hallmark_ontology.json

{
  "_comment": "MSigDB Hallmark 50개 경로를 생물학적으로 의미있는 계층 DAG로 구성. K562에 특히 관련된 경로 강조.",
  "nodes": [
    {"id": "biological_process",      "name": "Biological Process"},
    {"id": "cell_proliferation",      "name": "Cell Proliferation"},
    {"id": "cell_death",              "name": "Cell Death & Stress"},
    {"id": "metabolism",              "name": "Metabolic Process"},
    {"id": "immune_signaling",        "name": "Immune Signaling"},
    {"id": "signal_transduction",     "name": "Signal Transduction"},
    {"id": "stress_response",         "name": "Stress Response"},
    {"id": "development",             "name": "Development & Differentiation"},
    {"id": "E2F_Targets",             "name": "E2F Targets"},
    {"id": "G2M_Checkpoint",          "name": "G2-M Checkpoint"},
    {"id": "Mitotic_Spindle",         "name": "Mitotic Spindle"},
    {"id": "Myc_Targets_V1",          "name": "Myc Targets V1"},
    {"id": "Myc_Targets_V2",          "name": "Myc Targets V2"},
    {"id": "Apoptosis",               "name": "Apoptosis"},
    {"id": "p53_Pathway",             "name": "p53 Pathway"},
    {"id": "Oxidative_Phosphorylation","name": "Oxidative Phosphorylation"},
    {"id": "Glycolysis",              "name": "Glycolysis"},
    {"id": "Fatty_Acid_Metabolism",   "name": "Fatty Acid Metabolism"},
    {"id": "Cholesterol_Homeostasis", "name": "Cholesterol Homeostasis"},
    {"id": "mTORC1_Signaling",        "name": "mTORC1 Signaling"},
    {"id": "TNFa_NFkB",               "name": "TNF-alpha Signaling via NF-kB"},
    {"id": "IL6_JAK_STAT3",           "name": "IL-6/JAK/STAT3 Signaling"},
    {"id": "IL2_STAT5",               "name": "IL-2/STAT5 Signaling"},
    {"id": "Interferon_Alpha",        "name": "Interferon Alpha Response"},
    {"id": "Interferon_Gamma",        "name": "Interferon Gamma Response"},
    {"id": "Inflammatory_Response",   "name": "Inflammatory Response"},
    {"id": "Complement",              "name": "Complement"},
    {"id": "PI3K_AKT_mTOR",          "name": "PI3K/AKT/mTOR Signaling"},
    {"id": "KRAS_Up",                 "name": "KRAS Signaling Up"},
    {"id": "KRAS_Dn",                 "name": "KRAS Signaling Dn"},
    {"id": "Hedgehog",                "name": "Hedgehog Signaling"},
    {"id": "Notch",                   "name": "Notch Signaling"},
    {"id": "TGFb",                    "name": "TGF-beta Signaling"},
    {"id": "WNT",                     "name": "Wnt-beta Catenin Signaling"},
    {"id": "Hypoxia",                 "name": "Hypoxia"},
    {"id": "UV_Up",                   "name": "UV Response Up"},
    {"id": "UV_Dn",                   "name": "UV Response Dn"},
    {"id": "UPR",                     "name": "Unfolded Protein Response"},
    {"id": "ROS",                     "name": "Reactive Oxygen Species Pathway"},
    {"id": "DNA_Repair",              "name": "DNA Repair"},
    {"id": "Adipogenesis",            "name": "Adipogenesis"},
    {"id": "Myogenesis",              "name": "Myogenesis"},
    {"id": "Androgen_Response",       "name": "Androgen Response"},
    {"id": "Estrogen_Early",          "name": "Estrogen Response Early"},
    {"id": "Estrogen_Late",           "name": "Estrogen Response Late"},
    {"id": "Angiogenesis",            "name": "Angiogenesis"},
    {"id": "EMT",                     "name": "Epithelial Mesenchymal Transition"},
    {"id": "Coagulation",             "name": "Coagulation"},
    {"id": "Protein_Secretion",       "name": "Protein Secretion"},
    {"id": "Xenobiotic",              "name": "Xenobiotic Metabolism"},
    {"id": "Peroxisome",              "name": "Peroxisome"},
    {"id": "heme_Metabolism",         "name": "Heme Metabolism"}
  ],
  "edges": [
    {"child": "cell_proliferation",      "parent": "biological_process"},
    {"child": "cell_death",              "parent": "biological_process"},
    {"child": "metabolism",              "parent": "biological_process"},
    {"child": "immune_signaling",        "parent": "biological_process"},
    {"child": "signal_transduction",     "parent": "biological_process"},
    {"child": "stress_response",         "parent": "biological_process"},
    {"child": "development",             "parent": "biological_process"},

    {"child": "E2F_Targets",             "parent": "cell_proliferation"},
    {"child": "G2M_Checkpoint",          "parent": "cell_proliferation"},
    {"child": "Mitotic_Spindle",         "parent": "cell_proliferation"},
    {"child": "Myc_Targets_V1",          "parent": "cell_proliferation"},
    {"child": "Myc_Targets_V2",          "parent": "cell_proliferation"},

    {"child": "Apoptosis",               "parent": "cell_death"},
    {"child": "p53_Pathway",             "parent": "cell_death"},
    {"child": "Hypoxia",                 "parent": "cell_death"},

    {"child": "Oxidative_Phosphorylation","parent": "metabolism"},
    {"child": "Glycolysis",              "parent": "metabolism"},
    {"child": "Fatty_Acid_Metabolism",   "parent": "metabolism"},
    {"child": "Cholesterol_Homeostasis", "parent": "metabolism"},
    {"child": "mTORC1_Signaling",        "parent": "metabolism"},
    {"child": "Peroxisome",              "parent": "metabolism"},
    {"child": "Xenobiotic",              "parent": "metabolism"},
    {"child": "heme_Metabolism",         "parent": "metabolism"},

    {"child": "TNFa_NFkB",               "parent": "immune_signaling"},
    {"child": "IL6_JAK_STAT3",           "parent": "immune_signaling"},
    {"child": "IL2_STAT5",               "parent": "immune_signaling"},
    {"child": "Interferon_Alpha",        "parent": "immune_signaling"},
    {"child": "Interferon_Gamma",        "parent": "immune_signaling"},
    {"child": "Inflammatory_Response",   "parent": "immune_signaling"},
    {"child": "Complement",              "parent": "immune_signaling"},
    {"child": "Coagulation",             "parent": "immune_signaling"},

    {"child": "PI3K_AKT_mTOR",          "parent": "signal_transduction"},
    {"child": "KRAS_Up",                 "parent": "signal_transduction"},
    {"child": "KRAS_Dn",                 "parent": "signal_transduction"},
    {"child": "Hedgehog",                "parent": "signal_transduction"},
    {"child": "Notch",                   "parent": "signal_transduction"},
    {"child": "TGFb",                    "parent": "signal_transduction"},
    {"child": "WNT",                     "parent": "signal_transduction"},

    {"child": "UV_Up",                   "parent": "stress_response"},
    {"child": "UV_Dn",                   "parent": "stress_response"},
    {"child": "UPR",                     "parent": "stress_response"},
    {"child": "ROS",                     "parent": "stress_response"},
    {"child": "DNA_Repair",              "parent": "stress_response"},

    {"child": "Adipogenesis",            "parent": "development"},
    {"child": "Myogenesis",              "parent": "development"},
    {"child": "Androgen_Response",       "parent": "development"},
    {"child": "Estrogen_Early",          "parent": "development"},
    {"child": "Estrogen_Late",           "parent": "development"},
    {"child": "Angiogenesis",            "parent": "development"},
    {"child": "EMT",                     "parent": "development"},
    {"child": "Protein_Secretion",       "parent": "development"}
  ],
  "msigdb_key_map": {
    "E2F_Targets":              "E2F Targets",
    "G2M_Checkpoint":           "G2-M Checkpoint",
    "Mitotic_Spindle":          "Mitotic Spindle",
    "Myc_Targets_V1":           "Myc Targets V1",
    "Myc_Targets_V2":           "Myc Targets V2",
    "Apoptosis":                "Apoptosis",
    "p53_Pathway":              "p53 Pathway",
    "Hypoxia":                  "Hypoxia",
    "Oxidative_Phosphorylation":"Oxidative Phosphorylation",
    "Glycolysis":               "Glycolysis",
    "Fatty_Acid_Metabolism":    "Fatty Acid Metabolism",
    "Cholesterol_Homeostasis":  "Cholesterol Homeostasis",
    "mTORC1_Signaling":         "mTORC1 Signaling",
    "Peroxisome":               "Pperoxisome",
    "Xenobiotic":               "Xenobiotic Metabolism",
    "heme_Metabolism":          "heme Metabolism",
    "TNFa_NFkB":                "TNF-alpha Signaling via NF-kB",
    "IL6_JAK_STAT3":            "IL-6/JAK/STAT3 Signaling",
    "IL2_STAT5":                "IL-2/STAT5 Signaling",
    "Interferon_Alpha":         "Interferon Alpha Response",
    "Interferon_Gamma":         "Interferon Gamma Response",
    "Inflammatory_Response":    "Inflammatory Response",
    "Complement":               "Complement",
    "Coagulation":              "Coagulation",
    "PI3K_AKT_mTOR":            "PI3K/AKT/mTOR  Signaling",
    "KRAS_Up":                  "KRAS Signaling Up",
    "KRAS_Dn":                  "KRAS Signaling Dn",
    "Hedgehog":                 "Hedgehog Signaling",
    "Notch":                    "Notch Signaling",
    "TGFb":                     "TGF-beta Signaling",
    "WNT":                      "Wnt-beta Catenin Signaling",
    "UV_Up":                    "UV Response Up",
    "UV_Dn":                    "UV Response Dn",
    "UPR":                      "Unfolded Protein Response",
    "ROS":                      "Reactive Oxygen Species Pathway",
    "DNA_Repair":               "DNA Repair",
    "Adipogenesis":             "Adipogenesis",
    "Myogenesis":               "Myogenesis",
    "Androgen_Response":        "Androgen Response",
    "Estrogen_Early":           "Estrogen Response Early",
    "Estrogen_Late":            "Estrogen Response Late",
    "Angiogenesis":             "Angiogenesis",
    "EMT":                      "Epithelial Mesenchymal Transition",
    "Protein_Secretion":        "Protein Secretion"
  }
}