm": 0.39655446 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 2.14861249, "median_fpkm": 0, "mean_log1p_fpkm": 0.4903935 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.31640286 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.56224916 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.41166732 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 0.33362046 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.30539995 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.18744497 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.48723975 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.64637092 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.37204345 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.25640418 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.80232802, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.27414853, "trajectory_state": "no_strong_monotonic_pseudotime_association" }, { "gene": "ZNF236", "measured": true, "representative_ensembl_feature": "ENSG00000130856.11", "representative_feature_rule": "highest_mean_fpkm_row_per_gene_symbol", "detected_cells_gt_0": 127, "detected_fraction_gt_0": 0.46863469, "overall_mean_fpkm": 3.41568087, "physical_time_log2_ratio_72h_vs_0h_pseudocount_0_1": 1.25030112, "pseudotime_spearman_rho": -0.16206425, "pseudotime_spearman_p": 0.00751141, "physical_time_kruskal_wallis_p": 0.24145643, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_fpkm": 1.41373969, "median_fpkm": 0.0502515, "mean_log1p_fpkm": 0.50008631 }, { "hours": 24, "cell_count": 74, "mean_fpkm": 3.87116902, "median_fpkm": 0, "mean_log1p_fpkm": 0.5276825 }, { "hours": 48, "cell_count": 79, "mean_fpkm": 4.68460055, "median_fpkm": 0, "mean_log1p_fpkm": 0.68951035 }, { "hours": 72, "cell_count": 49, "mean_fpkm": 3.50105156, "median_fpkm": 0.304452, "mean_log1p_fpkm": 0.76318423 } ], "pseudotime_profile": [ { "bin": 1, "cell_count": 27, "median_pseudotime": 9.02226494, "mean_log1p_fpkm": 0.32257669 }, { "bin": 2, "cell_count": 27, "median_pseudotime": 19.3990258, "mean_log1p_fpkm": 0.64997691 }, { "bin": 3, "cell_count": 27, "median_pseudotime": 31.88462671, "mean_log1p_fpkm": 0.46281663 }, { "bin": 4, "cell_count": 27, "median_pseudotime": 41.82137577, "mean_log1p_fpkm": 1.23826713 }, { "bin": 5, "cell_count": 27, "median_pseudotime": 44.08333053, "mean_log1p_fpkm": 0.85690526 }, { "bin": 6, "cell_count": 27, "median_pseudotime": 46.16188448, "mean_log1p_fpkm": 0.57994334 }, { "bin": 7, "cell_count": 27, "median_pseudotime": 50.61779133, "mean_log1p_fpkm": 0.44015146 }, { "bin": 8, "cell_count": 27, "median_pseudotime": 57.09142445, "mean_log1p_fpkm": 0.60064821 }, { "bin": 9, "cell_count": 27, "median_pseudotime": 63.9866916, "mean_log1p_fpkm": 0.5330134 }, { "bin": 10, "cell_count": 28, "median_pseudotime": 73.10195975, "mean_log1p_fpkm": 0.42663328 } ], "interpretation": "Descriptive expression trajectory in unperturbed differentiating human primary skeletal myoblasts; not a perturbation response.", "pseudotime_spearman_fdr_among_21_candidates": 0.02854336, "physical_time_kruskal_wallis_fdr_among_21_candidates": 0.30584481, "trajectory_state": "no_strong_monotonic_pseudotime_association" } ], "program_records": [ { "program_id": "myogenic_contractile", "program_label": "Myogenic / contractile", "panel_gene_count": 17, "measured_gene_count": 17, "measured_genes": ["ACTA1", "ACTN2", "CAV3", "CKM", "DES", "MEF2C", "MYH1", "MYH2", "MYH3", "MYH7", "MYLPF", "MYOD1", "MYOG", "NCAM1", "PAX7", "TNNC1", "TNNC2"], "pseudotime_spearman_rho": 0.62990255, "pseudotime_spearman_p": 2.28685169e-31, "physical_time_kruskal_wallis_p": 0.00024458, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": -0.29020775 }, { "hours": 24, "cell_count": 74, "mean_z_score": -0.00164418 }, { "hours": 48, "cell_count": 79, "mean_z_score": 0.11032377 }, { "hours": 72, "cell_count": 49, "mean_z_score": 0.23327401 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 1.37211101e-30, "physical_time_kruskal_wallis_fdr_across_six_panels": 0.0002935 }, { "program_id": "ecm_fibrotic", "program_label": "ECM / fibrotic", "panel_gene_count": 16, "measured_gene_count": 16, "measured_genes": ["COL1A1", "COL1A2", "COL3A1", "COL6A1", "COL6A2", "COL6A3", "COMP", "CTHRC1", "DCN", "FN1", "LUM", "MMP2", "MMP9", "SPP1", "TGFBI", "TIMP1"], "pseudotime_spearman_rho": -0.10698394, "pseudotime_spearman_p": 0.07873286, "physical_time_kruskal_wallis_p": 5.8152785e-07, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": -0.21092108 }, { "hours": 24, "cell_count": 74, "mean_z_score": -0.00906232 }, { "hours": 48, "cell_count": 79, "mean_z_score": 0.0924469 }, { "hours": 72, "cell_count": 49, "mean_z_score": 0.16165022 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 0.09447943, "physical_time_kruskal_wallis_fdr_across_six_panels": 8.72291774e-07 }, { "program_id": "inflammatory_stress", "program_label": "Inflammatory / stress", "panel_gene_count": 15, "measured_gene_count": 15, "measured_genes": ["C3", "DDIT4", "HSPA1A", "IFI30", "IFIT1", "IFITM3", "IL6", "IRF1", "ISG15", "LITAF", "PYCARD", "SERPINA1", "SERPINA3", "SOD2", "STAT1"], "pseudotime_spearman_rho": -0.06918277, "pseudotime_spearman_p": 0.25638031, "physical_time_kruskal_wallis_p": 6.21390898e-09, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": -0.18718838 }, { "hours": 24, "cell_count": 74, "mean_z_score": -0.00321041 }, { "hours": 48, "cell_count": 79, "mean_z_score": 0.07015375 }, { "hours": 72, "cell_count": 49, "mean_z_score": 0.15533515 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 0.25638031, "physical_time_kruskal_wallis_fdr_across_six_panels": 1.2427818e-08 }, { "program_id": "cell_cycle", "program_label": "Cell cycle / proliferation", "panel_gene_count": 11, "measured_gene_count": 11, "measured_genes": ["BIRC5", "CCNB1", "CDC20", "CDK1", "CENPF", "MKI67", "PTTG1", "STMN1", "TOP2A", "TUBA1B", "TUBB"], "pseudotime_spearman_rho": -0.38843728, "pseudotime_spearman_p": 3.42642733e-11, "physical_time_kruskal_wallis_p": 4.74736599e-10, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": 0.56386628 }, { "hours": 24, "cell_count": 74, "mean_z_score": -0.21206207 }, { "hours": 48, "cell_count": 79, "mean_z_score": -0.27701257 }, { "hours": 72, "cell_count": 49, "mean_z_score": -0.02714668 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 6.85285466e-11, "physical_time_kruskal_wallis_fdr_across_six_panels": 1.4242098e-09 }, { "program_id": "metabolic_secretory", "program_label": "Metabolic / secretory", "panel_gene_count": 11, "measured_gene_count": 10, "measured_genes": ["ALB", "APOA1", "APOA2", "APOE", "FABP3", "FDFT1", "GPX3", "IGFBP1", "MLXIPL", "RBP4"], "pseudotime_spearman_rho": 0.32818214, "pseudotime_spearman_p": 3.17420711e-08, "physical_time_kruskal_wallis_p": 5.64918393e-19, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": -0.2395636 }, { "hours": 24, "cell_count": 74, "mean_z_score": 0.04698945 }, { "hours": 48, "cell_count": 79, "mean_z_score": 0.04443941 }, { "hours": 72, "cell_count": 49, "mean_z_score": 0.19473379 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 4.76131067e-08, "physical_time_kruskal_wallis_fdr_across_six_panels": 3.38951036e-18 }, { "program_id": "proteostasis_membrane", "program_label": "Proteostasis / membrane", "panel_gene_count": 12, "measured_gene_count": 12, "measured_genes": ["CALR", "CAV3", "DDIT4", "DYSF", "GPX3", "HSP90AA1", "HSPA1A", "HSPB1", "LAMP1", "SGCA", "SGCB", "VCP"], "pseudotime_spearman_rho": 0.41846345, "pseudotime_spearman_p": 6.49986111e-13, "physical_time_kruskal_wallis_p": 0.16027222, "time_profile": [ { "hours": 0, "cell_count": 69, "mean_z_score": -0.0950543 }, { "hours": 24, "cell_count": 74, "mean_z_score": 0.03334652 }, { "hours": 48, "cell_count": 79, "mean_z_score": 0.05081917 }, { "hours": 72, "cell_count": 49, "mean_z_score": 0.00155898 } ], "interpretation": "Mean per-gene z-score for the frozen project panel in unperturbed myogenic differentiation; descriptive only, not enrichment.", "pseudotime_spearman_fdr_across_six_panels": 1.94995833e-12, "physical_time_kruskal_wallis_fdr_across_six_panels": 0.16027222 } ], "interpretation": "A real-time-anchored, unperturbed human myogenic differentiation reference. It qualifies baseline trajectory context but does not unlock perturbation-conditioned velocity, fate or treatment simulation." }, "gse133344": { "source": { "file": "GSE133344_filtered_genes.tsv.gz", "size_bytes": 264791, "sha256": "0dcba3cf4f3095b3fc1fa31b402c562bca7eea8d7d9ffd753e7b446dc37b9e3d" }, "study_summary": { "cell_line": "K562", "perturbation_modality": "CRISPRa", "reported_perturbations": 287, "reported_single_target_gene_set": 112, "reported_gene_pairs": 132 }, "feature_qc": { "expression_features": 33694, "current_candidates_present_as_expression_features": 20, "current_candidate_total": 21, "current_candidates_absent_as_expression_features": "INTS13" }, "candidate_feature_records": [ { "gene": "ADAM10", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "CALR", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "CPEB1", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "DDX19B", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "DNAAF3", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "DNM1", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "EHMT2", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "EPS8L1", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "GFOD2", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "INTS13", "present_as_expression_feature": false, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "LMO2", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "MON1A", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "MPHOSPH6", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "NAGLU", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "RAC3", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "RNASEH2C", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "RNF8", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "WDR4", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "ZFP69B", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "ZNF133", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." }, { "gene": "ZNF236", "present_as_expression_feature": true, "confirmed_as_crispra_target": null, "interpretation": "Feature-list coverage only; target status is not inferable from the filtered-gene file." } ], "interpretation": "Cross-cell-line method calibration for CRISPRa and combinatorial perturbation design only; not direct evidence for current candidate overexpression effects in muscle or DMD." } }