| { |
| "canonical_recovery": { |
| "scregnet_top20": { |
| "Neftel_AC": { |
| "recovered": 1, |
| "total": 5, |
| "fraction": 0.2, |
| "recovered_names": [ |
| "NFIB" |
| ], |
| "canonical_ranks": { |
| "SOX9": 65, |
| "NFIA": 517, |
| "NFIB": 6, |
| "HES1": 855, |
| "HEY1": 135 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES1": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 33, |
| "RUNX2": 260, |
| "FOSL2": 169, |
| "BHLHE40": 435, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES2": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 51, |
| "RUNX2": 291, |
| "FOSL2": 158, |
| "BHLHE40": 428, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 305, |
| "SOX11": 774, |
| "DCX": -1, |
| "NEUROD1": 1578, |
| "NEUROG2": 1437 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 292, |
| "SOX11": 763, |
| "DCX": -1, |
| "NEUROD1": 1572, |
| "NEUROG2": 1506 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 806, |
| "OLIG2": 913, |
| "ASCL1": 558, |
| "NKX2-2": 968, |
| "SOX10": 701 |
| }, |
| "top_n": 20 |
| } |
| }, |
| "scregnet_top50": { |
| "Neftel_AC": { |
| "recovered": 1, |
| "total": 5, |
| "fraction": 0.2, |
| "recovered_names": [ |
| "NFIB" |
| ], |
| "canonical_ranks": { |
| "SOX9": 65, |
| "NFIA": 517, |
| "NFIB": 6, |
| "HES1": 855, |
| "HEY1": 135 |
| }, |
| "top_n": 50 |
| }, |
| "Neftel_MES1": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "RUNX1" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 33, |
| "RUNX2": 260, |
| "FOSL2": 169, |
| "BHLHE40": 435, |
| "WWTR1": -1 |
| }, |
| "top_n": 50 |
| }, |
| "Neftel_MES2": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 51, |
| "RUNX2": 291, |
| "FOSL2": 158, |
| "BHLHE40": 428, |
| "WWTR1": -1 |
| }, |
| "top_n": 50 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 305, |
| "SOX11": 774, |
| "DCX": -1, |
| "NEUROD1": 1578, |
| "NEUROG2": 1437 |
| }, |
| "top_n": 50 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 292, |
| "SOX11": 763, |
| "DCX": -1, |
| "NEUROD1": 1572, |
| "NEUROG2": 1506 |
| }, |
| "top_n": 50 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 806, |
| "OLIG2": 913, |
| "ASCL1": 558, |
| "NKX2-2": 968, |
| "SOX10": 701 |
| }, |
| "top_n": 50 |
| } |
| }, |
| "scregnet_top100": { |
| "Neftel_AC": { |
| "recovered": 2, |
| "total": 5, |
| "fraction": 0.4, |
| "recovered_names": [ |
| "SOX9", |
| "NFIB" |
| ], |
| "canonical_ranks": { |
| "SOX9": 65, |
| "NFIA": 517, |
| "NFIB": 6, |
| "HES1": 855, |
| "HEY1": 135 |
| }, |
| "top_n": 100 |
| }, |
| "Neftel_MES1": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "RUNX1" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 33, |
| "RUNX2": 260, |
| "FOSL2": 169, |
| "BHLHE40": 435, |
| "WWTR1": -1 |
| }, |
| "top_n": 100 |
| }, |
| "Neftel_MES2": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "RUNX1" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 1000, |
| "RUNX1": 51, |
| "RUNX2": 291, |
| "FOSL2": 158, |
| "BHLHE40": 428, |
| "WWTR1": -1 |
| }, |
| "top_n": 100 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 305, |
| "SOX11": 774, |
| "DCX": -1, |
| "NEUROD1": 1578, |
| "NEUROG2": 1437 |
| }, |
| "top_n": 100 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 292, |
| "SOX11": 763, |
| "DCX": -1, |
| "NEUROD1": 1572, |
| "NEUROG2": 1506 |
| }, |
| "top_n": 100 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 806, |
| "OLIG2": 913, |
| "ASCL1": 558, |
| "NKX2-2": 968, |
| "SOX10": 701 |
| }, |
| "top_n": 100 |
| } |
| }, |
| "competing_pan_malignant": { |
| "genie3": { |
| "pan_malignant": { |
| "recovered": 0, |
| "total": 0, |
| "recovered_names": [] |
| }, |
| "subtype_recovery_top20": { |
| "Neftel_AC": { |
| "recovered": 1, |
| "total": 5, |
| "fraction": 0.2, |
| "recovered_names": [ |
| "NFIA" |
| ], |
| "canonical_ranks": { |
| "SOX9": 83, |
| "NFIA": 18, |
| "NFIB": 102, |
| "HES1": 75, |
| "HEY1": 562 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES1": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 597, |
| "RUNX1": 104, |
| "RUNX2": 21, |
| "FOSL2": 36, |
| "BHLHE40": 391, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES2": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "CEBPB" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 6, |
| "RUNX1": 396, |
| "RUNX2": 253, |
| "FOSL2": 892, |
| "BHLHE40": 94, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 90, |
| "SOX11": 568, |
| "DCX": -1, |
| "NEUROD1": 1495, |
| "NEUROG2": 1385 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 86, |
| "SOX11": 132, |
| "DCX": -1, |
| "NEUROD1": 1491, |
| "NEUROG2": 1192 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 552, |
| "OLIG2": 445, |
| "ASCL1": 740, |
| "NKX2-2": 204, |
| "SOX10": 46 |
| }, |
| "top_n": 20 |
| } |
| }, |
| "available_subtypes": [ |
| "Neftel_AC", |
| "Neftel_MES1", |
| "Neftel_MES2", |
| "Neftel_NPC1", |
| "Neftel_NPC2", |
| "Neftel_OPC" |
| ] |
| }, |
| "grnboost2": { |
| "pan_malignant": { |
| "recovered": 0, |
| "total": 0, |
| "recovered_names": [] |
| }, |
| "subtype_recovery_top20": { |
| "Neftel_AC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX9": 115, |
| "NFIA": 38, |
| "NFIB": 36, |
| "HES1": 282, |
| "HEY1": 405 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES1": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "RUNX2" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 311, |
| "RUNX1": 103, |
| "RUNX2": 20, |
| "FOSL2": 152, |
| "BHLHE40": 528, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES2": { |
| "recovered": 1, |
| "total": 6, |
| "fraction": 0.1667, |
| "recovered_names": [ |
| "CEBPB" |
| ], |
| "canonical_ranks": { |
| "CEBPB": 12, |
| "RUNX1": 198, |
| "RUNX2": 289, |
| "FOSL2": 1184, |
| "BHLHE40": 158, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 58, |
| "SOX11": 109, |
| "DCX": -1, |
| "NEUROD1": 1337, |
| "NEUROG2": 275 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 56, |
| "SOX11": 33, |
| "DCX": -1, |
| "NEUROD1": 291, |
| "NEUROG2": 824 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 324, |
| "OLIG2": 155, |
| "ASCL1": 463, |
| "NKX2-2": 349, |
| "SOX10": 74 |
| }, |
| "top_n": 20 |
| } |
| }, |
| "available_subtypes": [ |
| "Neftel_AC", |
| "Neftel_MES1", |
| "Neftel_MES2", |
| "Neftel_NPC1", |
| "Neftel_NPC2", |
| "Neftel_OPC" |
| ] |
| }, |
| "correlation": { |
| "pan_malignant": { |
| "recovered": 0, |
| "total": 0, |
| "recovered_names": [] |
| }, |
| "subtype_recovery_top20": { |
| "Neftel_AC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX9": 1357, |
| "NFIA": 1450, |
| "NFIB": 1522, |
| "HES1": 1081, |
| "HEY1": 1116 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES1": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 1143, |
| "RUNX1": 1494, |
| "RUNX2": 1330, |
| "FOSL2": 1478, |
| "BHLHE40": 1255, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_MES2": { |
| "recovered": 0, |
| "total": 6, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "CEBPB": 1408, |
| "RUNX1": 1543, |
| "RUNX2": 942, |
| "FOSL2": 1176, |
| "BHLHE40": 1452, |
| "WWTR1": -1 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC1": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 1401, |
| "SOX11": 1437, |
| "DCX": -1, |
| "NEUROD1": 129, |
| "NEUROG2": 155 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_NPC2": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX4": 1527, |
| "SOX11": 1428, |
| "DCX": -1, |
| "NEUROD1": 146, |
| "NEUROG2": 375 |
| }, |
| "top_n": 20 |
| }, |
| "Neftel_OPC": { |
| "recovered": 0, |
| "total": 5, |
| "fraction": 0.0, |
| "recovered_names": [], |
| "canonical_ranks": { |
| "SOX2": 1499, |
| "OLIG2": 1113, |
| "ASCL1": 822, |
| "NKX2-2": 1178, |
| "SOX10": 1019 |
| }, |
| "top_n": 20 |
| } |
| }, |
| "available_subtypes": [ |
| "Neftel_AC", |
| "Neftel_MES1", |
| "Neftel_MES2", |
| "Neftel_NPC1", |
| "Neftel_NPC2", |
| "Neftel_OPC" |
| ] |
| }, |
| "scenic": { |
| "pan_malignant": { |
| "recovered": 0, |
| "total": 0, |
| "recovered_names": [] |
| }, |
| "subtype_recovery_top20": {}, |
| "available_subtypes": [] |
| } |
| } |
| }, |
| "specific_tfs": { |
| "Neftel_AC": { |
| "n_specific": 21, |
| "top_tfs": [ |
| "ATF7", |
| "FOXJ1", |
| "ZNF467", |
| "ZNF319", |
| "NANOG", |
| "TBX20", |
| "FEZF1", |
| "FOXB1", |
| "ZNF572", |
| "ZNF611", |
| "ZNF708", |
| "E2F8", |
| "ZNF750", |
| "ZSCAN23", |
| "ZNF565", |
| "ZNF10", |
| "FOXD1", |
| "NR2F2", |
| "HNF4G", |
| "ZNF746" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 1.985, |
| 1.947, |
| 1.939, |
| 1.872, |
| 1.871, |
| 1.742, |
| 1.622, |
| 1.558, |
| 1.54, |
| 1.532, |
| 1.527 |
| ] |
| }, |
| "Neftel_MES1": { |
| "n_specific": 198, |
| "top_tfs": [ |
| "ZNF292", |
| "HLX", |
| "DMRTA1", |
| "PAX2", |
| "TFAP2C", |
| "AIRE", |
| "IRF5", |
| "OSR1", |
| "TCF7L1", |
| "ZFP64", |
| "MXD1", |
| "MTF1", |
| "ZNF117", |
| "ZBTB21", |
| "CARF", |
| "ZNF793", |
| "ZNF365", |
| "PPARD", |
| "ZKSCAN2", |
| "CPEB1" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.2, |
| 2.199, |
| 2.179, |
| 2.148, |
| 2.086, |
| 2.083, |
| 2.057, |
| 2.049, |
| 2.043, |
| 2.041, |
| 2.036, |
| 2.033 |
| ] |
| }, |
| "Neftel_MES2": { |
| "n_specific": 11, |
| "top_tfs": [ |
| "DMBX1", |
| "GCM2", |
| "THAP5", |
| "ZNF506", |
| "HES7", |
| "TTF1", |
| "ZNF865", |
| "ATOH8", |
| "ZNF773", |
| "ZBTB16", |
| "ZNF75A" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.233, |
| 1.969, |
| 1.852, |
| 1.847, |
| 1.705, |
| 1.649 |
| ] |
| }, |
| "Neftel_NPC1": { |
| "n_specific": 5, |
| "top_tfs": [ |
| "ZNF165", |
| "GATA2", |
| "TFAP2B", |
| "PLAGL1", |
| "ZNF224" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 1.819, |
| 1.581 |
| ] |
| }, |
| "Neftel_NPC2": { |
| "n_specific": 58, |
| "top_tfs": [ |
| "ZNF491", |
| "BARHL1", |
| "ISL1", |
| "SP9", |
| "BHLHE22", |
| "SCRT1", |
| "NKX2-1", |
| "NHLH2", |
| "NEUROD6", |
| "NEUROD4", |
| "SIM1", |
| "EMX1", |
| "NEUROD2", |
| "ZNF550", |
| "JRKL", |
| "ZNF668", |
| "ZNF334", |
| "PRRX1", |
| "ZNF691", |
| "ZNF471" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.23, |
| 2.178, |
| 2.154, |
| 2.153, |
| 2.141 |
| ] |
| }, |
| "Neftel_OPC": { |
| "n_specific": 308, |
| "top_tfs": [ |
| "PAX7", |
| "DUX4", |
| "ZNF488", |
| "DMRT2", |
| "ZNF679", |
| "POU2AF1", |
| "TPRX1", |
| "ZNF469", |
| "ZNF730", |
| "MAX", |
| "ZNF300", |
| "ZNF2", |
| "ZNF592", |
| "PREB", |
| "BNC2", |
| "MEF2A", |
| "ZFP82", |
| "FOS", |
| "KDM2A", |
| "ZIC2" |
| ], |
| "top_scores": [ |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.236, |
| 2.228, |
| 2.177, |
| 2.143, |
| 2.126, |
| 2.116, |
| 2.1, |
| 2.1, |
| 2.082, |
| 2.081, |
| 2.076, |
| 2.067, |
| 2.049 |
| ] |
| } |
| }, |
| "module_enrichment": { |
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| "CCDC9B", |
| "ZNF750", |
| "KCNH8", |
| "ADGRB3", |
| "FBXL7", |
| "TENM2", |
| "TEX49", |
| "PHF21A", |
| "ZIC1", |
| "FRMD5", |
| "DELE1", |
| "SCEL", |
| "WDR49", |
| "SLC5A11", |
| "EBF3", |
| "RFX4", |
| "DTHD1", |
| "OR2H2", |
| "LDB3", |
| "DOCK5", |
| "GRK2", |
| "LRRC74A", |
| "C1orf87", |
| "RIMS1", |
| "SH3BGRL2", |
| "PLPPR1", |
| "MOG", |
| "APOBEC2", |
| "NIN", |
| "PRKN", |
| "MMD2", |
| "PIK3R6", |
| "GRIN2C", |
| "TIMP4" |
| ], |
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| }, |
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| }, |
| "Neftel_OPC_SOX10": { |
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| { |
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| { |
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| { |
| "term": "Regulation Of Plasma Membrane Repair (GO:1905684)", |
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| }, |
| { |
| "term": "Positive Regulation Of Response To External Stimulus (GO:0032103)", |
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| "kegg": { |
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| { |
| "term": "Salmonella infection", |
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| }, |
| "enrichment_status": "ok", |
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| }, |
| "module_enrichment_gseapy": { |
| "settings": { |
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| "fdr_cutoff": 0.05, |
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| "canonical_modules": "all subtype canonical TFs present in subtype TF ranking" |
| }, |
| "input_inspection": { |
| "n_gene_universe": 18716, |
| "canonical_tfs_tested_per_subtype": { |
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| } |
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| "summary": { |
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| "genes": [ |
| "PTPRD", |
| "NRG1", |
| "VEGFA", |
| "S100A10" |
| ] |
| } |
| ] |
| }, |
| "kegg": { |
| "library": "KEGG_2021_Human", |
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| { |
| "term": "ECM-receptor interaction", |
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| "genes": [ |
| "COL1A1", |
| "COL1A2", |
| "SPP1", |
| "CD36" |
| ] |
| }, |
| { |
| "term": "AGE-RAGE signaling pathway in diabetic complications", |
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| "p_value": 0.00014631030835113933, |
| "odds_ratio": 16.8207, |
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| "genes": [ |
| "COL1A1", |
| "COL3A1", |
| "COL1A2", |
| "VEGFA" |
| ] |
| }, |
| { |
| "term": "Platelet activation", |
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| "genes": [ |
| "COL1A1", |
| "COL3A1", |
| "FCER1G", |
| "COL1A2" |
| ] |
| }, |
| { |
| "term": "Relaxin signaling pathway", |
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| "odds_ratio": 12.8981, |
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| "genes": [ |
| "COL1A1", |
| "COL3A1", |
| "COL1A2", |
| "VEGFA" |
| ] |
| }, |
| { |
| "term": "Asthma", |
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| "odds_ratio": 29.8718, |
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| "genes": [ |
| "FCER1G", |
| "HLA-DRA" |
| ] |
| } |
| ] |
| }, |
| "enrichment_status": "ok", |
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| "in_top20": false, |
| "in_top50": false, |
| "in_top100": false |
| } |
| }, |
| "OLIG2": { |
| "module": { |
| "n_targets": 50, |
| "targets": [ |
| "PLPPR1", |
| "KNG1", |
| "DDT", |
| "VWF", |
| "DAAM2", |
| "ST8SIA5", |
| "ERG", |
| "GRID1", |
| "TEX49", |
| "ANXA10", |
| "NUGGC", |
| "WNT9B", |
| "OTOP1", |
| "NACC2", |
| "HBA1", |
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| "CCDC9B", |
| "SCEL", |
| "GLYAT", |
| "SLC6A1", |
| "ANO4", |
| "PHF21A", |
| "ALDOB", |
| "KLHL3", |
| "LDB3", |
| "PADI4", |
| "ZNF679", |
| "GALNT17", |
| "LRRC72", |
| "HAPLN4", |
| "POTEI", |
| "SPATA3", |
| "TMTC1", |
| "C21orf62", |
| "HAPLN2", |
| "NR1I3", |
| "C2orf78", |
| "NPPA", |
| "MDFIC2", |
| "GRM6", |
| "PIMREG", |
| "CELA3B", |
| "CDH17", |
| "CPLX2", |
| "BHMT", |
| "CARMIL3", |
| "ACER1", |
| "TERB1", |
| "FGFR2", |
| "CA5A" |
| ], |
| "top_k_targets": 50 |
| }, |
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| "library": "GO_Biological_Process_2023", |
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| }, |
| "kegg": { |
| "library": "KEGG_2021_Human", |
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| { |
| "term": "African trypanosomiasis", |
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| "genes": [ |
| "NPPA", |
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| "KNG1" |
| ] |
| } |
| ] |
| }, |
| "enrichment_status": "ok", |
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| } |
| }, |
| "ASCL1": { |
| "module": { |
| "n_targets": 50, |
| "targets": [ |
| "DUX4", |
| "C2orf78", |
| "GAB4", |
| "DCAF8L2", |
| "ZNF679", |
| "SPATA3", |
| "MDFIC2", |
| "MS4A5", |
| "OTOP1", |
| "TENT5D", |
| "CELA3B", |
| "KCNU1", |
| "OR5V1", |
| "OR4N2", |
| "APOL5", |
| "LRRC72", |
| "C11orf42", |
| "TGM6", |
| "TTLL2", |
| "ACP4", |
| "TEX49", |
| "GFRAL", |
| "ANXA10", |
| "NLRP8", |
| "TPRX1", |
| "C1orf141", |
| "OTP", |
| "TMPRSS15", |
| "C1orf185", |
| "INHBC", |
| "WNT9B", |
| "NLRP5", |
| "C3orf84", |
| "MARCOL", |
| "NLRP9", |
| "FBXO39", |
| "TOPAZ1", |
| "DEFB131B", |
| "SPDYE6", |
| "C1orf100", |
| "ACTL8", |
| "WEE2", |
| "TEX52", |
| "MOBP", |
| "CCDC83", |
| "TEKT1", |
| "DAZL", |
| "PKHD1", |
| "C1orf87", |
| "GML" |
| ], |
| "top_k_targets": 50 |
| }, |
| "go_bp": { |
| "library": "GO_Biological_Process_2023", |
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| }, |
| "kegg": { |
| "library": "KEGG_2021_Human", |
| "n_significant_terms": 0, |
| "top_terms": [] |
| }, |
| "enrichment_status": "ok", |
| "recovery_flags": { |
| "in_top20": false, |
| "in_top50": false, |
| "in_top100": false |
| } |
| }, |
| "NKX2-2": { |
| "module": { |
| "n_targets": 50, |
| "targets": [ |
| "SLC6A1", |
| "MYBPC3", |
| "PLIN5", |
| "ANO2", |
| "DAAM2", |
| "SOX11", |
| "JPH2", |
| "SLCO1A2", |
| "GRM3", |
| "FGF1", |
| "HEPACAM", |
| "ARMH1", |
| "THSD4", |
| "MOBP", |
| "HECW2", |
| "ERG", |
| "CCDC9B", |
| "ZNF750", |
| "KCNH8", |
| "ADGRB3", |
| "FBXL7", |
| "TENM2", |
| "TEX49", |
| "PHF21A", |
| "ZIC1", |
| "FRMD5", |
| "DELE1", |
| "SCEL", |
| "WDR49", |
| "SLC5A11", |
| "EBF3", |
| "RFX4", |
| "DTHD1", |
| "OR2H2", |
| "LDB3", |
| "DOCK5", |
| "GRK2", |
| "LRRC74A", |
| "C1orf87", |
| "RIMS1", |
| "SH3BGRL2", |
| "PLPPR1", |
| "MOG", |
| "APOBEC2", |
| "NIN", |
| "PRKN", |
| "MMD2", |
| "PIK3R6", |
| "GRIN2C", |
| "TIMP4" |
| ], |
| "top_k_targets": 50 |
| }, |
| "go_bp": { |
| "library": "GO_Biological_Process_2023", |
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| }, |
| "kegg": { |
| "library": "KEGG_2021_Human", |
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| }, |
| "enrichment_status": "ok", |
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| "in_top20": false, |
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| "in_top100": false |
| } |
| }, |
| "SOX10": { |
| "module": { |
| "n_targets": 50, |
| "targets": [ |
| "S100A11", |
| "TNFRSF12A", |
| "CSF2RA", |
| "OLFML3", |
| "CD14", |
| "FRMD4A", |
| "COL1A2", |
| "VIM", |
| "SPP1", |
| "PDE4B", |
| "ENPP2", |
| "HMOX1", |
| "LGALS1", |
| "SELENOP", |
| "NPC2", |
| "TSPAN4", |
| "MDK", |
| "ENTPD1", |
| "LY96", |
| "SULF2", |
| "JDP2", |
| "BASP1", |
| "PMP22", |
| "PHACTR1", |
| "ABCA1", |
| "UPP1", |
| "AIM2", |
| "EVA1B", |
| "IER3", |
| "S100A10", |
| "ENPP1", |
| "TIMP1", |
| "PKIB", |
| "CYBA", |
| "KCNMA1", |
| "CLIC4", |
| "UBE2C", |
| "PXDC1", |
| "ASS1", |
| "GPRC5C", |
| "PAK1", |
| "A1BG", |
| "AIG1", |
| "CD68", |
| "LAT2", |
| "RCN3", |
| "APBB1IP", |
| "ARL4C", |
| "ANXA2", |
| "ADAMTSL4" |
| ], |
| "top_k_targets": 50 |
| }, |
| "go_bp": { |
| "library": "GO_Biological_Process_2023", |
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| "top_terms": [ |
| { |
| "term": "Cellular Response To Molecule Of Bacterial Origin (GO:0071219)", |
| "adjusted_p_value": 0.005998085625857357, |
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| "genes": [ |
| "PDE4B", |
| "LY96", |
| "CD14", |
| "VIM", |
| "CD68" |
| ] |
| }, |
| { |
| "term": "Cellular Response To Lipopolysaccharide (GO:0071222)", |
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| "genes": [ |
| "PDE4B", |
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| "CD14", |
| "VIM", |
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| ] |
| }, |
| { |
| "term": "Cellular Response To Lipid (GO:0071396)", |
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| "genes": [ |
| "SPP1", |
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| "VIM", |
| "CD68" |
| ] |
| }, |
| { |
| "term": "Regulation Of Plasma Membrane Repair (GO:1905684)", |
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| "p_value": 6.958486114747632e-05, |
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| "genes": [ |
| "ANXA2", |
| "S100A10" |
| ] |
| }, |
| { |
| "term": "Positive Regulation Of Response To External Stimulus (GO:0032103)", |
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| "genes": [ |
| "LGALS1", |
| "AIM2", |
| "MDK", |
| "LY96", |
| "CYBA" |
| ] |
| } |
| ] |
| }, |
| "kegg": { |
| "library": "KEGG_2021_Human", |
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| { |
| "term": "Pyrimidine metabolism", |
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| "genes": [ |
| "ENTPD1", |
| "ENPP1", |
| "UPP1" |
| ] |
| }, |
| { |
| "term": "Salmonella infection", |
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| "odds_ratio": 8.4239, |
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| "genes": [ |
| "PAK1", |
| "ANXA2", |
| "LY96", |
| "CD14", |
| "S100A10" |
| ] |
| } |
| ] |
| }, |
| "enrichment_status": "ok", |
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| } |
| } |
| } |
| }, |
| "interesting_findings": [ |
| { |
| "subtype": "Neftel_NPC1", |
| "tf": "NEUROD1", |
| "source": "GO_BP", |
| "term": "Golgi Organization (GO:0007030)", |
| "adjusted_p_value": 2.996675124695898e-21, |
| "combined_score": 4125.2916 |
| }, |
| { |
| "subtype": "Neftel_NPC1", |
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| "source": "GO_BP", |
| "term": "Golgi Organization (GO:0007030)", |
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| "combined_score": 4125.2916 |
| }, |
| { |
| "subtype": "Neftel_NPC2", |
| "tf": "NEUROD1", |
| "source": "GO_BP", |
| "term": "Golgi Organization (GO:0007030)", |
| "adjusted_p_value": 2.996675124695898e-21, |
| "combined_score": 4125.2916 |
| }, |
| { |
| "subtype": "Neftel_NPC2", |
| "tf": "NEUROG2", |
| "source": "GO_BP", |
| "term": "Golgi Organization (GO:0007030)", |
| "adjusted_p_value": 2.996675124695898e-21, |
| "combined_score": 4125.2916 |
| }, |
| { |
| "subtype": "Neftel_NPC1", |
| "tf": "NEUROD1", |
| "source": "GO_BP", |
| "term": "Spindle Assembly (GO:0051225)", |
| "adjusted_p_value": 5.277583681741211e-21, |
| "combined_score": 5822.877 |
| }, |
| { |
| "subtype": "Neftel_NPC1", |
| "tf": "NEUROG2", |
| "source": "GO_BP", |
| "term": "Spindle Assembly (GO:0051225)", |
| "adjusted_p_value": 5.277583681741211e-21, |
| "combined_score": 5822.877 |
| }, |
| { |
| "subtype": "Neftel_NPC2", |
| "tf": "NEUROD1", |
| "source": "GO_BP", |
| "term": "Spindle Assembly (GO:0051225)", |
| "adjusted_p_value": 5.277583681741211e-21, |
| "combined_score": 5822.877 |
| }, |
| { |
| "subtype": "Neftel_NPC2", |
| "tf": "NEUROG2", |
| "source": "GO_BP", |
| "term": "Spindle Assembly (GO:0051225)", |
| "adjusted_p_value": 5.277583681741211e-21, |
| "combined_score": 5822.877 |
| } |
| ] |
| }, |
| "input_inspection": { |
| "n_total_edges": 1374450, |
| "n_unique_celltypes": 17, |
| "subtypes": [ |
| "Neftel_AC", |
| "Neftel_MES1", |
| "Neftel_MES2", |
| "Neftel_NPC1", |
| "Neftel_NPC2", |
| "Neftel_OPC" |
| ], |
| "subtype_edge_summary": { |
| "Neftel_AC": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3494, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| }, |
| "Neftel_MES1": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3456, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| }, |
| "Neftel_MES2": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3454, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| }, |
| "Neftel_NPC1": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3493, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| }, |
| "Neftel_NPC2": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3474, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| }, |
| "Neftel_OPC": { |
| "n_edges": 80850, |
| "n_regulators": 1617, |
| "n_targets": 3482, |
| "score_min": 0.0, |
| "score_max": 1.0 |
| } |
| }, |
| "canonical_tfs_per_subtype": { |
| "Neftel_AC": 5, |
| "Neftel_MES1": 6, |
| "Neftel_MES2": 6, |
| "Neftel_NPC1": 5, |
| "Neftel_NPC2": 5, |
| "Neftel_OPC": 5 |
| } |
| }, |
| "computation_logic": { |
| "canonical_recovery": "TFs are ranked by mean outgoing edge score per subtype; canonical recovery counts canonical TFs in score-ranked top-N.", |
| "specificity": "For each TF, activity is z-scored across Neftel subtypes; TFs with z>1.5 in a subtype are subtype-specific candidates.", |
| "module_enrichment": "For each subtype canonical TF present in subtype ranking, take top-50 non-self targets and run gseapy Enrichr for GO BP and KEGG; retain terms with FDR < 0.05 and record whether each TF is recovered in top-20/top-50/top-100." |
| }, |
| "subtypes": [ |
| "Neftel_AC", |
| "Neftel_MES1", |
| "Neftel_MES2", |
| "Neftel_NPC1", |
| "Neftel_NPC2", |
| "Neftel_OPC" |
| ], |
| "neftel_canonical": { |
| "Neftel_MES1": [ |
| "CEBPB", |
| "RUNX1", |
| "RUNX2", |
| "FOSL2", |
| "BHLHE40", |
| "WWTR1" |
| ], |
| "Neftel_MES2": [ |
| "CEBPB", |
| "RUNX1", |
| "RUNX2", |
| "FOSL2", |
| "BHLHE40", |
| "WWTR1" |
| ], |
| "Neftel_OPC": [ |
| "SOX2", |
| "OLIG2", |
| "ASCL1", |
| "NKX2-2", |
| "SOX10" |
| ], |
| "Neftel_AC": [ |
| "SOX9", |
| "NFIA", |
| "NFIB", |
| "HES1", |
| "HEY1" |
| ], |
| "Neftel_NPC1": [ |
| "SOX4", |
| "SOX11", |
| "DCX", |
| "NEUROD1", |
| "NEUROG2" |
| ], |
| "Neftel_NPC2": [ |
| "SOX4", |
| "SOX11", |
| "DCX", |
| "NEUROD1", |
| "NEUROG2" |
| ] |
| } |
| } |
