diff --git "a/results/experiments/exp_5/results.json" "b/results/experiments/exp_5/results.json" --- "a/results/experiments/exp_5/results.json" +++ "b/results/experiments/exp_5/results.json" @@ -2,16 +2,18 @@ "canonical_recovery": { "scregnet_top20": { "Neftel_AC": { - "recovered": 0, + "recovered": 1, "total": 5, - "fraction": 0.0, - "recovered_names": [], + "fraction": 0.2, + "recovered_names": [ + "NFIB" + ], "canonical_ranks": { - "SOX9": 846, - "NFIA": 585, - "NFIB": 586, - "HES1": 325, - "HEY1": 333 + "SOX9": 65, + "NFIA": 517, + "NFIB": 6, + "HES1": 855, + "HEY1": 135 }, "top_n": 20 }, @@ -21,11 +23,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 33, + "RUNX2": 260, + "FOSL2": 169, + "BHLHE40": 435, "WWTR1": -1 }, "top_n": 20 @@ -36,11 +38,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 51, + "RUNX2": 291, + "FOSL2": 158, + "BHLHE40": 428, "WWTR1": -1 }, "top_n": 20 @@ -51,11 +53,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX4": 841, - "SOX11": 830, + "SOX4": 305, + "SOX11": 774, "DCX": -1, - "NEUROD1": 569, - "NEUROG2": 574 + "NEUROD1": 1578, + "NEUROG2": 1437 }, "top_n": 20 }, @@ -65,11 +67,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX4": 841, - "SOX11": 830, + "SOX4": 292, + "SOX11": 763, "DCX": -1, - "NEUROD1": 569, - "NEUROG2": 574 + "NEUROD1": 1572, + "NEUROG2": 1506 }, "top_n": 20 }, @@ -79,41 +81,45 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX2": 837, - "OLIG2": 647, - "ASCL1": 30, - "NKX2-2": 603, - "SOX10": 829 + "SOX2": 806, + "OLIG2": 913, + "ASCL1": 558, + "NKX2-2": 968, + "SOX10": 701 }, "top_n": 20 } }, "scregnet_top50": { "Neftel_AC": { - "recovered": 0, + "recovered": 1, "total": 5, - "fraction": 0.0, - "recovered_names": [], + "fraction": 0.2, + "recovered_names": [ + "NFIB" + ], "canonical_ranks": { - "SOX9": 846, - "NFIA": 585, - "NFIB": 586, - "HES1": 325, - "HEY1": 333 + "SOX9": 65, + "NFIA": 517, + "NFIB": 6, + "HES1": 855, + "HEY1": 135 }, "top_n": 50 }, "Neftel_MES1": { - "recovered": 0, + "recovered": 1, "total": 6, - "fraction": 0.0, - "recovered_names": [], + "fraction": 0.1667, + "recovered_names": [ + "RUNX1" + ], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 33, + "RUNX2": 260, + "FOSL2": 169, + "BHLHE40": 435, "WWTR1": -1 }, "top_n": 50 @@ -124,11 +130,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 51, + "RUNX2": 291, + "FOSL2": 158, + "BHLHE40": 428, "WWTR1": -1 }, "top_n": 50 @@ -139,11 +145,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX4": 841, - "SOX11": 830, + "SOX4": 305, + "SOX11": 774, "DCX": -1, - "NEUROD1": 569, - "NEUROG2": 574 + "NEUROD1": 1578, + "NEUROG2": 1437 }, "top_n": 50 }, @@ -153,78 +159,77 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX4": 841, - "SOX11": 830, + "SOX4": 292, + "SOX11": 763, "DCX": -1, - "NEUROD1": 569, - "NEUROG2": 574 + "NEUROD1": 1572, + "NEUROG2": 1506 }, "top_n": 50 }, "Neftel_OPC": { - "recovered": 1, + "recovered": 0, "total": 5, - "fraction": 0.2, - "recovered_names": [ - "ASCL1" - ], + "fraction": 0.0, + "recovered_names": [], "canonical_ranks": { - "SOX2": 837, - "OLIG2": 647, - "ASCL1": 30, - "NKX2-2": 603, - "SOX10": 829 + "SOX2": 806, + "OLIG2": 913, + "ASCL1": 558, + "NKX2-2": 968, + "SOX10": 701 }, "top_n": 50 } }, "scregnet_top100": { "Neftel_AC": { - "recovered": 0, + "recovered": 2, "total": 5, - "fraction": 0.0, - "recovered_names": [], + "fraction": 0.4, + "recovered_names": [ + "SOX9", + "NFIB" + ], "canonical_ranks": { - "SOX9": 846, - "NFIA": 585, - "NFIB": 586, - "HES1": 325, - "HEY1": 333 + "SOX9": 65, + "NFIA": 517, + "NFIB": 6, + "HES1": 855, + "HEY1": 135 }, "top_n": 100 }, "Neftel_MES1": { - "recovered": 2, + "recovered": 1, "total": 6, - "fraction": 0.3333, + "fraction": 0.1667, "recovered_names": [ - "CEBPB", - "BHLHE40" + "RUNX1" ], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 33, + "RUNX2": 260, + "FOSL2": 169, + "BHLHE40": 435, "WWTR1": -1 }, "top_n": 100 }, "Neftel_MES2": { - "recovered": 2, + "recovered": 1, "total": 6, - "fraction": 0.3333, + "fraction": 0.1667, "recovered_names": [ - "CEBPB", - "BHLHE40" + "RUNX1" ], "canonical_ranks": { - "CEBPB": 89, - "RUNX1": 774, - "RUNX2": 775, - "FOSL2": 228, - "BHLHE40": 68, + "CEBPB": 1000, + "RUNX1": 51, + "RUNX2": 291, + "FOSL2": 158, + "BHLHE40": 428, "WWTR1": -1 }, "top_n": 100 @@ -235,11 +240,11 @@ "fraction": 0.0, "recovered_names": [], "canonical_ranks": { - "SOX4": 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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", + "tf": "NEUROG2", + "source": "GO_BP", + "term": "Golgi Organization (GO:0007030)", + "adjusted_p_value": 2.996675124695898e-21, + "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, + 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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",