From 6ebf1003ed5146d37ef0b6935e75adfee365cf70 Mon Sep 17 00:00:00 2001 From: nanglo123 Date: Thu, 25 Apr 2024 10:07:39 -0400 Subject: [PATCH] Add more comments to modeling regnet file and fix minor bug, rerun script to regenerate qual regnet amr --- mira/modeling/amr/regnet.py | 6 +- .../regnet_amr_sbml/Apoptosis.json | 42 +- .../regnet_amr_sbml/BIOMD0000000562.json | 4 +- .../regnet_amr_sbml/Coagulation-pathway.json | 178 ++-- .../regnet_amr_sbml/ER_Stress.json | 308 +++--- .../regnet_amr_sbml/ETC.json | 190 ++-- .../regnet_amr_sbml/E_protein.json | 36 +- .../regnet_amr_sbml/HMOX1_Pathway.json | 284 +++--- .../regnet_amr_sbml/IFN-lambda.json | 18 +- .../regnet_amr_sbml/Interferon1.json | 220 ++-- .../regnet_amr_sbml/JNK_pathway.json | 10 +- .../regnet_amr_sbml/Kynurenine_pathway.json | 412 ++++---- .../regnet_amr_sbml/NLRP3_Activation.json | 94 +- .../regnet_amr_sbml/Nsp14.json | 942 +++++++++--------- .../regnet_amr_sbml/Nsp4_Nsp6.json | 24 +- .../regnet_amr_sbml/Nsp9_protein.json | 272 ++--- .../regnet_amr_sbml/Orf10_Cul2_pathway.json | 120 +-- .../regnet_amr_sbml/Orf3a.json | 44 +- .../regnet_amr_sbml/PAMP_signaling.json | 104 +- .../Pyrimidine_deprivation.json | 154 +-- .../RTC-and-transcription.json | 16 +- .../regnet_amr_sbml/Renin_angiotensin.json | 178 ++-- .../regnet_amr_sbml/TGFB_pathway.json | 34 +- .../Virus_replication_cycle.json | 320 +++--- 24 files changed, 2006 insertions(+), 2004 deletions(-) diff --git a/mira/modeling/amr/regnet.py b/mira/modeling/amr/regnet.py index 021c694d..6dcdb65e 100644 --- a/mira/modeling/amr/regnet.py +++ b/mira/modeling/amr/regnet.py @@ -132,6 +132,7 @@ def __init__(self, model: Model): # Possibilities are: # - ControlledReplication / GroupedControlledProduction # - ControlledDegradation / GroupedControlledDegradation + # - ControlledProduction if the control and produced concept are not the same else: # If we have multiple controls then the thing that replicates # is both a control and a produced variable. @@ -146,7 +147,7 @@ def __init__(self, model: Model): # There is one corner case where both controllers are also # the same as the produced variable, in which case. if not indep_ctrl: - indep_ctrl = {transition.consumed[0].key} + indep_ctrl = {transition.produced[0].key} for controller in indep_ctrl: self.create_edge( @@ -163,7 +164,7 @@ def __init__(self, model: Model): transition.consumed[0].key } # There is one corner case where both controllers are also - # the same as the produced variable, in which case. + # the same as the consumed variable, in which case. if not indep_ctrl: indep_ctrl = {transition.consumed[0].key} @@ -177,6 +178,7 @@ def __init__(self, model: Model): edge_id += 1 else: + # ControlledProduction if produced and controller are not the same # ControlledDegradation target = vmap[ transition.consumed[0].key diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json index 49e808ff..8eca998f 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Apoptosis.json @@ -411,13 +411,13 @@ }, { "id": "t7", - "source": "TRADD", + "source": "FADD", "target": "TRADD/FADD_complex", "sign": true }, { "id": "t8", - "source": "FADD", + "source": "TRADD", "target": "TRADD/FADD_complex", "sign": true }, @@ -429,7 +429,7 @@ }, { "id": "t10", - "source": "AKT1", + "source": "CASP9_cell", "target": "Apoptosome_complex", "sign": true }, @@ -441,7 +441,7 @@ }, { "id": "t12", - "source": "CASP9_cell", + "source": "AKT1", "target": "Apoptosome_complex", "sign": true }, @@ -465,7 +465,7 @@ }, { "id": "t16", - "source": "BID", + "source": "BCL2/MCL1/BCL2L1_complex", "target": "BAX", "sign": true }, @@ -477,7 +477,7 @@ }, { "id": "t18", - "source": "BCL2/MCL1/BCL2L1_complex", + "source": "BID", "target": "BAX", "sign": true }, @@ -489,13 +489,13 @@ }, { "id": "t20", - "source": "BAX", + "source": "MAPK14", "target": "CYCS", "sign": true }, { "id": "t21", - "source": "MAPK14", + "source": "BAX", "target": "CYCS", "sign": true }, @@ -525,79 +525,79 @@ }, { "id": "t26", - "source": "CASP9_cell_active", + "source": "CASP8", "target": "CASP3", "sign": true }, { "id": "t27", - "source": "CASP8", + "source": "CASP9_cell_active", "target": "CASP3", "sign": true }, { "id": "t28", - "source": "TRADD/FADD_complex", + "source": "FADD", "target": "CASP8", "sign": true }, { "id": "t29", - "source": "Orf3a", + "source": "TRADD/FADD_complex", "target": "CASP8", "sign": true }, { "id": "t30", - "source": "FADD", + "source": "Orf3a", "target": "CASP8", "sign": true }, { "id": "t31", - "source": "CASP3", + "source": "N", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t32", - "source": "N", + "source": "S", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t33", - "source": "Orf8a", + "source": "Orf9b", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t34", - "source": "Orf9b", + "source": "CASP3", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t35", - "source": "Orf3b", + "source": "CASP7", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t36", - "source": "Orf6", + "source": "Orf8a", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t37", - "source": "S", + "source": "Orf3b", "target": "Apoptosis_phenotype", "sign": true }, { "id": "t38", - "source": "CASP7", + "source": "Orf6", "target": "Apoptosis_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json index 758c9803..94184185 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/BIOMD0000000562.json @@ -423,13 +423,13 @@ }, { "id": "t29", - "source": "egfr", + "source": "ph", "target": "sos", "sign": true }, { "id": "t30", - "source": "ph", + "source": "egfr", "target": "sos", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Coagulation-pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Coagulation-pathway.json index 128593bc..5154e284 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Coagulation-pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Coagulation-pathway.json @@ -1461,13 +1461,13 @@ "edges": [ { "id": "t1", - "source": "KLKB1", + "source": "KNG1", "target": "KNG1:KLKB1_complex", "sign": true }, { "id": "t2", - "source": "KNG1", + "source": "KLKB1", "target": "KNG1:KLKB1_complex", "sign": true }, @@ -1503,13 +1503,13 @@ }, { "id": "t8", - "source": "PLAT_blood", + "source": "SERPINE1", "target": "PLAT:SERPINE1_complex", "sign": true }, { "id": "t9", - "source": "SERPINE1", + "source": "PLAT_blood", "target": "PLAT:SERPINE1_complex", "sign": true }, @@ -1539,13 +1539,13 @@ }, { "id": "t14", - "source": "Thrombomodulin", + "source": "Thrombin_blood_active", "target": "Thrombin:Thrombomodulin_complex", "sign": true }, { "id": "t15", - "source": "Thrombin_blood_active", + "source": "Thrombomodulin", "target": "Thrombin:Thrombomodulin_complex", "sign": true }, @@ -1575,25 +1575,25 @@ }, { "id": "t20", - "source": "C5b:C6_complex", + "source": "C7", "target": "C5b:C6:C7_complex", "sign": true }, { "id": "t21", - "source": "C7", + "source": "C5b:C6_complex", "target": "C5b:C6:C7_complex", "sign": true }, { "id": "t22", - "source": "C9", + "source": "SARS-CoV-2 infection_phenotype", "target": "C5b-9_complex_endothelium, vascular", "sign": true }, { "id": "t23", - "source": "SARS-CoV-2 infection_phenotype", + "source": "C9", "target": "C5b-9_complex_endothelium, vascular", "sign": true }, @@ -1605,25 +1605,25 @@ }, { "id": "t25", - "source": "C6", + "source": "C5b", "target": "C5b:C6_complex", "sign": true }, { "id": "t26", - "source": "C5b", + "source": "C6", "target": "C5b:C6_complex", "sign": true }, { "id": "t27", - "source": "C4b", + "source": "C2a", "target": "C2a:C4b_complex", "sign": true }, { "id": "t28", - "source": "C2a", + "source": "C4b", "target": "C2a:C4b_complex", "sign": true }, @@ -1641,19 +1641,19 @@ }, { "id": "t31", - "source": "SARS-CoV-2 infection_phenotype", + "source": "SERPINF2", "target": "SERPINF2:Plasmin_complex", "sign": true }, { "id": "t32", - "source": "Plasmin", + "source": "SARS-CoV-2 infection_phenotype", "target": "SERPINF2:Plasmin_complex", "sign": true }, { "id": "t33", - "source": "SERPINF2", + "source": "Plasmin", "target": "SERPINF2:Plasmin_complex", "sign": true }, @@ -1671,25 +1671,25 @@ }, { "id": "t36", - "source": "VWF", + "source": "GP6:alpha2:beta1_complex", "target": "GP6:alpha2beta1:VWF_complex", "sign": true }, { "id": "t37", - "source": "GP6:alpha2:beta1_complex", + "source": "VWF", "target": "GP6:alpha2beta1:VWF_complex", "sign": true }, { "id": "t38", - "source": "GP6", + "source": "ITGA2:ITGAB1_complex", "target": "GP6:alpha2:beta1_complex", "sign": true }, { "id": "t39", - "source": "ITGA2:ITGAB1_complex", + "source": "GP6", "target": "GP6:alpha2:beta1_complex", "sign": true }, @@ -1701,97 +1701,97 @@ }, { "id": "t41", - "source": "F12", + "source": "KLKB1", "target": "F12a", "sign": true }, { "id": "t42", - "source": "KLKB1", + "source": "F12", "target": "F12a", "sign": true }, { "id": "t43", - "source": "F8", + "source": "ACE", "target": "Small peptide", "sign": true }, { "id": "t44", - "source": "ACE", + "source": "F10", "target": "Small peptide", "sign": true }, { "id": "t45", - "source": "Antithrombin", + "source": "F12", "target": "Small peptide", "sign": true }, { "id": "t46", - "source": "PROC", + "source": "Bradykinin", "target": "Small peptide", "sign": true }, { "id": "t47", - "source": "F10", + "source": "F8", "target": "Small peptide", "sign": true }, { "id": "t48", - "source": "F12", + "source": "KLKB1", "target": "Small peptide", "sign": true }, { "id": "t49", - "source": "KLKB1", + "source": "PROC", "target": "Small peptide", "sign": true }, { "id": "t50", - "source": "F9a", + "source": "Thrombin_blood_active", "target": "Small peptide", "sign": true }, { "id": "t51", - "source": "Thrombin_blood_active", + "source": "Antithrombin", "target": "Small peptide", "sign": true }, { "id": "t52", - "source": "Bradykinin", + "source": "F9a", "target": "Small peptide", "sign": true }, { "id": "t53", - "source": "Thrombin_blood_active", + "source": "F12a", "target": "F11", "sign": true }, { "id": "t54", - "source": "F12a", + "source": "Thrombin_blood_active", "target": "F11", "sign": true }, { "id": "t55", - "source": "Thrombin_blood_active", + "source": "F12a", "target": "F11a", "sign": true }, { "id": "t56", - "source": "F12a", + "source": "Thrombin_blood_active", "target": "F11a", "sign": true }, @@ -1815,13 +1815,13 @@ }, { "id": "t60", - "source": "F10", + "source": "Antithrombin", "target": "F10a", "sign": true }, { "id": "t61", - "source": "Antithrombin", + "source": "F10", "target": "F10a", "sign": true }, @@ -1869,19 +1869,19 @@ }, { "id": "t69", - "source": "SARS-CoV-2 infection_phenotype", + "source": "ACE", "target": "angiotensin II_simple_molecule", "sign": true }, { "id": "t70", - "source": "ACE", + "source": "angiotensin I_simple_molecule", "target": "angiotensin II_simple_molecule", "sign": true }, { "id": "t71", - "source": "angiotensin I_simple_molecule", + "source": "SARS-CoV-2 infection_phenotype", "target": "angiotensin II_simple_molecule", "sign": true }, @@ -1923,13 +1923,13 @@ }, { "id": "t78", - "source": "Thrombin:Thrombomodulin_complex", + "source": "PROC", "target": "F5a", "sign": true }, { "id": "t79", - "source": "PROC", + "source": "Thrombin:Thrombomodulin_complex", "target": "F5a", "sign": true }, @@ -1965,19 +1965,19 @@ }, { "id": "t85", - "source": "Fibrin polymer", + "source": "Plasmin", "target": "D-dimer", "sign": true }, { "id": "t86", - "source": "Plasmin", + "source": "TAFI", "target": "D-dimer", "sign": true }, { "id": "t87", - "source": "TAFI", + "source": "Fibrin polymer", "target": "D-dimer", "sign": true }, @@ -1989,43 +1989,43 @@ }, { "id": "t89", - "source": "PLAU", + "source": "F11a", "target": "Plasmin", "sign": true }, { "id": "t90", - "source": "F11a", + "source": "Plasminogen", "target": "Plasmin", "sign": true }, { "id": "t91", - "source": "Plasminogen", + "source": "PLAT_blood_active", "target": "Plasmin", "sign": true }, { "id": "t92", - "source": "KLKB1", + "source": "PLAU", "target": "Plasmin", "sign": true }, { "id": "t93", - "source": "PLAT_blood_active", + "source": "KLKB1", "target": "Plasmin", "sign": true }, { "id": "t94", - "source": "PROC", + "source": "Bradykinin", "target": "PLAT_blood_active", "sign": true }, { "id": "t95", - "source": "angiotensin I-7_simple_molecule", + "source": "SERPINE1", "target": "PLAT_blood_active", "sign": true }, @@ -2037,25 +2037,25 @@ }, { "id": "t97", - "source": "PLAT_blood", + "source": "angiotensin I-7_simple_molecule", "target": "PLAT_blood_active", "sign": true }, { "id": "t98", - "source": "SERPINE1", + "source": "PLAT_blood", "target": "PLAT_blood_active", "sign": true }, { "id": "t99", - "source": "Bradykinin", + "source": "PROC", "target": "PLAT_blood_active", "sign": true }, { "id": "t100", - "source": "AGTR1_blood", + "source": "angiotensin II_simple_molecule", "target": "SERPINE1", "sign": true }, @@ -2067,19 +2067,19 @@ }, { "id": "t102", - "source": "angiotensin II_simple_molecule", + "source": "IL6", "target": "SERPINE1", "sign": true }, { "id": "t103", - "source": "aldosterone_simple_molecule_blood", + "source": "AGTR1_blood", "target": "SERPINE1", "sign": true }, { "id": "t104", - "source": "IL6", + "source": "aldosterone_simple_molecule_blood", "target": "SERPINE1", "sign": true }, @@ -2139,13 +2139,13 @@ }, { "id": "t114", - "source": "KLKB1", + "source": "F12a", "target": "Kallikrein", "sign": true }, { "id": "t115", - "source": "F12a", + "source": "KLKB1", "target": "Kallikrein", "sign": true }, @@ -2163,31 +2163,31 @@ }, { "id": "t118", - "source": "C2a:C4b_complex", + "source": "SARS-CoV-2 infection_phenotype", "target": "C5a", "sign": true }, { "id": "t119", - "source": "SARS-CoV-2 infection_phenotype", + "source": "C5", "target": "C5a", "sign": true }, { "id": "t120", - "source": "C5", + "source": "Plasmin", "target": "C5a", "sign": true }, { "id": "t121", - "source": "Plasmin", + "source": "C2a:C4b_complex", "target": "C5a", "sign": true }, { "id": "t122", - "source": "VWF", + "source": "C5b-9_complex_endothelium, vascular", "target": "Thrombosis_phenotype_blood", "sign": true }, @@ -2205,13 +2205,13 @@ }, { "id": "t125", - "source": "CRP", + "source": "IL1B", "target": "Thrombosis_phenotype_blood", "sign": true }, { "id": "t126", - "source": "C5b-9_complex_endothelium, vascular", + "source": "C4d", "target": "Thrombosis_phenotype_blood", "sign": true }, @@ -2223,19 +2223,19 @@ }, { "id": "t128", - "source": "IL2RA", + "source": "CRP", "target": "Thrombosis_phenotype_blood", "sign": true }, { "id": "t129", - "source": "C4d", + "source": "IL2RA", "target": "Thrombosis_phenotype_blood", "sign": true }, { "id": "t130", - "source": "IL1B", + "source": "VWF", "target": "Thrombosis_phenotype_blood", "sign": true }, @@ -2313,7 +2313,7 @@ }, { "id": "t143", - "source": "C2a:C4b_complex", + "source": "C3b:Bb:C3b_complex", "target": "C5b", "sign": true }, @@ -2325,7 +2325,7 @@ }, { "id": "t145", - "source": "C3b:Bb:C3b_complex", + "source": "C2a:C4b_complex", "target": "C5b", "sign": true }, @@ -2361,37 +2361,37 @@ }, { "id": "t151", - "source": "C2", + "source": "MASP1", "target": "C2a", "sign": true }, { "id": "t152", - "source": "MASP1", + "source": "C2", "target": "C2a", "sign": true }, { "id": "t153", - "source": "C2", + "source": "MASP1", "target": "C2b", "sign": true }, { "id": "t154", - "source": "MASP1", + "source": "C2", "target": "C2b", "sign": true }, { "id": "t155", - "source": "CFI", + "source": "SARS-CoV-2 infection_phenotype", "target": "C4d", "sign": true }, { "id": "t156", - "source": "SARS-CoV-2 infection_phenotype", + "source": "CFI", "target": "C4d", "sign": true }, @@ -2481,13 +2481,13 @@ }, { "id": "t171", - "source": "ACE", + "source": "Bradykinin", "target": "Bradykinin(1-5)", "sign": true }, { "id": "t172", - "source": "Bradykinin", + "source": "ACE", "target": "Bradykinin(1-5)", "sign": true }, @@ -2589,25 +2589,25 @@ }, { "id": "t189", - "source": "AGTR1_blood", + "source": "SARS-CoV-2 infection_phenotype", "target": "aldosterone_simple_molecule_blood", "sign": true }, { "id": "t190", - "source": "K+_ion", + "source": "angiotensin II_simple_molecule", "target": "aldosterone_simple_molecule_blood", "sign": true }, { "id": "t191", - "source": "angiotensin II_simple_molecule", + "source": "K+_ion", "target": "aldosterone_simple_molecule_blood", "sign": true }, { "id": "t192", - "source": "SARS-CoV-2 infection_phenotype", + "source": "AGTR1_blood", "target": "aldosterone_simple_molecule_blood", "sign": true }, @@ -2655,13 +2655,13 @@ }, { "id": "t200", - "source": "NR3C2", + "source": "AGTR1_blood", "target": "Thrombosis_phenotype_human host", "sign": true }, { "id": "t201", - "source": "AGTR1_blood", + "source": "NR3C2", "target": "Thrombosis_phenotype_human host", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/ER_Stress.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/ER_Stress.json index 2f5c20ef..50948447 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/ER_Stress.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/ER_Stress.json @@ -1957,73 +1957,73 @@ }, { "id": "t2", - "source": "EIF2S1_phosphorylated", + "source": "EIF2S2", "target": "EIF2-P:GDP_complex", "sign": true }, { "id": "t3", - "source": "EIF2S2", + "source": "EIF2S1_phosphorylated", "target": "EIF2-P:GDP_complex", "sign": true }, { "id": "t4", - "source": "BAX_endoplasmic reticulum", + "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t5", - "source": "BAX:ERN1_complex", + "source": "BCL2", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t6", - "source": "BCL2L1", + "source": "ERN1:Unfolded_space_protein_complex", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t7", - "source": "ERN1:Unfolded_space_protein_complex", + "source": "BCL2L1", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t8", - "source": "BCL2", + "source": "TRAF2", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t9", - "source": "TRAF2", + "source": "BAK1", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t10", - "source": "BAK1", + "source": "BAX:ERN1_complex", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t11", - "source": "BAK1:ERN1_complex", + "source": "BAX_endoplasmic reticulum", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t12", - "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", + "source": "BAK1:ERN1_complex", "target": "TRAF2:ERN1_complex", "sign": true }, { "id": "t13", - "source": "Ca2+space_ER_space_depletion_phenotype", + "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", "target": "SIGMAR1:ITPR3_complex", "sign": true }, @@ -2035,31 +2035,31 @@ }, { "id": "t15", - "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", + "source": "ER_space_stress_phenotype", "target": "SIGMAR1:ITPR3_complex", "sign": true }, { "id": "t16", - "source": "ER_space_stress_phenotype", + "source": "Ca2+space_ER_space_depletion_phenotype", "target": "SIGMAR1:ITPR3_complex", "sign": true }, { "id": "t17", - "source": "Met-tRNA_rna", + "source": "Ternary_space_Complex_complex", "target": "EIF2:GDP:Met-tRNA_complex", "sign": true }, { "id": "t18", - "source": "Ternary_space_Complex_complex", + "source": "GDP_simple_molecule", "target": "EIF2:GDP:Met-tRNA_complex", "sign": true }, { "id": "t19", - "source": "GDP_simple_molecule", + "source": "Met-tRNA_rna", "target": "EIF2:GDP:Met-tRNA_complex", "sign": true }, @@ -2071,13 +2071,13 @@ }, { "id": "t21", - "source": "SQSTM1_space_", + "source": "CASP8:CASP8-ubq:FADD_complex", "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "sign": true }, { "id": "t22", - "source": "MAP1LC3A", + "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "sign": true }, @@ -2089,19 +2089,19 @@ }, { "id": "t24", - "source": "CASP8:CASP8-ubq:FADD_complex", + "source": "TRIM13", "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "sign": true }, { "id": "t25", - "source": "TRIM13", + "source": "MAP1LC3A", "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "sign": true }, { "id": "t26", - "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", + "source": "SQSTM1_space_", "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "sign": true }, @@ -2119,13 +2119,13 @@ }, { "id": "t29", - "source": "SIGMAR1_endoplasmic reticulum", + "source": "HSPA5_endoplasmic reticulum", "target": "SIGMAR1:HSPA5_complex", "sign": true }, { "id": "t30", - "source": "HSPA5_endoplasmic reticulum", + "source": "SIGMAR1_endoplasmic reticulum", "target": "SIGMAR1:HSPA5_complex", "sign": true }, @@ -2143,7 +2143,7 @@ }, { "id": "t33", - "source": "EIF2B_complex", + "source": "EIF2:GDP:Met-tRNA_complex", "target": "Ternary_space_Complex_complex", "sign": true }, @@ -2155,19 +2155,19 @@ }, { "id": "t35", - "source": "EIF2:GDP:Met-tRNA_complex", + "source": "EIF2B_complex", "target": "Ternary_space_Complex_complex", "sign": true }, { "id": "t36", - "source": "PACS2_early_space_endosome", + "source": "ADAM17_early_space_endosome", "target": "PACS2-ADAM17_space_interaction_complex", "sign": true }, { "id": "t37", - "source": "ADAM17_early_space_endosome", + "source": "PACS2_early_space_endosome", "target": "PACS2-ADAM17_space_interaction_complex", "sign": true }, @@ -2185,19 +2185,19 @@ }, { "id": "t40", - "source": "MFN2_endoplasmic reticulum", + "source": "MFN2_mitochondrion", "target": "MFN2:MFN2_complex", "sign": true }, { "id": "t41", - "source": "MFN2_mitochondrion", + "source": "MFN2_endoplasmic reticulum", "target": "MFN2:MFN2_complex", "sign": true }, { "id": "t42", - "source": "BBC3", + "source": "Persistant_space_ER_space_Stress_phenotype_cell", "target": "ERN1:BBC3_complex", "sign": true }, @@ -2209,7 +2209,7 @@ }, { "id": "t44", - "source": "Persistant_space_ER_space_Stress_phenotype_cell", + "source": "BBC3", "target": "ERN1:BBC3_complex", "sign": true }, @@ -2233,43 +2233,43 @@ }, { "id": "t48", - "source": "MFN2_endoplasmic reticulum", + "source": "MFN1", "target": "MFN1:MFN2_complex", "sign": true }, { "id": "t49", - "source": "MFN1", + "source": "MFN2_endoplasmic reticulum", "target": "MFN1:MFN2_complex", "sign": true }, { "id": "t50", - "source": "MCU2", + "source": "MCU1", "target": "MCU:MICU1:MICU2:SMDT1_complex", "sign": true }, { "id": "t51", - "source": "SMDT1", + "source": "MCU2", "target": "MCU:MICU1:MICU2:SMDT1_complex", "sign": true }, { "id": "t52", - "source": "MCU1", + "source": "MCU", "target": "MCU:MICU1:MICU2:SMDT1_complex", "sign": true }, { "id": "t53", - "source": "MCU", + "source": "SMDT1", "target": "MCU:MICU1:MICU2:SMDT1_complex", "sign": true }, { "id": "t54", - "source": "BCL2L11_endoplasmic reticulum", + "source": "Persistant_space_ER_space_Stress_phenotype_cell", "target": "ERN1:BCL2L11_complex", "sign": true }, @@ -2281,19 +2281,19 @@ }, { "id": "t56", - "source": "Persistant_space_ER_space_Stress_phenotype_cell", + "source": "BCL2L11_endoplasmic reticulum", "target": "ERN1:BCL2L11_complex", "sign": true }, { "id": "t57", - "source": "CAPN1", + "source": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", "target": "CAPN1:Ca2+_complex", "sign": true }, { "id": "t58", - "source": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "source": "CAPN1", "target": "CAPN1:Ca2+_complex", "sign": true }, @@ -2305,19 +2305,19 @@ }, { "id": "t60", - "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", + "source": "EIF2AK3", "target": "EIF2AK3:EIF2AK3_complex", "sign": true }, { "id": "t61", - "source": "Unfolded_space_protein", + "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic reticulum", "target": "EIF2AK3:EIF2AK3_complex", "sign": true }, { "id": "t62", - "source": "EIF2AK3", + "source": "Unfolded_space_protein", "target": "EIF2AK3:EIF2AK3_complex", "sign": true }, @@ -2329,25 +2329,25 @@ }, { "id": "t64", - "source": "ACE2", + "source": "S", "target": "ACE2:Spike_complex", "sign": true }, { "id": "t65", - "source": "S", + "source": "ACE2", "target": "ACE2:Spike_complex", "sign": true }, { "id": "t66", - "source": "HSPA5_default_compartment", + "source": "S", "target": "HSPA5-Spike interaction_complex", "sign": true }, { "id": "t67", - "source": "S", + "source": "HSPA5_default_compartment", "target": "HSPA5-Spike interaction_complex", "sign": true }, @@ -2371,13 +2371,13 @@ }, { "id": "t71", - "source": "ATF4", + "source": "DDIT3", "target": "PPP1R15A_rna", "sign": true }, { "id": "t72", - "source": "DDIT3", + "source": "ATF4", "target": "PPP1R15A_rna", "sign": true }, @@ -2401,7 +2401,7 @@ }, { "id": "t76", - "source": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "source": "MBTPS2", "target": "ATF6_Golgi apparatus", "sign": true }, @@ -2413,13 +2413,13 @@ }, { "id": "t78", - "source": "MBTPS2", + "source": "ATF6_endoplasmic reticulum", "target": "ATF6_Golgi apparatus", "sign": true }, { "id": "t79", - "source": "ATF6_endoplasmic reticulum", + "source": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", "target": "ATF6_Golgi apparatus", "sign": true }, @@ -2449,55 +2449,55 @@ }, { "id": "t84", - "source": "ER_space_stress_phenotype", + "source": "Ca2+space_ER_space_depletion_phenotype", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t85", - "source": "SIGMAR1:HSPA5_complex", + "source": "Unfolded_space_protein", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t86", - "source": "ACE2", + "source": "SIGMAR1:HSPA5_complex", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t87", - "source": "Ca2+space_ER_space_depletion_phenotype", + "source": "ATF6:HSPA5_complex", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t88", - "source": "Unfolded_space_protein", + "source": "HSPA5_rna", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t89", - "source": "ATF6:HSPA5_complex", + "source": "ER_space_stress_phenotype", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t90", - "source": "HSPA5_rna", + "source": "ACE2", "target": "HSPA5_endoplasmic reticulum", "sign": true }, { "id": "t91", - "source": "TMBIM6", + "source": "ERO1A_endoplasmic reticulum", "target": "ITPR", "sign": true }, { "id": "t92", - "source": "ERO1A_endoplasmic reticulum", + "source": "TMBIM6", "target": "ITPR", "sign": true }, @@ -2521,43 +2521,43 @@ }, { "id": "t96", - "source": "ACE2", + "source": "S", "target": "HSPA5_rna", "sign": true }, { "id": "t97", - "source": "S", + "source": "ACE2", "target": "HSPA5_rna", "sign": true }, { "id": "t98", - "source": "ATF6_Golgi apparatus", + "source": "EIF2AK3:EIF2AK3_complex", "target": "UPR_phenotype", "sign": true }, { "id": "t99", - "source": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "source": "XBP1", "target": "UPR_phenotype", "sign": true }, { "id": "t100", - "source": "XBP1", + "source": "ATF6_Golgi apparatus", "target": "UPR_phenotype", "sign": true }, { "id": "t101", - "source": "EIF2AK3:EIF2AK3_complex", + "source": "TRAF2:ERN1_complex", "target": "UPR_phenotype", "sign": true }, { "id": "t102", - "source": "TRAF2:ERN1_complex", + "source": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", "target": "UPR_phenotype", "sign": true }, @@ -2569,13 +2569,13 @@ }, { "id": "t104", - "source": "FIS1", + "source": "VAPB", "target": "Ca2+space_mitochondrial_space_concentration_phenotype", "sign": true }, { "id": "t105", - "source": "VAPB", + "source": "FIS1", "target": "Ca2+space_mitochondrial_space_concentration_phenotype", "sign": true }, @@ -2611,31 +2611,31 @@ }, { "id": "t111", - "source": "ATF4", + "source": "DDIT3_gene", "target": "DDIT3_rna", "sign": true }, { "id": "t112", - "source": "Persistant_space_ER_space_Stress_phenotype_cell", + "source": "XBP1", "target": "DDIT3_rna", "sign": true }, { "id": "t113", - "source": "XBP1", + "source": "ATF4", "target": "DDIT3_rna", "sign": true }, { "id": "t114", - "source": "ATF6_nucleus", + "source": "Persistant_space_ER_space_Stress_phenotype_cell", "target": "DDIT3_rna", "sign": true }, { "id": "t115", - "source": "DDIT3_gene", + "source": "ATF6_nucleus", "target": "DDIT3_rna", "sign": true }, @@ -2665,19 +2665,19 @@ }, { "id": "t120", - "source": "DDIT3", + "source": "TRIB3_gene", "target": "TRIB3_rna", "sign": true }, { "id": "t121", - "source": "TRIB3_gene", + "source": "DDIT3", "target": "TRIB3_rna", "sign": true }, { "id": "t122", - "source": "ITPR3:HSPA9:VDAC1_complex", + "source": "SIGMAR1:ITPR3_complex", "target": "Ca2+_ion_mitochondrion", "sign": true }, @@ -2689,7 +2689,7 @@ }, { "id": "t124", - "source": "SIGMAR1:ITPR3_complex", + "source": "ITPR3:HSPA9:VDAC1_complex", "target": "Ca2+_ion_mitochondrion", "sign": true }, @@ -2701,49 +2701,49 @@ }, { "id": "t126", - "source": "PPP1R15A", + "source": "EIF2S1_phosphorylated", "target": "EIF2S1", "sign": true }, { "id": "t127", - "source": "EIF2S1_phosphorylated", + "source": "EIF2AK1", "target": "EIF2S1", "sign": true }, { "id": "t128", - "source": "EIF2AK1", + "source": "PPP1R15A", "target": "EIF2S1", "sign": true }, { "id": "t129", - "source": "cleaved~CASP4", + "source": "CASP9", "target": "cleaved~CASP9", "sign": true }, { "id": "t130", - "source": "CASP9", + "source": "cleaved~CASP4", "target": "cleaved~CASP9", "sign": true }, { "id": "t131", - "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "source": "ITPR3", "target": "RMDN3", "sign": false }, { "id": "t132", - "source": "ITPR3", + "source": "VAPB", "target": "RMDN3", "sign": false }, { "id": "t133", - "source": "VAPB", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "target": "RMDN3", "sign": false }, @@ -2767,13 +2767,13 @@ }, { "id": "t137", - "source": "Ca2+space_ER_space_depletion_phenotype", + "source": "ER_space_stress_phenotype", "target": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", "sign": true }, { "id": "t138", - "source": "ER_space_stress_phenotype", + "source": "Ca2+space_ER_space_depletion_phenotype", "target": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", "sign": true }, @@ -2785,55 +2785,55 @@ }, { "id": "t140", - "source": "ERN1:BCL2L11_complex", + "source": "XBP1_gene", "target": "XBP1_rna", "sign": true }, { "id": "t141", - "source": "ERN1:BBC3_complex", + "source": "ERN1:BCL2L11_complex", "target": "XBP1_rna", "sign": true }, { "id": "t142", - "source": "ATF6_nucleus", + "source": "TRAF2:ERN1_complex", "target": "XBP1_rna", "sign": true }, { "id": "t143", - "source": "TRAF2:ERN1_complex", + "source": "ATF6_nucleus", "target": "XBP1_rna", "sign": true }, { "id": "t144", - "source": "XBP1_gene", + "source": "ERN1:BBC3_complex", "target": "XBP1_rna", "sign": true }, { "id": "t145", - "source": "Unfolded_space_protein", + "source": "ERAD_phenotype", "target": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", "sign": true }, { "id": "t146", - "source": "ERAD_phenotype", + "source": "Unfolded_space_protein", "target": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", "sign": true }, { "id": "t147", - "source": "BCL2_gene", + "source": "DDIT3_phosphorylated", "target": "BCL2_rna", "sign": true }, { "id": "t148", - "source": "DDIT3_phosphorylated", + "source": "BCL2_gene", "target": "BCL2_rna", "sign": true }, @@ -2857,13 +2857,13 @@ }, { "id": "t152", - "source": "MAPK14", + "source": "MAP3K5_phosphorylated", "target": "MAPK14_phosphorylated", "sign": true }, { "id": "t153", - "source": "MAP3K5_phosphorylated", + "source": "MAPK14", "target": "MAPK14_phosphorylated", "sign": true }, @@ -2899,13 +2899,13 @@ }, { "id": "t159", - "source": "presence_space_of_space_dsRNA_phenotype", + "source": "DNAJC3", "target": "EIF2AK2", "sign": true }, { "id": "t160", - "source": "DNAJC3", + "source": "presence_space_of_space_dsRNA_phenotype", "target": "EIF2AK2", "sign": true }, @@ -2929,43 +2929,43 @@ }, { "id": "t164", - "source": "MAPK8_phosphorylated", + "source": "MAPK14_phosphorylated", "target": "BAX_phosphorylated", "sign": true }, { "id": "t165", - "source": "MAPK14_phosphorylated", + "source": "MAPK8_phosphorylated", "target": "BAX_phosphorylated", "sign": true }, { "id": "t166", - "source": "EIF2AK3:EIF2AK3_complex", + "source": "ATF6_endoplasmic reticulum", "target": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", "sign": true }, { "id": "t167", - "source": "ATF6_endoplasmic reticulum", + "source": "EIF2AK3:EIF2AK3_complex", "target": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", "sign": true }, { "id": "t168", - "source": "MAP3K4_phosphorylated", + "source": "MAPK8", "target": "MAPK8_phosphorylated", "sign": true }, { "id": "t169", - "source": "MAPK8", + "source": "MAP3K5_phosphorylated", "target": "MAPK8_phosphorylated", "sign": true }, { "id": "t170", - "source": "MAP3K5_phosphorylated", + "source": "MAP3K4_phosphorylated", "target": "MAPK8_phosphorylated", "sign": true }, @@ -3013,7 +3013,7 @@ }, { "id": "t178", - "source": "ACE2", + "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", "target": "ER_space_stress_phenotype", "sign": true }, @@ -3025,7 +3025,7 @@ }, { "id": "t180", - "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", + "source": "ACE2", "target": "ER_space_stress_phenotype", "sign": true }, @@ -3037,97 +3037,97 @@ }, { "id": "t182", - "source": "cleaved~CASP4", + "source": "CASP3", "target": "cleaved~CASP3", "sign": true }, { "id": "t183", - "source": "CASP3", + "source": "cleaved~CASP4", "target": "cleaved~CASP3", "sign": true }, { "id": "t184", - "source": "EIF2S1", + "source": "EIF2AK3:EIF2AK3_complex", "target": "EIF2S1_phosphorylated", "sign": true }, { "id": "t185", - "source": "GCN2:ATP_complex", + "source": "EIF2AK2", "target": "EIF2S1_phosphorylated", "sign": true }, { "id": "t186", - "source": "EIF2AK2", + "source": "DNAJC3", "target": "EIF2S1_phosphorylated", "sign": true }, { "id": "t187", - "source": "DNAJC3", + "source": "EIF2S1", "target": "EIF2S1_phosphorylated", "sign": true }, { "id": "t188", - "source": "EIF2AK3:EIF2AK3_complex", + "source": "GCN2:ATP_complex", "target": "EIF2S1_phosphorylated", "sign": true }, { "id": "t189", - "source": "PACS2_endoplasmic reticulum", + "source": "MFN1:MFN2_complex", "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "sign": true }, { "id": "t190", - "source": "MFN1:MFN2_complex", + "source": "VAPB:RMDN3_complex", "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "sign": true }, { "id": "t191", - "source": "FIS1:BCAP31_complex", + "source": "PACS2_endoplasmic reticulum", "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "sign": true }, { "id": "t192", - "source": "MFN2:MFN2_complex", + "source": "FIS1:BCAP31_complex", "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "sign": true }, { "id": "t193", - "source": "VAPB:RMDN3_complex", + "source": "MFN2:MFN2_complex", "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", "sign": true }, { "id": "t194", - "source": "DDIT3", + "source": "AP-1", "target": "AP-1_phosphorylated_phosphorylated", "sign": true }, { "id": "t195", - "source": "MAPK8_phosphorylated", + "source": "DDIT3", "target": "AP-1_phosphorylated_phosphorylated", "sign": true }, { "id": "t196", - "source": "AP-1", + "source": "MAPK8_phosphorylated", "target": "AP-1_phosphorylated_phosphorylated", "sign": true }, { "id": "t197", - "source": "EIF2B_complex", + "source": "EIF2:GDP:Met-tRNA_complex", "target": "GDP_simple_molecule", "sign": true }, @@ -3139,7 +3139,7 @@ }, { "id": "t199", - "source": "EIF2:GDP:Met-tRNA_complex", + "source": "EIF2B_complex", "target": "GDP_simple_molecule", "sign": true }, @@ -3193,25 +3193,25 @@ }, { "id": "t208", - "source": "TRAF2:ERN1_complex", + "source": "MAP3K5", "target": "MAP3K5_phosphorylated", "sign": true }, { "id": "t209", - "source": "MAP3K5", + "source": "TRAF2", "target": "MAP3K5_phosphorylated", "sign": true }, { "id": "t210", - "source": "TRAF2", + "source": "TRAF2:ERN1_complex", "target": "MAP3K5_phosphorylated", "sign": true }, { "id": "t211", - "source": "MFN2_endoplasmic reticulum", + "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", "target": "Apoptosis_phenotype_endoplasmic reticulum", "sign": true }, @@ -3223,19 +3223,19 @@ }, { "id": "t213", - "source": "SIGMAR1_mitochondria-associated endoplasmic reticulum membrane", + "source": "MFN2_endoplasmic reticulum", "target": "Apoptosis_phenotype_endoplasmic reticulum", "sign": true }, { "id": "t214", - "source": "DNAJC3_gene", + "source": "ATF6_nucleus", "target": "DNAJC3_rna", "sign": true }, { "id": "t215", - "source": "ATF6_nucleus", + "source": "DNAJC3_gene", "target": "DNAJC3_rna", "sign": true }, @@ -3277,7 +3277,7 @@ }, { "id": "t222", - "source": "DDIT3_phosphorylated", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", "target": "Apoptosis_phenotype_cell", "sign": true }, @@ -3289,37 +3289,37 @@ }, { "id": "t224", - "source": "MAPK14_phosphorylated", + "source": "DDIT3_phosphorylated", "target": "Apoptosis_phenotype_cell", "sign": true }, { "id": "t225", - "source": "BAX_phosphorylated", + "source": "BID_phosphorylated", "target": "Apoptosis_phenotype_cell", "sign": true }, { "id": "t226", - "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "source": "BAX_phosphorylated", "target": "Apoptosis_phenotype_cell", "sign": true }, { "id": "t227", - "source": "cleaved~CASP3", + "source": "TRIB3", "target": "Apoptosis_phenotype_cell", "sign": true }, { "id": "t228", - "source": "BID_phosphorylated", + "source": "MAPK14_phosphorylated", "target": "Apoptosis_phenotype_cell", "sign": true }, { "id": "t229", - "source": "TRIB3", + "source": "cleaved~CASP3", "target": "Apoptosis_phenotype_cell", "sign": true }, @@ -3361,13 +3361,13 @@ }, { "id": "t236", - "source": "Ca2+_ion_cell", + "source": "release_space_of_space_ER_space_Ca2+_phenotype", "target": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", "sign": true }, { "id": "t237", - "source": "release_space_of_space_ER_space_Ca2+_phenotype", + "source": "Ca2+_ion_cell", "target": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", "sign": true }, @@ -3379,13 +3379,13 @@ }, { "id": "t239", - "source": "MFN2_endoplasmic reticulum", + "source": "HSPA5_endoplasmic reticulum", "target": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", "sign": true }, { "id": "t240", - "source": "HSPA5_endoplasmic reticulum", + "source": "MFN2_endoplasmic reticulum", "target": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", "sign": true }, @@ -3439,13 +3439,13 @@ }, { "id": "t249", - "source": "DDIT3", + "source": "ATF6_nucleus", "target": "ERO1A_rna", "sign": true }, { "id": "t250", - "source": "ATF6_nucleus", + "source": "DDIT3", "target": "ERO1A_rna", "sign": true }, @@ -3469,25 +3469,25 @@ }, { "id": "t254", - "source": "HSPA5-Spike interaction_complex", + "source": "SARS-CoV infection_phenotype", "target": "viral entry into host cell_phenotype", "sign": true }, { "id": "t255", - "source": "ACE2,_space_soluble", + "source": "ACE2-SARS-CoV interaction_complex", "target": "viral entry into host cell_phenotype", "sign": true }, { "id": "t256", - "source": "ACE2-SARS-CoV interaction_complex", + "source": "ACE2,_space_soluble", "target": "viral entry into host cell_phenotype", "sign": true }, { "id": "t257", - "source": "SARS-CoV infection_phenotype", + "source": "HSPA5-Spike interaction_complex", "target": "viral entry into host cell_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/ETC.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/ETC.json index 6811ee49..746958cc 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/ETC.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/ETC.json @@ -922,13 +922,13 @@ }, { "id": "t4", - "source": "F-ATPase_complex_mitochondrial matrix", + "source": "H+_ion_mitochondrion", "target": "ATP_space_Synthase_complex", "sign": true }, { "id": "t5", - "source": "H+_ion_mitochondrion", + "source": "F-ATPase_complex_mitochondrial matrix", "target": "ATP_space_Synthase_complex", "sign": true }, @@ -940,19 +940,19 @@ }, { "id": "t7", - "source": "Mt_space_translation_complex", + "source": "mt_space_mRNA_rna", "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial matrix", "sign": true }, { "id": "t8", - "source": "Nsp8-affected Mt ribosomal proteins_complex", + "source": "Mt_space_translation_complex", "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial matrix", "sign": true }, { "id": "t9", - "source": "mt_space_mRNA_rna", + "source": "Nsp8-affected Mt ribosomal proteins_complex", "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial matrix", "sign": true }, @@ -964,13 +964,13 @@ }, { "id": "t11", - "source": "NDUFB9", + "source": "OXPHOS_space_factors_complex", "target": "Complex_space_1_complex", "sign": true }, { "id": "t12", - "source": "NDUFA1", + "source": "NDUFB9", "target": "Complex_space_1_complex", "sign": true }, @@ -982,7 +982,7 @@ }, { "id": "t14", - "source": "OXPHOS_space_factors_complex", + "source": "NDUFA1", "target": "Complex_space_1_complex", "sign": true }, @@ -1000,19 +1000,19 @@ }, { "id": "t17", - "source": "ACAD9", + "source": "NDUFAF7", "target": "OXPHOS_space_factors_complex", "sign": true }, { "id": "t18", - "source": "NDUFAF7", + "source": "ECSIT", "target": "OXPHOS_space_factors_complex", "sign": true }, { "id": "t19", - "source": "ECSIT", + "source": "ACAD9", "target": "OXPHOS_space_factors_complex", "sign": true }, @@ -1024,19 +1024,19 @@ }, { "id": "t21", - "source": "Q_simple_molecule_mitochondrial matrix", + "source": "SIRT3", "target": "complex_space_2_complex_mitochondrial matrix", "sign": true }, { "id": "t22", - "source": "SIRT3", + "source": "OXPHOS_space_factors_complex", "target": "complex_space_2_complex_mitochondrial matrix", "sign": true }, { "id": "t23", - "source": "OXPHOS_space_factors_complex", + "source": "Q_simple_molecule_mitochondrial matrix", "target": "complex_space_2_complex_mitochondrial matrix", "sign": true }, @@ -1048,19 +1048,19 @@ }, { "id": "t25", - "source": "Q_simple_molecule_mitochondrial matrix", + "source": "OXPHOS_space_factors_complex", "target": "complex_space_3_complex", "sign": true }, { "id": "t26", - "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial matrix", + "source": "Q_simple_molecule_mitochondrial matrix", "target": "complex_space_3_complex", "sign": true }, { "id": "t27", - "source": "OXPHOS_space_factors_complex", + "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial matrix", "target": "complex_space_3_complex", "sign": true }, @@ -1144,25 +1144,25 @@ }, { "id": "t41", - "source": "Nsp6", + "source": "ATP5MG", "target": "F-ATPase:Nsp6_complex", "sign": true }, { "id": "t42", - "source": "ATP5MG", + "source": "Nsp6", "target": "F-ATPase:Nsp6_complex", "sign": true }, { "id": "t43", - "source": "H2O2_simple_molecule", + "source": "Fe2+_ion", "target": "Fe3+_ion", "sign": true }, { "id": "t44", - "source": "Fe2+_ion", + "source": "H2O2_simple_molecule", "target": "Fe3+_ion", "sign": true }, @@ -1174,7 +1174,7 @@ }, { "id": "t46", - "source": "paraquat_space_dication_complex", + "source": "superoxide_simple_molecule", "target": "paraquat_simple_molecule", "sign": true }, @@ -1186,7 +1186,7 @@ }, { "id": "t48", - "source": "superoxide_simple_molecule", + "source": "paraquat_space_dication_complex", "target": "paraquat_simple_molecule", "sign": true }, @@ -1222,13 +1222,13 @@ }, { "id": "t54", - "source": "H+_ion_mitochondrial matrix", + "source": "superoxide_simple_molecule", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t55", - "source": "superoxide_simple_molecule", + "source": "SOD2", "target": "H2O2_simple_molecule", "sign": true }, @@ -1240,19 +1240,19 @@ }, { "id": "t57", - "source": "SOD2", + "source": "H+_ion_mitochondrial matrix", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t58", - "source": "Fe3+_ion", + "source": "H2O2_simple_molecule", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t59", - "source": "H2O2_simple_molecule", + "source": "hydroxide_simple_molecule", "target": "H+_ion_mitochondrial matrix", "sign": true }, @@ -1264,7 +1264,7 @@ }, { "id": "t61", - "source": "hydroxide_simple_molecule", + "source": "Fe3+_ion", "target": "H+_ion_mitochondrial matrix", "sign": true }, @@ -1276,109 +1276,109 @@ }, { "id": "t63", - "source": "Complex_space_1_complex", + "source": "NADH_simple_molecule", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t64", - "source": "NADH_simple_molecule", + "source": "Complex_space_1_complex", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t65", - "source": "Mt-dNTP_space_pool_complex", + "source": "TFAM", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t66", - "source": "TFAM", + "source": "Mt-DNA_space_repair_complex", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t67", - "source": "Mt-DNA_space_repair_complex", + "source": "mt_space_DNA_space_replication_phenotype", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t68", - "source": "mt_space_DNA_space_damage_phenotype", + "source": "damaged_space_mt_space_DNA_gene", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t69", - "source": "damaged_space_mt_space_DNA_gene", + "source": "Mt-dNTP_space_pool_complex", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t70", - "source": "mt_space_DNA_space_replication_phenotype", + "source": "mt_space_DNA_space_damage_phenotype", "target": "mt_space_DNA_gene", "sign": true }, { "id": "t71", - "source": "Fe3+_ion", + "source": "superoxide_simple_molecule", "target": "Fe2+_ion", "sign": true }, { "id": "t72", - "source": "superoxide_simple_molecule", + "source": "Fe3+_ion", "target": "Fe2+_ion", "sign": true }, { "id": "t73", - "source": "GPX1", + "source": "TXN2", "target": "H2O_simple_molecule", "sign": true }, { "id": "t74", - "source": "GPX4", + "source": "PRDX_complex", "target": "H2O_simple_molecule", "sign": true }, { "id": "t75", - "source": "H2O2_simple_molecule", + "source": "GPX1", "target": "H2O_simple_molecule", "sign": true }, { "id": "t76", - "source": "CAT", + "source": "H2O2_simple_molecule", "target": "H2O_simple_molecule", "sign": true }, { "id": "t77", - "source": "TXN2", + "source": "hydroxide_simple_molecule", "target": "H2O_simple_molecule", "sign": true }, { "id": "t78", - "source": "hydroxide_simple_molecule", + "source": "glutathione_simple_molecule", "target": "H2O_simple_molecule", "sign": true }, { "id": "t79", - "source": "glutathione_simple_molecule", + "source": "GPX4", "target": "H2O_simple_molecule", "sign": true }, { "id": "t80", - "source": "PRDX_complex", + "source": "CAT", "target": "H2O_simple_molecule", "sign": true }, @@ -1390,13 +1390,13 @@ }, { "id": "t82", - "source": "ubiquinol_simple_molecule_mitochondrial matrix", + "source": "H+_ion_mitochondrial matrix", "target": "Q_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t83", - "source": "H+_ion_mitochondrial matrix", + "source": "ubiquinol_simple_molecule_mitochondrial matrix", "target": "Q_simple_molecule_mitochondrial matrix", "sign": true }, @@ -1414,37 +1414,37 @@ }, { "id": "t86", - "source": "H2O2_simple_molecule", + "source": "superoxide_simple_molecule", "target": "ROS_simple_molecule", "sign": true }, { "id": "t87", - "source": "hydroxide_simple_molecule", + "source": "H2O2_simple_molecule", "target": "ROS_simple_molecule", "sign": true }, { "id": "t88", - "source": "superoxide_simple_molecule", + "source": "hydroxide_simple_molecule", "target": "ROS_simple_molecule", "sign": true }, { "id": "t89", - "source": "NADPH_simple_molecule", + "source": "TXNRD2", "target": "TXN2", "sign": true }, { "id": "t90", - "source": "H2O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "TXN2", "sign": true }, { "id": "t91", - "source": "TXNRD2", + "source": "H2O2_simple_molecule", "target": "TXN2", "sign": true }, @@ -1456,43 +1456,43 @@ }, { "id": "t93", - "source": "GSR", + "source": "TXN2", "target": "NADP(+)_simple_molecule", "sign": true }, { "id": "t94", - "source": "TXNRD2", + "source": "glutathione_space_disulfide_simple_molecule", "target": "NADP(+)_simple_molecule", "sign": true }, { "id": "t95", - "source": "TXN2", + "source": "NADPH_simple_molecule", "target": "NADP(+)_simple_molecule", "sign": true }, { "id": "t96", - "source": "NADPH_simple_molecule", + "source": "TXNRD2", "target": "NADP(+)_simple_molecule", "sign": true }, { "id": "t97", - "source": "glutathione_space_disulfide_simple_molecule", + "source": "GSR", "target": "NADP(+)_simple_molecule", "sign": true }, { "id": "t98", - "source": "H2O2_simple_molecule", + "source": "Fe2+_ion", "target": "HO_simple_molecule", "sign": true }, { "id": "t99", - "source": "Fe2+_ion", + "source": "H2O2_simple_molecule", "target": "HO_simple_molecule", "sign": true }, @@ -1504,13 +1504,13 @@ }, { "id": "t101", - "source": "Fe3+_ion", + "source": "superoxide_simple_molecule", "target": "O2_simple_molecule", "sign": true }, { "id": "t102", - "source": "superoxide_simple_molecule", + "source": "Fe3+_ion", "target": "O2_simple_molecule", "sign": true }, @@ -1522,13 +1522,13 @@ }, { "id": "t104", - "source": "ubiquinol_simple_molecule_mitochondrial matrix", + "source": "H+_ion_mitochondrial matrix", "target": "H+_ion_mitochondrion", "sign": true }, { "id": "t105", - "source": "H+_ion_mitochondrial matrix", + "source": "ubiquinol_simple_molecule_mitochondrial matrix", "target": "H+_ion_mitochondrion", "sign": true }, @@ -1540,13 +1540,13 @@ }, { "id": "t107", - "source": "Complex_space_1_complex", + "source": "CYCS_mitochondrial matrix", "target": "H+_ion_mitochondrion", "sign": true }, { "id": "t108", - "source": "CYCS_mitochondrial matrix", + "source": "Complex_space_1_complex", "target": "H+_ion_mitochondrion", "sign": true }, @@ -1582,31 +1582,31 @@ }, { "id": "t114", - "source": "mt_space_DNA_gene", + "source": "mt_space_DNA_space_damage_phenotype", "target": "damaged_space_mt_space_DNA_gene", "sign": true }, { "id": "t115", - "source": "mt_space_DNA_space_damage_phenotype", + "source": "mt_space_DNA_gene", "target": "damaged_space_mt_space_DNA_gene", "sign": true }, { "id": "t116", - "source": "H2O2_simple_molecule", + "source": "Fe2+_ion", "target": "hydroxide_simple_molecule", "sign": true }, { "id": "t117", - "source": "Fe2+_ion", + "source": "H2O2_simple_molecule", "target": "hydroxide_simple_molecule", "sign": true }, { "id": "t118", - "source": "ATP_space_Synthase_complex", + "source": "H+_ion_mitochondrial matrix", "target": "ATP_simple_molecule", "sign": true }, @@ -1624,25 +1624,25 @@ }, { "id": "t121", - "source": "H+_ion_mitochondrial matrix", + "source": "ATP_space_Synthase_complex", "target": "ATP_simple_molecule", "sign": true }, { "id": "t122", - "source": "complex_space_2_complex_mitochondrial matrix", + "source": "Complex_space_1_complex", "target": "ubiquinol_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t123", - "source": "Q_simple_molecule_mitochondrial matrix", + "source": "complex_space_2_complex_mitochondrial matrix", "target": "ubiquinol_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t124", - "source": "Complex_space_1_complex", + "source": "Q_simple_molecule_mitochondrial matrix", "target": "ubiquinol_simple_molecule_mitochondrial matrix", "sign": true }, @@ -1666,13 +1666,13 @@ }, { "id": "t128", - "source": "NADPH_simple_molecule", + "source": "glutathione_space_disulfide_simple_molecule", "target": "glutathione_simple_molecule", "sign": true }, { "id": "t129", - "source": "glutathione_space_disulfide_simple_molecule", + "source": "NADPH_simple_molecule", "target": "glutathione_simple_molecule", "sign": true }, @@ -1690,49 +1690,49 @@ }, { "id": "t132", - "source": "GPX1", + "source": "H2O2_simple_molecule", "target": "glutathione_space_disulfide_simple_molecule", "sign": true }, { "id": "t133", - "source": "H2O2_simple_molecule", + "source": "glutathione_simple_molecule", "target": "glutathione_space_disulfide_simple_molecule", "sign": true }, { "id": "t134", - "source": "glutathione_simple_molecule", + "source": "GPX4", "target": "glutathione_space_disulfide_simple_molecule", "sign": true }, { "id": "t135", - "source": "GPX4", + "source": "GPX1", "target": "glutathione_space_disulfide_simple_molecule", "sign": true }, { "id": "t136", - "source": "TIM_space_complex:Nsp4_complex", + "source": "TOM_space_complex_complex_mitochondrion", "target": "precursor_space_protein_space_N-terminus_space_binding", "sign": true }, { "id": "t137", - "source": "TIM_space_complex_complex", + "source": "TIM23_space_complex_complex", "target": "precursor_space_protein_space_N-terminus_space_binding", "sign": true }, { "id": "t138", - "source": "TOM_space_complex_complex_mitochondrion", + "source": "TIM_space_complex:Nsp4_complex", "target": "precursor_space_protein_space_N-terminus_space_binding", "sign": true }, { "id": "t139", - "source": "TIM23_space_complex_complex", + "source": "TIM_space_complex_complex", "target": "precursor_space_protein_space_N-terminus_space_binding", "sign": true }, @@ -1756,13 +1756,13 @@ }, { "id": "t143", - "source": "Complex_space_1_complex", + "source": "NADH_simple_molecule", "target": "NAD+_simple_molecule", "sign": true }, { "id": "t144", - "source": "NADH_simple_molecule", + "source": "Complex_space_1_complex", "target": "NAD+_simple_molecule", "sign": true }, @@ -1774,13 +1774,13 @@ }, { "id": "t146", - "source": "ubiquinol_simple_molecule_mitochondrial matrix", + "source": "H+_ion_mitochondrial matrix", "target": "O2-_simple_molecule", "sign": true }, { "id": "t147", - "source": "H+_ion_mitochondrial matrix", + "source": "ubiquinol_simple_molecule_mitochondrial matrix", "target": "O2-_simple_molecule", "sign": true }, @@ -1816,25 +1816,25 @@ }, { "id": "t153", - "source": "O2_simple_molecule", + "source": "complex_space_3_complex", "target": "CYCS_mitochondrial matrix", "sign": true }, { "id": "t154", - "source": "ubiquinol_simple_molecule_mitochondrial matrix", + "source": "H+_ion_mitochondrial matrix", "target": "CYCS_mitochondrial matrix", "sign": true }, { "id": "t155", - "source": "complex_space_3_complex", + "source": "O2_simple_molecule", "target": "CYCS_mitochondrial matrix", "sign": true }, { "id": "t156", - "source": "H+_ion_mitochondrial matrix", + "source": "ubiquinol_simple_molecule_mitochondrial matrix", "target": "CYCS_mitochondrial matrix", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/E_protein.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/E_protein.json index 0cf6529d..bea08f12 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/E_protein.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/E_protein.json @@ -335,43 +335,43 @@ }, { "id": "t3", - "source": "H2BC21", + "source": "H4-16", "target": "histone_complex_nucleus", "sign": true }, { "id": "t4", - "source": "H4C14", + "source": "H2BC21", "target": "histone_complex_nucleus", "sign": true }, { "id": "t5", - "source": "H4C9", + "source": "H4C1", "target": "histone_complex_nucleus", "sign": true }, { "id": "t6", - "source": "H3C15", + "source": "H4C14", "target": "histone_complex_nucleus", "sign": true }, { "id": "t7", - "source": "H4-16", + "source": "H4C9", "target": "histone_complex_nucleus", "sign": true }, { "id": "t8", - "source": "H4C1", + "source": "H3C1", "target": "histone_complex_nucleus", "sign": true }, { "id": "t9", - "source": "H3C1", + "source": "H3C15", "target": "histone_complex_nucleus", "sign": true }, @@ -383,37 +383,37 @@ }, { "id": "t11", - "source": "CRB3", + "source": "PATJ", "target": "CRB3:PALS1:PATJ complex_complex", "sign": true }, { "id": "t12", - "source": "MPP5", + "source": "CRB3", "target": "CRB3:PALS1:PATJ complex_complex", "sign": true }, { "id": "t13", - "source": "PATJ", + "source": "MPP5", "target": "CRB3:PALS1:PATJ complex_complex", "sign": true }, { "id": "t14", - "source": "E_cell", + "source": "ASIC1", "target": "ASIC1 trimer:H+:STOML3_complex", "sign": true }, { "id": "t15", - "source": "ASIC1", + "source": "STOML3", "target": "ASIC1 trimer:H+:STOML3_complex", "sign": true }, { "id": "t16", - "source": "STOML3", + "source": "E_cell", "target": "ASIC1 trimer:H+:STOML3_complex", "sign": true }, @@ -473,13 +473,13 @@ }, { "id": "t26", - "source": "JQ-1_simple_molecule", + "source": "E_nucleus", "target": "BRD2", "sign": true }, { "id": "t27", - "source": "E_nucleus", + "source": "JQ-1_simple_molecule", "target": "BRD2", "sign": true }, @@ -503,19 +503,19 @@ }, { "id": "t31", - "source": "ATP1A:ATP1B:FXYDs_complex", + "source": "ASIC1 trimer:H+:STOML3_complex", "target": "Activity of sodium channels_phenotype", "sign": true }, { "id": "t32", - "source": "ASIC1 trimer:H+:STOML3_complex", + "source": "STOML3", "target": "Activity of sodium channels_phenotype", "sign": true }, { "id": "t33", - "source": "STOML3", + "source": "ATP1A:ATP1B:FXYDs_complex", "target": "Activity of sodium channels_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/HMOX1_Pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/HMOX1_Pathway.json index 3f4f7cb4..5689054f 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/HMOX1_Pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/HMOX1_Pathway.json @@ -1703,13 +1703,13 @@ "edges": [ { "id": "t1", - "source": "MAF", + "source": "NRF2_phosphorylated_nucleus", "target": "Nrf2/Maf_complex", "sign": true }, { "id": "t2", - "source": "NRF2_phosphorylated_nucleus", + "source": "MAF", "target": "Nrf2/Maf_complex", "sign": true }, @@ -1775,13 +1775,13 @@ }, { "id": "t13", - "source": "Neddylated CUL3:RBX1_complex", + "source": "CAND1", "target": "Ubiquitin Ligase Complex_complex_cell", "sign": true }, { "id": "t14", - "source": "CAND1", + "source": "Neddylated CUL3:RBX1_complex", "target": "Ubiquitin Ligase Complex_complex_cell", "sign": true }, @@ -1835,25 +1835,25 @@ }, { "id": "t23", - "source": "TXNIP", + "source": "NLRP3_cell", "target": "TXNIP:NLRP3_complex", "sign": true }, { "id": "t24", - "source": "NLRP3_cell", + "source": "TXNIP", "target": "TXNIP:NLRP3_complex", "sign": true }, { "id": "t25", - "source": "SUGT1:HSP90AB1_complex", + "source": "NLRP3_cell", "target": "NLRP3:SUGT1:HSP90_complex", "sign": true }, { "id": "t26", - "source": "NLRP3_cell", + "source": "SUGT1:HSP90AB1_complex", "target": "NLRP3:SUGT1:HSP90_complex", "sign": true }, @@ -1871,13 +1871,13 @@ }, { "id": "t29", - "source": "TXN_cell", + "source": "TXNIP", "target": "Thioredoxin:TXNIP_complex", "sign": true }, { "id": "t30", - "source": "TXNIP", + "source": "TXN_cell", "target": "Thioredoxin:TXNIP_complex", "sign": true }, @@ -1895,7 +1895,7 @@ }, { "id": "t33", - "source": "CTSG", + "source": "ASC", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, @@ -1907,13 +1907,13 @@ }, { "id": "t35", - "source": "ASC", + "source": "NLRP3 oligomer:ASC:Caspase1_complex", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, { "id": "t36", - "source": "NLRP3 oligomer:ASC:Caspase1_complex", + "source": "CTSG", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, @@ -1991,79 +1991,79 @@ }, { "id": "t49", - "source": "Heme_simple_molecule_cell", + "source": "NADPH_simple_molecule", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t50", - "source": "HMOX1_cell_active", + "source": "O2_simple_molecule_cell", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t51", - "source": "O2_simple_molecule_cell", + "source": "Heme_simple_molecule_cell", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t52", - "source": "NADPH_simple_molecule", + "source": "HMOX1_cell_active", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t53", - "source": "Fe2+_ion_mitochondrial matrix", + "source": "FECH", "target": "Heme_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t54", - "source": "FECH", + "source": "Fe2+_ion_mitochondrial matrix", "target": "Heme_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t55", - "source": "PRIN9_simple_molecule_mitochondrial matrix", + "source": "Pb2+_ion", "target": "Heme_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t56", - "source": "Pb2+_ion", + "source": "PRIN9_simple_molecule_mitochondrial matrix", "target": "Heme_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t57", - "source": "Heme_simple_molecule_cell", + "source": "dALA_simple_molecule_cell", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t58", - "source": "O2_simple_molecule_cell", + "source": "Heme_simple_molecule_cell", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t59", - "source": "NADPH_simple_molecule", + "source": "O2_simple_molecule_cell", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t60", - "source": "HMOX1_cell_active", + "source": "NADPH_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t61", - "source": "dALA_simple_molecule_cell", + "source": "HMOX1_cell_active", "target": "H2O_simple_molecule_cell", "sign": true }, @@ -2075,91 +2075,91 @@ }, { "id": "t63", - "source": "Heme_simple_molecule_cell", + "source": "Biliverdin_simple_molecule", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t64", - "source": "BLVRB", + "source": "BLVRA:Zn2+_complex", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t65", - "source": "O2_simple_molecule_cell", + "source": "Heme_simple_molecule_cell", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t66", - "source": "NADPH_simple_molecule", + "source": "O2_simple_molecule_cell", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t67", - "source": "HMOX1_cell_active", + "source": "NADPH_simple_molecule", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t68", - "source": "BLVRA:Zn2+_complex", + "source": "BLVRB", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t69", - "source": "Biliverdin_simple_molecule", + "source": "HMOX1_cell_active", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t70", - "source": "Heme_simple_molecule_cell", + "source": "SLC11A2", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t71", - "source": "O2_simple_molecule_cell", + "source": "Heme_simple_molecule_cell", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t72", - "source": "NADPH_simple_molecule", + "source": "Fe2+_ion_default_compartment", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t73", - "source": "HMOX1_cell_active", + "source": "O2_simple_molecule_cell", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t74", - "source": "MCOLN1", + "source": "Fe2+_ion_endosome", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t75", - "source": "SLC11A2", + "source": "NADPH_simple_molecule", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t76", - "source": "Fe2+_ion_default_compartment", + "source": "MCOLN1", "target": "Fe2+_ion_cell", "sign": true }, { "id": "t77", - "source": "Fe2+_ion_endosome", + "source": "HMOX1_cell_active", "target": "Fe2+_ion_cell", "sign": true }, @@ -2171,49 +2171,49 @@ }, { "id": "t79", - "source": "Heme_simple_molecule_cell", + "source": "NADPH_simple_molecule", "target": "CO_simple_molecule", "sign": true }, { "id": "t80", - "source": "HMOX1_cell_active", + "source": "O2_simple_molecule_cell", "target": "CO_simple_molecule", "sign": true }, { "id": "t81", - "source": "O2_simple_molecule_cell", + "source": "Heme_simple_molecule_cell", "target": "CO_simple_molecule", "sign": true }, { "id": "t82", - "source": "NADPH_simple_molecule", + "source": "HMOX1_cell_active", "target": "CO_simple_molecule", "sign": true }, { "id": "t83", - "source": "NADPH_simple_molecule", + "source": "Biliverdin_simple_molecule", "target": "Bilirubin_simple_molecule_cell", "sign": true }, { "id": "t84", - "source": "Biliverdin_simple_molecule", + "source": "NADPH_simple_molecule", "target": "Bilirubin_simple_molecule_cell", "sign": true }, { "id": "t85", - "source": "BLVRA:Zn2+_complex", + "source": "BLVRB", "target": "Bilirubin_simple_molecule_cell", "sign": true }, { "id": "t86", - "source": "BLVRB", + "source": "BLVRA:Zn2+_complex", "target": "Bilirubin_simple_molecule_cell", "sign": true }, @@ -2279,55 +2279,55 @@ }, { "id": "t97", - "source": "Fe2+_ion_mitochondrial matrix", + "source": "FECH", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t98", - "source": "FECH", + "source": "Fe2+_ion_mitochondrial matrix", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t99", - "source": "PRIN9_simple_molecule_mitochondrial matrix", + "source": "Pb2+_ion", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t100", - "source": "Pb2+_ion", + "source": "PRIN9_simple_molecule_mitochondrial matrix", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t101", - "source": "H+_ion_mitochondrial matrix", + "source": "Panhematin_drug", "target": "dALA_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t102", - "source": "Panhematin_drug", + "source": "Heme_simple_molecule_mitochondrial matrix", "target": "dALA_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t103", - "source": "Gly_simple_molecule", + "source": "H+_ion_mitochondrial matrix", "target": "dALA_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t104", - "source": "ALAS1:ALAS2_complex", + "source": "Gly_simple_molecule", "target": "dALA_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t105", - "source": "Heme_simple_molecule_mitochondrial matrix", + "source": "ALAS1:ALAS2_complex", "target": "dALA_simple_molecule_mitochondrial matrix", "sign": true }, @@ -2339,31 +2339,31 @@ }, { "id": "t107", - "source": "H+_ion_mitochondrial matrix", + "source": "Panhematin_drug", "target": "CO2_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t108", - "source": "Panhematin_drug", + "source": "Heme_simple_molecule_mitochondrial matrix", "target": "CO2_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t109", - "source": "Gly_simple_molecule", + "source": "H+_ion_mitochondrial matrix", "target": "CO2_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t110", - "source": "ALAS1:ALAS2_complex", + "source": "Gly_simple_molecule", "target": "CO2_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t111", - "source": "Heme_simple_molecule_mitochondrial matrix", + "source": "ALAS1:ALAS2_complex", "target": "CO2_simple_molecule_mitochondrial matrix", "sign": true }, @@ -2375,31 +2375,31 @@ }, { "id": "t113", - "source": "H+_ion_mitochondrial matrix", + "source": "Panhematin_drug", "target": "CoA-SH_simple_molecule", "sign": true }, { "id": "t114", - "source": "Panhematin_drug", + "source": "Heme_simple_molecule_mitochondrial matrix", "target": "CoA-SH_simple_molecule", "sign": true }, { "id": "t115", - "source": "Gly_simple_molecule", + "source": "H+_ion_mitochondrial matrix", "target": "CoA-SH_simple_molecule", "sign": true }, { "id": "t116", - "source": "ALAS1:ALAS2_complex", + "source": "Gly_simple_molecule", "target": "CoA-SH_simple_molecule", "sign": true }, { "id": "t117", - "source": "Heme_simple_molecule_mitochondrial matrix", + "source": "ALAS1:ALAS2_complex", "target": "CoA-SH_simple_molecule", "sign": true }, @@ -2417,31 +2417,31 @@ }, { "id": "t120", - "source": "dALA_simple_molecule_cell", + "source": "ALAD:Zn2+_complex", "target": "PBG_simple_molecule", "sign": true }, { "id": "t121", - "source": "ALAD:Zn2+_complex", + "source": "dALA_simple_molecule_cell", "target": "PBG_simple_molecule", "sign": true }, { "id": "t122", - "source": "dALA_simple_molecule_cell", + "source": "ALAD:Zn2+_complex", "target": "H+_ion_cell", "sign": true }, { "id": "t123", - "source": "ALAD:Zn2+_complex", + "source": "dALA_simple_molecule_cell", "target": "H+_ion_cell", "sign": true }, { "id": "t124", - "source": "PBG_simple_molecule", + "source": "HMBS:DIPY_complex", "target": "HMBL_simple_molecule", "sign": true }, @@ -2453,13 +2453,13 @@ }, { "id": "t126", - "source": "HMBS:DIPY_complex", + "source": "PBG_simple_molecule", "target": "HMBL_simple_molecule", "sign": true }, { "id": "t127", - "source": "PBG_simple_molecule", + "source": "HMBS:DIPY_complex", "target": "NH4+_ion", "sign": true }, @@ -2471,19 +2471,19 @@ }, { "id": "t129", - "source": "HMBS:DIPY_complex", + "source": "PBG_simple_molecule", "target": "NH4+_ion", "sign": true }, { "id": "t130", - "source": "UROS", + "source": "HMBL_simple_molecule", "target": "URO3_simple_molecule", "sign": true }, { "id": "t131", - "source": "HMBL_simple_molecule", + "source": "UROS", "target": "URO3_simple_molecule", "sign": true }, @@ -2507,73 +2507,73 @@ }, { "id": "t135", - "source": "O2_simple_molecule_mitochondrion", + "source": "CPOX", "target": "PPGEN9_simple_molecule", "sign": true }, { "id": "t136", - "source": "CPOX", + "source": "COPRO3_simple_molecule_mitochondrion", "target": "PPGEN9_simple_molecule", "sign": true }, { "id": "t137", - "source": "COPRO3_simple_molecule_mitochondrion", + "source": "O2_simple_molecule_mitochondrion", "target": "PPGEN9_simple_molecule", "sign": true }, { "id": "t138", - "source": "PPGEN9_simple_molecule", + "source": "PPO:FAD_complex", "target": "PRIN9_simple_molecule_mitochondrion", "sign": true }, { "id": "t139", - "source": "O2_simple_molecule_mitochondrion", + "source": "PPGEN9_simple_molecule", "target": "PRIN9_simple_molecule_mitochondrion", "sign": true }, { "id": "t140", - "source": "PPO:FAD_complex", + "source": "O2_simple_molecule_mitochondrion", "target": "PRIN9_simple_molecule_mitochondrion", "sign": true }, { "id": "t141", - "source": "O2_simple_molecule_mitochondrion", + "source": "CPOX", "target": "CO2_simple_molecule_mitochondrion", "sign": true }, { "id": "t142", - "source": "CPOX", + "source": "COPRO3_simple_molecule_mitochondrion", "target": "CO2_simple_molecule_mitochondrion", "sign": true }, { "id": "t143", - "source": "COPRO3_simple_molecule_mitochondrion", + "source": "O2_simple_molecule_mitochondrion", "target": "CO2_simple_molecule_mitochondrion", "sign": true }, { "id": "t144", - "source": "PPGEN9_simple_molecule", + "source": "CPOX", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t145", - "source": "O2_simple_molecule_mitochondrion", + "source": "PPO:FAD_complex", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t146", - "source": "PPO:FAD_complex", + "source": "PPGEN9_simple_molecule", "target": "H2O2_simple_molecule", "sign": true }, @@ -2585,7 +2585,7 @@ }, { "id": "t148", - "source": "CPOX", + "source": "O2_simple_molecule_mitochondrion", "target": "H2O2_simple_molecule", "sign": true }, @@ -2615,61 +2615,61 @@ }, { "id": "t153", - "source": "Fe3+_ion_default_compartment", + "source": "Fe2+_ion_cell", "target": "Fe2+_ion_default_compartment", "sign": true }, { "id": "t154", - "source": "SLC40A1:HEPH:Cu2+_complex", + "source": "SLC40A1:CP:Cu2+_complex", "target": "Fe2+_ion_default_compartment", "sign": true }, { "id": "t155", - "source": "CYBRD1:Heme_complex", + "source": "SLC40A1:HEPH:Cu2+_complex", "target": "Fe2+_ion_default_compartment", "sign": true }, { "id": "t156", - "source": "Fe2+_ion_cell", + "source": "CYBRD1:Heme_complex", "target": "Fe2+_ion_default_compartment", "sign": true }, { "id": "t157", - "source": "SLC40A1:CP:Cu2+_complex", + "source": "Fe3+_ion_default_compartment", "target": "Fe2+_ion_default_compartment", "sign": true }, { "id": "t158", - "source": "H+_ion_default_compartment", + "source": "O2_simple_molecule_default_compartment", "target": "Fe3+_ion_default_compartment", "sign": true }, { "id": "t159", - "source": "SLC40A1:HEPH:Cu2+_complex", + "source": "Fe2+_ion_default_compartment", "target": "Fe3+_ion_default_compartment", "sign": true }, { "id": "t160", - "source": "Fe2+_ion_default_compartment", + "source": "SLC40A1:CP:Cu2+_complex", "target": "Fe3+_ion_default_compartment", "sign": true }, { "id": "t161", - "source": "O2_simple_molecule_default_compartment", + "source": "SLC40A1:HEPH:Cu2+_complex", "target": "Fe3+_ion_default_compartment", "sign": true }, { "id": "t162", - "source": "SLC40A1:CP:Cu2+_complex", + "source": "H+_ion_default_compartment", "target": "Fe3+_ion_default_compartment", "sign": true }, @@ -2735,31 +2735,31 @@ }, { "id": "t173", - "source": "H+_ion_default_compartment", + "source": "O2_simple_molecule_default_compartment", "target": "H2O_simple_molecule_default_compartment", "sign": true }, { "id": "t174", - "source": "SLC40A1:HEPH:Cu2+_complex", + "source": "Fe2+_ion_default_compartment", "target": "H2O_simple_molecule_default_compartment", "sign": true }, { "id": "t175", - "source": "Fe2+_ion_default_compartment", + "source": "SLC40A1:CP:Cu2+_complex", "target": "H2O_simple_molecule_default_compartment", "sign": true }, { "id": "t176", - "source": "O2_simple_molecule_default_compartment", + "source": "SLC40A1:HEPH:Cu2+_complex", "target": "H2O_simple_molecule_default_compartment", "sign": true }, { "id": "t177", - "source": "SLC40A1:CP:Cu2+_complex", + "source": "H+_ion_default_compartment", "target": "H2O_simple_molecule_default_compartment", "sign": true }, @@ -2807,55 +2807,55 @@ }, { "id": "t185", - "source": "PKC", + "source": "CK2", "target": "NRF2_phosphorylated_cell", "sign": true }, { "id": "t186", - "source": "CK2", + "source": "PKC", "target": "NRF2_phosphorylated_cell", "sign": true }, { "id": "t187", - "source": "Heme_simple_molecule_cell", + "source": "ATP_simple_molecule", "target": "Heme_simple_molecule_default_compartment", "sign": true }, { "id": "t188", - "source": "ATP_simple_molecule", + "source": "Heme_simple_molecule_cell", "target": "Heme_simple_molecule_default_compartment", "sign": true }, { "id": "t189", - "source": "ABCG2", + "source": "H2O_simple_molecule_cell", "target": "Heme_simple_molecule_default_compartment", "sign": true }, { "id": "t190", - "source": "H2O_simple_molecule_cell", + "source": "FLVCR1-1", "target": "Heme_simple_molecule_default_compartment", "sign": true }, { "id": "t191", - "source": "FLVCR1-1", + "source": "ABCG2", "target": "Heme_simple_molecule_default_compartment", "sign": true }, { "id": "t192", - "source": "Heme_simple_molecule_cell", + "source": "ABCG2", "target": "ADP_simple_molecule", "sign": true }, { "id": "t193", - "source": "ABCG2", + "source": "ATP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, @@ -2867,19 +2867,19 @@ }, { "id": "t195", - "source": "ATP_simple_molecule", + "source": "Heme_simple_molecule_cell", "target": "ADP_simple_molecule", "sign": true }, { "id": "t196", - "source": "Heme_simple_molecule_cell", + "source": "ABCG2", "target": "Pi_simple_molecule", "sign": true }, { "id": "t197", - "source": "ABCG2", + "source": "ATP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, @@ -2891,7 +2891,7 @@ }, { "id": "t199", - "source": "ATP_simple_molecule", + "source": "Heme_simple_molecule_cell", "target": "Pi_simple_molecule", "sign": true }, @@ -2915,19 +2915,19 @@ }, { "id": "t203", - "source": "Fe3+_ion_endosome", + "source": "e-_ion_endosome", "target": "Fe2+_ion_endosome", "sign": true }, { "id": "t204", - "source": "e-_ion_endosome", + "source": "STEAP3", "target": "Fe2+_ion_endosome", "sign": true }, { "id": "t205", - "source": "STEAP3", + "source": "Fe3+_ion_endosome", "target": "Fe2+_ion_endosome", "sign": true }, @@ -2939,13 +2939,13 @@ }, { "id": "t207", - "source": "NLRP3:SUGT1:HSP90_complex", + "source": "NLRP3_rna", "target": "NLRP3_cell", "sign": true }, { "id": "t208", - "source": "NLRP3_rna", + "source": "NLRP3:SUGT1:HSP90_complex", "target": "NLRP3_cell", "sign": true }, @@ -2981,49 +2981,49 @@ }, { "id": "t214", - "source": "CTSG", + "source": "NLRP3 oligomer:ASC:Caspase1_complex", "target": "CASP1_cell", "sign": true }, { "id": "t215", - "source": "NLRP3 oligomer:ASC:Caspase1_complex", + "source": "CTSG", "target": "CASP1_cell", "sign": true }, { "id": "t216", - "source": "CTSG", + "source": "NLRP3 oligomer:ASC:Caspase1_complex", "target": "CASP1_cell", "sign": true }, { "id": "t217", - "source": "NLRP3 oligomer:ASC:Caspase1_complex", + "source": "CTSG", "target": "CASP1_cell", "sign": true }, { "id": "t218", - "source": "CTSG", + "source": "NLRP3 oligomer:ASC:Caspase1_complex", "target": "CASP1_cell", "sign": true }, { "id": "t219", - "source": "NLRP3 oligomer:ASC:Caspase1_complex", + "source": "CTSG", "target": "CASP1_cell", "sign": true }, { "id": "t220", - "source": "CTSG", + "source": "NLRP3 oligomer:ASC:Caspase1_complex", "target": "CASP1_cell", "sign": true }, { "id": "t221", - "source": "NLRP3 oligomer:ASC:Caspase1_complex", + "source": "CTSG", "target": "CASP1_cell", "sign": true }, @@ -3041,13 +3041,13 @@ }, { "id": "t224", - "source": "proIL-1B_cell", + "source": "Caspase-1 Tetramer_complex", "target": "IL-1B_cell", "sign": true }, { "id": "t225", - "source": "Caspase-1 Tetramer_complex", + "source": "proIL-1B_cell", "target": "IL-1B_cell", "sign": true }, @@ -3083,49 +3083,49 @@ }, { "id": "t231", - "source": "SARS Orf3a", + "source": "DAMPs_phenotype", "target": "NLRP3_cell_active", "sign": true }, { "id": "t232", - "source": "NLRP3_cell", + "source": "PAMPs_phenotype", "target": "NLRP3_cell_active", "sign": true }, { "id": "t233", - "source": "SARS E", + "source": "Reactive Oxygen Species_simple_molecule", "target": "NLRP3_cell_active", "sign": true }, { "id": "t234", - "source": "PAMPs_phenotype", + "source": "NLRP3 Elicitor Small Molecules_simple_molecule", "target": "NLRP3_cell_active", "sign": true }, { "id": "t235", - "source": "Reactive Oxygen Species_simple_molecule", + "source": "SARS E", "target": "NLRP3_cell_active", "sign": true }, { "id": "t236", - "source": "NLRP3 Elicitor Small Molecules_simple_molecule", + "source": "NLRP3_cell", "target": "NLRP3_cell_active", "sign": true }, { "id": "t237", - "source": "DAMPs_phenotype", + "source": "TXNIP:NLRP3_complex", "target": "NLRP3_cell_active", "sign": true }, { "id": "t238", - "source": "TXNIP:NLRP3_complex", + "source": "SARS Orf3a", "target": "NLRP3_cell_active", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/IFN-lambda.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/IFN-lambda.json index f0e732dc..41a0b06c 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/IFN-lambda.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/IFN-lambda.json @@ -484,13 +484,13 @@ }, { "id": "t12", - "source": "RIG-I-mitoMAVS_complex", + "source": "IKK-TBK1_complex", "target": "RIG-I-MAVS_complex_mitochondrion", "sign": true }, { "id": "t13", - "source": "IKK-TBK1_complex", + "source": "RIG-I-mitoMAVS_complex", "target": "RIG-I-MAVS_complex_mitochondrion", "sign": true }, @@ -538,31 +538,31 @@ }, { "id": "t21", - "source": "M", + "source": "RIG-I", "target": "RIG-1 M-Protein_complex", "sign": true }, { "id": "t22", - "source": "RIG-I", + "source": "M", "target": "RIG-1 M-Protein_complex", "sign": true }, { "id": "t23", - "source": "dsRNA_rna", + "source": "RIG-I", "target": "RIG-I:dsRNA_complex_mitochondrion", "sign": true }, { "id": "t24", - "source": "RIG-I", + "source": "PLPro", "target": "RIG-I:dsRNA_complex_mitochondrion", "sign": true }, { "id": "t25", - "source": "PLPro", + "source": "dsRNA_rna", "target": "RIG-I:dsRNA_complex_mitochondrion", "sign": true }, @@ -664,13 +664,13 @@ }, { "id": "t42", - "source": "dsRNA_vesicle_rna", + "source": "RNA_rna", "target": "dsRNA_rna", "sign": true }, { "id": "t43", - "source": "RNA_rna", + "source": "dsRNA_vesicle_rna", "target": "dsRNA_rna", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Interferon1.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Interferon1.json index 1d592bcd..337e373b 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Interferon1.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Interferon1.json @@ -1295,85 +1295,85 @@ }, { "id": "t9", - "source": "JAK1_TYK2_complex", + "source": "IRF9", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t10", - "source": "TREML4", + "source": "STAT2_phosphorylated", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t11", - "source": "STAT1_phosphorylated", + "source": "Orf6", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t12", - "source": "IRF9", + "source": "Nsp5", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t13", - "source": "STAT2_phosphorylated", + "source": "JAK1_TYK2_complex", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t14", - "source": "Nsp5", + "source": "TREML4", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t15", - "source": "Orf6", + "source": "STAT1_phosphorylated", "target": "STAT1/2_IRF9_complex", "sign": true }, { "id": "t16", - "source": "Orf6", + "source": "STAT1/2_IRF9_complex", "target": "ISRE_complex", "sign": true }, { "id": "t17", - "source": "STAT1/2_IRF9_complex", + "source": "Orf6", "target": "ISRE_complex", "sign": true }, { "id": "t18", - "source": "TYK2", + "source": "JAK1", "target": "JAK1_TYK2_complex", "sign": true }, { "id": "t19", - "source": "IFNB1_IFNAR_complex", + "source": "TYK2", "target": "JAK1_TYK2_complex", "sign": true }, { "id": "t20", - "source": "IFNA1_IFNAR_complex", + "source": "IFNB1_IFNAR_complex", "target": "JAK1_TYK2_complex", "sign": true }, { "id": "t21", - "source": "JAK1", + "source": "IFNA1_IFNAR_complex", "target": "JAK1_TYK2_complex", "sign": true }, { "id": "t22", - "source": "JUN", + "source": "MAPK8/14_complex", "target": "AP-1_complex_cell", "sign": true }, @@ -1385,13 +1385,13 @@ }, { "id": "t24", - "source": "E", + "source": "JUN", "target": "AP-1_complex_cell", "sign": true }, { "id": "t25", - "source": "MAPK8/14_complex", + "source": "E", "target": "AP-1_complex_cell", "sign": true }, @@ -1409,19 +1409,19 @@ }, { "id": "t28", - "source": "OAS2_cell_active", + "source": "EIF2AK", "target": "OAS1_EIF2AK_complex", "sign": true }, { "id": "t29", - "source": "EIF2AK", + "source": "OAS3_cell_active", "target": "OAS1_EIF2AK_complex", "sign": true }, { "id": "t30", - "source": "OAS3_cell_active", + "source": "OAS2_cell_active", "target": "OAS1_EIF2AK_complex", "sign": true }, @@ -1433,13 +1433,13 @@ }, { "id": "t32", - "source": "Nsp3", + "source": "TRAF3", "target": "TBK1_IKBKE_complex", "sign": true }, { "id": "t33", - "source": "TRAF3", + "source": "NAP1", "target": "TBK1_IKBKE_complex", "sign": true }, @@ -1451,19 +1451,19 @@ }, { "id": "t35", - "source": "NAP1", + "source": "TBK1", "target": "TBK1_IKBKE_complex", "sign": true }, { "id": "t36", - "source": "TBK1", + "source": "Nsp3", "target": "TBK1_IKBKE_complex", "sign": true }, { "id": "t37", - "source": "TREML4", + "source": "TLR7", "target": "MYD88_TRAM_complex", "sign": true }, @@ -1475,7 +1475,7 @@ }, { "id": "t39", - "source": "TLR7", + "source": "Viral dsRNA_rna_endosome", "target": "MYD88_TRAM_complex", "sign": true }, @@ -1493,43 +1493,43 @@ }, { "id": "t42", - "source": "Viral dsRNA_rna_endosome", + "source": "TREML4", "target": "MYD88_TRAM_complex", "sign": true }, { "id": "t43", - "source": "TANK", + "source": "TRAF3_TBK1_IKBKE_complex_cell_active", "target": "TRAF3_TANK_TBK1_IKKepsilon_complex", "sign": true }, { "id": "t44", - "source": "MAVS", + "source": "M", "target": "TRAF3_TANK_TBK1_IKKepsilon_complex", "sign": true }, { "id": "t45", - "source": "M", + "source": "MAVS", "target": "TRAF3_TANK_TBK1_IKKepsilon_complex", "sign": true }, { "id": "t46", - "source": "TLR3_TRIF_complex", + "source": "TANK", "target": "TRAF3_TANK_TBK1_IKKepsilon_complex", "sign": true }, { "id": "t47", - "source": "TRAF3_TBK1_IKBKE_complex_cell_active", + "source": "TLR3_TRIF_complex", "target": "TRAF3_TANK_TBK1_IKKepsilon_complex", "sign": true }, { "id": "t48", - "source": "TRAF3", + "source": "TBK1_IKBKE_complex", "target": "TRAF3_TBK1_IKBKE_complex_cell", "sign": true }, @@ -1541,109 +1541,109 @@ }, { "id": "t50", - "source": "TBK1_IKBKE_complex", + "source": "TRAF3", "target": "TRAF3_TBK1_IKBKE_complex_cell", "sign": true }, { "id": "t51", - "source": "TRAF3_TBK1_IKBKE_complex_cell", + "source": "pp1ab", "target": "TRAF3_TBK1_IKBKE_complex_cell_active", "sign": true }, { "id": "t52", - "source": "pp1ab", + "source": "STING1_ubiquitinated", "target": "TRAF3_TBK1_IKBKE_complex_cell_active", "sign": true }, { "id": "t53", - "source": "STING1_ubiquitinated", + "source": "TRAF3_TBK1_IKBKE_complex_cell", "target": "TRAF3_TBK1_IKBKE_complex_cell_active", "sign": true }, { "id": "t54", - "source": "Nsp10", + "source": "Nsp16", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t55", - "source": "Nsp15", + "source": "M", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t56", - "source": "N", + "source": "Nsp14", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t57", - "source": "Nsp14", + "source": "DDX58_ubiquitinated", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t58", - "source": "Nsp16", + "source": "IFIH1", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t59", - "source": "IFIH1", + "source": "Nsp10", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t60", - "source": "M", + "source": "Viral dsRNA_rna_cell", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t61", - "source": "DDX58_ubiquitinated", + "source": "Nsp15", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t62", - "source": "Viral dsRNA_rna_cell", + "source": "N", "target": "RIG1_MDA5_complex", "sign": true }, { "id": "t63", - "source": "E", + "source": "MNS_drug", "target": "NLRP3_inflammasome_complex", "sign": true }, { "id": "t64", - "source": "MNS_drug", + "source": "p50_p65_complex_nucleus", "target": "NLRP3_inflammasome_complex", "sign": true }, { "id": "t65", - "source": "p50_p65_complex_nucleus", + "source": "E", "target": "NLRP3_inflammasome_complex", "sign": true }, { "id": "t66", - "source": "MAPK8", + "source": "MAPK14", "target": "MAPK8/14_complex", "sign": true }, { "id": "t67", - "source": "MAPK14", + "source": "MAP3K7", "target": "MAPK8/14_complex", "sign": true }, @@ -1655,7 +1655,7 @@ }, { "id": "t69", - "source": "MAP3K7", + "source": "MAPK8", "target": "MAPK8/14_complex", "sign": true }, @@ -1673,13 +1673,13 @@ }, { "id": "t72", - "source": "TRIF", + "source": "Viral dsRNA_rna_endosome", "target": "TLR3_TRIF_complex", "sign": true }, { "id": "t73", - "source": "Viral dsRNA_rna_endosome", + "source": "TRIF", "target": "TLR3_TRIF_complex", "sign": true }, @@ -1691,13 +1691,13 @@ }, { "id": "t75", - "source": "TLR3_TRIF_complex", + "source": "RIP1", "target": "TLR3_TRIF_RIPK1_complex", "sign": true }, { "id": "t76", - "source": "RIP1", + "source": "TLR3_TRIF_complex", "target": "TLR3_TRIF_RIPK1_complex", "sign": true }, @@ -1721,13 +1721,13 @@ }, { "id": "t80", - "source": "TAB1", + "source": "TAK1", "target": "TAB1/2_TRAF6_TAK1_complex", "sign": true }, { "id": "t81", - "source": "TAK1", + "source": "TAB1", "target": "TAB1/2_TRAF6_TAK1_complex", "sign": true }, @@ -1805,13 +1805,13 @@ }, { "id": "t94", - "source": "ISG15", + "source": "GRL0617_drug", "target": "ISG15_Nsp3_complex", "sign": true }, { "id": "t95", - "source": "GRL0617_drug", + "source": "ISG15", "target": "ISG15_Nsp3_complex", "sign": true }, @@ -1847,7 +1847,7 @@ }, { "id": "t101", - "source": "Azithromycin_drug", + "source": "IRF7_homodimer_complex", "target": "IFNB1_rna", "sign": true }, @@ -1859,19 +1859,19 @@ }, { "id": "t103", - "source": "IRF7_homodimer_complex", + "source": "Azithromycin_drug", "target": "IFNB1_rna", "sign": true }, { "id": "t104", - "source": "IRF3_homodimer_complex_nucleus", + "source": "AP-1_complex_nucleus", "target": "IFNB1_rna", "sign": true }, { "id": "t105", - "source": "AP-1_complex_nucleus", + "source": "IRF3_homodimer_complex_nucleus", "target": "IFNB1_rna", "sign": true }, @@ -1931,103 +1931,103 @@ }, { "id": "t115", - "source": "Nsp15", + "source": "EIF2AK_rna", "target": "EIF2AK", "sign": true }, { "id": "t116", - "source": "EIF2AK_rna", + "source": "Nsp15", "target": "EIF2AK", "sign": true }, { "id": "t117", - "source": "Nsp3", + "source": "ITCH", "target": "TRAF6_ubiquitinated", "sign": true }, { "id": "t118", - "source": "ITCH", + "source": "MYD88_TRAM_complex", "target": "TRAF6_ubiquitinated", "sign": true }, { "id": "t119", - "source": "MYD88_TRAM_complex", + "source": "Nsp3", "target": "TRAF6_ubiquitinated", "sign": true }, { "id": "t120", - "source": "STING1_ubiquitinated", + "source": "Nsp13", "target": "TBK1", "sign": true }, { "id": "t121", - "source": "MAVS", + "source": "STING1_ubiquitinated", "target": "TBK1", "sign": true }, { "id": "t122", - "source": "IKBKE", + "source": "MAVS", "target": "TBK1", "sign": true }, { "id": "t123", - "source": "Nsp13", + "source": "IKBKE", "target": "TBK1", "sign": true }, { "id": "t124", - "source": "Nsp6", + "source": "M", "target": "Nsp1", "sign": false }, { "id": "t125", - "source": "Orf7b", + "source": "Orf3a", "target": "Nsp1", "sign": false }, { "id": "t126", - "source": "Nsp13", + "source": "Nsp6", "target": "Nsp1", "sign": false }, { "id": "t127", - "source": "M", + "source": "Nsp13", "target": "Nsp1", "sign": false }, { "id": "t128", - "source": "Orf3a", + "source": "Orf7b", "target": "Nsp1", "sign": false }, { "id": "t129", - "source": "Nsp6", + "source": "Nsp13", "target": "Orf7a", "sign": false }, { "id": "t130", - "source": "Orf7b", + "source": "Nsp6", "target": "Orf7a", "sign": false }, { "id": "t131", - "source": "Nsp13", + "source": "Orf7b", "target": "Orf7a", "sign": false }, @@ -2069,55 +2069,55 @@ }, { "id": "t138", - "source": "Nsp15", + "source": "OAS3_cell", "target": "OAS3_cell_active", "sign": true }, { "id": "t139", - "source": "OAS3_cell", + "source": "Nsp15", "target": "OAS3_cell_active", "sign": true }, { "id": "t140", - "source": "ISG15", + "source": "OAS1_EIF2AK_complex", "target": "ISG expression_antiviral response_phenotype", "sign": true }, { "id": "t141", - "source": "Azithromycin_drug", + "source": "ISG15", "target": "ISG expression_antiviral response_phenotype", "sign": true }, { "id": "t142", - "source": "Nsp3", + "source": "p50_p65_complex_nucleus", "target": "ISG expression_antiviral response_phenotype", "sign": true }, { "id": "t143", - "source": "p50_p65_complex_nucleus", + "source": "Azithromycin_drug", "target": "ISG expression_antiviral response_phenotype", "sign": true }, { "id": "t144", - "source": "OAS1_EIF2AK_complex", + "source": "Nsp3", "target": "ISG expression_antiviral response_phenotype", "sign": true }, { "id": "t145", - "source": "Nsp3", + "source": "MYD88_TRAM_complex", "target": "TRAF3", "sign": true }, { "id": "t146", - "source": "MYD88_TRAM_complex", + "source": "Nsp3", "target": "TRAF3", "sign": true }, @@ -2129,13 +2129,13 @@ }, { "id": "t148", - "source": "Nsp3", + "source": "TBK1", "target": "IKBKE", "sign": true }, { "id": "t149", - "source": "TBK1", + "source": "Nsp3", "target": "IKBKE", "sign": true }, @@ -2147,19 +2147,19 @@ }, { "id": "t151", - "source": "TRAF3_TANK_TBK1_IKKepsilon_complex", + "source": "MAVS", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t152", - "source": "Nsp15", + "source": "Orf8_complex", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t153", - "source": "N", + "source": "TRAF3_TANK_TBK1_IKKepsilon_complex", "target": "IRF3_phosphorylated", "sign": true }, @@ -2171,43 +2171,43 @@ }, { "id": "t155", - "source": "Orf8_complex", + "source": "Orf6", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t156", - "source": "pp1ab", + "source": "N", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t157", - "source": "Orf6", + "source": "Nsp15", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t158", - "source": "MAVS", + "source": "pp1ab", "target": "IRF3_phosphorylated", "sign": true }, { "id": "t159", - "source": "RIG1_MDA5_complex", + "source": "ITCH", "target": "MAVS", "sign": true }, { "id": "t160", - "source": "ITCH", + "source": "Orf9b", "target": "MAVS", "sign": true }, { "id": "t161", - "source": "Orf9b", + "source": "RIG1_MDA5_complex", "target": "MAVS", "sign": true }, @@ -2225,31 +2225,31 @@ }, { "id": "t164", - "source": "N", + "source": "Azithromycin_drug", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t165", - "source": "Azithromycin_drug", + "source": "RNF135", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t166", - "source": "TRIM25", + "source": "Nsp5", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t167", - "source": "Nsp5", + "source": "N", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t168", - "source": "RNF135", + "source": "TRIM25", "target": "DDX58_ubiquitinated", "sign": true }, @@ -2285,7 +2285,7 @@ }, { "id": "t174", - "source": "IFNB1_extracellular space", + "source": "IFNA1_extracellular space", "target": "Viral dsRNA_rna_cell", "sign": true }, @@ -2297,7 +2297,7 @@ }, { "id": "t176", - "source": "IFNA1_extracellular space", + "source": "IFNB1_extracellular space", "target": "Viral dsRNA_rna_cell", "sign": true }, @@ -2327,13 +2327,13 @@ }, { "id": "t181", - "source": "IFNB1_extracellular space", + "source": "IFNA1_extracellular space", "target": "type I IFN response_phenotype", "sign": true }, { "id": "t182", - "source": "IFNA1_extracellular space", + "source": "IFNB1_extracellular space", "target": "type I IFN response_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/JNK_pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/JNK_pathway.json index c10ea658..a4e95e32 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/JNK_pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/JNK_pathway.json @@ -171,31 +171,31 @@ "edges": [ { "id": "t1", - "source": "7a", + "source": "MAP2K7_phosphorylated", "target": "JNK_complex_cell", "sign": true }, { "id": "t2", - "source": "MAP2K7_phosphorylated", + "source": "S", "target": "JNK_complex_cell", "sign": true }, { "id": "t3", - "source": "S", + "source": "7a", "target": "JNK_complex_cell", "sign": true }, { "id": "t4", - "source": "3a", + "source": "MAP2K4_phosphorylated", "target": "JNK_complex_cell", "sign": true }, { "id": "t5", - "source": "MAP2K4_phosphorylated", + "source": "3a", "target": "JNK_complex_cell", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Kynurenine_pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Kynurenine_pathway.json index 79e95b29..635343c4 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Kynurenine_pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Kynurenine_pathway.json @@ -1653,13 +1653,13 @@ }, { "id": "t4", - "source": "apo-IDO1", + "source": "Heme_simple_molecule", "target": "IDO1_complex", "sign": true }, { "id": "t5", - "source": "Heme_simple_molecule", + "source": "apo-IDO1", "target": "IDO1_complex", "sign": true }, @@ -1689,67 +1689,67 @@ }, { "id": "t10", - "source": "QUIN_simple_molecule", + "source": "O2_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t11", - "source": "Heme_simple_molecule", + "source": "QUIN_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t12", - "source": "ACS_simple_molecule", + "source": "Heme_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t13", - "source": "H+_ion_cell", + "source": "L-Kynurenine_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t14", - "source": "O2_simple_molecule", + "source": "ACS_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t15", - "source": "AP-DOBu_simple_molecule", + "source": "PRPP_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t16", - "source": "HMOX1_cell", + "source": "QPRT", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t17", - "source": "PRPP_simple_molecule", + "source": "NADPH_simple_molecule_cell", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t18", - "source": "NADPH_simple_molecule_cell", + "source": "AP-DOBu_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t19", - "source": "L-Kynurenine_simple_molecule", + "source": "H+_ion_cell", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t20", - "source": "QPRT", + "source": "HMOX1_cell", "target": "H2O_simple_molecule_cell", "sign": true }, @@ -1761,13 +1761,13 @@ }, { "id": "t22", - "source": "L-Tryptophan_simple_molecule_cell", + "source": "IDO2", "target": "NFK_simple_molecule", "sign": true }, { "id": "t23", - "source": "IDO2", + "source": "L-Tryptophan_simple_molecule_cell", "target": "NFK_simple_molecule", "sign": true }, @@ -1785,37 +1785,37 @@ }, { "id": "t26", - "source": "I3LACT", + "source": "PYR_simple_molecule", "target": "AP-DOBu_simple_molecule", "sign": true }, { "id": "t27", - "source": "I3PROPA", + "source": "L-Kynurenine_simple_molecule", "target": "AP-DOBu_simple_molecule", "sign": true }, { "id": "t28", - "source": "L-Kynurenine_simple_molecule", + "source": "L-Phe_simple_molecule", "target": "AP-DOBu_simple_molecule", "sign": true }, { "id": "t29", - "source": "L-Phe_simple_molecule", + "source": "I3PROPA", "target": "AP-DOBu_simple_molecule", "sign": true }, { "id": "t30", - "source": "PYR_simple_molecule", + "source": "PXLP-KYAT1_complex", "target": "AP-DOBu_simple_molecule", "sign": true }, { "id": "t31", - "source": "PXLP-KYAT1_complex", + "source": "I3LACT", "target": "AP-DOBu_simple_molecule", "sign": true }, @@ -1863,7 +1863,7 @@ }, { "id": "t39", - "source": "ATP_simple_molecule_cell", + "source": "O2_simple_molecule", "target": "NADP+_simple_molecule_cell", "sign": true }, @@ -1875,85 +1875,85 @@ }, { "id": "t41", - "source": "NAD+_simple_molecule_cell", + "source": "NADK:Zn2+ tetramer_complex", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t42", - "source": "H+_ion_cell", + "source": "NAD+_simple_molecule_cell", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t43", - "source": "O2_simple_molecule", + "source": "L-Kynurenine_simple_molecule", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t44", - "source": "HMOX1_cell", + "source": "L-Arginine_simple_molecule", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t45", - "source": "NADPH_simple_molecule_cell", + "source": "iNOS", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t46", - "source": "L-Kynurenine_simple_molecule", + "source": "NADPH_simple_molecule_cell", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t47", - "source": "NADK:Zn2+ tetramer_complex", + "source": "ATP_simple_molecule_cell", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t48", - "source": "L-Arginine_simple_molecule", + "source": "H+_ion_cell", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t49", - "source": "iNOS", + "source": "HMOX1_cell", "target": "NADP+_simple_molecule_cell", "sign": true }, { "id": "t50", - "source": "ATP_simple_molecule_cell", + "source": "NMRK2", "target": "H+_ion_cell", "sign": true }, { "id": "t51", - "source": "NAD+_simple_molecule_cell", + "source": "O2_simple_molecule", "target": "H+_ion_cell", "sign": true }, { "id": "t52", - "source": "2AMA_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "H+_ion_cell", "sign": true }, { "id": "t53", - "source": "NAR_simple_molecule", + "source": "NMRK1", "target": "H+_ion_cell", "sign": true }, { "id": "t54", - "source": "O2_simple_molecule", + "source": "L-Arginine_simple_molecule", "target": "H+_ion_cell", "sign": true }, @@ -1965,37 +1965,37 @@ }, { "id": "t56", - "source": "NADPH_simple_molecule_cell", + "source": "NR_simple_molecule", "target": "H+_ion_cell", "sign": true }, { "id": "t57", - "source": "NMRK1", + "source": "iNOS", "target": "H+_ion_cell", "sign": true }, { "id": "t58", - "source": "NR_simple_molecule", + "source": "ATP_simple_molecule_cell", "target": "H+_ion_cell", "sign": true }, { "id": "t59", - "source": "L-Arginine_simple_molecule", + "source": "NAR_simple_molecule", "target": "H+_ion_cell", "sign": true }, { "id": "t60", - "source": "NMRK2", + "source": "NADPH_simple_molecule_cell", "target": "H+_ion_cell", "sign": true }, { "id": "t61", - "source": "iNOS", + "source": "2AMA_simple_molecule", "target": "H+_ion_cell", "sign": true }, @@ -2007,79 +2007,79 @@ }, { "id": "t63", - "source": "I3LACT", + "source": "3HKYN_simple_molecule", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t64", - "source": "CCBL2", + "source": "PYR_simple_molecule", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t65", - "source": "I3PROPA", + "source": "L-Kynurenine_simple_molecule", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t66", - "source": "H2O_simple_molecule_cell", + "source": "L-Phe_simple_molecule", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t67", - "source": "KYNU", + "source": "H2O_simple_molecule_cell", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t68", - "source": "L-Kynurenine_simple_molecule", + "source": "I3PROPA", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t69", - "source": "L-Phe_simple_molecule", + "source": "PXLP-KYAT1_complex", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t70", - "source": "PYR_simple_molecule", + "source": "I3LACT", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t71", - "source": "PXLP-KYAT1_complex", + "source": "KYNU", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t72", - "source": "3HKYN_simple_molecule", + "source": "CCBL2", "target": "L-Ala_simple_molecule", "sign": true }, { "id": "t73", - "source": "H2O_simple_molecule_cell", + "source": "3HKYN_simple_molecule", "target": "3HAA_simple_molecule", "sign": true }, { "id": "t74", - "source": "KYNU", + "source": "H2O_simple_molecule_cell", "target": "3HAA_simple_molecule", "sign": true }, { "id": "t75", - "source": "3HKYN_simple_molecule", + "source": "KYNU", "target": "3HAA_simple_molecule", "sign": true }, @@ -2091,13 +2091,13 @@ }, { "id": "t77", - "source": "H+_ion_cell", + "source": "O2_simple_molecule", "target": "3HKYN_simple_molecule", "sign": true }, { "id": "t78", - "source": "O2_simple_molecule", + "source": "L-Kynurenine_simple_molecule", "target": "3HKYN_simple_molecule", "sign": true }, @@ -2109,37 +2109,37 @@ }, { "id": "t80", - "source": "L-Kynurenine_simple_molecule", + "source": "H+_ion_cell", "target": "3HKYN_simple_molecule", "sign": true }, { "id": "t81", - "source": "AHR/L-KYN_complex", + "source": "3HAA_simple_molecule", "target": "Regulatory T-cell generation_phenotype", "sign": true }, { "id": "t82", - "source": "3HAA_simple_molecule", + "source": "AHR/L-KYN_complex", "target": "Regulatory T-cell generation_phenotype", "sign": true }, { "id": "t83", - "source": "O2_simple_molecule", + "source": "3HAA_simple_molecule", "target": "ACS_simple_molecule", "sign": true }, { "id": "t84", - "source": "HAAO", + "source": "O2_simple_molecule", "target": "ACS_simple_molecule", "sign": true }, { "id": "t85", - "source": "3HAA_simple_molecule", + "source": "HAAO", "target": "ACS_simple_molecule", "sign": true }, @@ -2157,13 +2157,13 @@ }, { "id": "t88", - "source": "H+_ion_cell", + "source": "PRPP_simple_molecule", "target": "CO2_simple_molecule", "sign": true }, { "id": "t89", - "source": "PRPP_simple_molecule", + "source": "QPRT", "target": "CO2_simple_molecule", "sign": true }, @@ -2175,7 +2175,7 @@ }, { "id": "t91", - "source": "QPRT", + "source": "H+_ion_cell", "target": "CO2_simple_molecule", "sign": true }, @@ -2187,25 +2187,25 @@ }, { "id": "t93", - "source": "2AMA_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "NADH_simple_molecule_cell", "sign": true }, { "id": "t94", - "source": "H2O_simple_molecule_cell", + "source": "2AMA_simple_molecule", "target": "NADH_simple_molecule_cell", "sign": true }, { "id": "t95", - "source": "NAD+_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "NADH_simple_molecule_cell", "sign": true }, { "id": "t96", - "source": "ATP_simple_molecule_cell", + "source": "NAAD_simple_molecule_cell", "target": "NAD+_simple_molecule_cell", "sign": true }, @@ -2217,19 +2217,19 @@ }, { "id": "t98", - "source": "NAAD_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "NAD+_simple_molecule_cell", "sign": true }, { "id": "t99", - "source": "NMNAT2:Mg2+_complex", + "source": "NADSYN1 hexamer", "target": "NAD+_simple_molecule_cell", "sign": true }, { "id": "t100", - "source": "NADSYN1 hexamer", + "source": "ATP_simple_molecule_cell", "target": "NAD+_simple_molecule_cell", "sign": true }, @@ -2241,7 +2241,7 @@ }, { "id": "t102", - "source": "H2O_simple_molecule_cell", + "source": "NMNAT2:Mg2+_complex", "target": "NAD+_simple_molecule_cell", "sign": true }, @@ -2259,37 +2259,37 @@ }, { "id": "t105", - "source": "2AMA_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "2AM_simple_molecule", "sign": true }, { "id": "t106", - "source": "H2O_simple_molecule_cell", + "source": "2AMA_simple_molecule", "target": "2AM_simple_molecule", "sign": true }, { "id": "t107", - "source": "NAD+_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "2AM_simple_molecule", "sign": true }, { "id": "t108", - "source": "IFN-G", + "source": "CO_simple_molecule", "target": "iNOS_rna", "sign": true }, { "id": "t109", - "source": "CO_simple_molecule", + "source": "Nf-KB Complex_complex", "target": "iNOS_rna", "sign": true }, { "id": "t110", - "source": "Nf-KB Complex_complex", + "source": "IFN-G", "target": "iNOS_rna", "sign": true }, @@ -2325,61 +2325,61 @@ }, { "id": "t116", - "source": "IFN-G", + "source": "NO_simple_molecule", "target": "IDO1_rna", "sign": true }, { "id": "t117", - "source": "NO_simple_molecule", + "source": "IFN-G", "target": "IDO1_rna", "sign": true }, { "id": "t118", - "source": "ATP_simple_molecule_mitochondrial matrix", + "source": "NAMN_simple_molecule_mitochondrial matrix", "target": "PPi (3-)_simple_molecule", "sign": true }, { "id": "t119", - "source": "NMNAT3:Mg2+_complex", + "source": "ATP_simple_molecule_mitochondrial matrix", "target": "PPi (3-)_simple_molecule", "sign": true }, { "id": "t120", - "source": "NAMN_simple_molecule_mitochondrial matrix", + "source": "NMNAT3:Mg2+_complex", "target": "PPi (3-)_simple_molecule", "sign": true }, { "id": "t121", - "source": "ATP_simple_molecule_mitochondrial matrix", + "source": "NAMN_simple_molecule_mitochondrial matrix", "target": "NAAD_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t122", - "source": "NMNAT3:Mg2+_complex", + "source": "ATP_simple_molecule_mitochondrial matrix", "target": "NAAD_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t123", - "source": "NAMN_simple_molecule_mitochondrial matrix", + "source": "NMNAT3:Mg2+_complex", "target": "NAAD_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t124", - "source": "NAD+_simple_molecule_mitochondrial matrix", + "source": "CARKD", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t125", - "source": "S-NADPHX_simple_molecule", + "source": "NAD+_simple_molecule_mitochondrial matrix", "target": "H+_ion_mitochondrial matrix", "sign": true }, @@ -2391,25 +2391,25 @@ }, { "id": "t127", - "source": "NADK2", + "source": "S-NADPHX_simple_molecule", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t128", - "source": "CARKD", + "source": "NADK2", "target": "H+_ion_mitochondrial matrix", "sign": true }, { "id": "t129", - "source": "NAD+_simple_molecule_mitochondrial matrix", + "source": "CARKD", "target": "ADP_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t130", - "source": "S-NADPHX_simple_molecule", + "source": "NAD+_simple_molecule_mitochondrial matrix", "target": "ADP_simple_molecule_mitochondrial matrix", "sign": true }, @@ -2421,13 +2421,13 @@ }, { "id": "t132", - "source": "NADK2", + "source": "S-NADPHX_simple_molecule", "target": "ADP_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t133", - "source": "CARKD", + "source": "NADK2", "target": "ADP_simple_molecule_mitochondrial matrix", "sign": true }, @@ -2463,13 +2463,13 @@ }, { "id": "t139", - "source": "NAD+_simple_molecule_mitochondrial matrix", + "source": "ATP_simple_molecule_mitochondrial matrix", "target": "NADP+_simple_molecule_mitochondrial matrix", "sign": true }, { "id": "t140", - "source": "ATP_simple_molecule_mitochondrial matrix", + "source": "NAD+_simple_molecule_mitochondrial matrix", "target": "NADP+_simple_molecule_mitochondrial matrix", "sign": true }, @@ -2505,43 +2505,43 @@ }, { "id": "t146", - "source": "ATP_simple_molecule_cell", + "source": "Mg2+_ion", "target": "PPi_simple_molecule", "sign": true }, { "id": "t147", - "source": "L-Gln_simple_molecule", + "source": "NAAD_simple_molecule_cell", "target": "PPi_simple_molecule", "sign": true }, { "id": "t148", - "source": "H+_ion_cell", + "source": "L-Gln_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t149", - "source": "NAM_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "PPi_simple_molecule", "sign": true }, { "id": "t150", - "source": "NAAD_simple_molecule_cell", + "source": "NAMPT", "target": "PPi_simple_molecule", "sign": true }, { "id": "t151", - "source": "Mg2+_ion", + "source": "PRPP_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t152", - "source": "NADSYN1 hexamer", + "source": "NCA_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, @@ -2553,103 +2553,103 @@ }, { "id": "t154", - "source": "PRPP_simple_molecule", + "source": "ATP_simple_molecule_cell", "target": "PPi_simple_molecule", "sign": true }, { "id": "t155", - "source": "H2O_simple_molecule_cell", + "source": "NADSYN1 hexamer", "target": "PPi_simple_molecule", "sign": true }, { "id": "t156", - "source": "NCA_simple_molecule", + "source": "H+_ion_cell", "target": "PPi_simple_molecule", "sign": true }, { "id": "t157", - "source": "NAMPT", + "source": "NAM_simple_molecule_cell", "target": "PPi_simple_molecule", "sign": true }, { "id": "t158", - "source": "ATP_simple_molecule_cell", + "source": "NMRK2", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t159", - "source": "QUIN_simple_molecule", + "source": "Mg2+_ion", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t160", - "source": "H+_ion_cell", + "source": "QUIN_simple_molecule", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t161", - "source": "NAM_simple_molecule_cell", + "source": "NMRK1", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t162", - "source": "NAR_simple_molecule", + "source": "NAMPT", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t163", - "source": "Mg2+_ion", + "source": "PRPP_simple_molecule", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t164", - "source": "NAPRT1", + "source": "NCA_simple_molecule", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t165", - "source": "PRPP_simple_molecule", + "source": "QPRT", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t166", - "source": "NMRK1", + "source": "ATP_simple_molecule_cell", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t167", - "source": "NCA_simple_molecule", + "source": "NAR_simple_molecule", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t168", - "source": "QPRT", + "source": "NAPRT1", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t169", - "source": "NAMPT", + "source": "H+_ion_cell", "target": "NAMN_simple_molecule_cell", "sign": true }, { "id": "t170", - "source": "NMRK2", + "source": "NAM_simple_molecule_cell", "target": "NAMN_simple_molecule_cell", "sign": true }, @@ -2667,31 +2667,31 @@ }, { "id": "t173", - "source": "ATP_simple_molecule_cell", + "source": "NMN_simple_molecule_cell", "target": "PPi(3-)_simple_molecule_cell", "sign": true }, { "id": "t174", - "source": "NMN_simple_molecule_cell", + "source": "NMNAT2:Mg2+_complex", "target": "PPi(3-)_simple_molecule_cell", "sign": true }, { "id": "t175", - "source": "NMNAT2:Mg2+_complex", + "source": "NAMN_simple_molecule_cell", "target": "PPi(3-)_simple_molecule_cell", "sign": true }, { "id": "t176", - "source": "NAMN_simple_molecule_cell", + "source": "ATP_simple_molecule_cell", "target": "PPi(3-)_simple_molecule_cell", "sign": true }, { "id": "t177", - "source": "ATP_simple_molecule_cell", + "source": "NAAD_simple_molecule_cell", "target": "L-Glu_simple_molecule", "sign": true }, @@ -2703,25 +2703,25 @@ }, { "id": "t179", - "source": "NAAD_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "L-Glu_simple_molecule", "sign": true }, { "id": "t180", - "source": "NADSYN1 hexamer", + "source": "ATP_simple_molecule_cell", "target": "L-Glu_simple_molecule", "sign": true }, { "id": "t181", - "source": "H2O_simple_molecule_cell", + "source": "NADSYN1 hexamer", "target": "L-Glu_simple_molecule", "sign": true }, { "id": "t182", - "source": "ATP_simple_molecule_cell", + "source": "NAAD_simple_molecule_cell", "target": "AMP_simple_molecule_cell", "sign": true }, @@ -2733,37 +2733,37 @@ }, { "id": "t184", - "source": "NAAD_simple_molecule_cell", + "source": "H2O_simple_molecule_cell", "target": "AMP_simple_molecule_cell", "sign": true }, { "id": "t185", - "source": "NADSYN1 hexamer", + "source": "ATP_simple_molecule_cell", "target": "AMP_simple_molecule_cell", "sign": true }, { "id": "t186", - "source": "H2O_simple_molecule_cell", + "source": "NADSYN1 hexamer", "target": "AMP_simple_molecule_cell", "sign": true }, { "id": "t187", - "source": "ATP_simple_molecule_cell", + "source": "NMRK2", "target": "ADP_simple_molecule_cell", "sign": true }, { "id": "t188", - "source": "NAD+_simple_molecule_cell", + "source": "NADK:Zn2+ tetramer_complex", "target": "ADP_simple_molecule_cell", "sign": true }, { "id": "t189", - "source": "NAR_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "ADP_simple_molecule_cell", "sign": true }, @@ -2781,13 +2781,13 @@ }, { "id": "t192", - "source": "NMRK2", + "source": "ATP_simple_molecule_cell", "target": "ADP_simple_molecule_cell", "sign": true }, { "id": "t193", - "source": "NADK:Zn2+ tetramer_complex", + "source": "NAR_simple_molecule", "target": "ADP_simple_molecule_cell", "sign": true }, @@ -2811,37 +2811,37 @@ }, { "id": "t197", - "source": "PARPs", + "source": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", "target": "NAM_simple_molecule_cell", "sign": true }, { "id": "t198", - "source": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "NAM_simple_molecule_cell", "sign": true }, { "id": "t199", - "source": "NAD+_simple_molecule_cell", + "source": "PARPs", "target": "NAM_simple_molecule_cell", "sign": true }, { "id": "t200", - "source": "NR_simple_molecule", + "source": "NMRK2", "target": "NMN_simple_molecule_cell", "sign": true }, { "id": "t201", - "source": "ATP_simple_molecule_cell", + "source": "NR_simple_molecule", "target": "NMN_simple_molecule_cell", "sign": true }, { "id": "t202", - "source": "NMRK2", + "source": "ATP_simple_molecule_cell", "target": "NMN_simple_molecule_cell", "sign": true }, @@ -2871,151 +2871,151 @@ }, { "id": "t207", - "source": "PARPs", + "source": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", "target": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", "sign": true }, { "id": "t208", - "source": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", + "source": "NAD+_simple_molecule_cell", "target": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", "sign": true }, { "id": "t209", - "source": "NAD+_simple_molecule_cell", + "source": "PARPs", "target": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", "sign": true }, { "id": "t210", - "source": "CD38", + "source": "NAD+_simple_molecule_human host", "target": "H+_ion_human host", "sign": true }, { "id": "t211", - "source": "NAD+_simple_molecule_human host", + "source": "H2O_simple_molecule_human host", "target": "H+_ion_human host", "sign": true }, { "id": "t212", - "source": "BST1", + "source": "CD38", "target": "H+_ion_human host", "sign": true }, { "id": "t213", - "source": "H2O_simple_molecule_human host", + "source": "BST1", "target": "H+_ion_human host", "sign": true }, { "id": "t214", - "source": "CD38", + "source": "NAD+_simple_molecule_human host", "target": "NAM_simple_molecule_human host", "sign": true }, { "id": "t215", - "source": "NAD+_simple_molecule_human host", + "source": "H2O_simple_molecule_human host", "target": "NAM_simple_molecule_human host", "sign": true }, { "id": "t216", - "source": "BST1", + "source": "CD38", "target": "NAM_simple_molecule_human host", "sign": true }, { "id": "t217", - "source": "H2O_simple_molecule_human host", + "source": "BST1", "target": "NAM_simple_molecule_human host", "sign": true }, { "id": "t218", - "source": "H+_ion_human host", + "source": "RNLS:FAD_complex", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t219", - "source": "O2_ion", + "source": "dh-beta-NAD_simple_molecule", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t220", - "source": "dh-beta-NAD_simple_molecule", + "source": "O2_ion", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t221", - "source": "RNLS:FAD_complex", + "source": "H+_ion_human host", "target": "H2O2_simple_molecule", "sign": true }, { "id": "t222", - "source": "H+_ion_human host", + "source": "RNLS:FAD_complex", "target": "NAD+_simple_molecule_human host", "sign": true }, { "id": "t223", - "source": "O2_ion", + "source": "dh-beta-NAD_simple_molecule", "target": "NAD+_simple_molecule_human host", "sign": true }, { "id": "t224", - "source": "dh-beta-NAD_simple_molecule", + "source": "O2_ion", "target": "NAD+_simple_molecule_human host", "sign": true }, { "id": "t225", - "source": "RNLS:FAD_complex", + "source": "H+_ion_human host", "target": "NAD+_simple_molecule_human host", "sign": true }, { "id": "t226", - "source": "CD38", + "source": "NAD+_simple_molecule_human host", "target": "ADP-ribose_simple_molecule", "sign": true }, { "id": "t227", - "source": "NAD+_simple_molecule_human host", + "source": "H2O_simple_molecule_human host", "target": "ADP-ribose_simple_molecule", "sign": true }, { "id": "t228", - "source": "BST1", + "source": "CD38", "target": "ADP-ribose_simple_molecule", "sign": true }, { "id": "t229", - "source": "H2O_simple_molecule_human host", + "source": "BST1", "target": "ADP-ribose_simple_molecule", "sign": true }, { "id": "t230", - "source": "NMN_simple_molecule_human host", + "source": "NAD+_simple_molecule_human host", "target": "Pi_ion", "sign": true }, { "id": "t231", - "source": "NAD+_simple_molecule_human host", + "source": "H2O_simple_molecule_human host", "target": "Pi_ion", "sign": true }, @@ -3027,7 +3027,7 @@ }, { "id": "t233", - "source": "H2O_simple_molecule_human host", + "source": "NMN_simple_molecule_human host", "target": "Pi_ion", "sign": true }, @@ -3039,31 +3039,31 @@ }, { "id": "t235", - "source": "NT5E:Zn2+_complex", + "source": "H2O_simple_molecule_human host", "target": "NMN_simple_molecule_human host", "sign": true }, { "id": "t236", - "source": "H2O_simple_molecule_human host", + "source": "NT5E:Zn2+_complex", "target": "NMN_simple_molecule_human host", "sign": true }, { "id": "t237", - "source": "NMN_simple_molecule_human host", + "source": "NT5E:Zn2+_complex", "target": "NRNAM_simple_molecule", "sign": true }, { "id": "t238", - "source": "NT5E:Zn2+_complex", + "source": "H2O_simple_molecule_human host", "target": "NRNAM_simple_molecule", "sign": true }, { "id": "t239", - "source": "H2O_simple_molecule_human host", + "source": "NMN_simple_molecule_human host", "target": "NRNAM_simple_molecule", "sign": true }, @@ -3117,13 +3117,13 @@ }, { "id": "t248", - "source": "NAMN_simple_molecule_nucleus", + "source": "NMNAT1:Zn2+_complex", "target": "NAAD_simple_molecule_nucleus", "sign": true }, { "id": "t249", - "source": "NMNAT1:Zn2+_complex", + "source": "NAMN_simple_molecule_nucleus", "target": "NAAD_simple_molecule_nucleus", "sign": true }, @@ -3135,13 +3135,13 @@ }, { "id": "t251", - "source": "NAMN_simple_molecule_nucleus", + "source": "NMNAT1:Zn2+_complex", "target": "PPi(3-)_simple_molecule_nucleus", "sign": true }, { "id": "t252", - "source": "NMNAT1:Zn2+_complex", + "source": "NAMN_simple_molecule_nucleus", "target": "PPi(3-)_simple_molecule_nucleus", "sign": true }, @@ -3165,73 +3165,73 @@ }, { "id": "t256", - "source": "H+_ion_endoplasmic reticulum", + "source": "PGG2_simple_molecule", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t257", - "source": "PGG2_simple_molecule", + "source": "e-_ion", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t258", - "source": "e-_ion", + "source": "MNA_simple_molecule", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t259", - "source": "PTGS2", + "source": "PTCS2:celecoxib_complex", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t260", - "source": "PTCS2:celecoxib_complex", + "source": "H+_ion_endoplasmic reticulum", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t261", - "source": "MNA_simple_molecule", + "source": "PTGS2", "target": "PGH2_simple_molecule", "sign": true }, { "id": "t262", - "source": "H+_ion_endoplasmic reticulum", + "source": "PGG2_simple_molecule", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, { "id": "t263", - "source": "PGG2_simple_molecule", + "source": "e-_ion", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, { "id": "t264", - "source": "e-_ion", + "source": "MNA_simple_molecule", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, { "id": "t265", - "source": "PTGS2", + "source": "PTCS2:celecoxib_complex", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, { "id": "t266", - "source": "PTCS2:celecoxib_complex", + "source": "H+_ion_endoplasmic reticulum", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, { "id": "t267", - "source": "MNA_simple_molecule", + "source": "PTGS2", "target": "H2O_simple_molecule_endoplasmic reticulum", "sign": true }, @@ -3243,13 +3243,13 @@ }, { "id": "t269", - "source": "SLC5A8", + "source": "Na+_ion_human host", "target": "monocarboxylates transported by SLC5A8_simple_molecule_cell", "sign": true }, { "id": "t270", - "source": "Na+_ion_human host", + "source": "SLC5A8", "target": "monocarboxylates transported by SLC5A8_simple_molecule_cell", "sign": true }, @@ -3261,19 +3261,19 @@ }, { "id": "t272", - "source": "SLC5A8", + "source": "Na+_ion_human host", "target": "Na+_ion_cell", "sign": true }, { "id": "t273", - "source": "Na+_ion_human host", + "source": "SLC5A8", "target": "Na+_ion_cell", "sign": true }, { "id": "t274", - "source": "IFN-G", + "source": "3HAA_simple_molecule", "target": "HMOX1_rna", "sign": true }, @@ -3285,7 +3285,7 @@ }, { "id": "t276", - "source": "3HAA_simple_molecule", + "source": "IFN-G", "target": "HMOX1_rna", "sign": true }, @@ -3309,13 +3309,13 @@ }, { "id": "t280", - "source": "HMOX1_cell", + "source": "Heme_simple_molecule", "target": "Fe2+_ion", "sign": true }, { "id": "t281", - "source": "Heme_simple_molecule", + "source": "HMOX1_cell", "target": "Fe2+_ion", "sign": true }, @@ -3333,13 +3333,13 @@ }, { "id": "t284", - "source": "HMOX1_cell", + "source": "Heme_simple_molecule", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t285", - "source": "Heme_simple_molecule", + "source": "HMOX1_cell", "target": "Biliverdin_simple_molecule", "sign": true }, @@ -3357,13 +3357,13 @@ }, { "id": "t288", - "source": "HMOX1_cell", + "source": "Heme_simple_molecule", "target": "CO_simple_molecule", "sign": true }, { "id": "t289", - "source": "Heme_simple_molecule", + "source": "HMOX1_cell", "target": "CO_simple_molecule", "sign": true }, @@ -3405,13 +3405,13 @@ }, { "id": "t296", - "source": "CA_simple_molecule", + "source": "3HKYN_simple_molecule", "target": "T-cell apoptosis_phenotype", "sign": true }, { "id": "t297", - "source": "3HKYN_simple_molecule", + "source": "CA_simple_molecule", "target": "T-cell apoptosis_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/NLRP3_Activation.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/NLRP3_Activation.json index 2c8959bf..94f06207 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/NLRP3_Activation.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/NLRP3_Activation.json @@ -644,49 +644,49 @@ }, { "id": "t3", - "source": "SUGT1:HSP90AB1_complex", + "source": "NLRP3_cell", "target": "NLRP3:SUGT1:HSP90_complex", "sign": true }, { "id": "t4", - "source": "NLRP3_cell", + "source": "SUGT1:HSP90AB1_complex", "target": "NLRP3:SUGT1:HSP90_complex", "sign": true }, { "id": "t5", - "source": "CASP1_cell", + "source": "NLRP3 oligomer:ASC_complex", "target": "NLRP3 oligomer:ASC:proCaspase1_complex", "sign": true }, { "id": "t6", - "source": "NLRP3 oligomer:ASC_complex", + "source": "CASP1_cell", "target": "NLRP3 oligomer:ASC:proCaspase1_complex", "sign": true }, { "id": "t7", - "source": "CTSG", + "source": "NLRP3 oligomer:ASC:proCaspase1_complex", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, { "id": "t8", - "source": "NLRP3 oligomer:ASC:proCaspase1_complex", + "source": "NLRP3_cell", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, { "id": "t9", - "source": "ASC_ubiquitinated", + "source": "CTSG", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, { "id": "t10", - "source": "NLRP3_cell", + "source": "ASC_ubiquitinated", "target": "NLRP3 oligomer:ASC_complex", "sign": true }, @@ -698,13 +698,13 @@ }, { "id": "t12", - "source": "TXNIP", + "source": "NLRP3_cell", "target": "TXNIP:NLRP3_complex", "sign": true }, { "id": "t13", - "source": "NLRP3_cell", + "source": "TXNIP", "target": "TXNIP:NLRP3_complex", "sign": true }, @@ -734,13 +734,13 @@ }, { "id": "t18", - "source": "p50", + "source": "p65", "target": "Nf-KB Complex_complex_cell", "sign": true }, { "id": "t19", - "source": "p65", + "source": "p50", "target": "Nf-KB Complex_complex_cell", "sign": true }, @@ -758,13 +758,13 @@ }, { "id": "t22", - "source": "TXN_cell", + "source": "TXNIP", "target": "Thioredoxin:TXNIP_complex", "sign": true }, { "id": "t23", - "source": "TXNIP", + "source": "TXN_cell", "target": "Thioredoxin:TXNIP_complex", "sign": true }, @@ -794,49 +794,49 @@ }, { "id": "t28", - "source": "Ca2+_ion", + "source": "NLRP3 Elicitor Proteins", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t29", - "source": "NLRP3 Elicitor Proteins", + "source": "DAMPs_phenotype", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t30", - "source": "NLRP3:SUGT1:HSP90_complex", + "source": "PAMPs_phenotype", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t31", - "source": "PAMPs_phenotype", + "source": "Reactive Oxygen Species_simple_molecule", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t32", - "source": "Reactive Oxygen Species_simple_molecule", + "source": "NLRP3 Elicitor Small Molecules_simple_molecule", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t33", - "source": "NLRP3 Elicitor Small Molecules_simple_molecule", + "source": "TXNIP:NLRP3_complex", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t34", - "source": "DAMPs_phenotype", + "source": "Ca2+_ion", "target": "SUGT1:HSP90AB1_complex", "sign": true }, { "id": "t35", - "source": "TXNIP:NLRP3_complex", + "source": "NLRP3:SUGT1:HSP90_complex", "target": "SUGT1:HSP90AB1_complex", "sign": true }, @@ -878,13 +878,13 @@ }, { "id": "t42", - "source": "proIL-1B_cell", + "source": "Caspase-1 Tetramer_complex", "target": "IL-1B_cell", "sign": true }, { "id": "t43", - "source": "Caspase-1 Tetramer_complex", + "source": "proIL-1B_cell", "target": "IL-1B_cell", "sign": true }, @@ -938,49 +938,49 @@ }, { "id": "t52", - "source": "Ca2+_ion", + "source": "NLRP3 Elicitor Proteins", "target": "NLRP3_cell", "sign": true }, { "id": "t53", - "source": "NLRP3 Elicitor Proteins", + "source": "DAMPs_phenotype", "target": "NLRP3_cell", "sign": true }, { "id": "t54", - "source": "NLRP3:SUGT1:HSP90_complex", + "source": "PAMPs_phenotype", "target": "NLRP3_cell", "sign": true }, { "id": "t55", - "source": "PAMPs_phenotype", + "source": "Reactive Oxygen Species_simple_molecule", "target": "NLRP3_cell", "sign": true }, { "id": "t56", - "source": "Reactive Oxygen Species_simple_molecule", + "source": "NLRP3 Elicitor Small Molecules_simple_molecule", "target": "NLRP3_cell", "sign": true }, { "id": "t57", - "source": "NLRP3 Elicitor Small Molecules_simple_molecule", + "source": "TXNIP:NLRP3_complex", "target": "NLRP3_cell", "sign": true }, { "id": "t58", - "source": "DAMPs_phenotype", + "source": "Ca2+_ion", "target": "NLRP3_cell", "sign": true }, { "id": "t59", - "source": "TXNIP:NLRP3_complex", + "source": "NLRP3:SUGT1:HSP90_complex", "target": "NLRP3_cell", "sign": true }, @@ -1010,13 +1010,13 @@ }, { "id": "t64", - "source": "O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t65", - "source": "HMOX1", + "source": "O2_simple_molecule", "target": "NADP+_simple_molecule", "sign": true }, @@ -1028,19 +1028,19 @@ }, { "id": "t67", - "source": "NADPH_simple_molecule", + "source": "HMOX1", "target": "NADP+_simple_molecule", "sign": true }, { "id": "t68", - "source": "O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t69", - "source": "HMOX1", + "source": "O2_simple_molecule", "target": "Biliverdin_simple_molecule", "sign": true }, @@ -1052,19 +1052,19 @@ }, { "id": "t71", - "source": "NADPH_simple_molecule", + "source": "HMOX1", "target": "Biliverdin_simple_molecule", "sign": true }, { "id": "t72", - "source": "O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "H2O_simple_molecule", "sign": true }, { "id": "t73", - "source": "HMOX1", + "source": "O2_simple_molecule", "target": "H2O_simple_molecule", "sign": true }, @@ -1076,19 +1076,19 @@ }, { "id": "t75", - "source": "NADPH_simple_molecule", + "source": "HMOX1", "target": "H2O_simple_molecule", "sign": true }, { "id": "t76", - "source": "O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "CO_simple_molecule", "sign": true }, { "id": "t77", - "source": "HMOX1", + "source": "O2_simple_molecule", "target": "CO_simple_molecule", "sign": true }, @@ -1100,19 +1100,19 @@ }, { "id": "t79", - "source": "NADPH_simple_molecule", + "source": "HMOX1", "target": "CO_simple_molecule", "sign": true }, { "id": "t80", - "source": "O2_simple_molecule", + "source": "NADPH_simple_molecule", "target": "Fe2+_ion", "sign": true }, { "id": "t81", - "source": "HMOX1", + "source": "O2_simple_molecule", "target": "Fe2+_ion", "sign": true }, @@ -1124,7 +1124,7 @@ }, { "id": "t83", - "source": "NADPH_simple_molecule", + "source": "HMOX1", "target": "Fe2+_ion", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp14.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp14.json index 6a98c0d4..08b98449 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp14.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp14.json @@ -1807,109 +1807,109 @@ "edges": [ { "id": "t1", - "source": "SIRT5", + "source": "Nsp14_mitochondrion", "target": "SIRT5:Nsp14_complex", "sign": true }, { "id": "t2", - "source": "Nsp14_mitochondrion", + "source": "SIRT5", "target": "SIRT5:Nsp14_complex", "sign": true }, { "id": "t3", - "source": "GLA", + "source": "Nsp14_cell", "target": "GLA:Nsp14_complex", "sign": true }, { "id": "t4", - "source": "Nsp14_cell", + "source": "GLA", "target": "GLA:Nsp14_complex", "sign": true }, { "id": "t5", - "source": "IMPDH2", + "source": "Nsp14_cell", "target": "IMPDH2:Nsp14_complex", "sign": true }, { "id": "t6", - "source": "Nsp14_cell", + "source": "IMPDH2", "target": "IMPDH2:Nsp14_complex", "sign": true }, { "id": "t7", - "source": "NADP_simple_molecule", + "source": "Raffinose_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t8", - "source": "LCT", + "source": "Stachyose_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t9", - "source": "AKR1B1", + "source": "GLA", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t10", - "source": "Galacitol_simple_molecule", + "source": "Lactose_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t11", - "source": "Melibiose_simple_molecule", + "source": "NADP_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t12", - "source": "GLA:Nsp14_complex", + "source": "GLB1", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t13", - "source": "Migalastat_drug", + "source": "LCT", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t14", - "source": "Lactose_simple_molecule", + "source": "Melibiose_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t15", - "source": "GLB1", + "source": "GLA:Nsp14_complex", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t16", - "source": "GLA", + "source": "Migalastat_drug", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t17", - "source": "Raffinose_simple_molecule", + "source": "AKR1B1", "target": "D-Galactose_simple_molecule", "sign": true }, { "id": "t18", - "source": "Stachyose_simple_molecule", + "source": "Galacitol_simple_molecule", "target": "D-Galactose_simple_molecule", "sign": true }, @@ -1921,79 +1921,79 @@ }, { "id": "t20", - "source": "D-Galactose_simple_molecule", + "source": "GALM", "target": "_alpha_-D-Galactose_simple_molecule", "sign": true }, { "id": "t21", - "source": "GALM", + "source": "D-Galactose_simple_molecule", "target": "_alpha_-D-Galactose_simple_molecule", "sign": true }, { "id": "t22", - "source": "_alpha_-D-Galactose_simple_molecule", + "source": "ATP_simple_molecule", "target": "_alpha_-D-Galactose-1P_simple_molecule", "sign": true }, { "id": "t23", - "source": "ATP_simple_molecule", + "source": "GALK1", "target": "_alpha_-D-Galactose-1P_simple_molecule", "sign": true }, { "id": "t24", - "source": "GALK1", + "source": "_alpha_-D-Galactose_simple_molecule", "target": "_alpha_-D-Galactose-1P_simple_molecule", "sign": true }, { "id": "t25", - "source": "DCK", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t26", - "source": "NME6", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t27", - "source": "GMP_simple_molecule", + "source": "NME7", "target": "ADP_simple_molecule", "sign": true }, { "id": "t28", - "source": "AK1", + "source": "ADK", "target": "ADP_simple_molecule", "sign": true }, { "id": "t29", - "source": "ADK", + "source": "NRK1", "target": "ADP_simple_molecule", "sign": true }, { "id": "t30", - "source": "GUK1", + "source": "Deoxyadenosine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t31", - "source": "NAD_simple_molecule", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t32", - "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "source": "GUK1", "target": "ADP_simple_molecule", "sign": true }, @@ -2005,223 +2005,223 @@ }, { "id": "t34", - "source": "Adenosine_simple_molecule", + "source": "GALK1", "target": "ADP_simple_molecule", "sign": true }, { "id": "t35", - "source": "GALK1", + "source": "_alpha_-D-Galactose_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t36", - "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "source": "AK7", "target": "ADP_simple_molecule", "sign": true }, { "id": "t37", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "Deamino-NAD_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t38", - "source": "dAMP_simple_molecule", + "source": "L-Aspartate_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t39", - "source": "NADK", + "source": "AMP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t40", - "source": "L-Aspartate_simple_molecule", + "source": "Glycine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t41", - "source": "AMP_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t42", - "source": "L-Glutamine_simple_molecule", + "source": "NADK", "target": "ADP_simple_molecule", "sign": true }, { "id": "t43", - "source": "NME7", + "source": "L-Glutamine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t44", - "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "source": "GMP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t45", - "source": "PFAS", + "source": "AK8", "target": "ADP_simple_molecule", "sign": true }, { "id": "t46", - "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "source": "Adenosine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t47", - "source": "AK5", + "source": "NAPRT1", "target": "ADP_simple_molecule", "sign": true }, { "id": "t48", - "source": "H2O_simple_molecule_cell", + "source": "dGDP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t49", - "source": "dADP_simple_molecule", + "source": "NME5", "target": "ADP_simple_molecule", "sign": true }, { "id": "t50", - "source": "NME5", + "source": "Nicotinate_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t51", - "source": "NAPRT1", + "source": "PAICS", "target": "ADP_simple_molecule", "sign": true }, { "id": "t52", - "source": "Nicotinate_simple_molecule", + "source": "NME3", "target": "ADP_simple_molecule", "sign": true }, { "id": "t53", - "source": "GART", + "source": "NADSYN1", "target": "ADP_simple_molecule", "sign": true }, { "id": "t54", - "source": "dGDP_simple_molecule", + "source": "Nucleoside diphosphate kinase_complex_cell", "target": "ADP_simple_molecule", "sign": true }, { "id": "t55", - "source": "NME3", + "source": "ATP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t56", - "source": "N-Ribosyl-nicotinamide_simple_molecule", + "source": "dAMP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t57", - "source": "AK7", + "source": "NME6", "target": "ADP_simple_molecule", "sign": true }, { "id": "t58", - "source": "ATP_simple_molecule", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t59", - "source": "Deoxyguanosine_simple_molecule", + "source": "PFAS", "target": "ADP_simple_molecule", "sign": true }, { "id": "t60", - "source": "PAICS", + "source": "GDP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t61", - "source": "Nucleoside diphosphate kinase_complex_cell", + "source": "DCK", "target": "ADP_simple_molecule", "sign": true }, { "id": "t62", - "source": "NADSYN1", + "source": "dADP_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t63", - "source": "AK8", + "source": "Deoxyguanosine_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t64", - "source": "Deoxyadenosine_simple_molecule", + "source": "NAD_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t65", - "source": "_alpha_-D-Galactose_simple_molecule", + "source": "AK5", "target": "ADP_simple_molecule", "sign": true }, { "id": "t66", - "source": "NRK1", + "source": "N-Ribosyl-nicotinamide_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t67", - "source": "Glycine_simple_molecule", + "source": "GART", "target": "ADP_simple_molecule", "sign": true }, { "id": "t68", - "source": "GDP_simple_molecule", + "source": "H2O_simple_molecule_cell", "target": "ADP_simple_molecule", "sign": true }, { "id": "t69", - "source": "Deamino-NAD_simple_molecule", + "source": "AK1", "target": "ADP_simple_molecule", "sign": true }, { "id": "t70", - "source": "_alpha_-D-Galactose-1P_simple_molecule", + "source": "GALE", "target": "UDP-_alpha_-D-Galactose_simple_molecule", "sign": true }, @@ -2239,7 +2239,7 @@ }, { "id": "t73", - "source": "GALE", + "source": "_alpha_-D-Galactose-1P_simple_molecule", "target": "UDP-_alpha_-D-Galactose_simple_molecule", "sign": true }, @@ -2251,103 +2251,103 @@ }, { "id": "t75", - "source": "UGP2", + "source": "GALT", "target": "_alpha_-D-Glucose-1-P_simple_molecule", "sign": true }, { "id": "t76", - "source": "_alpha_-D-Galactose-1P_simple_molecule", + "source": "PPi_simple_molecule", "target": "_alpha_-D-Glucose-1-P_simple_molecule", "sign": true }, { "id": "t77", - "source": "GALT", + "source": "UGP2", "target": "_alpha_-D-Glucose-1-P_simple_molecule", "sign": true }, { "id": "t78", - "source": "PPi_simple_molecule", + "source": "_alpha_-D-Galactose-1P_simple_molecule", "target": "_alpha_-D-Glucose-1-P_simple_molecule", "sign": true }, { "id": "t79", - "source": "PPi_simple_molecule", + "source": "UDP-_alpha_-D-Glucose_simple_molecule", "target": "UTP_simple_molecule", "sign": true }, { "id": "t80", - "source": "UDP-_alpha_-D-Glucose_simple_molecule", + "source": "UGP2", "target": "UTP_simple_molecule", "sign": true }, { "id": "t81", - "source": "UGP2", + "source": "PPi_simple_molecule", "target": "UTP_simple_molecule", "sign": true }, { "id": "t82", - "source": "Nicotinamide_simple_molecule", + "source": "HPRT1", "target": "PPi_simple_molecule", "sign": true }, { "id": "t83", - "source": "NMNAT3", + "source": "ITPA", "target": "PPi_simple_molecule", "sign": true }, { "id": "t84", - "source": "NAPRT1", + "source": "APRT", "target": "PPi_simple_molecule", "sign": true }, { "id": "t85", - "source": "Guanine_simple_molecule", + "source": "NMNAT1", "target": "PPi_simple_molecule", "sign": true }, { "id": "t86", - "source": "Nicotinate_simple_molecule", + "source": "GMPS", "target": "PPi_simple_molecule", "sign": true }, { "id": "t87", - "source": "HPRT1", + "source": "Hypoxanthine_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t88", - "source": "GMPS", + "source": "QPRT", "target": "PPi_simple_molecule", "sign": true }, { "id": "t89", - "source": "dGTP_simple_molecule", + "source": "PPAT", "target": "PPi_simple_molecule", "sign": true }, { "id": "t90", - "source": "PPAT", + "source": "Nicotinate_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t91", - "source": "APRT", + "source": "dGTP_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, @@ -2359,91 +2359,91 @@ }, { "id": "t93", - "source": "QPRT", + "source": "NAMPT", "target": "PPi_simple_molecule", "sign": true }, { "id": "t94", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "NMNAT3", "target": "PPi_simple_molecule", "sign": true }, { "id": "t95", - "source": "Nicotinamide D-ribonucleotide_simple_molecule", + "source": "Quinolinate_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t96", - "source": "Hypoxanthine_simple_molecule", + "source": "Guanine_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t97", - "source": "NMNAT2", + "source": "Nicotinate D-ribonucleotide_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t98", - "source": "Adenine_simple_molecule", + "source": "H_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t99", - "source": "H_simple_molecule", + "source": "Nicotinamide_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t100", - "source": "L-Glutamine_simple_molecule", + "source": "XMP_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t101", - "source": "NMNAT1", + "source": "Nicotinamide D-ribonucleotide_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t102", - "source": "Quinolinate_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t103", - "source": "ENPP1", + "source": "ENPP3", "target": "PPi_simple_molecule", "sign": true }, { "id": "t104", - "source": "ENPP3", + "source": "Adenine_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t105", - "source": "XMP_simple_molecule", + "source": "L-Glutamine_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t106", - "source": "NAMPT", + "source": "ENPP1", "target": "PPi_simple_molecule", "sign": true }, { "id": "t107", - "source": "Nicotinate D-ribonucleotide_simple_molecule", + "source": "NAPRT1", "target": "PPi_simple_molecule", "sign": true }, @@ -2455,7 +2455,7 @@ }, { "id": "t109", - "source": "ITPA", + "source": "NMNAT2", "target": "PPi_simple_molecule", "sign": true }, @@ -2467,25 +2467,25 @@ }, { "id": "t111", - "source": "UDP-_alpha_-D-Galactose_simple_molecule", + "source": "lactose synthetase_complex", "target": "Lactose_simple_molecule", "sign": true }, { "id": "t112", - "source": "lactose synthetase_complex", + "source": "UDP-_alpha_-D-Galactose_simple_molecule", "target": "Lactose_simple_molecule", "sign": true }, { "id": "t113", - "source": "Melibiose_simple_molecule", + "source": "GLA", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, { "id": "t114", - "source": "LCT", + "source": "Lactose_simple_molecule", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, @@ -2497,25 +2497,25 @@ }, { "id": "t116", - "source": "Migalastat_drug", + "source": "GLB1", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, { "id": "t117", - "source": "Lactose_simple_molecule", + "source": "LCT", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, { "id": "t118", - "source": "GLB1", + "source": "Melibiose_simple_molecule", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, { "id": "t119", - "source": "GLA", + "source": "Migalastat_drug", "target": "_alpha_-D-Glucose_simple_molecule", "sign": true }, @@ -2533,13 +2533,13 @@ }, { "id": "t122", - "source": "UDP-_alpha_-D-Galactose_simple_molecule", + "source": "lactose synthetase_complex", "target": "UDP_simple_molecule", "sign": true }, { "id": "t123", - "source": "lactose synthetase_complex", + "source": "UDP-_alpha_-D-Galactose_simple_molecule", "target": "UDP_simple_molecule", "sign": true }, @@ -2551,13 +2551,13 @@ }, { "id": "t125", - "source": "ATIC", + "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t126", - "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "source": "ADP_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, @@ -2569,37 +2569,37 @@ }, { "id": "t128", - "source": "Thioredoxin_simple_molecule", + "source": "ATIC", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t129", - "source": "ADP_simple_molecule", + "source": "Thioredoxin_simple_molecule", "target": "H2O_simple_molecule_cell", "sign": true }, { "id": "t130", - "source": "NADK", + "source": "NADPH_simple_molecule", "target": "NADP_simple_molecule", "sign": true }, { "id": "t131", - "source": "NADPH_simple_molecule", + "source": "NADK", "target": "NADP_simple_molecule", "sign": true }, { "id": "t132", - "source": "NNT", + "source": "NAD_simple_molecule", "target": "NADP_simple_molecule", "sign": true }, { "id": "t133", - "source": "NAD_simple_molecule", + "source": "NNT", "target": "NADP_simple_molecule", "sign": true }, @@ -2611,295 +2611,295 @@ }, { "id": "t135", - "source": "NADP_simple_molecule", + "source": "IMP_simple_molecule", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t136", - "source": "AKR1B1", + "source": "NADP_simple_molecule", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t137", - "source": "Galacitol_simple_molecule", + "source": "Ammonium_simple_molecule", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t138", - "source": "GMPR2", + "source": "GMPR", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t139", - "source": "Ammonium_simple_molecule", + "source": "AKR1B1", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t140", - "source": "GMPR", + "source": "GMPR2", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t141", - "source": "IMP_simple_molecule", + "source": "Galacitol_simple_molecule", "target": "NADPH_simple_molecule", "sign": true }, { "id": "t142", - "source": "DCK", + "source": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t143", - "source": "NADP_simple_molecule", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t144", - "source": "GTP_simple_molecule", + "source": "ENTPD5", "target": "H_simple_molecule", "sign": true }, { "id": "t145", - "source": "Ribavirin_drug", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t146", - "source": "Merimepodib_drug", + "source": "IMP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t147", - "source": "ENTPD5", + "source": "GMPS", "target": "H_simple_molecule", "sign": true }, { "id": "t148", - "source": "ADK", + "source": "Hypoxanthine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t149", - "source": "NAD_simple_molecule", + "source": "NRK1", "target": "H_simple_molecule", "sign": true }, { "id": "t150", - "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "source": "ADK", "target": "H_simple_molecule", "sign": true }, { "id": "t151", - "source": "10-Formyltetrahydrofolate_simple_molecule", + "source": "Deoxyadenosine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t152", - "source": "Adenosine_simple_molecule", + "source": "Ammonium_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t153", - "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "source": "IMPDH2:Nsp14_complex", "target": "H_simple_molecule", "sign": true }, { "id": "t154", - "source": "NADK", + "source": "Ribavirin_drug", "target": "H_simple_molecule", "sign": true }, { "id": "t155", - "source": "CD38", + "source": "CANT1", "target": "H_simple_molecule", "sign": true }, { "id": "t156", - "source": "L-Aspartate_simple_molecule", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t157", - "source": "IMPDH1", + "source": "Mycophenolic acid_drug", "target": "H_simple_molecule", "sign": true }, { "id": "t158", - "source": "AKR1B1", + "source": "GMPR2", "target": "H_simple_molecule", "sign": true }, { "id": "t159", - "source": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "source": "ENTPD2", "target": "H_simple_molecule", "sign": true }, { "id": "t160", - "source": "CANT1", + "source": "Merimepodib_drug", "target": "H_simple_molecule", "sign": true }, { "id": "t161", - "source": "L-Glutamine_simple_molecule", + "source": "Deamino-NAD_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t162", - "source": "GMPR2", + "source": "CD38", "target": "H_simple_molecule", "sign": true }, { "id": "t163", - "source": "Hypoxanthine_simple_molecule", + "source": "L-Aspartate_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t164", - "source": "XDH", + "source": "XMP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t165", - "source": "CO2_simple_molecule", + "source": "Glycine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t166", - "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "source": "ENPP3", "target": "H_simple_molecule", "sign": true }, { "id": "t167", - "source": "ENPP3", + "source": "NADK", "target": "H_simple_molecule", "sign": true }, { "id": "t168", - "source": "Aminoimidazole ribotide_simple_molecule", + "source": "L-Glutamine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t169", - "source": "PFAS", + "source": "IMPDH2", "target": "H_simple_molecule", "sign": true }, { "id": "t170", - "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "source": "GTP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t171", - "source": "IMPDH2", + "source": "ENPP1", "target": "H_simple_molecule", "sign": true }, { "id": "t172", - "source": "H2O_simple_molecule_cell", + "source": "Adenosine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t173", - "source": "ENTPD4", + "source": "AKR1B1", "target": "H_simple_molecule", "sign": true }, { "id": "t174", - "source": "IMPDH2:Nsp14_complex", + "source": "Aminoimidazole ribotide_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t175", - "source": "ENTPD6", + "source": "CO2_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t176", - "source": "GART", + "source": "ITPA", "target": "H_simple_molecule", "sign": true }, { "id": "t177", - "source": "Ammonium_simple_molecule", + "source": "NTPCR", "target": "H_simple_molecule", "sign": true }, { "id": "t178", - "source": "N-Ribosyl-nicotinamide_simple_molecule", + "source": "NADP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t179", - "source": "GMPS", + "source": "IMPDH1", "target": "H_simple_molecule", "sign": true }, { "id": "t180", - "source": "dGTP_simple_molecule", + "source": "PAICS", "target": "H_simple_molecule", "sign": true }, { "id": "t181", - "source": "ATP_simple_molecule", + "source": "NADSYN1", "target": "H_simple_molecule", "sign": true }, { "id": "t182", - "source": "Mycophenolic acid_drug", + "source": "dGTP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t183", - "source": "Deoxyguanosine_simple_molecule", + "source": "ATP_simple_molecule", "target": "H_simple_molecule", "sign": true }, @@ -2911,109 +2911,109 @@ }, { "id": "t185", - "source": "PAICS", + "source": "XDH", "target": "H_simple_molecule", "sign": true }, { "id": "t186", - "source": "ENTPD2", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t187", - "source": "NADSYN1", + "source": "PFAS", "target": "H_simple_molecule", "sign": true }, { "id": "t188", - "source": "ENPP1", + "source": "ENTPD4", "target": "H_simple_molecule", "sign": true }, { "id": "t189", - "source": "Deoxyadenosine_simple_molecule", + "source": "GDP_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t190", - "source": "NRK1", + "source": "DCK", "target": "H_simple_molecule", "sign": true }, { "id": "t191", - "source": "Glycine_simple_molecule", + "source": "ENTPD6", "target": "H_simple_molecule", "sign": true }, { "id": "t192", - "source": "XMP_simple_molecule", + "source": "Deoxyguanosine_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t193", - "source": "GMPR", + "source": "NAD_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t194", - "source": "GDP_simple_molecule", + "source": "GMPR", "target": "H_simple_molecule", "sign": true }, { "id": "t195", - "source": "IMP_simple_molecule", + "source": "N-Ribosyl-nicotinamide_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t196", - "source": "NTPCR", + "source": "10-Formyltetrahydrofolate_simple_molecule", "target": "H_simple_molecule", "sign": true }, { "id": "t197", - "source": "Deamino-NAD_simple_molecule", + "source": "GART", "target": "H_simple_molecule", "sign": true }, { "id": "t198", - "source": "ITPA", + "source": "H2O_simple_molecule_cell", "target": "H_simple_molecule", "sign": true }, { "id": "t199", - "source": "GLA:Nsp14_complex", + "source": "Stachyose_simple_molecule", "target": "Raffinose_simple_molecule", "sign": true }, { "id": "t200", - "source": "Migalastat_drug", + "source": "GLA", "target": "Raffinose_simple_molecule", "sign": true }, { "id": "t201", - "source": "GLA", + "source": "Migalastat_drug", "target": "Raffinose_simple_molecule", "sign": true }, { "id": "t202", - "source": "Stachyose_simple_molecule", + "source": "GLA:Nsp14_complex", "target": "Raffinose_simple_molecule", "sign": true }, @@ -3025,25 +3025,25 @@ }, { "id": "t204", - "source": "GLA:Nsp14_complex", + "source": "Raffinose_simple_molecule", "target": "Sucrose_simple_molecule", "sign": true }, { "id": "t205", - "source": "Migalastat_drug", + "source": "GLA", "target": "Sucrose_simple_molecule", "sign": true }, { "id": "t206", - "source": "GLA", + "source": "GLA:Nsp14_complex", "target": "Sucrose_simple_molecule", "sign": true }, { "id": "t207", - "source": "Raffinose_simple_molecule", + "source": "Migalastat_drug", "target": "Sucrose_simple_molecule", "sign": true }, @@ -3055,13 +3055,13 @@ }, { "id": "t209", - "source": "PNP", + "source": "CD38", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t210", - "source": "CD38", + "source": "H2O_simple_molecule_mitochondrion", "target": "Nicotinamide_simple_molecule", "sign": true }, @@ -3073,37 +3073,37 @@ }, { "id": "t212", - "source": "Pi_simple_molecule", + "source": "SIRT5:Nsp14_complex", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t213", - "source": "Histone N6-acetyl-L-lysine_simple_molecule", + "source": "Pi_simple_molecule", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t214", - "source": "H2O_simple_molecule_mitochondrion", + "source": "NAD_simple_molecule", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t215", - "source": "Nicotinate_simple_molecule", + "source": "Histone N6-acetyl-L-lysine_simple_molecule", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t216", - "source": "NAD_simple_molecule", + "source": "SIRT5", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t217", - "source": "SIRT5", + "source": "Nicotinate_simple_molecule", "target": "Nicotinamide_simple_molecule", "sign": true }, @@ -3115,13 +3115,13 @@ }, { "id": "t219", - "source": "SIRT5:Nsp14_complex", + "source": "H2O_simple_molecule_cell", "target": "Nicotinamide_simple_molecule", "sign": true }, { "id": "t220", - "source": "H2O_simple_molecule_cell", + "source": "PNP", "target": "Nicotinamide_simple_molecule", "sign": true }, @@ -3151,37 +3151,37 @@ }, { "id": "t225", - "source": "NAD_simple_molecule", + "source": "ENPP3", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t226", - "source": "ENPP1", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t227", - "source": "N-Ribosyl-nicotinamide_simple_molecule", + "source": "NRK1", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t228", - "source": "ENPP3", + "source": "NAD_simple_molecule", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t229", - "source": "NRK1", + "source": "ENPP1", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t230", - "source": "NAMPT", + "source": "N-Ribosyl-nicotinamide_simple_molecule", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, @@ -3193,37 +3193,37 @@ }, { "id": "t232", - "source": "H2O_simple_molecule_cell", + "source": "NAMPT", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t233", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "H2O_simple_molecule_cell", "target": "Nicotinamide D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t234", - "source": "Nicotinamide D-ribonucleotide_simple_molecule", + "source": "Deamino-NAD_simple_molecule", "target": "NAD_simple_molecule", "sign": true }, { "id": "t235", - "source": "NMNAT2", + "source": "H_simple_molecule", "target": "NAD_simple_molecule", "sign": true }, { "id": "t236", - "source": "H_simple_molecule", + "source": "NMNAT1", "target": "NAD_simple_molecule", "sign": true }, { "id": "t237", - "source": "L-Glutamine_simple_molecule", + "source": "Nicotinamide D-ribonucleotide_simple_molecule", "target": "NAD_simple_molecule", "sign": true }, @@ -3235,7 +3235,7 @@ }, { "id": "t239", - "source": "NMNAT1", + "source": "L-Glutamine_simple_molecule", "target": "NAD_simple_molecule", "sign": true }, @@ -3259,13 +3259,13 @@ }, { "id": "t243", - "source": "Deamino-NAD_simple_molecule", + "source": "NMNAT2", "target": "NAD_simple_molecule", "sign": true }, { "id": "t244", - "source": "NMNAT2", + "source": "Nicotinate D-ribonucleotide_simple_molecule", "target": "Deamino-NAD_simple_molecule", "sign": true }, @@ -3277,25 +3277,25 @@ }, { "id": "t246", - "source": "NMNAT3", + "source": "NMNAT1", "target": "Deamino-NAD_simple_molecule", "sign": true }, { "id": "t247", - "source": "NMNAT1", + "source": "ATP_simple_molecule", "target": "Deamino-NAD_simple_molecule", "sign": true }, { "id": "t248", - "source": "Nicotinate D-ribonucleotide_simple_molecule", + "source": "NMNAT3", "target": "Deamino-NAD_simple_molecule", "sign": true }, { "id": "t249", - "source": "ATP_simple_molecule", + "source": "NMNAT2", "target": "Deamino-NAD_simple_molecule", "sign": true }, @@ -3307,31 +3307,31 @@ }, { "id": "t251", - "source": "NAPRT1", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t252", - "source": "Nicotinate_simple_molecule", + "source": "QPRT", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t253", - "source": "Quinolinate_simple_molecule", + "source": "Nicotinate_simple_molecule", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t254", - "source": "ATP_simple_molecule", + "source": "NAPRT1", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t255", - "source": "QPRT", + "source": "ATP_simple_molecule", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, @@ -3343,25 +3343,25 @@ }, { "id": "t257", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "Quinolinate_simple_molecule", "target": "Nicotinate D-ribonucleotide_simple_molecule", "sign": true }, { "id": "t258", - "source": "Mycophenolic acid_drug", + "source": "Merimepodib_drug", "target": "NADH_simple_molecule", "sign": true }, { "id": "t259", - "source": "IMPDH1", + "source": "NADPH_simple_molecule", "target": "NADH_simple_molecule", "sign": true }, { "id": "t260", - "source": "NADPH_simple_molecule", + "source": "IMP_simple_molecule", "target": "NADH_simple_molecule", "sign": true }, @@ -3373,49 +3373,49 @@ }, { "id": "t262", - "source": "Ribavirin_drug", + "source": "NAD_simple_molecule", "target": "NADH_simple_molecule", "sign": true }, { "id": "t263", - "source": "NNT", + "source": "IMPDH2", "target": "NADH_simple_molecule", "sign": true }, { "id": "t264", - "source": "IMPDH2:Nsp14_complex", + "source": "IMPDH1", "target": "NADH_simple_molecule", "sign": true }, { "id": "t265", - "source": "XDH", + "source": "IMPDH2:Nsp14_complex", "target": "NADH_simple_molecule", "sign": true }, { "id": "t266", - "source": "Merimepodib_drug", + "source": "NNT", "target": "NADH_simple_molecule", "sign": true }, { "id": "t267", - "source": "NAD_simple_molecule", + "source": "Ribavirin_drug", "target": "NADH_simple_molecule", "sign": true }, { "id": "t268", - "source": "IMPDH2", + "source": "Mycophenolic acid_drug", "target": "NADH_simple_molecule", "sign": true }, { "id": "t269", - "source": "IMP_simple_molecule", + "source": "XDH", "target": "NADH_simple_molecule", "sign": true }, @@ -3427,49 +3427,49 @@ }, { "id": "t271", - "source": "L-Glutamine_simple_molecule", + "source": "PFAS", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t272", - "source": "NADSYN1", + "source": "Deamino-NAD_simple_molecule", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t273", - "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "source": "XMP_simple_molecule", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t274", - "source": "XMP_simple_molecule", + "source": "GMPS", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t275", - "source": "PPAT", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t276", - "source": "PFAS", + "source": "L-Glutamine_simple_molecule", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t277", - "source": "GMPS", + "source": "PPAT", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t278", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "NADSYN1", "target": "L-Glutamate_simple_molecule", "sign": true }, @@ -3487,37 +3487,37 @@ }, { "id": "t281", - "source": "Deamino-NAD_simple_molecule", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "target": "L-Glutamate_simple_molecule", "sign": true }, { "id": "t282", - "source": "ADK", + "source": "APRT", "target": "AMP_simple_molecule", "sign": true }, { "id": "t283", - "source": "NAD_simple_molecule", + "source": "PRPS1L1", "target": "AMP_simple_molecule", "sign": true }, { "id": "t284", - "source": "Adenosine_simple_molecule", + "source": "GMPS", "target": "AMP_simple_molecule", "sign": true }, { "id": "t285", - "source": "GMPS", + "source": "ADK", "target": "AMP_simple_molecule", "sign": true }, { "id": "t286", - "source": "APRT", + "source": "D-Ribose 5P_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, @@ -3529,31 +3529,31 @@ }, { "id": "t288", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "XMP_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t289", - "source": "PRPS2", + "source": "ENPP3", "target": "AMP_simple_molecule", "sign": true }, { "id": "t290", - "source": "Adenine_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t291", - "source": "D-Ribose 5P_simple_molecule", + "source": "Adenine_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t292", - "source": "PRPS1", + "source": "NAD_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, @@ -3571,19 +3571,19 @@ }, { "id": "t295", - "source": "ENPP3", + "source": "Adenosine_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t296", - "source": "XMP_simple_molecule", + "source": "PRPS1", "target": "AMP_simple_molecule", "sign": true }, { "id": "t297", - "source": "PRPS1L1", + "source": "PRPS2", "target": "AMP_simple_molecule", "sign": true }, @@ -3595,127 +3595,127 @@ }, { "id": "t299", - "source": "PNP", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t300", - "source": "GTP_simple_molecule", + "source": "ENTPD5", "target": "Pi_simple_molecule", "sign": true }, { "id": "t301", - "source": "GMP_simple_molecule", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t302", - "source": "ENTPD5", + "source": "IMP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t303", - "source": "NT5E", + "source": "Hypoxanthine_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t304", - "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "source": "NT5E", "target": "Pi_simple_molecule", "sign": true }, { "id": "t305", - "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "source": "CANT1", "target": "Pi_simple_molecule", "sign": true }, { "id": "t306", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t307", - "source": "L-Aspartate_simple_molecule", + "source": "ENTPD2", "target": "Pi_simple_molecule", "sign": true }, { "id": "t308", - "source": "Hypoxanthine_simple_molecule", + "source": "L-Aspartate_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t309", - "source": "AMP_simple_molecule", + "source": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t310", - "source": "CANT1", + "source": "XMP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t311", - "source": "L-Glutamine_simple_molecule", + "source": "AMP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t312", - "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "source": "Glycine_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t313", - "source": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", + "source": "Nicotinamide D-ribonucleotide_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t314", - "source": "PFAS", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t315", - "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "source": "L-Glutamine_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t316", - "source": "H2O_simple_molecule_cell", + "source": "GMP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t317", - "source": "ENTPD4", + "source": "GTP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t318", - "source": "ENTPD6", + "source": "NAPRT1", "target": "Pi_simple_molecule", "sign": true }, { "id": "t319", - "source": "NAPRT1", + "source": "NTPCR", "target": "Pi_simple_molecule", "sign": true }, @@ -3727,7 +3727,7 @@ }, { "id": "t321", - "source": "GART", + "source": "PAICS", "target": "Pi_simple_molecule", "sign": true }, @@ -3739,61 +3739,61 @@ }, { "id": "t323", - "source": "Nicotinamide D-ribonucleotide_simple_molecule", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t324", - "source": "PAICS", + "source": "PNP", "target": "Pi_simple_molecule", "sign": true }, { "id": "t325", - "source": "ENTPD2", + "source": "PFAS", "target": "Pi_simple_molecule", "sign": true }, { "id": "t326", - "source": "Glycine_simple_molecule", + "source": "ENTPD4", "target": "Pi_simple_molecule", "sign": true }, { "id": "t327", - "source": "XMP_simple_molecule", + "source": "GDP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t328", - "source": "GDP_simple_molecule", + "source": "ENTPD6", "target": "Pi_simple_molecule", "sign": true }, { "id": "t329", - "source": "IMP_simple_molecule", + "source": "GART", "target": "Pi_simple_molecule", "sign": true }, { "id": "t330", - "source": "NTPCR", + "source": "H2O_simple_molecule_cell", "target": "Pi_simple_molecule", "sign": true }, { "id": "t331", - "source": "CD38", + "source": "NADP_simple_molecule", "target": "nicotinate-adenine dinucleotide phosphate_simple_molecule", "sign": true }, { "id": "t332", - "source": "NADP_simple_molecule", + "source": "CD38", "target": "nicotinate-adenine dinucleotide phosphate_simple_molecule", "sign": true }, @@ -3805,19 +3805,19 @@ }, { "id": "t334", - "source": "D-Ribose 5P_simple_molecule", + "source": "PRPS1L1", "target": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "sign": true }, { "id": "t335", - "source": "PRPS1", + "source": "D-Ribose 5P_simple_molecule", "target": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "sign": true }, { "id": "t336", - "source": "PRPS1L1", + "source": "PRPS1", "target": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "sign": true }, @@ -3835,25 +3835,25 @@ }, { "id": "t339", - "source": "PNP", + "source": "Xanthosine_simple_molecule", "target": "_alpha_-D-Ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t340", - "source": "Pi_simple_molecule", + "source": "Guanosine_simple_molecule", "target": "_alpha_-D-Ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t341", - "source": "Inosine_simple_molecule", + "source": "Pi_simple_molecule", "target": "_alpha_-D-Ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t342", - "source": "Xanthosine_simple_molecule", + "source": "Inosine_simple_molecule", "target": "_alpha_-D-Ribose 1-phosphate_simple_molecule", "sign": true }, @@ -3871,67 +3871,67 @@ }, { "id": "t345", - "source": "Guanosine_simple_molecule", + "source": "PNP", "target": "_alpha_-D-Ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t346", - "source": "Histone N6-acetyl-L-lysine_simple_molecule", + "source": "H2O_simple_molecule_mitochondrion", "target": "Histone-L-lysine_simple_molecule", "sign": true }, { "id": "t347", - "source": "H2O_simple_molecule_mitochondrion", + "source": "SIRT5:Nsp14_complex", "target": "Histone-L-lysine_simple_molecule", "sign": true }, { "id": "t348", - "source": "NAD_simple_molecule", + "source": "Histone N6-acetyl-L-lysine_simple_molecule", "target": "Histone-L-lysine_simple_molecule", "sign": true }, { "id": "t349", - "source": "SIRT5", + "source": "NAD_simple_molecule", "target": "Histone-L-lysine_simple_molecule", "sign": true }, { "id": "t350", - "source": "SIRT5:Nsp14_complex", + "source": "SIRT5", "target": "Histone-L-lysine_simple_molecule", "sign": true }, { "id": "t351", - "source": "Histone N6-acetyl-L-lysine_simple_molecule", + "source": "H2O_simple_molecule_mitochondrion", "target": "O-Acetyl-ADP-ribose_simple_molecule", "sign": true }, { "id": "t352", - "source": "H2O_simple_molecule_mitochondrion", + "source": "SIRT5:Nsp14_complex", "target": "O-Acetyl-ADP-ribose_simple_molecule", "sign": true }, { "id": "t353", - "source": "NAD_simple_molecule", + "source": "Histone N6-acetyl-L-lysine_simple_molecule", "target": "O-Acetyl-ADP-ribose_simple_molecule", "sign": true }, { "id": "t354", - "source": "SIRT5", + "source": "NAD_simple_molecule", "target": "O-Acetyl-ADP-ribose_simple_molecule", "sign": true }, { "id": "t355", - "source": "SIRT5:Nsp14_complex", + "source": "SIRT5", "target": "O-Acetyl-ADP-ribose_simple_molecule", "sign": true }, @@ -3955,85 +3955,85 @@ }, { "id": "t359", - "source": "Quinolinate_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "CO2_simple_molecule", "sign": true }, { "id": "t360", - "source": "QPRT", + "source": "H_simple_molecule", "target": "CO2_simple_molecule", "sign": true }, { "id": "t361", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "Quinolinate_simple_molecule", "target": "CO2_simple_molecule", "sign": true }, { "id": "t362", - "source": "H_simple_molecule", + "source": "QPRT", "target": "CO2_simple_molecule", "sign": true }, { "id": "t363", - "source": "PGM2", + "source": "_alpha_D-Ribose 1P_simple_molecule", "target": "D-Ribose 5P_simple_molecule", "sign": true }, { "id": "t364", - "source": "_alpha_D-Ribose 1P_simple_molecule", + "source": "PGM2", "target": "D-Ribose 5P_simple_molecule", "sign": true }, { "id": "t365", - "source": "L-Glutamine_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "5-phospho-beta-D-ribosylamine_simple_molecule", "sign": true }, { "id": "t366", - "source": "PPAT", + "source": "H2O_simple_molecule_cell", "target": "5-phospho-beta-D-ribosylamine_simple_molecule", "sign": true }, { "id": "t367", - "source": "H2O_simple_molecule_cell", + "source": "PPAT", "target": "5-phospho-beta-D-ribosylamine_simple_molecule", "sign": true }, { "id": "t368", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "L-Glutamine_simple_molecule", "target": "5-phospho-beta-D-ribosylamine_simple_molecule", "sign": true }, { "id": "t369", - "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "source": "Glycine_simple_molecule", "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "sign": true }, { "id": "t370", - "source": "Glycine_simple_molecule", + "source": "ATP_simple_molecule", "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "sign": true }, { "id": "t371", - "source": "ATP_simple_molecule", + "source": "GART", "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "sign": true }, { "id": "t372", - "source": "GART", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "sign": true }, @@ -4045,13 +4045,13 @@ }, { "id": "t374", - "source": "10-Formyltetrahydrofolate_simple_molecule", + "source": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "sign": true }, { "id": "t375", - "source": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "source": "10-Formyltetrahydrofolate_simple_molecule", "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", "sign": true }, @@ -4069,43 +4069,43 @@ }, { "id": "t378", - "source": "ATIC", + "source": "10-Formyltetrahydrofolate_simple_molecule", "target": "Tetrahydrofolate_simple_molecule", "sign": true }, { "id": "t379", - "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "source": "ATIC", "target": "Tetrahydrofolate_simple_molecule", "sign": true }, { "id": "t380", - "source": "10-Formyltetrahydrofolate_simple_molecule", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", "target": "Tetrahydrofolate_simple_molecule", "sign": true }, { "id": "t381", - "source": "L-Glutamine_simple_molecule", + "source": "PFAS", "target": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "sign": true }, { "id": "t382", - "source": "PFAS", + "source": "L-Glutamine_simple_molecule", "target": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "sign": true }, { "id": "t383", - "source": "H2O_simple_molecule_cell", + "source": "ATP_simple_molecule", "target": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "sign": true }, { "id": "t384", - "source": "ATP_simple_molecule", + "source": "H2O_simple_molecule_cell", "target": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "sign": true }, @@ -4117,7 +4117,7 @@ }, { "id": "t386", - "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "source": "ATP_simple_molecule", "target": "Aminoimidazole ribotide_simple_molecule", "sign": true }, @@ -4129,19 +4129,19 @@ }, { "id": "t388", - "source": "ATP_simple_molecule", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", "target": "Aminoimidazole ribotide_simple_molecule", "sign": true }, { "id": "t389", - "source": "CO2_simple_molecule", + "source": "Aminoimidazole ribotide_simple_molecule", "target": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "sign": true }, { "id": "t390", - "source": "Aminoimidazole ribotide_simple_molecule", + "source": "CO2_simple_molecule", "target": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "sign": true }, @@ -4153,121 +4153,121 @@ }, { "id": "t392", - "source": "L-Aspartate_simple_molecule", + "source": "ATP_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "sign": true }, { "id": "t393", - "source": "ATP_simple_molecule", + "source": "L-Aspartate_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "sign": true }, { "id": "t394", - "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "source": "PAICS", "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "sign": true }, { "id": "t395", - "source": "PAICS", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "sign": true }, { "id": "t396", - "source": "ADSL", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", "sign": true }, { "id": "t397", - "source": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "source": "ADSL", "target": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", "sign": true }, { "id": "t398", - "source": "ADSL", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", "target": "Fumarate_simple_molecule", "sign": true }, { "id": "t399", - "source": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "source": "ADSL", "target": "Fumarate_simple_molecule", "sign": true }, { "id": "t400", - "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "source": "ATIC", "target": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", "sign": true }, { "id": "t401", - "source": "10-Formyltetrahydrofolate_simple_molecule", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", "sign": true }, { "id": "t402", - "source": "ATIC", + "source": "10-Formyltetrahydrofolate_simple_molecule", "target": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", "sign": true }, { "id": "t403", - "source": "Hypoxanthine_simple_molecule", + "source": "HPRT1", "target": "IMP_simple_molecule", "sign": true }, { "id": "t404", - "source": "AMP_simple_molecule", + "source": "H_simple_molecule", "target": "IMP_simple_molecule", "sign": true }, { "id": "t405", - "source": "H_simple_molecule", + "source": "AMP_simple_molecule", "target": "IMP_simple_molecule", "sign": true }, { "id": "t406", - "source": "AMPD1", + "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", "target": "IMP_simple_molecule", "sign": true }, { "id": "t407", - "source": "AMDP2", + "source": "Hypoxanthine_simple_molecule", "target": "IMP_simple_molecule", "sign": true }, { "id": "t408", - "source": "AMPD3", + "source": "AMPD1", "target": "IMP_simple_molecule", "sign": true }, { "id": "t409", - "source": "ATIC", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "IMP_simple_molecule", "sign": true }, { "id": "t410", - "source": "HPRT1", + "source": "AMPD3", "target": "IMP_simple_molecule", "sign": true }, { "id": "t411", - "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "source": "ATIC", "target": "IMP_simple_molecule", "sign": true }, @@ -4279,55 +4279,55 @@ }, { "id": "t413", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "AMDP2", "target": "IMP_simple_molecule", "sign": true }, { "id": "t414", - "source": "Mycophenolic acid_drug", + "source": "Merimepodib_drug", "target": "XMP_simple_molecule", "sign": true }, { "id": "t415", - "source": "IMPDH1", + "source": "IMP_simple_molecule", "target": "XMP_simple_molecule", "sign": true }, { "id": "t416", - "source": "Ribavirin_drug", + "source": "NAD_simple_molecule", "target": "XMP_simple_molecule", "sign": true }, { "id": "t417", - "source": "IMPDH2:Nsp14_complex", + "source": "IMPDH2", "target": "XMP_simple_molecule", "sign": true }, { "id": "t418", - "source": "Merimepodib_drug", + "source": "IMPDH1", "target": "XMP_simple_molecule", "sign": true }, { "id": "t419", - "source": "NAD_simple_molecule", + "source": "IMPDH2:Nsp14_complex", "target": "XMP_simple_molecule", "sign": true }, { "id": "t420", - "source": "IMPDH2", + "source": "Ribavirin_drug", "target": "XMP_simple_molecule", "sign": true }, { "id": "t421", - "source": "IMP_simple_molecule", + "source": "Mycophenolic acid_drug", "target": "XMP_simple_molecule", "sign": true }, @@ -4339,115 +4339,115 @@ }, { "id": "t423", - "source": "NADP_simple_molecule", + "source": "HPRT1", "target": "GMP_simple_molecule", "sign": true }, { "id": "t424", - "source": "ENTPD4", + "source": "ENTPD5", "target": "GMP_simple_molecule", "sign": true }, { "id": "t425", - "source": "GTP_simple_molecule", + "source": "IMP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t426", - "source": "ENTPD6", + "source": "GMPS", "target": "GMP_simple_molecule", "sign": true }, { "id": "t427", - "source": "Guanine_simple_molecule", + "source": "NADP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t428", - "source": "ENTPD5", + "source": "Ammonium_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t429", - "source": "Ammonium_simple_molecule", + "source": "CANT1", "target": "GMP_simple_molecule", "sign": true }, { "id": "t430", - "source": "HPRT1", + "source": "GMPR2", "target": "GMP_simple_molecule", "sign": true }, { "id": "t431", - "source": "GMPS", + "source": "ATP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t432", - "source": "ATP_simple_molecule", + "source": "Guanine_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t433", - "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", + "source": "ENTPD2", "target": "GMP_simple_molecule", "sign": true }, { "id": "t434", - "source": "CANT1", + "source": "ENTPD4", "target": "GMP_simple_molecule", "sign": true }, { "id": "t435", - "source": "L-Glutamine_simple_molecule", + "source": "GDP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t436", - "source": "GMPR2", + "source": "XMP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t437", - "source": "ENTPD2", + "source": "ENTPD6", "target": "GMP_simple_molecule", "sign": true }, { "id": "t438", - "source": "XMP_simple_molecule", + "source": "5-phospho-_alpha_-D-ribose 1-diphosphate_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t439", - "source": "GMPR", + "source": "L-Glutamine_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t440", - "source": "GDP_simple_molecule", + "source": "GTP_simple_molecule", "target": "GMP_simple_molecule", "sign": true }, { "id": "t441", - "source": "IMP_simple_molecule", + "source": "GMPR", "target": "GMP_simple_molecule", "sign": true }, @@ -4459,49 +4459,49 @@ }, { "id": "t443", - "source": "GTP_simple_molecule", + "source": "ENTPD2", "target": "GDP_simple_molecule", "sign": true }, { "id": "t444", - "source": "GMP_simple_molecule", + "source": "NTPCR", "target": "GDP_simple_molecule", "sign": true }, { "id": "t445", - "source": "ENTPD2", + "source": "GTP_simple_molecule", "target": "GDP_simple_molecule", "sign": true }, { "id": "t446", - "source": "GUK1", + "source": "GMP_simple_molecule", "target": "GDP_simple_molecule", "sign": true }, { "id": "t447", - "source": "H2O_simple_molecule_cell", + "source": "ATP_simple_molecule", "target": "GDP_simple_molecule", "sign": true }, { "id": "t448", - "source": "ATP_simple_molecule", + "source": "GUK1", "target": "GDP_simple_molecule", "sign": true }, { "id": "t449", - "source": "NTPCR", + "source": "H2O_simple_molecule_cell", "target": "GDP_simple_molecule", "sign": true }, { "id": "t450", - "source": "NME6", + "source": "GDP_simple_molecule", "target": "GTP_simple_molecule", "sign": true }, @@ -4513,31 +4513,31 @@ }, { "id": "t452", - "source": "Nucleoside diphosphate kinase_complex_cell", + "source": "NME7", "target": "GTP_simple_molecule", "sign": true }, { "id": "t453", - "source": "NME7", + "source": "NME3", "target": "GTP_simple_molecule", "sign": true }, { "id": "t454", - "source": "NME3", + "source": "Nucleoside diphosphate kinase_complex_cell", "target": "GTP_simple_molecule", "sign": true }, { "id": "t455", - "source": "GDP_simple_molecule", + "source": "ATP_simple_molecule", "target": "GTP_simple_molecule", "sign": true }, { "id": "t456", - "source": "ATP_simple_molecule", + "source": "NME6", "target": "GTP_simple_molecule", "sign": true }, @@ -4549,31 +4549,31 @@ }, { "id": "t458", - "source": "GUK1", + "source": "ribonucleoside reductase_complex_cell", "target": "dGDP_simple_molecule", "sign": true }, { "id": "t459", - "source": "dGMP_simple_molecule", + "source": "ATP_simple_molecule", "target": "dGDP_simple_molecule", "sign": true }, { "id": "t460", - "source": "ribonucleoside reductase_complex_cell", + "source": "Thioredoxin_simple_molecule", "target": "dGDP_simple_molecule", "sign": true }, { "id": "t461", - "source": "ATP_simple_molecule", + "source": "GUK1", "target": "dGDP_simple_molecule", "sign": true }, { "id": "t462", - "source": "Thioredoxin_simple_molecule", + "source": "dGMP_simple_molecule", "target": "dGDP_simple_molecule", "sign": true }, @@ -4585,7 +4585,7 @@ }, { "id": "t464", - "source": "ribonucleoside reductase_complex_cell", + "source": "ADP_simple_molecule", "target": "Thioredoxin disulfide_simple_molecule", "sign": true }, @@ -4597,49 +4597,49 @@ }, { "id": "t466", - "source": "ADP_simple_molecule", + "source": "ribonucleoside reductase_complex_cell", "target": "Thioredoxin disulfide_simple_molecule", "sign": true }, { "id": "t467", - "source": "NME6", + "source": "NME5", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t468", - "source": "NME5", + "source": "NME7", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t469", - "source": "Nucleoside diphosphate kinase_complex_cell", + "source": "NME3", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t470", - "source": "NME7", + "source": "Nucleoside diphosphate kinase_complex_cell", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t471", - "source": "dGDP_simple_molecule", + "source": "ATP_simple_molecule", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t472", - "source": "NME3", + "source": "dGDP_simple_molecule", "target": "dGTP_simple_molecule", "sign": true }, { "id": "t473", - "source": "ATP_simple_molecule", + "source": "NME6", "target": "dGTP_simple_molecule", "sign": true }, @@ -4651,49 +4651,49 @@ }, { "id": "t475", - "source": "Deoxyguanosine_simple_molecule", + "source": "ITPA", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t476", - "source": "ENPP1", + "source": "ENPP3", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t477", - "source": "ENPP3", + "source": "Deoxyguanosine_simple_molecule", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t478", - "source": "dGTP_simple_molecule", + "source": "ENPP1", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t479", - "source": "ATP_simple_molecule", + "source": "dGTP_simple_molecule", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t480", - "source": "H2O_simple_molecule_cell", + "source": "ATP_simple_molecule", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t481", - "source": "ITPA", + "source": "H2O_simple_molecule_cell", "target": "dGMP_simple_molecule", "sign": true }, { "id": "t482", - "source": "PNP", + "source": "Guanosine_simple_molecule", "target": "Guanine_simple_molecule", "sign": true }, @@ -4711,7 +4711,7 @@ }, { "id": "t485", - "source": "Guanosine_simple_molecule", + "source": "PNP", "target": "Guanine_simple_molecule", "sign": true }, @@ -4735,31 +4735,31 @@ }, { "id": "t489", - "source": "PNP", + "source": "Deoxyguanosine_simple_molecule", "target": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t490", - "source": "Deoxyguanosine_simple_molecule", + "source": "Pi_simple_molecule", "target": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t491", - "source": "Pi_simple_molecule", + "source": "PNP", "target": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", "sign": true }, { "id": "t492", - "source": "AMP_simple_molecule", + "source": "Guanine_simple_molecule", "target": "Ammonium_simple_molecule", "sign": true }, { "id": "t493", - "source": "AMPD1", + "source": "GDA", "target": "Ammonium_simple_molecule", "sign": true }, @@ -4771,19 +4771,19 @@ }, { "id": "t495", - "source": "Guanine_simple_molecule", + "source": "AMP_simple_molecule", "target": "Ammonium_simple_molecule", "sign": true }, { "id": "t496", - "source": "AMDP2", + "source": "H2O_simple_molecule_cell", "target": "Ammonium_simple_molecule", "sign": true }, { "id": "t497", - "source": "AMPD3", + "source": "AMPD1", "target": "Ammonium_simple_molecule", "sign": true }, @@ -4795,19 +4795,19 @@ }, { "id": "t499", - "source": "GDA", + "source": "Adenosine_simple_molecule", "target": "Ammonium_simple_molecule", "sign": true }, { "id": "t500", - "source": "Adenosine_simple_molecule", + "source": "AMPD3", "target": "Ammonium_simple_molecule", "sign": true }, { "id": "t501", - "source": "H2O_simple_molecule_cell", + "source": "AMDP2", "target": "Ammonium_simple_molecule", "sign": true }, @@ -4837,61 +4837,61 @@ }, { "id": "t506", - "source": "PNP", + "source": "Xanthosine_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t507", - "source": "Hypoxanthine_simple_molecule", + "source": "Guanine_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t508", - "source": "Pi_simple_molecule", + "source": "GDA", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t509", - "source": "XDH", + "source": "H_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t510", - "source": "H_simple_molecule", + "source": "Hypoxanthine_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t511", - "source": "Guanine_simple_molecule", + "source": "Pi_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t512", - "source": "Xanthosine_simple_molecule", + "source": "NAD_simple_molecule", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t513", - "source": "NAD_simple_molecule", + "source": "XDH", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t514", - "source": "GDA", + "source": "H2O_simple_molecule_cell", "target": "Xanthine_simple_molecule", "sign": true }, { "id": "t515", - "source": "H2O_simple_molecule_cell", + "source": "PNP", "target": "Xanthine_simple_molecule", "sign": true }, @@ -4903,19 +4903,19 @@ }, { "id": "t517", - "source": "NT5E", + "source": "IMP_simple_molecule", "target": "Inosine_simple_molecule", "sign": true }, { "id": "t518", - "source": "Adenosine_simple_molecule", + "source": "NT5E", "target": "Inosine_simple_molecule", "sign": true }, { "id": "t519", - "source": "IMP_simple_molecule", + "source": "Adenosine_simple_molecule", "target": "Inosine_simple_molecule", "sign": true }, @@ -4933,7 +4933,7 @@ }, { "id": "t522", - "source": "PNP", + "source": "Inosine_simple_molecule", "target": "Hypoxanthine_simple_molecule", "sign": true }, @@ -4945,19 +4945,19 @@ }, { "id": "t524", - "source": "Inosine_simple_molecule", + "source": "PNP", "target": "Hypoxanthine_simple_molecule", "sign": true }, { "id": "t525", - "source": "H2O_simple_molecule_cell", + "source": "AMP_simple_molecule", "target": "Adenosine_simple_molecule", "sign": true }, { "id": "t526", - "source": "AMP_simple_molecule", + "source": "H2O_simple_molecule_cell", "target": "Adenosine_simple_molecule", "sign": true }, @@ -4969,7 +4969,7 @@ }, { "id": "t528", - "source": "PNP", + "source": "Adenosine_simple_molecule", "target": "Adenine_simple_molecule", "sign": true }, @@ -4981,55 +4981,55 @@ }, { "id": "t530", - "source": "Adenosine_simple_molecule", + "source": "PNP", "target": "Adenine_simple_molecule", "sign": true }, { "id": "t531", - "source": "Hypoxanthine_simple_molecule", + "source": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t532", - "source": "PNP", + "source": "H_simple_molecule", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t533", - "source": "H_simple_molecule", + "source": "Hypoxanthine_simple_molecule", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t534", - "source": "2-deoxy-_alpha_-D-ribose 1-phosphate_simple_molecule", + "source": "Deoxyadenosine_simple_molecule", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t535", - "source": "Deoxyadenosine_simple_molecule", + "source": "H2O_simple_molecule_cell", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t536", - "source": "H2O_simple_molecule_cell", + "source": "ADA", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t537", - "source": "ADA", + "source": "PNP", "target": "Deoxyinosine_simple_molecule", "sign": true }, { "id": "t538", - "source": "Deoxyadenosine_simple_molecule", + "source": "ATP_simple_molecule", "target": "dAMP_simple_molecule", "sign": true }, @@ -5041,13 +5041,13 @@ }, { "id": "t540", - "source": "ATP_simple_molecule", + "source": "Deoxyadenosine_simple_molecule", "target": "dAMP_simple_molecule", "sign": true }, { "id": "t541", - "source": "ribonucleoside reductase_complex_cell", + "source": "dAMP_simple_molecule", "target": "dADP_simple_molecule", "sign": true }, @@ -5059,67 +5059,67 @@ }, { "id": "t543", - "source": "ATP_simple_molecule", + "source": "ADP_simple_molecule", "target": "dADP_simple_molecule", "sign": true }, { "id": "t544", - "source": "Thioredoxin_simple_molecule", + "source": "ribonucleoside reductase_complex_cell", "target": "dADP_simple_molecule", "sign": true }, { "id": "t545", - "source": "dAMP_simple_molecule", + "source": "ATP_simple_molecule", "target": "dADP_simple_molecule", "sign": true }, { "id": "t546", - "source": "ADP_simple_molecule", + "source": "Thioredoxin_simple_molecule", "target": "dADP_simple_molecule", "sign": true }, { "id": "t547", - "source": "dADP_simple_molecule", + "source": "NME5", "target": "dATP_simple_molecule", "sign": true }, { "id": "t548", - "source": "NME6", + "source": "dADP_simple_molecule", "target": "dATP_simple_molecule", "sign": true }, { "id": "t549", - "source": "NME5", + "source": "NME7", "target": "dATP_simple_molecule", "sign": true }, { "id": "t550", - "source": "Nucleoside diphosphate kinase_complex_cell", + "source": "NME3", "target": "dATP_simple_molecule", "sign": true }, { "id": "t551", - "source": "NME7", + "source": "Nucleoside diphosphate kinase_complex_cell", "target": "dATP_simple_molecule", "sign": true }, { "id": "t552", - "source": "NME3", + "source": "ATP_simple_molecule", "target": "dATP_simple_molecule", "sign": true }, { "id": "t553", - "source": "ATP_simple_molecule", + "source": "NME6", "target": "dATP_simple_molecule", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp4_Nsp6.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp4_Nsp6.json index be960294..a3c21224 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp4_Nsp6.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp4_Nsp6.json @@ -712,13 +712,13 @@ }, { "id": "t4", - "source": "Nsp4_cell", + "source": "ALG11_endoplasmic reticulum", "target": "Nsp4_ALG11_complex_endoplasmic reticulum", "sign": true }, { "id": "t5", - "source": "ALG11_endoplasmic reticulum", + "source": "Nsp4_cell", "target": "Nsp4_ALG11_complex_endoplasmic reticulum", "sign": true }, @@ -730,25 +730,25 @@ }, { "id": "t7", - "source": "DNAJC11", + "source": "Nsp4_cell", "target": "Nsp4:DNAJC11_complex", "sign": true }, { "id": "t8", - "source": "Nsp4_cell", + "source": "DNAJC11", "target": "Nsp4:DNAJC11_complex", "sign": true }, { "id": "t9", - "source": "F-ATPase_complex_mitochondrial matrix", + "source": "Nsp6", "target": "F-ATPase:Nsp6_complex", "sign": true }, { "id": "t10", - "source": "Nsp6", + "source": "F-ATPase_complex_mitochondrial matrix", "target": "F-ATPase:Nsp6_complex", "sign": true }, @@ -760,13 +760,13 @@ }, { "id": "t12", - "source": "Nsp4_cell", + "source": "NUP210_endoplasmic reticulum", "target": "Nsp4:NUP210_complex_endoplasmic reticulum", "sign": true }, { "id": "t13", - "source": "NUP210_endoplasmic reticulum", + "source": "Nsp4_cell", "target": "Nsp4:NUP210_complex_endoplasmic reticulum", "sign": true }, @@ -856,13 +856,13 @@ }, { "id": "t28", - "source": "P-ATPase_complex_cell", + "source": "Nsp6", "target": "P-ATPase:Nsp6_complex", "sign": true }, { "id": "t29", - "source": "Nsp6", + "source": "P-ATPase_complex_cell", "target": "P-ATPase:Nsp6_complex", "sign": true }, @@ -1018,13 +1018,13 @@ }, { "id": "t55", - "source": "TOM complex_complex", + "source": "Nsp4_cell", "target": "Nsp4_mitochondrion", "sign": true }, { "id": "t56", - "source": "Nsp4_cell", + "source": "TOM complex_complex", "target": "Nsp4_mitochondrion", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp9_protein.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp9_protein.json index 60e27a51..b5936551 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp9_protein.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Nsp9_protein.json @@ -2518,13 +2518,13 @@ "edges": [ { "id": "t1", - "source": "Nsp9_cell", + "source": "Fibrillin_complex_human host", "target": "Fibrillincomp_complex", "sign": true }, { "id": "t2", - "source": "Fibrillin_complex_human host", + "source": "Nsp9_cell", "target": "Fibrillincomp_complex", "sign": true }, @@ -2554,25 +2554,25 @@ }, { "id": "t7", - "source": "MIB1", + "source": "DLL1", "target": "MIBcomp_complex", "sign": true }, { "id": "t8", - "source": "DLL1", + "source": "MIB1", "target": "MIBcomp_complex", "sign": true }, { "id": "t9", - "source": "Vpr", + "source": "COPS_complex_nucleus", "target": "COPS_complex_nucleus", "sign": true }, { "id": "t10", - "source": "COPS_complex_nucleus", + "source": "Vpr", "target": "COPS_complex_nucleus", "sign": true }, @@ -2590,55 +2590,55 @@ }, { "id": "t13", - "source": "S-Adenosylmethionine_drug", + "source": "MAT1A", "target": "SAdComp_complex", "sign": true }, { "id": "t14", - "source": "MAT1A", + "source": "S-Adenosylmethionine_drug", "target": "SAdComp_complex", "sign": true }, { "id": "t15", - "source": "nup1_complex", + "source": "nup2_complex", "target": "Nuclear Pore_complex", "sign": true }, { "id": "t16", - "source": "nup2_complex", + "source": "nup1_complex", "target": "Nuclear Pore_complex", "sign": true }, { "id": "t17", - "source": "EXOSC2", + "source": "EXOSC5", "target": "EXOCcomp_complex", "sign": true }, { "id": "t18", - "source": "Nsp8", + "source": "EXOSC8", "target": "EXOCcomp_complex", "sign": true }, { "id": "t19", - "source": "EXOSC5", + "source": "EXOSC3", "target": "EXOCcomp_complex", "sign": true }, { "id": "t20", - "source": "EXOSC3", + "source": "Nsp8", "target": "EXOCcomp_complex", "sign": true }, { "id": "t21", - "source": "EXOSC8", + "source": "EXOSC2", "target": "EXOCcomp_complex", "sign": true }, @@ -2686,55 +2686,55 @@ }, { "id": "t29", - "source": "Nsp9_nucleus", + "source": "ZNF503", "target": "znfcomp_complex", "sign": true }, { "id": "t30", - "source": "ZNF503", + "source": "Nsp9_nucleus", "target": "znfcomp_complex", "sign": true }, { "id": "t31", - "source": "Nsp8", + "source": "Nsp7", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t32", - "source": "Nsp7", + "source": "Nsp12", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t33", - "source": "Nsp12", + "source": "Nsp8", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t34", - "source": "Nsp7812_complex_cell", + "source": "remdesivir _drug", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t35", - "source": "remdesivir _drug", + "source": "favipiravir_drug", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t36", - "source": "RdRpassembled_rna", + "source": "Nsp7812_complex_cell", "target": "Nsp7812_complex_cell", "sign": true }, { "id": "t37", - "source": "favipiravir_drug", + "source": "RdRpassembled_rna", "target": "Nsp7812_complex_cell", "sign": true }, @@ -2746,13 +2746,13 @@ }, { "id": "t39", - "source": "NUP58", + "source": "NUP54", "target": "nup1_complex", "sign": true }, { "id": "t40", - "source": "NUP54", + "source": "NUP58", "target": "nup1_complex", "sign": true }, @@ -2770,13 +2770,13 @@ }, { "id": "t43", - "source": "EDN1-homo_complex_nucleus", + "source": "BAG6", "target": "EDN1-homo_complex_nucleus", "sign": true }, { "id": "t44", - "source": "BAG6", + "source": "EDN1-homo_complex_nucleus", "target": "EDN1-homo_complex_nucleus", "sign": true }, @@ -2788,49 +2788,49 @@ }, { "id": "t46", - "source": "NEK7", + "source": "NEK9", "target": "NEKs_complex", "sign": true }, { "id": "t47", - "source": "NEK9", + "source": "NEK7", "target": "NEKs_complex", "sign": true }, { "id": "t48", - "source": "POLR2E", + "source": "POLR2A", "target": "gtfrnapoly_complex", "sign": true }, { "id": "t49", - "source": "POLR2B", + "source": "POLR2G", "target": "gtfrnapoly_complex", "sign": true }, { "id": "t50", - "source": "POLR2A", + "source": "GTF2F2", "target": "gtfrnapoly_complex", "sign": true }, { "id": "t51", - "source": "GTF2F2", + "source": "POLR2E", "target": "gtfrnapoly_complex", "sign": true }, { "id": "t52", - "source": "GTF2B", + "source": "POLR2B", "target": "gtfrnapoly_complex", "sign": true }, { "id": "t53", - "source": "POLR2G", + "source": "GTF2B", "target": "gtfrnapoly_complex", "sign": true }, @@ -2860,25 +2860,25 @@ }, { "id": "t58", - "source": "COPS5", + "source": "COPS6", "target": "COPS_complex_nucleus", "sign": true }, { "id": "t59", - "source": "COPS4", + "source": "COPS2", "target": "COPS_complex_nucleus", "sign": true }, { "id": "t60", - "source": "COPS8", + "source": "COPS4", "target": "COPS_complex_nucleus", "sign": true }, { "id": "t61", - "source": "COPS2", + "source": "COPS5", "target": "COPS_complex_nucleus", "sign": true }, @@ -2890,7 +2890,7 @@ }, { "id": "t63", - "source": "COPS6", + "source": "COPS8", "target": "COPS_complex_nucleus", "sign": true }, @@ -2926,13 +2926,13 @@ }, { "id": "t69", - "source": "TAT", + "source": "GTF2F2", "target": "TAT-HIV_complex", "sign": true }, { "id": "t70", - "source": "GTF2F2", + "source": "TAT", "target": "TAT-HIV_complex", "sign": true }, @@ -2950,13 +2950,13 @@ }, { "id": "t73", - "source": "AIFM1", + "source": "SPART", "target": "SPARTcomp_complex", "sign": true }, { "id": "t74", - "source": "SPART", + "source": "AIFM1", "target": "SPARTcomp_complex", "sign": true }, @@ -2974,13 +2974,13 @@ }, { "id": "t77", - "source": "Nsp10_cell", + "source": "Nsp9_cell", "target": "pathogen_complex", "sign": true }, { "id": "t78", - "source": "Nsp9_cell", + "source": "Nsp10_cell", "target": "pathogen_complex", "sign": true }, @@ -3004,7 +3004,7 @@ }, { "id": "t82", - "source": "FOCAD", + "source": "Nsp7", "target": "FOCADcomp_complex", "sign": true }, @@ -3016,7 +3016,7 @@ }, { "id": "t84", - "source": "Nsp7", + "source": "FOCAD", "target": "FOCADcomp_complex", "sign": true }, @@ -3070,13 +3070,13 @@ }, { "id": "t93", - "source": "Rofecoxib_drug", + "source": "PTGS2", "target": "PTGScomp_complex", "sign": true }, { "id": "t94", - "source": "PTGS2", + "source": "Rofecoxib_drug", "target": "PTGScomp_complex", "sign": true }, @@ -3100,13 +3100,13 @@ }, { "id": "t98", - "source": "MAT2A", + "source": "MAT2B", "target": "MAT_complex", "sign": true }, { "id": "t99", - "source": "MAT2B", + "source": "MAT2A", "target": "MAT_complex", "sign": true }, @@ -3124,25 +3124,25 @@ }, { "id": "t102", - "source": "Flavin adenine dinucleotide_drug", + "source": "AIFM1", "target": "AIFMFlaComp_complex", "sign": true }, { "id": "t103", - "source": "AIFM1", + "source": "Flavin adenine dinucleotide_drug", "target": "AIFMFlaComp_complex", "sign": true }, { "id": "t104", - "source": "Sitaxentan_drug", + "source": "EDNRA", "target": "EDNRASitaComp_complex", "sign": true }, { "id": "t105", - "source": "EDNRA", + "source": "Sitaxentan_drug", "target": "EDNRASitaComp_complex", "sign": true }, @@ -3160,25 +3160,25 @@ }, { "id": "t108", - "source": "EDNRA", + "source": "Acetylsalicylic acid_drug", "target": "EDNRAcetComp_complex", "sign": true }, { "id": "t109", - "source": "Acetylsalicylic acid_drug", + "source": "EDNRA", "target": "EDNRAcetComp_complex", "sign": true }, { "id": "t110", - "source": "Macitentan_drug", + "source": "EDNRA", "target": "EDNRMacComp_complex", "sign": true }, { "id": "t111", - "source": "EDNRA", + "source": "Macitentan_drug", "target": "EDNRMacComp_complex", "sign": true }, @@ -3196,25 +3196,25 @@ }, { "id": "t114", - "source": "MYCBP2", + "source": "Nsp12", "target": "MYCBPcomp_complex", "sign": true }, { "id": "t115", - "source": "Nsp12", + "source": "MYCBP2", "target": "MYCBPcomp_complex", "sign": true }, { "id": "t116", - "source": "SBNO1", + "source": "Nsp12", "target": "SBNOcomp_complex", "sign": true }, { "id": "t117", - "source": "Nsp12", + "source": "SBNO1", "target": "SBNOcomp_complex", "sign": true }, @@ -3232,25 +3232,25 @@ }, { "id": "t120", - "source": "ADP_simple_molecule", + "source": "BCKDK", "target": "ADPcomp_complex", "sign": true }, { "id": "t121", - "source": "BCKDK", + "source": "ADP_simple_molecule", "target": "ADPcomp_complex", "sign": true }, { "id": "t122", - "source": "DCAF7", + "source": "ZNF503", "target": "dcafznf_complex", "sign": true }, { "id": "t123", - "source": "ZNF503", + "source": "DCAF7", "target": "dcafznf_complex", "sign": true }, @@ -3268,13 +3268,13 @@ }, { "id": "t126", - "source": "ZNF318", + "source": "Nsp12", "target": "ZNFcomp_complex", "sign": true }, { "id": "t127", - "source": "Nsp12", + "source": "ZNF318", "target": "ZNFcomp_complex", "sign": true }, @@ -3292,13 +3292,13 @@ }, { "id": "t130", - "source": "SRP54", + "source": "Nsp8", "target": "SRP54comp_complex", "sign": true }, { "id": "t131", - "source": "Nsp8", + "source": "SRP54", "target": "SRP54comp_complex", "sign": true }, @@ -3310,13 +3310,13 @@ }, { "id": "t133", - "source": "ZC3H7A ", + "source": "Nsp12", "target": "ZC3H7Acomp_complex", "sign": true }, { "id": "t134", - "source": "Nsp12", + "source": "ZC3H7A ", "target": "ZC3H7Acomp_complex", "sign": true }, @@ -3346,37 +3346,37 @@ }, { "id": "t139", - "source": "CA12", + "source": "Nsp7", "target": "CA12comp_complex", "sign": true }, { "id": "t140", - "source": "Nsp7", + "source": "CA12", "target": "CA12comp_complex", "sign": true }, { "id": "t141", - "source": "CA12", + "source": "Zonisamide_drug", "target": "ZonisamideComp_complex", "sign": true }, { "id": "t142", - "source": "Zonisamide_drug", + "source": "CA12", "target": "ZonisamideComp_complex", "sign": true }, { "id": "t143", - "source": "Ellagic Acid_drug", + "source": "CA12", "target": "EAcomp_complex", "sign": true }, { "id": "t144", - "source": "CA12", + "source": "Ellagic Acid_drug", "target": "EAcomp_complex", "sign": true }, @@ -3394,13 +3394,13 @@ }, { "id": "t147", - "source": "CA12", + "source": "Benzthiazide_drug", "target": "BZcomp_complex", "sign": true }, { "id": "t148", - "source": "Benzthiazide_drug", + "source": "CA12", "target": "BZcomp_complex", "sign": true }, @@ -3418,31 +3418,31 @@ }, { "id": "t151", - "source": "ELN", + "source": "PLG", "target": "Fibrillin_complex_human host", "sign": true }, { "id": "t152", - "source": "Fibrillin_complex_human host", + "source": "ELN", "target": "Fibrillin_complex_human host", "sign": true }, { "id": "t153", - "source": "PLG", + "source": "Fibrillin_complex_human host", "target": "Fibrillin_complex_human host", "sign": true }, { "id": "t154", - "source": "ELN", + "source": "Rofecoxib_drug", "target": "RofecoxibComp_complex", "sign": true }, { "id": "t155", - "source": "Rofecoxib_drug", + "source": "ELN", "target": "RofecoxibComp_complex", "sign": true }, @@ -3460,13 +3460,13 @@ }, { "id": "t158", - "source": "ENV", + "source": "PCSK1", "target": "NECENVComp_complex", "sign": true }, { "id": "t159", - "source": "PCSK1", + "source": "ENV", "target": "NECENVComp_complex", "sign": true }, @@ -3508,13 +3508,13 @@ }, { "id": "t166", - "source": "COMT", + "source": "Nsp7", "target": "COMT_complex", "sign": true }, { "id": "t167", - "source": "Nsp7", + "source": "COMT", "target": "COMT_complex", "sign": true }, @@ -3568,13 +3568,13 @@ }, { "id": "t176", - "source": "3,5-Dinitrocatechol_drug", + "source": "COMT", "target": "DCcomp_complex", "sign": true }, { "id": "t177", - "source": "COMT", + "source": "3,5-Dinitrocatechol_drug", "target": "DCcomp_complex", "sign": true }, @@ -3592,25 +3592,25 @@ }, { "id": "t180", - "source": "(3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE_drug", + "source": "COMT", "target": "DNCcomp_complex", "sign": true }, { "id": "t181", - "source": "COMT", + "source": "(3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE_drug", "target": "DNCcomp_complex", "sign": true }, { "id": "t182", - "source": "COMT", + "source": "2-Methoxyestradiol_drug", "target": "MCcomp_complex", "sign": true }, { "id": "t183", - "source": "2-Methoxyestradiol_drug", + "source": "COMT", "target": "MCcomp_complex", "sign": true }, @@ -3628,37 +3628,37 @@ }, { "id": "t186", - "source": "GDP_simple_molecule", + "source": "RAB7A", "target": "RGcomp_complex_cell", "sign": true }, { "id": "t187", - "source": "RAB7A", + "source": "GDP_simple_molecule", "target": "RGcomp_complex_cell", "sign": true }, { "id": "t188", - "source": "Suramin_drug", + "source": "SIRT5", "target": "SScomp_complex", "sign": true }, { "id": "t189", - "source": "SIRT5", + "source": "Suramin_drug", "target": "SScomp_complex", "sign": true }, { "id": "t190", - "source": "GDP_simple_molecule", + "source": "RHOA", "target": "RGcomp_complex_cell", "sign": true }, { "id": "t191", - "source": "RHOA", + "source": "GDP_simple_molecule", "target": "RGcomp_complex_cell", "sign": true }, @@ -3712,7 +3712,7 @@ }, { "id": "t200", - "source": "MRPS5", + "source": "Nsp8", "target": "MRPScomp_complex", "sign": true }, @@ -3724,25 +3724,25 @@ }, { "id": "t202", - "source": "Nsp8", + "source": "MRPS5", "target": "MRPScomp_complex", "sign": true }, { "id": "t203", - "source": "IMPDH2", + "source": "Ribavirin_drug", "target": "IRcomp_complex", "sign": true }, { "id": "t204", - "source": "Ribavirin_drug", + "source": "IMPDH2", "target": "IRcomp_complex", "sign": true }, { "id": "t205", - "source": "LOXL1", + "source": "FBLN5", "target": "LOXcomp_complex", "sign": true }, @@ -3754,7 +3754,7 @@ }, { "id": "t207", - "source": "FBLN5", + "source": "LOXL1", "target": "LOXcomp_complex", "sign": true }, @@ -3784,25 +3784,25 @@ }, { "id": "t212", - "source": "SRP72", + "source": "Nsp7", "target": "SRP72comp_complex", "sign": true }, { "id": "t213", - "source": "Nsp7", + "source": "SRP72", "target": "SRP72comp_complex", "sign": true }, { "id": "t214", - "source": "NARS2", + "source": "L-Asparagine_simple_molecule", "target": "NLcomp_complex", "sign": true }, { "id": "t215", - "source": "L-Asparagine_simple_molecule", + "source": "NARS2", "target": "NLcomp_complex", "sign": true }, @@ -3820,25 +3820,25 @@ }, { "id": "t218", - "source": "Nsp8", + "source": "AATF", "target": "AATFcomp_complex", "sign": true }, { "id": "t219", - "source": "AATF", + "source": "Nsp8", "target": "AATFcomp_complex", "sign": true }, { "id": "t220", - "source": "IMPDH2", + "source": "Nsp14_nucleus", "target": "INPDH2comp_complex", "sign": true }, { "id": "t221", - "source": "Nsp14_nucleus", + "source": "IMPDH2", "target": "INPDH2comp_complex", "sign": true }, @@ -3856,25 +3856,25 @@ }, { "id": "t224", - "source": "TCF12", + "source": "Nsp12", "target": "TCFcomp_complex", "sign": true }, { "id": "t225", - "source": "Nsp12", + "source": "TCF12", "target": "TCFcomp_complex", "sign": true }, { "id": "t226", - "source": "Nsp10_nucleus", + "source": "ERGIC1", "target": "ERGIC1comp_complex", "sign": true }, { "id": "t227", - "source": "ERGIC1", + "source": "Nsp10_nucleus", "target": "ERGIC1comp_complex", "sign": true }, @@ -3892,13 +3892,13 @@ }, { "id": "t230", - "source": "GFER", + "source": "FAD_simple_molecule", "target": "FGCOMP_complex", "sign": true }, { "id": "t231", - "source": "FAD_simple_molecule", + "source": "GFER", "target": "FGCOMP_complex", "sign": true }, @@ -3928,25 +3928,25 @@ }, { "id": "t236", - "source": "Nsp8", + "source": "NGDN", "target": "NGDNcomp_complex", "sign": true }, { "id": "t237", - "source": "NGDN", + "source": "Nsp8", "target": "NGDNcomp_complex", "sign": true }, { "id": "t238", - "source": "CCDC86", + "source": "Nsp8", "target": "CCDCcomp_complex", "sign": true }, { "id": "t239", - "source": "Nsp8", + "source": "CCDC86", "target": "CCDCcomp_complex", "sign": true }, @@ -3976,37 +3976,37 @@ }, { "id": "t244", - "source": "NARS2", + "source": "Nsp8", "target": "NARS2comp_complex", "sign": true }, { "id": "t245", - "source": "Nsp8", + "source": "NARS2", "target": "NARS2comp_complex", "sign": true }, { "id": "t246", - "source": "ZNF250", + "source": "Nsp14_nucleus", "target": "ZNF250comp_complex", "sign": true }, { "id": "t247", - "source": "Nsp14_nucleus", + "source": "ZNF250", "target": "ZNF250comp_complex", "sign": true }, { "id": "t248", - "source": "Nsp14_cell", + "source": "PEG10", "target": "PEG10comp_complex", "sign": true }, { "id": "t249", - "source": "PEG10", + "source": "Nsp14_cell", "target": "PEG10comp_complex", "sign": true }, @@ -4042,13 +4042,13 @@ }, { "id": "t255", - "source": "PLAT", + "source": "Nafamostat_drug", "target": "PLG", "sign": true }, { "id": "t256", - "source": "Nafamostat_drug", + "source": "PLAT", "target": "PLG", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf10_Cul2_pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf10_Cul2_pathway.json index a2815c60..071d3ab6 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf10_Cul2_pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf10_Cul2_pathway.json @@ -620,7 +620,7 @@ }, { "id": "t2", - "source": "Rbx1:Cul2_complex", + "source": "Zyg11B:EloBC_complex", "target": "Cul2 ubiquitin ligase_complex", "sign": true }, @@ -632,19 +632,19 @@ }, { "id": "t4", - "source": "Zyg11B:EloBC_complex", + "source": "Rbx1:Cul2_complex", "target": "Cul2 ubiquitin ligase_complex", "sign": true }, { "id": "t5", - "source": "CSN5_complex", + "source": "Cul2 ubiquitin ligase:substrate_complex_cell", "target": "Cul2 ubiquitin ligase_complex", "sign": true }, { "id": "t6", - "source": "Cul2 ubiquitin ligase:substrate_complex_cell", + "source": "CSN5_complex", "target": "Cul2 ubiquitin ligase_complex", "sign": true }, @@ -668,19 +668,19 @@ }, { "id": "t10", - "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", + "source": "Orf10", "target": "Cul2 ubiquitin ligase:Orf10_complex", "sign": true }, { "id": "t11", - "source": "Cul2 ubiquitin ligase_complex", + "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "target": "Cul2 ubiquitin ligase:Orf10_complex", "sign": true }, { "id": "t12", - "source": "Orf10", + "source": "Cul2 ubiquitin ligase_complex", "target": "Cul2 ubiquitin ligase:Orf10_complex", "sign": true }, @@ -710,13 +710,13 @@ }, { "id": "t17", - "source": "Zyg11B:EloBC_complex", + "source": "ELOB", "target": "ELOB:ELOC_complex", "sign": true }, { "id": "t18", - "source": "ELOB", + "source": "Zyg11B:EloBC_complex", "target": "ELOB:ELOC_complex", "sign": true }, @@ -740,43 +740,43 @@ }, { "id": "t22", - "source": "NEDD8", + "source": "NAE_complex", "target": "NAE:NEDD8_complex", "sign": true }, { "id": "t23", - "source": "NAE_complex", + "source": "NEDD8", "target": "NAE:NEDD8_complex", "sign": true }, { "id": "t24", - "source": "CUL2", + "source": "Cul2 ubiquitin ligase_complex", "target": "Rbx1:Cul2_complex", "sign": true }, { "id": "t25", - "source": "Cul2 ubiquitin ligase_complex", + "source": "RBX1", "target": "Rbx1:Cul2_complex", "sign": true }, { "id": "t26", - "source": "RBX1", + "source": "CUL2", "target": "Rbx1:Cul2_complex", "sign": true }, { "id": "t27", - "source": "Cul2 ubiquitin ligase:Orf10_complex", + "source": "ubit_traget", "target": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "sign": true }, { "id": "t28", - "source": "ubit_traget", + "source": "Cul2 ubiquitin ligase:Orf10_complex", "target": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "sign": true }, @@ -788,19 +788,19 @@ }, { "id": "t30", - "source": "Cul2 ubiquitin ligase:N8:E2-Ub:substrate_complex", + "source": "UBE2M:NEDD8_complex", "target": "Cul2 ubiquitin ligase:substrate_complex_cell", "sign": true }, { "id": "t31", - "source": "Cul2 ubiquitin ligase:N8:E2:substrate_complex", + "source": "Cul2 ubiquitin ligase:N8:E2-Ub:substrate_complex", "target": "Cul2 ubiquitin ligase:substrate_complex_cell", "sign": true }, { "id": "t32", - "source": "UBE2M:NEDD8_complex", + "source": "Cul2 ubiquitin ligase:N8:E2:substrate_complex", "target": "Cul2 ubiquitin ligase:substrate_complex_cell", "sign": true }, @@ -812,13 +812,13 @@ }, { "id": "t34", - "source": "Cul2 ubiquitin ligase:substrate_complex_cell", + "source": "E2_ubiquitinated", "target": "Cul2 ubiquitin ligase:N8:E2-Ub:substrate_complex", "sign": true }, { "id": "t35", - "source": "E2_ubiquitinated", + "source": "Cul2 ubiquitin ligase:substrate_complex_cell", "target": "Cul2 ubiquitin ligase:N8:E2-Ub:substrate_complex", "sign": true }, @@ -854,37 +854,37 @@ }, { "id": "t41", - "source": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", + "source": "E2_ubiquitinated", "target": "Cul2 ubiquitin ligase:N8:Orf10:E2-Ub:substrate_complex", "sign": true }, { "id": "t42", - "source": "E2_ubiquitinated", + "source": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", "target": "Cul2 ubiquitin ligase:N8:Orf10:E2-Ub:substrate_complex", "sign": true }, { "id": "t43", - "source": "Cul2 ubiquitin ligase:N8:Orf10:E2-Ub:substrate_complex", + "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "target": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", "sign": true }, { "id": "t44", - "source": "Cul2 ubiquitin ligase:N8:Orf10:0E2:substrate_complex", + "source": "Cul2 ubiquitin ligase:N8:Orf10:E2-Ub:substrate_complex", "target": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", "sign": true }, { "id": "t45", - "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", + "source": "UBE2M:NEDD8_complex", "target": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", "sign": true }, { "id": "t46", - "source": "UBE2M:NEDD8_complex", + "source": "Cul2 ubiquitin ligase:N8:Orf10:0E2:substrate_complex", "target": "Cul2 ubiquitin ligase:N8:Orf10:substrate_complex", "sign": true }, @@ -902,13 +902,13 @@ }, { "id": "t49", - "source": "UBE2M", + "source": "NAE:NEDD8_complex", "target": "UBE2M:NEDD8_complex", "sign": true }, { "id": "t50", - "source": "NAE:NEDD8_complex", + "source": "UBE2M", "target": "UBE2M:NEDD8_complex", "sign": true }, @@ -920,49 +920,49 @@ }, { "id": "t52", - "source": "NAE1", + "source": "UBA3", "target": "NAE_complex", "sign": true }, { "id": "t53", - "source": "UBA3", + "source": "NAE1", "target": "NAE_complex", "sign": true }, { "id": "t54", - "source": "ELOB:ELOC_complex", + "source": "ELOB_rna", "target": "ELOB", "sign": true }, { "id": "t55", - "source": "ELOB_rna", + "source": "ELOB:ELOC_complex", "target": "ELOB", "sign": true }, { "id": "t56", - "source": "ELOC_rna", + "source": "ELOB:ELOC_complex", "target": "ELOC", "sign": true }, { "id": "t57", - "source": "ELOB:ELOC_complex", + "source": "ELOC_rna", "target": "ELOC", "sign": true }, { "id": "t58", - "source": "Zyg11B:EloBC_complex", + "source": "ZYG11B_rna", "target": "ZYG11B", "sign": true }, { "id": "t59", - "source": "ZYG11B_rna", + "source": "Zyg11B:EloBC_complex", "target": "ZYG11B", "sign": true }, @@ -980,13 +980,13 @@ }, { "id": "t62", - "source": "Rbx1:Cul2_complex", + "source": "CUL2_rna", "target": "CUL2", "sign": true }, { "id": "t63", - "source": "CUL2_rna", + "source": "Rbx1:Cul2_complex", "target": "CUL2", "sign": true }, @@ -1010,7 +1010,7 @@ }, { "id": "t67", - "source": "E2_rna", + "source": "Cul2 ubiquitin ligase:N8:Orf10:0E2:substrate_complex", "target": "E2", "sign": true }, @@ -1022,13 +1022,13 @@ }, { "id": "t69", - "source": "Cul2 ubiquitin ligase:N8:Orf10:0E2:substrate_complex", + "source": "Cul2 ubiquitin ligase:N8:E2:substrate_complex", "target": "E2", "sign": true }, { "id": "t70", - "source": "Cul2 ubiquitin ligase:N8:E2:substrate_complex", + "source": "E2_rna", "target": "E2", "sign": true }, @@ -1040,19 +1040,19 @@ }, { "id": "t72", - "source": "E1", + "source": "Ub_simple_molecule", "target": "E1_ubiquitinated", "sign": true }, { "id": "t73", - "source": "Ub_simple_molecule", + "source": "ATP_simple_molecule", "target": "E1_ubiquitinated", "sign": true }, { "id": "t74", - "source": "ATP_simple_molecule", + "source": "E1", "target": "E1_ubiquitinated", "sign": true }, @@ -1082,37 +1082,37 @@ }, { "id": "t79", - "source": "E1", + "source": "Ub_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t80", - "source": "Ub_simple_molecule", + "source": "ATP_simple_molecule", "target": "AMP_simple_molecule", "sign": true }, { "id": "t81", - "source": "ATP_simple_molecule", + "source": "E1", "target": "AMP_simple_molecule", "sign": true }, { "id": "t82", - "source": "E1", + "source": "Ub_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t83", - "source": "Ub_simple_molecule", + "source": "ATP_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t84", - "source": "ATP_simple_molecule", + "source": "E1", "target": "PPi_simple_molecule", "sign": true }, @@ -1124,19 +1124,19 @@ }, { "id": "t86", - "source": "Orf10 (+)ss sgmRNA_rna", + "source": "Cul2 ubiquitin ligase:Orf10_complex", "target": "Orf10", "sign": true }, { "id": "t87", - "source": "Cul2 ubiquitin ligase:Orf10_complex", + "source": "Orf10 (+)ss sgmRNA_rna", "target": "Orf10", "sign": true }, { "id": "t88", - "source": "UBE2M:NEDD8_complex", + "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "target": "UBE2M", "sign": true }, @@ -1148,7 +1148,7 @@ }, { "id": "t90", - "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", + "source": "UBE2M:NEDD8_complex", "target": "UBE2M", "sign": true }, @@ -1160,19 +1160,19 @@ }, { "id": "t92", - "source": "ubit_traget_ubiquitinated", + "source": "DUB", "target": "ubit_traget", "sign": true }, { "id": "t93", - "source": "DUB", + "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", "target": "ubit_traget", "sign": true }, { "id": "t94", - "source": "Cul2 ubiquitin ligase:Orf10:substrate_complex", + "source": "ubit_traget_ubiquitinated", "target": "ubit_traget", "sign": true }, @@ -1214,13 +1214,13 @@ }, { "id": "t101", - "source": "UBA3_rna", + "source": "NAE_complex", "target": "UBA3", "sign": true }, { "id": "t102", - "source": "NAE_complex", + "source": "UBA3_rna", "target": "UBA3", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf3a.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf3a.json index a6187865..fc3e64ea 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf3a.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Orf3a.json @@ -499,31 +499,31 @@ }, { "id": "t7", - "source": "Orf3a", + "source": "E", "target": "P65/P015_complex", "sign": true }, { "id": "t8", - "source": "IKBKG/IKBKB/CHUK_complex", + "source": "Orf3a", "target": "P65/P015_complex", "sign": true }, { "id": "t9", - "source": "E", + "source": "IKBKG/IKBKB/CHUK_complex", "target": "P65/P015_complex", "sign": true }, { "id": "t10", - "source": "TRIM30a/TRIM38_complex", + "source": "TRAF6", "target": "TAB2/TAB3/TAK1_complex", "sign": true }, { "id": "t11", - "source": "TRAF6", + "source": "TRIM30a/TRIM38_complex", "target": "TAB2/TAB3/TAK1_complex", "sign": true }, @@ -535,49 +535,49 @@ }, { "id": "t13", - "source": "TAB2/TAB3/TAK1_complex", + "source": "TRIM22", "target": "NEMO/IKKA/IKKB_complex", "sign": true }, { "id": "t14", - "source": "TRIM29", + "source": "TRIM27/TRIM21_complex", "target": "NEMO/IKKA/IKKB_complex", "sign": true }, { "id": "t15", - "source": "TRIM14/TRIM23_complex", + "source": "TAB2/TAB3/TAK1_complex", "target": "NEMO/IKKA/IKKB_complex", "sign": true }, { "id": "t16", - "source": "TRIM22", + "source": "TRIM14/TRIM23_complex", "target": "NEMO/IKKA/IKKB_complex", "sign": true }, { "id": "t17", - "source": "TRIM27/TRIM21_complex", + "source": "TRIM29", "target": "NEMO/IKKA/IKKB_complex", "sign": true }, { "id": "t18", - "source": "NFKB1", + "source": "NFKBIA_phosphorylated_ubiquitinated_ubiquitinated_ubiquitinated", "target": "NFKB1:NFKNIA_complex", "sign": true }, { "id": "t19", - "source": "CACTIN", + "source": "NFKB1", "target": "NFKB1:NFKNIA_complex", "sign": true }, { "id": "t20", - "source": "NFKBIA_phosphorylated_ubiquitinated_ubiquitinated_ubiquitinated", + "source": "CACTIN", "target": "NFKB1:NFKNIA_complex", "sign": true }, @@ -625,7 +625,7 @@ }, { "id": "t28", - "source": "TRIM38", + "source": "TRIM23", "target": "TRAF6", "sign": true }, @@ -637,7 +637,7 @@ }, { "id": "t30", - "source": "TRIM23", + "source": "TRIM38", "target": "TRAF6", "sign": true }, @@ -649,25 +649,25 @@ }, { "id": "t32", - "source": "TRIM38", + "source": "TLR3", "target": "TICAM1", "sign": true }, { "id": "t33", - "source": "TLR3", + "source": "TRIM38", "target": "TICAM1", "sign": true }, { "id": "t34", - "source": "TRIM59", + "source": "TLR7/8/9_complex", "target": "MYD88", "sign": true }, { "id": "t35", - "source": "TLR7/8/9_complex", + "source": "TRIM59", "target": "MYD88", "sign": true }, @@ -715,19 +715,19 @@ }, { "id": "t43", - "source": "P65/P015_complex", + "source": "CASP1", "target": "IL1b", "sign": true }, { "id": "t44", - "source": "E", + "source": "P65/P015_complex", "target": "IL1b", "sign": true }, { "id": "t45", - "source": "CASP1", + "source": "E", "target": "IL1b", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/PAMP_signaling.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/PAMP_signaling.json index abf62bac..4ddf4dfc 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/PAMP_signaling.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/PAMP_signaling.json @@ -770,13 +770,13 @@ }, { "id": "t2", - "source": "IRAK4", + "source": "IRAK1", "target": "MYD88:IRAK:TRAF_complex", "sign": true }, { "id": "t3", - "source": "IRAK1", + "source": "IRAK4", "target": "MYD88:IRAK:TRAF_complex", "sign": true }, @@ -794,7 +794,7 @@ }, { "id": "t6", - "source": "MAVS", + "source": "TRAF6", "target": "MAVS:TRAF_complex", "sign": true }, @@ -806,19 +806,19 @@ }, { "id": "t8", - "source": "TRAF6", + "source": "MAVS", "target": "MAVS:TRAF_complex", "sign": true }, { "id": "t9", - "source": "TRADD", + "source": "MAVS", "target": "MAVS:TRADD_complex", "sign": true }, { "id": "t10", - "source": "MAVS", + "source": "TRADD", "target": "MAVS:TRADD_complex", "sign": true }, @@ -848,25 +848,25 @@ }, { "id": "t15", - "source": "IKBKG", + "source": "CHUK", "target": "IKK Complex_complex_cell", "sign": true }, { "id": "t16", - "source": "CHUK", + "source": "IKBKG", "target": "IKK Complex_complex_cell", "sign": true }, { "id": "t17", - "source": "NFKBIA", + "source": "NFKB1", "target": "NFKB:NFKBIA_complex_cell", "sign": true }, { "id": "t18", - "source": "NFKB1", + "source": "NFKBIA", "target": "NFKB:NFKBIA_complex_cell", "sign": true }, @@ -878,19 +878,19 @@ }, { "id": "t20", - "source": "Nsp3", + "source": "MAVS:TRADD_complex", "target": "TANK:TRAF3:IKBKE_complex_cell", "sign": true }, { "id": "t21", - "source": "M", + "source": "Nsp3", "target": "TANK:TRAF3:IKBKE_complex_cell", "sign": true }, { "id": "t22", - "source": "MAVS:TRADD_complex", + "source": "M", "target": "TANK:TRAF3:IKBKE_complex_cell", "sign": true }, @@ -938,13 +938,13 @@ }, { "id": "t30", - "source": "ssRNA_rna", + "source": "TLR7", "target": "TLR7:ssRNA_complex", "sign": true }, { "id": "t31", - "source": "TLR7", + "source": "ssRNA_rna", "target": "TLR7:ssRNA_complex", "sign": true }, @@ -968,7 +968,7 @@ }, { "id": "t35", - "source": "M", + "source": "dsRNA_rna_cell", "target": "DDX58:dsRNA_complex", "sign": true }, @@ -980,31 +980,31 @@ }, { "id": "t37", - "source": "dsRNA_rna_cell", + "source": "M", "target": "DDX58:dsRNA_complex", "sign": true }, { "id": "t38", - "source": "Nsp3", + "source": "M", "target": "IFIH1:dsRNA_complex", "sign": true }, { "id": "t39", - "source": "M", + "source": "Nsp3", "target": "IFIH1:dsRNA_complex", "sign": true }, { "id": "t40", - "source": "dsRNA_rna_cell", + "source": "IFIH1", "target": "IFIH1:dsRNA_complex", "sign": true }, { "id": "t41", - "source": "IFIH1", + "source": "dsRNA_rna_cell", "target": "IFIH1:dsRNA_complex", "sign": true }, @@ -1040,19 +1040,19 @@ }, { "id": "t47", - "source": "Nsp15", + "source": "EIF2AK2", "target": "EIF2AK2:dsRNA_complex", "sign": true }, { "id": "t48", - "source": "EIF2AK2", + "source": "dsRNA_rna_cell", "target": "EIF2AK2:dsRNA_complex", "sign": true }, { "id": "t49", - "source": "dsRNA_rna_cell", + "source": "Nsp15", "target": "EIF2AK2:dsRNA_complex", "sign": true }, @@ -1070,7 +1070,7 @@ }, { "id": "t52", - "source": "M", + "source": "CASP10", "target": "IKK Complex_complex_cell", "sign": true }, @@ -1082,19 +1082,19 @@ }, { "id": "t54", - "source": "CASP10", + "source": "M", "target": "IKK Complex_complex_cell", "sign": true }, { "id": "t55", - "source": "JNK_complex", + "source": "MAPK14_phosphorylated", "target": "AP1_complex", "sign": true }, { "id": "t56", - "source": "MAPK14_phosphorylated", + "source": "JNK_complex", "target": "AP1_complex", "sign": true }, @@ -1112,37 +1112,37 @@ }, { "id": "t59", - "source": "TLR3:dsRNA_complex", + "source": "TICAM1_cell", "target": "TICAM1_cell", "sign": true }, { "id": "t60", - "source": "TICAM1_cell", + "source": "TLR3:dsRNA_complex", "target": "TICAM1_cell", "sign": true }, { "id": "t61", - "source": "TBK1_cell", + "source": "TANK:TRAF3:IKBKE_complex_cell", "target": "TBK1_cell", "sign": true }, { "id": "t62", - "source": "TANK:TRAF3:IKBKE_complex_cell", + "source": "TBK1_cell", "target": "TBK1_cell", "sign": true }, { "id": "t63", - "source": "Nsp3", + "source": "TANK:TRAF3:IKBKE_complex_cell", "target": "IKBKE_cell", "sign": true }, { "id": "t64", - "source": "TANK:TRAF3:IKBKE_complex_cell", + "source": "Nsp3", "target": "IKBKE_cell", "sign": true }, @@ -1154,19 +1154,19 @@ }, { "id": "t66", - "source": "Nsp3", + "source": "Orf3b", "target": "IRF3_phosphorylated_cell", "sign": true }, { "id": "t67", - "source": "Orf3b", + "source": "Nsp3", "target": "IRF3_phosphorylated_cell", "sign": true }, { "id": "t68", - "source": "TBK1_cell", + "source": "Orf8", "target": "IRF3_phosphorylated_cell", "sign": true }, @@ -1178,43 +1178,43 @@ }, { "id": "t70", - "source": "Orf8", + "source": "TBK1_cell", "target": "IRF3_phosphorylated_cell", "sign": true }, { "id": "t71", - "source": "RNF135", + "source": "TRIM25", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t72", - "source": "DDX58:dsRNA_complex", + "source": "RNF135", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t73", - "source": "TRIM25", + "source": "N", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t74", - "source": "N", + "source": "DDX58:dsRNA_complex", "target": "DDX58_ubiquitinated", "sign": true }, { "id": "t75", - "source": "IFIH1:dsRNA_complex", + "source": "DDX58_ubiquitinated", "target": "MAVS", "sign": true }, { "id": "t76", - "source": "DDX58_ubiquitinated", + "source": "IFIH1:dsRNA_complex", "target": "MAVS", "sign": true }, @@ -1262,7 +1262,7 @@ }, { "id": "t84", - "source": "UBE2N", + "source": "MYD88:IRAK:TRAF_complex", "target": "TRAF6_ubiquitinated", "sign": true }, @@ -1274,7 +1274,7 @@ }, { "id": "t86", - "source": "MYD88:IRAK:TRAF_complex", + "source": "UBE2N", "target": "TRAF6_ubiquitinated", "sign": true }, @@ -1322,13 +1322,13 @@ }, { "id": "t94", - "source": "MAP3K7", + "source": "EIF2AK2:dsRNA_complex", "target": "MAP2K6_phosphorylated", "sign": true }, { "id": "t95", - "source": "EIF2AK2:dsRNA_complex", + "source": "MAP3K7", "target": "MAP2K6_phosphorylated", "sign": true }, @@ -1364,25 +1364,25 @@ }, { "id": "t101", - "source": "IRF3_phosphorylated_nucleus", + "source": "NFKB_complex", "target": "transcription of proinflammatory proteins_phenotype", "sign": true }, { "id": "t102", - "source": "IRF7_phosphorylated", + "source": "AP1_complex", "target": "transcription of proinflammatory proteins_phenotype", "sign": true }, { "id": "t103", - "source": "AP1_complex", + "source": "IRF3_phosphorylated_nucleus", "target": "transcription of proinflammatory proteins_phenotype", "sign": true }, { "id": "t104", - "source": "NFKB_complex", + "source": "IRF7_phosphorylated", "target": "transcription of proinflammatory proteins_phenotype", "sign": true } diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Pyrimidine_deprivation.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Pyrimidine_deprivation.json index 38a97e14..6cade6b3 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Pyrimidine_deprivation.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Pyrimidine_deprivation.json @@ -970,13 +970,13 @@ "edges": [ { "id": "t1", - "source": "NF-kB_complex", + "source": "IRF3_phosphorylated", "target": "IFNB1_space_expression_space_complex_complex", "sign": true }, { "id": "t2", - "source": "IRF3_phosphorylated", + "source": "NF-kB_complex", "target": "IFNB1_space_expression_space_complex_complex", "sign": true }, @@ -1006,13 +1006,13 @@ }, { "id": "t7", - "source": "cGAMP-STING_complex_endoplasmic reticulum-Golgi intermediate compartment", + "source": "LC3", "target": "cGAMP:STING:LC3_complex", "sign": true }, { "id": "t8", - "source": "LC3", + "source": "cGAMP-STING_complex_endoplasmic reticulum-Golgi intermediate compartment", "target": "cGAMP:STING:LC3_complex", "sign": true }, @@ -1024,55 +1024,55 @@ }, { "id": "t10", - "source": "cGAS", + "source": "dsDNA_simple_molecule", "target": "cGAS:dsDNA_complex", "sign": true }, { "id": "t11", - "source": "dsDNA_simple_molecule", + "source": "cGAS", "target": "cGAS:dsDNA_complex", "sign": true }, { "id": "t12", - "source": "MRE11", + "source": "dsDNA_simple_molecule", "target": "MRE11:dsDNA_complex", "sign": true }, { "id": "t13", - "source": "dsDNA_simple_molecule", + "source": "MRE11", "target": "MRE11:dsDNA_complex", "sign": true }, { "id": "t14", - "source": "cGAMP:STING_complex_Golgi apparatus", + "source": "TBK1", "target": "STING:TBK1_complex_Golgi apparatus", "sign": true }, { "id": "t15", - "source": "TBK1", + "source": "STING_Golgi apparatus", "target": "STING:TBK1_complex_Golgi apparatus", "sign": true }, { "id": "t16", - "source": "STING_Golgi apparatus", + "source": "cGAMP:STING_complex_Golgi apparatus", "target": "STING:TBK1_complex_Golgi apparatus", "sign": true }, { "id": "t17", - "source": "SAR1A", + "source": "cGAMP:STING_complex_endoplasmic reticulum", "target": "cGAMP-STING_complex_COPII-coated vesicle", "sign": true }, { "id": "t18", - "source": "cGAMP:STING_complex_endoplasmic reticulum", + "source": "SAR1A", "target": "cGAMP-STING_complex_COPII-coated vesicle", "sign": true }, @@ -1108,19 +1108,19 @@ }, { "id": "t24", - "source": "H+simple_molecule", + "source": "CAD", "target": "H2O_simple_molecule", "sign": true }, { "id": "t25", - "source": "CAD", + "source": "H+simple_molecule", "target": "H2O_simple_molecule", "sign": true }, { "id": "t26", - "source": "UMPS", + "source": "orotidine_space_5'-monophosphate_simple_molecule", "target": "UMP_simple_molecule", "sign": true }, @@ -1132,13 +1132,13 @@ }, { "id": "t28", - "source": "uridine_simple_molecule", + "source": "UMPS", "target": "UMP_simple_molecule", "sign": true }, { "id": "t29", - "source": "orotidine_space_5'-monophosphate_simple_molecule", + "source": "uridine_simple_molecule", "target": "UMP_simple_molecule", "sign": true }, @@ -1150,13 +1150,13 @@ }, { "id": "t31", - "source": "cGAS:dsDNA_complex", + "source": "ATP_simple_molecule", "target": "cGAMP_simple_molecule", "sign": true }, { "id": "t32", - "source": "ATP_simple_molecule", + "source": "cGAS:dsDNA_complex", "target": "cGAMP_simple_molecule", "sign": true }, @@ -1168,25 +1168,25 @@ }, { "id": "t34", - "source": "CDP_simple_molecule", + "source": "ribonucleoside-diphosphate reductase_complex", "target": "dCDP_simple_molecule", "sign": true }, { "id": "t35", - "source": "ribonucleoside-diphosphate reductase_complex", + "source": "CDP_simple_molecule", "target": "dCDP_simple_molecule", "sign": true }, { "id": "t36", - "source": "UMP_simple_molecule", + "source": "CMPK", "target": "UDP_simple_molecule", "sign": true }, { "id": "t37", - "source": "CMPK", + "source": "UMP_simple_molecule", "target": "UDP_simple_molecule", "sign": true }, @@ -1210,25 +1210,25 @@ }, { "id": "t41", - "source": "L-Gln_simple_molecule", + "source": "L-Asp_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t42", - "source": "L-Asp_simple_molecule", + "source": "CAD", "target": "Pi_simple_molecule", "sign": true }, { "id": "t43", - "source": "H2O_simple_molecule", + "source": "L-Gln_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t44", - "source": "CAD", + "source": "H2O_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, @@ -1240,13 +1240,13 @@ }, { "id": "t46", - "source": "CAP_simple_molecule", + "source": "HCO3-simple_molecule", "target": "Pi_simple_molecule", "sign": true }, { "id": "t47", - "source": "HCO3-simple_molecule", + "source": "CAP_simple_molecule", "target": "Pi_simple_molecule", "sign": true }, @@ -1258,31 +1258,31 @@ }, { "id": "t49", - "source": "H+simple_molecule", + "source": "CAD", "target": "(S)-dihydroorotate_simple_molecule", "sign": true }, { "id": "t50", - "source": "CAD", + "source": "H+simple_molecule", "target": "(S)-dihydroorotate_simple_molecule", "sign": true }, { "id": "t51", - "source": "L-Gln_simple_molecule", + "source": "CAD", "target": "ADP_simple_molecule", "sign": true }, { "id": "t52", - "source": "H2O_simple_molecule", + "source": "L-Gln_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t53", - "source": "HCO3-simple_molecule", + "source": "H2O_simple_molecule", "target": "ADP_simple_molecule", "sign": true }, @@ -1294,49 +1294,49 @@ }, { "id": "t55", - "source": "CAD", + "source": "HCO3-simple_molecule", "target": "ADP_simple_molecule", "sign": true }, { "id": "t56", - "source": "dCMP_simple_molecule", + "source": "DCTD", "target": "dUMP_simple_molecule", "sign": true }, { "id": "t57", - "source": "DUT", + "source": "dUTP_simple_molecule", "target": "dUMP_simple_molecule", "sign": true }, { "id": "t58", - "source": "DCTD", + "source": "DUT", "target": "dUMP_simple_molecule", "sign": true }, { "id": "t59", - "source": "dUTP_simple_molecule", + "source": "dCMP_simple_molecule", "target": "dUMP_simple_molecule", "sign": true }, { "id": "t60", - "source": "CAP_simple_molecule", + "source": "L-Asp_simple_molecule", "target": "N-carbamoyl-L-aspartate_simple_molecule", "sign": true }, { "id": "t61", - "source": "L-Asp_simple_molecule", + "source": "CAD", "target": "N-carbamoyl-L-aspartate_simple_molecule", "sign": true }, { "id": "t62", - "source": "CAD", + "source": "CAP_simple_molecule", "target": "N-carbamoyl-L-aspartate_simple_molecule", "sign": true }, @@ -1372,7 +1372,7 @@ }, { "id": "t68", - "source": "dTTP_simple_molecule", + "source": "dsDNA_simple_molecule", "target": "DNA_gene", "sign": true }, @@ -1384,13 +1384,13 @@ }, { "id": "t70", - "source": "dsDNA_simple_molecule", + "source": "virus_space_replication_phenotype", "target": "DNA_gene", "sign": true }, { "id": "t71", - "source": "virus_space_replication_phenotype", + "source": "dTTP_simple_molecule", "target": "DNA_gene", "sign": true }, @@ -1444,31 +1444,31 @@ }, { "id": "t80", - "source": "UMPS", + "source": "PRPP_simple_molecule", "target": "PPi_simple_molecule", "sign": true }, { "id": "t81", - "source": "PRPP_simple_molecule", + "source": "UMPS", "target": "PPi_simple_molecule", "sign": true }, { "id": "t82", - "source": "L-Gln_simple_molecule", + "source": "CAD", "target": "L-Glu_simple_molecule", "sign": true }, { "id": "t83", - "source": "H2O_simple_molecule", + "source": "L-Gln_simple_molecule", "target": "L-Glu_simple_molecule", "sign": true }, { "id": "t84", - "source": "HCO3-simple_molecule", + "source": "H2O_simple_molecule", "target": "L-Glu_simple_molecule", "sign": true }, @@ -1480,7 +1480,7 @@ }, { "id": "t86", - "source": "CAD", + "source": "HCO3-simple_molecule", "target": "L-Glu_simple_molecule", "sign": true }, @@ -1510,19 +1510,19 @@ }, { "id": "t91", - "source": "L-Gln_simple_molecule", + "source": "CAD", "target": "CAP_simple_molecule", "sign": true }, { "id": "t92", - "source": "H2O_simple_molecule", + "source": "L-Gln_simple_molecule", "target": "CAP_simple_molecule", "sign": true }, { "id": "t93", - "source": "HCO3-simple_molecule", + "source": "H2O_simple_molecule", "target": "CAP_simple_molecule", "sign": true }, @@ -1534,7 +1534,7 @@ }, { "id": "t95", - "source": "CAD", + "source": "HCO3-simple_molecule", "target": "CAP_simple_molecule", "sign": true }, @@ -1552,13 +1552,13 @@ }, { "id": "t98", - "source": "MRE11:RAD50:DNA_complex_endoplasmic reticulum", + "source": "STING_endoplasmic reticulum", "target": "STING_Golgi apparatus", "sign": true }, { "id": "t99", - "source": "STING_endoplasmic reticulum", + "source": "MRE11:RAD50:DNA_complex_endoplasmic reticulum", "target": "STING_Golgi apparatus", "sign": true }, @@ -1582,7 +1582,7 @@ }, { "id": "t103", - "source": "(S)-dihydroorotate_simple_molecule", + "source": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", "target": "QH2_simple_molecule", "sign": true }, @@ -1594,19 +1594,19 @@ }, { "id": "t105", - "source": "P1788_simple_molecule", + "source": "CoQ_simple_molecule", "target": "QH2_simple_molecule", "sign": true }, { "id": "t106", - "source": "CoQ_simple_molecule", + "source": "P1788_simple_molecule", "target": "QH2_simple_molecule", "sign": true }, { "id": "t107", - "source": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", + "source": "(S)-dihydroorotate_simple_molecule", "target": "QH2_simple_molecule", "sign": true }, @@ -1618,31 +1618,31 @@ }, { "id": "t109", - "source": "UMPS", + "source": "PRPP_simple_molecule", "target": "orotidine_space_5'-monophosphate_simple_molecule", "sign": true }, { "id": "t110", - "source": "PRPP_simple_molecule", + "source": "UMPS", "target": "orotidine_space_5'-monophosphate_simple_molecule", "sign": true }, { "id": "t111", - "source": "NME1", + "source": "dUDP_simple_molecule", "target": "dUTP_simple_molecule", "sign": true }, { "id": "t112", - "source": "dUDP_simple_molecule", + "source": "NME1", "target": "dUTP_simple_molecule", "sign": true }, { "id": "t113", - "source": "(S)-dihydroorotate_simple_molecule", + "source": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", "target": "orotate_simple_molecule", "sign": true }, @@ -1654,49 +1654,49 @@ }, { "id": "t115", - "source": "P1788_simple_molecule", + "source": "CoQ_simple_molecule", "target": "orotate_simple_molecule", "sign": true }, { "id": "t116", - "source": "CoQ_simple_molecule", + "source": "P1788_simple_molecule", "target": "orotate_simple_molecule", "sign": true }, { "id": "t117", - "source": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", + "source": "(S)-dihydroorotate_simple_molecule", "target": "orotate_simple_molecule", "sign": true }, { "id": "t118", - "source": "UMPS", + "source": "orotidine_space_5'-monophosphate_simple_molecule", "target": "CO2_simple_molecule", "sign": true }, { "id": "t119", - "source": "orotidine_space_5'-monophosphate_simple_molecule", + "source": "UMPS", "target": "CO2_simple_molecule", "sign": true }, { "id": "t120", - "source": "CDP_simple_molecule", + "source": "UTP_simple_molecule", "target": "CTP_simple_molecule", "sign": true }, { "id": "t121", - "source": "UTP_simple_molecule", + "source": "NME1", "target": "CTP_simple_molecule", "sign": true }, { "id": "t122", - "source": "NME1", + "source": "CDP_simple_molecule", "target": "CTP_simple_molecule", "sign": true }, @@ -1708,13 +1708,13 @@ }, { "id": "t124", - "source": "UDP_simple_molecule", + "source": "ribonucleoside-diphosphate reductase_complex", "target": "dUDP_simple_molecule", "sign": true }, { "id": "t125", - "source": "ribonucleoside-diphosphate reductase_complex", + "source": "UDP_simple_molecule", "target": "dUDP_simple_molecule", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/RTC-and-transcription.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/RTC-and-transcription.json index 8bec1221..8b70c26f 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/RTC-and-transcription.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/RTC-and-transcription.json @@ -310,25 +310,25 @@ "edges": [ { "id": "t1", - "source": "(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_cell", + "source": "nsp9_cell", "target": "Replication_space_transcription_space_complex_space__complex_double membrane vesicle viral factory", "sign": true }, { "id": "t2", - "source": "complex_complex_cell", + "source": "CoV_space_poly-br_merase_space_complex_complex_cell", "target": "Replication_space_transcription_space_complex_space__complex_double membrane vesicle viral factory", "sign": true }, { "id": "t3", - "source": "CoV_space_poly-br_merase_space_complex_complex_cell", + "source": "complex_complex_cell", "target": "Replication_space_transcription_space_complex_space__complex_double membrane vesicle viral factory", "sign": true }, { "id": "t4", - "source": "nsp9_cell", + "source": "(+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_cell", "target": "Replication_space_transcription_space_complex_space__complex_double membrane vesicle viral factory", "sign": true }, @@ -340,25 +340,25 @@ }, { "id": "t6", - "source": "nsp8_space_(II)", + "source": "nsp7", "target": "complex_complex_cell", "sign": true }, { "id": "t7", - "source": "nsp7", + "source": "nsp8_space_(II)", "target": "complex_complex_cell", "sign": true }, { "id": "t8", - "source": "nsp14", + "source": "nsp10", "target": "CoV_space_poly-br_merase_space_complex_complex_cell", "sign": true }, { "id": "t9", - "source": "nsp10", + "source": "nsp14", "target": "CoV_space_poly-br_merase_space_complex_complex_cell", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Renin_angiotensin.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Renin_angiotensin.json index 2ed1e239..41846515 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Renin_angiotensin.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Renin_angiotensin.json @@ -841,7 +841,7 @@ "edges": [ { "id": "t1", - "source": "AGTR1_cell", + "source": "angiotensin II_simple_molecule_cell", "target": "ACE2:AGTR1_complex", "sign": true }, @@ -853,31 +853,31 @@ }, { "id": "t3", - "source": "angiotensin II_simple_molecule_cell", + "source": "AGTR1_cell", "target": "ACE2:AGTR1_complex", "sign": true }, { "id": "t4", - "source": "Camostat mesilate_drug", + "source": "ACE2_cell", "target": "ACE2-Spike complex_complex", "sign": true }, { "id": "t5", - "source": "S", + "source": "TMPRSS2", "target": "ACE2-Spike complex_complex", "sign": true }, { "id": "t6", - "source": "TMPRSS2", + "source": "Camostat mesilate_drug", "target": "ACE2-Spike complex_complex", "sign": true }, { "id": "t7", - "source": "ACE2_cell", + "source": "S", "target": "ACE2-Spike complex_complex", "sign": true }, @@ -895,37 +895,37 @@ }, { "id": "t10", - "source": "REN", + "source": "AGT", "target": "angiotensin I_simple_molecule", "sign": true }, { "id": "t11", - "source": "AGT", + "source": "ACE_cell", "target": "angiotensin I_simple_molecule", "sign": true }, { "id": "t12", - "source": "ACE_cell", + "source": "REN", "target": "angiotensin I_simple_molecule", "sign": true }, { "id": "t13", - "source": "angiotensin 1-12_simple_molecule", + "source": "CTSG", "target": "angiotensin I_simple_molecule", "sign": true }, { "id": "t14", - "source": "CTSG", + "source": "CTSD", "target": "angiotensin I_simple_molecule", "sign": true }, { "id": "t15", - "source": "CTSD", + "source": "angiotensin 1-12_simple_molecule", "target": "angiotensin I_simple_molecule", "sign": true }, @@ -949,25 +949,25 @@ }, { "id": "t19", - "source": "angiotensin 1-12_simple_molecule", + "source": "CMA1", "target": "angiotensin II_simple_molecule_cell", "sign": true }, { "id": "t20", - "source": "angiotensin I_simple_molecule", + "source": "KLK1", "target": "angiotensin II_simple_molecule_cell", "sign": true }, { "id": "t21", - "source": "CMA1", + "source": "angiotensin 1-12_simple_molecule", "target": "angiotensin II_simple_molecule_cell", "sign": true }, { "id": "t22", - "source": "KLK1", + "source": "angiotensin I_simple_molecule", "target": "angiotensin II_simple_molecule_cell", "sign": true }, @@ -979,31 +979,31 @@ }, { "id": "t24", - "source": "THOP1", + "source": "angiotensin 1-9_simple_molecule", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t25", - "source": "MME_cell", + "source": "PREP", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t26", - "source": "PREP", + "source": "THOP1", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t27", - "source": "angiotensin 1-12_simple_molecule", + "source": "ACE_cell_active", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t28", - "source": "angiotensin 1-9_simple_molecule", + "source": "ACE2_cell", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, @@ -1015,79 +1015,79 @@ }, { "id": "t30", - "source": "ACE_cell_active", + "source": "angiotensin II_simple_molecule_cell", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t31", - "source": "angiotensin II_simple_molecule_cell", + "source": "PRCP", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t32", - "source": "PRCP", + "source": "MME_cell", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t33", - "source": "ACE2_cell", + "source": "angiotensin 1-12_simple_molecule", "target": "angiotensin 1-7_simple_molecule_cell", "sign": true }, { "id": "t34", - "source": "CGP42112A_drug", + "source": "angiotensin 1-9_simple_molecule", "target": "AGTR2_cell_active", "sign": true }, { "id": "t35", - "source": "angiotensin 1-9_simple_molecule", + "source": "angiotensin A_simple_molecule", "target": "AGTR2_cell_active", "sign": true }, { "id": "t36", - "source": "AGTR2_cell", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "AGTR2_cell_active", "sign": true }, { "id": "t37", - "source": "angiotensin A_simple_molecule", + "source": "AGTR2_cell", "target": "AGTR2_cell_active", "sign": true }, { "id": "t38", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "angiotensin II_simple_molecule_cell", "target": "AGTR2_cell_active", "sign": true }, { "id": "t39", - "source": "angiotensin II_simple_molecule_cell", + "source": "CGP42112A_drug", "target": "AGTR2_cell_active", "sign": true }, { "id": "t40", - "source": "MAS1_cell", + "source": "angiotensin 1-5_simple_molecule", "target": "MAS1_cell_active", "sign": true }, { "id": "t41", - "source": "angiotensin 1-5_simple_molecule", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "MAS1_cell_active", "sign": true }, { "id": "t42", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "MAS1_cell", "target": "MAS1_cell_active", "sign": true }, @@ -1099,37 +1099,37 @@ }, { "id": "t44", - "source": "Calcitriol_simple_molecule", + "source": "estradiol_simple_molecule", "target": "ACE_cell", "sign": true }, { "id": "t45", - "source": "estradiol_simple_molecule", + "source": "Calcitriol_simple_molecule", "target": "ACE_cell", "sign": true }, { "id": "t46", - "source": "ACE2_gene", + "source": "hypertension_phenotype", "target": "ACE2_cell", "sign": true }, { "id": "t47", - "source": "Calcitriol_simple_molecule", + "source": "aging_phenotype", "target": "ACE2_cell", "sign": true }, { "id": "t48", - "source": "SARS-CoV-2 infection_phenotype", + "source": "Calcitriol_simple_molecule", "target": "ACE2_cell", "sign": true }, { "id": "t49", - "source": "aging_phenotype", + "source": "SARS-CoV-2 infection_phenotype", "target": "ACE2_cell", "sign": true }, @@ -1141,19 +1141,19 @@ }, { "id": "t51", - "source": "hypertension_phenotype", + "source": "ACE2_gene", "target": "ACE2_cell", "sign": true }, { "id": "t52", - "source": "S", + "source": " Diabetes mellitus, type II_phenotype", "target": "ACE2_cell", "sign": true }, { "id": "t53", - "source": " Diabetes mellitus, type II_phenotype", + "source": "S", "target": "ACE2_cell", "sign": true }, @@ -1183,37 +1183,37 @@ }, { "id": "t58", - "source": "angiotensin A_simple_molecule", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "alamandine_simple_molecule", "sign": true }, { "id": "t59", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "ACE2_cell", "target": "alamandine_simple_molecule", "sign": true }, { "id": "t60", - "source": "ACE2_cell", + "source": "angiotensin A_simple_molecule", "target": "alamandine_simple_molecule", "sign": true }, { "id": "t61", - "source": "MRGPRD_cell", + "source": "alamandine_simple_molecule", "target": "MRGPRD_cell_active", "sign": true }, { "id": "t62", - "source": "alamandine_simple_molecule", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "MRGPRD_cell_active", "sign": true }, { "id": "t63", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "MRGPRD_cell", "target": "MRGPRD_cell_active", "sign": true }, @@ -1225,55 +1225,55 @@ }, { "id": "t65", - "source": "AGTR1_cell_active", + "source": "MAS1_cell_active", "target": "vasoconstriction_phenotype", "sign": true }, { "id": "t66", - "source": "AGTR2_cell_active", + "source": "LNPEP_cell_active", "target": "vasoconstriction_phenotype", "sign": true }, { "id": "t67", - "source": "MAS1_cell_active", + "source": "MRGPRD_cell_active", "target": "vasoconstriction_phenotype", "sign": true }, { "id": "t68", - "source": "MRGPRD_cell_active", + "source": "AGTR1_cell_active", "target": "vasoconstriction_phenotype", "sign": true }, { "id": "t69", - "source": "LNPEP_cell_active", + "source": "AGTR2_cell_active", "target": "vasoconstriction_phenotype", "sign": true }, { "id": "t70", - "source": "LNPEP_cell_active", + "source": "MAS1_cell_active", "target": "inflammatory response_phenotype", "sign": true }, { "id": "t71", - "source": "MAS1_cell_active", + "source": "MRGPRD_cell_active", "target": "inflammatory response_phenotype", "sign": true }, { "id": "t72", - "source": "MRGPRD_cell_active", + "source": "AGTR1_cell_active", "target": "inflammatory response_phenotype", "sign": true }, { "id": "t73", - "source": "AGTR1_cell_active", + "source": "LNPEP_cell_active", "target": "inflammatory response_phenotype", "sign": true }, @@ -1303,13 +1303,13 @@ }, { "id": "t78", - "source": "sex, male_phenotype", + "source": "ENPEP_cell", "target": "ENPEP_cell_active", "sign": true }, { "id": "t79", - "source": "ENPEP_cell", + "source": "sex, male_phenotype", "target": "ENPEP_cell_active", "sign": true }, @@ -1369,73 +1369,73 @@ }, { "id": "t89", - "source": "sex, male_phenotype", + "source": "aging_phenotype", "target": "ACE2_cell_active", "sign": true }, { "id": "t90", - "source": "hypertension_phenotype", + "source": "sex, male_phenotype", "target": "ACE2_cell_active", "sign": true }, { "id": "t91", - "source": "aging_phenotype", + "source": "ACE2_cell", "target": "ACE2_cell_active", "sign": true }, { "id": "t92", - "source": "ACE2_cell", + "source": "hypertension_phenotype", "target": "ACE2_cell_active", "sign": true }, { "id": "t93", - "source": "sex, male_phenotype", + "source": "aldosterone_simple_molecule", "target": "ACE_cell_active", "sign": true }, { "id": "t94", - "source": "Lisinopril_drug", + "source": "hypertension_phenotype", "target": "ACE_cell_active", "sign": true }, { "id": "t95", - "source": "ACE_cell", + "source": "aging_phenotype", "target": "ACE_cell_active", "sign": true }, { "id": "t96", - "source": "ABO blood group system_phenotype", + "source": "ACE_cell", "target": "ACE_cell_active", "sign": true }, { "id": "t97", - "source": "aging_phenotype", + "source": "ABO blood group system_phenotype", "target": "ACE_cell_active", "sign": true }, { "id": "t98", - "source": "aldosterone_simple_molecule", + "source": "Lisinopril_drug", "target": "ACE_cell_active", "sign": true }, { "id": "t99", - "source": "hypertension_phenotype", + "source": "sex, male_phenotype", "target": "ACE_cell_active", "sign": true }, { "id": "t100", - "source": "MAS1:AGTR1_complex", + "source": "angiotensin IV_simple_molecule", "target": "AGTR1_cell_active", "sign": true }, @@ -1447,43 +1447,43 @@ }, { "id": "t102", - "source": "angiotensin IV_simple_molecule", + "source": "angiotensin A_simple_molecule", "target": "AGTR1_cell_active", "sign": true }, { "id": "t103", - "source": "angiotensin A_simple_molecule", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "AGTR1_cell_active", "sign": true }, { "id": "t104", - "source": "AGTR1_cell", + "source": "angiotensin II_simple_molecule_cell", "target": "AGTR1_cell_active", "sign": true }, { "id": "t105", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "MAS1:AGTR1_complex", "target": "AGTR1_cell_active", "sign": true }, { "id": "t106", - "source": "angiotensin II_simple_molecule_cell", + "source": "AGTR1_cell", "target": "AGTR1_cell_active", "sign": true }, { "id": "t107", - "source": "angiotensin 1-12_simple_molecule", + "source": "MME_cell", "target": "angiotensin 1-4_simple_molecule", "sign": true }, { "id": "t108", - "source": "MME_cell", + "source": "angiotensin 1-12_simple_molecule", "target": "angiotensin 1-4_simple_molecule", "sign": true }, @@ -1495,13 +1495,13 @@ }, { "id": "t110", - "source": "LNPEP_cell", + "source": "angiotensin IV_simple_molecule", "target": "LNPEP_cell_active", "sign": true }, { "id": "t111", - "source": "angiotensin IV_simple_molecule", + "source": "LNPEP_cell", "target": "LNPEP_cell_active", "sign": true }, @@ -1519,13 +1519,13 @@ }, { "id": "t114", - "source": "angiotensin 1-7_simple_molecule_cell", + "source": "angiotensin IV_simple_molecule", "target": "angiotensin 3-7_simple_molecule", "sign": true }, { "id": "t115", - "source": "angiotensin IV_simple_molecule", + "source": "angiotensin 1-7_simple_molecule_cell", "target": "angiotensin 3-7_simple_molecule", "sign": true }, @@ -1543,13 +1543,13 @@ }, { "id": "t118", - "source": "AGTR2_cell_active", + "source": "MAS1_cell_active", "target": "fibrosis_phenotype", "sign": true }, { "id": "t119", - "source": "MAS1_cell_active", + "source": "AGTR2_cell_active", "target": "fibrosis_phenotype", "sign": true }, @@ -1579,13 +1579,13 @@ }, { "id": "t124", - "source": "sex, male_phenotype", + "source": "MME_cell", "target": "MME_cell_active", "sign": true }, { "id": "t125", - "source": "MME_cell", + "source": "sex, male_phenotype", "target": "MME_cell_active", "sign": true }, @@ -1597,13 +1597,13 @@ }, { "id": "t127", - "source": "LNPEP_cell_active", + "source": "AGTR1_cell_active", "target": "cognition_phenotype", "sign": true }, { "id": "t128", - "source": "AGTR1_cell_active", + "source": "LNPEP_cell_active", "target": "cognition_phenotype", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/TGFB_pathway.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/TGFB_pathway.json index 92ad36a7..a35415b8 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/TGFB_pathway.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/TGFB_pathway.json @@ -201,37 +201,37 @@ "edges": [ { "id": "t1", - "source": "BMPR1/2/ACTR2_complex", + "source": "MAPK3", "target": "SMAD1/5/8_complex", "sign": true }, { "id": "t2", - "source": "Orf3a", + "source": "E", "target": "SMAD1/5/8_complex", "sign": true }, { "id": "t3", - "source": "Nsp7b_cell", + "source": "Orf3a", "target": "SMAD1/5/8_complex", "sign": true }, { "id": "t4", - "source": "E", + "source": "BAMBI", "target": "SMAD1/5/8_complex", "sign": true }, { "id": "t5", - "source": "BAMBI", + "source": "BMPR1/2/ACTR2_complex", "target": "SMAD1/5/8_complex", "sign": true }, { "id": "t6", - "source": "MAPK3", + "source": "Nsp7b_cell", "target": "SMAD1/5/8_complex", "sign": true }, @@ -243,19 +243,19 @@ }, { "id": "t8", - "source": "Nsp7b_default_compartment", + "source": "TGFB/TGFBR_complex", "target": "SMAD2/3_complex", "sign": true }, { "id": "t9", - "source": "TGFB/TGFBR_complex", + "source": "MAPK3", "target": "SMAD2/3_complex", "sign": true }, { "id": "t10", - "source": "Orf3a", + "source": "ACVR1", "target": "SMAD2/3_complex", "sign": true }, @@ -273,13 +273,13 @@ }, { "id": "t13", - "source": "MAPK3", + "source": "Orf3a", "target": "SMAD2/3_complex", "sign": true }, { "id": "t14", - "source": "ACVR1", + "source": "Nsp7b_default_compartment", "target": "SMAD2/3_complex", "sign": true }, @@ -291,37 +291,37 @@ }, { "id": "t16", - "source": "LTBP1", + "source": "BAMBI", "target": "TGFB/TGFBR_complex", "sign": true }, { "id": "t17", - "source": "BAMBI", + "source": "LTBP1", "target": "TGFB/TGFBR_complex", "sign": true }, { "id": "t18", - "source": "TGFB/TGFBR_complex", + "source": "Orf7a", "target": "PP2A_complex", "sign": true }, { "id": "t19", - "source": "Orf7a", + "source": "TGFB/TGFBR_complex", "target": "PP2A_complex", "sign": true }, { "id": "t20", - "source": "TGFB/TGFBR_complex", + "source": "Nsp7", "target": "RHOA", "sign": true }, { "id": "t21", - "source": "Nsp7", + "source": "TGFB/TGFBR_complex", "target": "RHOA", "sign": true }, diff --git a/scripts/covid19_diseasemaps/regnet_amr_sbml/Virus_replication_cycle.json b/scripts/covid19_diseasemaps/regnet_amr_sbml/Virus_replication_cycle.json index a3622c02..d976ee82 100644 --- a/scripts/covid19_diseasemaps/regnet_amr_sbml/Virus_replication_cycle.json +++ b/scripts/covid19_diseasemaps/regnet_amr_sbml/Virus_replication_cycle.json @@ -1947,13 +1947,13 @@ "edges": [ { "id": "t1", - "source": "Nsp10", + "source": "Nsp16", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t2", - "source": "Nsp3", + "source": "Nsp9", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, @@ -1965,37 +1965,37 @@ }, { "id": "t4", - "source": "Nsp4_endoplasmic reticulum", + "source": "Nsp3", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t5", - "source": "Nsp14", + "source": "Nsp7", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t6", - "source": "Nsp16", + "source": "Nsp14", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t7", - "source": "Nsp13", + "source": "Nsp6_endoplasmic reticulum", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t8", - "source": "Nsp7", + "source": "Nsp10", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t9", - "source": "Nsp9", + "source": "Nsp8", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, @@ -2007,31 +2007,31 @@ }, { "id": "t11", - "source": "Nsp15", + "source": "Nsp4_endoplasmic reticulum", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t12", - "source": "Nsp6_endoplasmic reticulum", + "source": "Nsp15", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t13", - "source": "Nsp8", + "source": "Nsp13", "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "sign": true }, { "id": "t14", - "source": "S_SARS-CoV-2_space_virion", + "source": "ACE2_epithelial_space_cell", "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "sign": true }, { "id": "t15", - "source": "ACE2_epithelial_space_cell", + "source": "S_SARS-CoV-2_space_virion", "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "sign": true }, @@ -2043,55 +2043,55 @@ }, { "id": "t17", - "source": "S1:NRP1_space_complex_complex", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t18", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "E_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t19", - "source": "S2_SARS-CoV-2_space_virion", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t20", - "source": "cholesterol_simple_molecule", + "source": "S2_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t21", - "source": "S2_epithelial_space_cell", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t22", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t23", - "source": "M_SARS-CoV-2_space_virion", + "source": "cholesterol_simple_molecule", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t24", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_epithelial_space_cell", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, { "id": "t25", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "S1:NRP1_space_complex_complex", "target": "Nucleocapsid_complex_epithelial_space_cell", "sign": true }, @@ -2103,13 +2103,13 @@ }, { "id": "t27", - "source": "S1_default_compartment", + "source": "NRP1", "target": "S1:NRP1_space_complex_complex", "sign": true }, { "id": "t28", - "source": "NRP1", + "source": "S1_default_compartment", "target": "S1:NRP1_space_complex_complex", "sign": true }, @@ -2127,13 +2127,13 @@ }, { "id": "t31", - "source": "S_SARS-CoV-2_space_virion", + "source": "ACE2_epithelial_space_cell", "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "sign": true }, { "id": "t32", - "source": "ACE2_epithelial_space_cell", + "source": "S_SARS-CoV-2_space_virion", "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "sign": true }, @@ -2193,13 +2193,13 @@ }, { "id": "t42", - "source": "SIGMAR1_endoplasmic reticulum", + "source": "SARS-CoV2 candidate drugs_complex", "target": "SIGMAR1: drug complex_complex", "sign": true }, { "id": "t43", - "source": "SARS-CoV2 candidate drugs_complex", + "source": "SIGMAR1_endoplasmic reticulum", "target": "SIGMAR1: drug complex_complex", "sign": true }, @@ -2271,25 +2271,25 @@ }, { "id": "t55", - "source": "Selinexor_drug", + "source": "NUP210_endoplasmic reticulum", "target": "NUP210:Selinexor_complex", "sign": true }, { "id": "t56", - "source": "NUP210_endoplasmic reticulum", + "source": "Selinexor_drug", "target": "NUP210:Selinexor_complex", "sign": true }, { "id": "t57", - "source": "Nsp6_epithelial_space_cell", + "source": "SIGMAR1_endoplasmic reticulum", "target": "Nsp6:SIGMAR1_complex_endoplasmic reticulum", "sign": true }, { "id": "t58", - "source": "SIGMAR1_endoplasmic reticulum", + "source": "Nsp6_epithelial_space_cell", "target": "Nsp6:SIGMAR1_complex_endoplasmic reticulum", "sign": true }, @@ -2319,37 +2319,37 @@ }, { "id": "t63", - "source": "Ca+2_simple_molecule", + "source": "RAB7A", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, { "id": "t64", - "source": "RAB7A", + "source": "ARL8B", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, { "id": "t65", - "source": "ARL8B", + "source": "Ca+2_simple_molecule", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, { "id": "t66", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "RAB7A", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, { "id": "t67", - "source": "RAB7A", + "source": "ARL8B", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, { "id": "t68", - "source": "ARL8B", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "sign": true }, @@ -2373,13 +2373,13 @@ }, { "id": "t72", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t73", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -2391,13 +2391,13 @@ }, { "id": "t75", - "source": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf9b_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t76", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "Orf9b_space_ds_space_sgmRNA_rna", "sign": true }, @@ -2415,13 +2415,13 @@ }, { "id": "t79", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t80", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -2433,13 +2433,13 @@ }, { "id": "t82", - "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "source": "E (+)ss sgmRNA_rna_epithelial_space_cell", "target": "E_rough_space_endoplasmic_space_reticulum", "sign": true }, { "id": "t83", - "source": "E (+)ss sgmRNA_rna_epithelial_space_cell", + "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", "target": "E_rough_space_endoplasmic_space_reticulum", "sign": true }, @@ -2451,13 +2451,13 @@ }, { "id": "t85", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "M_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t86", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "M_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -2511,25 +2511,25 @@ }, { "id": "t95", - "source": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "E_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t96", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "E_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t97", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t98", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -2559,19 +2559,19 @@ }, { "id": "t103", - "source": "pp1a_space_Nsp6-11", + "source": "pp1ab_space_nsp6-16", "target": "Nsp7", "sign": true }, { "id": "t104", - "source": "pp1ab_space_nsp6-16", + "source": "Nsp5_endoplasmic reticulum", "target": "Nsp7", "sign": true }, { "id": "t105", - "source": "Nsp5_endoplasmic reticulum", + "source": "pp1a_space_Nsp6-11", "target": "Nsp7", "sign": true }, @@ -2637,13 +2637,13 @@ }, { "id": "t116", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "ds_space_gRNA_rna", "sign": true }, { "id": "t117", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "ds_space_gRNA_rna", "sign": true }, @@ -2661,25 +2661,25 @@ }, { "id": "t120", - "source": "Camostat_space_mesylate_drug", + "source": "FURIN", "target": "S2_epithelial_space_cell", "sign": true }, { "id": "t121", - "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "source": "TMPRSS2", "target": "S2_epithelial_space_cell", "sign": true }, { "id": "t122", - "source": "FURIN", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "target": "S2_epithelial_space_cell", "sign": true }, { "id": "t123", - "source": "TMPRSS2", + "source": "Camostat_space_mesylate_drug", "target": "S2_epithelial_space_cell", "sign": true }, @@ -2697,43 +2697,43 @@ }, { "id": "t126", - "source": "Camostat_space_mesylate_drug", + "source": "FURIN", "target": "ACE2_epithelial_space_cell", "sign": true }, { "id": "t127", - "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "source": "TMPRSS2", "target": "ACE2_epithelial_space_cell", "sign": true }, { "id": "t128", - "source": "FURIN", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "target": "ACE2_epithelial_space_cell", "sign": true }, { "id": "t129", - "source": "TMPRSS2", + "source": "Camostat_space_mesylate_drug", "target": "ACE2_epithelial_space_cell", "sign": true }, { "id": "t130", - "source": "pp1a_space_Nsp6-11", + "source": "pp1ab_space_nsp6-16", "target": "Nsp10", "sign": true }, { "id": "t131", - "source": "pp1ab_space_nsp6-16", + "source": "Nsp5_endoplasmic reticulum", "target": "Nsp10", "sign": true }, { "id": "t132", - "source": "Nsp5_endoplasmic reticulum", + "source": "pp1a_space_Nsp6-11", "target": "Nsp10", "sign": true }, @@ -2745,61 +2745,61 @@ }, { "id": "t134", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "E_SARS-CoV-2_space_virion", "target": "Orf7a_endosome", "sign": true }, { "id": "t135", - "source": "S2_SARS-CoV-2_space_virion", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "Orf7a_endosome", "sign": true }, { "id": "t136", - "source": "M_SARS-CoV-2_space_virion", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "Orf7a_endosome", "sign": true }, { "id": "t137", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_SARS-CoV-2_space_virion", "target": "Orf7a_endosome", "sign": true }, { "id": "t138", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "Orf7a_endosome", "sign": true }, { "id": "t139", - "source": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf7b_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t140", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "Orf7b_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t141", - "source": "N_space_space_(-)ss_space_sgmRNA_rna", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "N_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t142", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "N_space_space_(-)ss_space_sgmRNA_rna", "target": "N_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t143", - "source": "pp1a_space_Nsp6-11", + "source": "pp1ab_space_nsp6-16", "target": "Nsp9", "sign": true }, @@ -2811,7 +2811,7 @@ }, { "id": "t145", - "source": "pp1ab_space_nsp6-16", + "source": "pp1a_space_Nsp6-11", "target": "Nsp9", "sign": true }, @@ -2823,13 +2823,13 @@ }, { "id": "t147", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "N_space_space_(-)ss_space_sgmRNA_rna", "sign": true }, { "id": "t148", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "N_space_space_(-)ss_space_sgmRNA_rna", "sign": true }, @@ -2895,43 +2895,43 @@ }, { "id": "t159", - "source": "S1:NRP1_space_complex_complex", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t160", - "source": "cholesterol_simple_molecule", + "source": "E_SARS-CoV-2_space_virion", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t161", - "source": "S2_epithelial_space_cell", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t162", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t163", - "source": "M_SARS-CoV-2_space_virion", + "source": "cholesterol_simple_molecule", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t164", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_epithelial_space_cell", "target": "Orf7a_epithelial_space_cell", "sign": true }, { "id": "t165", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "S1:NRP1_space_complex_complex", "target": "Orf7a_epithelial_space_cell", "sign": true }, @@ -2955,13 +2955,13 @@ }, { "id": "t169", - "source": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf6_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t170", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "Orf6_space_ds_space_sgmRNA_rna", "sign": true }, @@ -2979,7 +2979,7 @@ }, { "id": "t173", - "source": "pp1a_space_Nsp6-11", + "source": "pp1ab_space_nsp6-16", "target": "Nsp8", "sign": true }, @@ -2991,7 +2991,7 @@ }, { "id": "t175", - "source": "pp1ab_space_nsp6-16", + "source": "pp1a_space_Nsp6-11", "target": "Nsp8", "sign": true }, @@ -3003,7 +3003,7 @@ }, { "id": "t177", - "source": "pp1a_space_Nsp6-11", + "source": "pp1ab_space_nsp6-16", "target": "Nsp6_endoplasmic reticulum", "sign": true }, @@ -3015,7 +3015,7 @@ }, { "id": "t179", - "source": "pp1ab_space_nsp6-16", + "source": "pp1a_space_Nsp6-11", "target": "Nsp6_endoplasmic reticulum", "sign": true }, @@ -3051,19 +3051,19 @@ }, { "id": "t185", - "source": "Nucleocapsid_complex_epithelial_space_cell", + "source": "Host_space_translation_space_complex_complex_epithelial_space_cell", "target": "N_epithelial_space_cell", "sign": true }, { "id": "t186", - "source": "Host_space_translation_space_complex_complex_epithelial_space_cell", + "source": "N (+)ss sgmRNA_rna_epithelial_space_cell", "target": "N_epithelial_space_cell", "sign": true }, { "id": "t187", - "source": "N (+)ss sgmRNA_rna_epithelial_space_cell", + "source": "Nucleocapsid_complex_epithelial_space_cell", "target": "N_epithelial_space_cell", "sign": true }, @@ -3075,13 +3075,13 @@ }, { "id": "t189", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "S_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t190", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "S_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -3105,37 +3105,37 @@ }, { "id": "t194", - "source": "Camostat_space_mesylate_drug", + "source": "FURIN", "target": "ACE2_default_compartment", "sign": true }, { "id": "t195", - "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "source": "TMPRSS2", "target": "ACE2_default_compartment", "sign": true }, { "id": "t196", - "source": "FURIN", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "target": "ACE2_default_compartment", "sign": true }, { "id": "t197", - "source": "TMPRSS2", + "source": "Camostat_space_mesylate_drug", "target": "ACE2_default_compartment", "sign": true }, { "id": "t198", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf8_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t199", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf8_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -3153,31 +3153,31 @@ }, { "id": "t202", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "E_SARS-CoV-2_space_virion", "target": "E_endosome", "sign": true }, { "id": "t203", - "source": "S2_SARS-CoV-2_space_virion", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "E_endosome", "sign": true }, { "id": "t204", - "source": "M_SARS-CoV-2_space_virion", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "E_endosome", "sign": true }, { "id": "t205", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_SARS-CoV-2_space_virion", "target": "E_endosome", "sign": true }, { "id": "t206", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "E_endosome", "sign": true }, @@ -3189,19 +3189,19 @@ }, { "id": "t208", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t209", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t210", - "source": "CTSB", + "source": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", "target": "S2_SARS-CoV-2_space_virion", "sign": true }, @@ -3213,37 +3213,37 @@ }, { "id": "t212", - "source": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "source": "CTSB", "target": "S2_SARS-CoV-2_space_virion", "sign": true }, { "id": "t213", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "E_SARS-CoV-2_space_virion", "target": "M_endosome", "sign": true }, { "id": "t214", - "source": "S2_SARS-CoV-2_space_virion", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "M_endosome", "sign": true }, { "id": "t215", - "source": "M_SARS-CoV-2_space_virion", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "M_endosome", "sign": true }, { "id": "t216", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_SARS-CoV-2_space_virion", "target": "M_endosome", "sign": true }, { "id": "t217", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "M_endosome", "sign": true }, @@ -3273,49 +3273,49 @@ }, { "id": "t222", - "source": "Camostat_space_mesylate_drug", + "source": "FURIN", "target": "S1_default_compartment", "sign": true }, { "id": "t223", - "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "source": "TMPRSS2", "target": "S1_default_compartment", "sign": true }, { "id": "t224", - "source": "FURIN", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", "target": "S1_default_compartment", "sign": true }, { "id": "t225", - "source": "TMPRSS2", + "source": "Camostat_space_mesylate_drug", "target": "S1_default_compartment", "sign": true }, { "id": "t226", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t227", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t228", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf14_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t229", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf14_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -3333,121 +3333,121 @@ }, { "id": "t232", - "source": "S1:NRP1_space_complex_complex", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t233", - "source": "cholesterol_simple_molecule", + "source": "E_SARS-CoV-2_space_virion", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t234", - "source": "S2_epithelial_space_cell", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t235", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t236", - "source": "M_SARS-CoV-2_space_virion", + "source": "cholesterol_simple_molecule", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t237", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_epithelial_space_cell", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t238", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "S1:NRP1_space_complex_complex", "target": "M_epithelial_space_cell", "sign": true }, { "id": "t239", - "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "source": "Orf7b (+)ss sgmRNA_rna_epithelial_space_cell", "target": "Orf7b_rough_space_endoplasmic_space_reticulum", "sign": true }, { "id": "t240", - "source": "Orf7b (+)ss sgmRNA_rna_epithelial_space_cell", + "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", "target": "Orf7b_rough_space_endoplasmic_space_reticulum", "sign": true }, { "id": "t241", - "source": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf7a_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t242", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "Orf7a_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t243", - "source": "pp1a_space_Nsp6-11", + "source": "Nsp5_endoplasmic reticulum", "target": "Nsp11", "sign": true }, { "id": "t244", - "source": "Nsp5_endoplasmic reticulum", + "source": "pp1a_space_Nsp6-11", "target": "Nsp11", "sign": true }, { "id": "t245", - "source": "S1:NRP1_space_complex_complex", + "source": "Orf7a_SARS-CoV-2_space_virion", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t246", - "source": "cholesterol_simple_molecule", + "source": "E_SARS-CoV-2_space_virion", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t247", - "source": "S2_epithelial_space_cell", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t248", - "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "source": "M_SARS-CoV-2_space_virion", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t249", - "source": "M_SARS-CoV-2_space_virion", + "source": "cholesterol_simple_molecule", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t250", - "source": "E_SARS-CoV-2_space_virion", + "source": "S2_epithelial_space_cell", "target": "E_epithelial_space_cell", "sign": true }, { "id": "t251", - "source": "Orf7a_SARS-CoV-2_space_virion", + "source": "S1:NRP1_space_complex_complex", "target": "E_epithelial_space_cell", "sign": true }, @@ -3459,7 +3459,7 @@ }, { "id": "t253", - "source": "CTSB", + "source": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", "target": "S1_endosome", "sign": true }, @@ -3471,7 +3471,7 @@ }, { "id": "t255", - "source": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "source": "CTSB", "target": "S1_endosome", "sign": true }, @@ -3495,13 +3495,13 @@ }, { "id": "t259", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", "target": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t260", - "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "sign": true }, @@ -3543,13 +3543,13 @@ }, { "id": "t267", - "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "source": "Orf8 (+)ss sgmRNA_rna_epithelial_space_cell", "target": "Orf8_rough_space_endoplasmic_space_reticulum", "sign": true }, { "id": "t268", - "source": "Orf8 (+)ss sgmRNA_rna_epithelial_space_cell", + "source": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", "target": "Orf8_rough_space_endoplasmic_space_reticulum", "sign": true }, @@ -3591,13 +3591,13 @@ }, { "id": "t275", - "source": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf3a_space_ds_space_sgmRNA_rna", "sign": true }, { "id": "t276", - "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", "target": "Orf3a_space_ds_space_sgmRNA_rna", "sign": true }, @@ -3645,19 +3645,19 @@ }, { "id": "t284", - "source": "Nsp3", + "source": "Nsp6_endoplasmic reticulum", "target": "double membrane vesicle viral factory assembly_phenotype", "sign": true }, { "id": "t285", - "source": "Nsp4_endoplasmic reticulum", + "source": "Nsp3", "target": "double membrane vesicle viral factory assembly_phenotype", "sign": true }, { "id": "t286", - "source": "Nsp6_endoplasmic reticulum", + "source": "Nsp4_endoplasmic reticulum", "target": "double membrane vesicle viral factory assembly_phenotype", "sign": true }, @@ -3855,13 +3855,13 @@ }, { "id": "t319", - "source": "Orf7b (+)ss sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "source": "DMV molecular pore_complex", "target": "Orf7b (+)ss sgmRNA_rna_epithelial_space_cell", "sign": true }, { "id": "t320", - "source": "DMV molecular pore_complex", + "source": "Orf7b (+)ss sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", "target": "Orf7b (+)ss sgmRNA_rna_epithelial_space_cell", "sign": true },