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Commit e9c4f512 authored by artenobot's avatar artenobot
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Update models

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<?xml version='1.0' encoding='utf-8'?>
<sbml level="3" version="1" layout:required="false" xmlns="http://www.sbml.org/sbml/level3/version1/core" qual:required="true" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1"><model id="model_id"><listOfCompartments><compartment constant="true" id="comp1" /></listOfCompartments><layout:listOfLayouts><layout:layout id="layout1"><layout:dimensions width="4010" height="4010" /><layout:listOfAdditionalGraphicalObjects /></layout:layout></layout:listOfLayouts><qual:listOfQualitativeSpecies /><qual:listOfTransitions /></model></sbml>
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FADD POSITIVE FAS/FASL_complex
BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex
BAX POSITIVE BAD/BBC3/BCL2L11_complex
Orf7a POSITIVE BCL2/MCL1/BCL2L1_complex
E POSITIVE BCL2/MCL1/BCL2L1_complex
BAD NEGATIVE BCL2/MCL1/BCL2L1_complex
BAX NEGATIVE BCL2/MCL1/BCL2L1_complex
CYCS POSITIVE Apoptosome_complex
AKT1 NEGATIVE Apoptosome_complex
CASP9_Cytoplasm POSITIVE Apoptosome_complex
MAPK14 POSITIVE CYCS
CASP9_Cytoplasm NEGATIVE AKT1
M NEGATIVE AKT1
BAD NEGATIVE AKT1
TRADD/FADD_complex POSITIVE TNF/TNFRSF1A_complex
FADD POSITIVE TRADD/FADD_complex
TRADD POSITIVE TRADD/FADD_complex
CASP8 POSITIVE TRADD/FADD_complex
CASP8 POSITIVE FADD
CASP3 POSITIVE CASP8
BID POSITIVE CASP8
CASP7 POSITIVE CASP8
CASP9_Cytoplasm POSITIVE CASP3
Apoptosis_phenotype POSITIVE CASP3
CASP7 POSITIVE CASP9_Cytoplasm
BAX POSITIVE BID
Orf3a POSITIVE MAPK14
Apoptosis_phenotype POSITIVE CASP7
Orf3b POSITIVE Apoptosis_phenotype
Orf8a POSITIVE Apoptosis_phenotype
N POSITIVE Apoptosis_phenotype
S POSITIVE Apoptosis_phenotype
Orf9b POSITIVE Apoptosis_phenotype
Orf6 POSITIVE Apoptosis_phenotype
C5b:C6:C7_complex POSITIVE C5b:C6:C7:C8A:C8B:C8G_complex
C5b-9_complex POSITIVE C5b:C6:C7:C8A:C8B:C8G_complex
GP6:Fibrinogen_complex POSITIVE GP6:alpha2beta1:VWF_complex
platelet activation_phenotype POSITIVE GP6:alpha2beta1:VWF_complex
GP6 POSITIVE GP6:Fibrinogen_complex
ITGA2:ITGAB1_complex POSITIVE GP6:Fibrinogen_complex
GP6 POSITIVE Fibrinogen:GP6_complex
platelet activation_phenotype POSITIVE Fibrinogen:GP6_complex
thrombus formation_phenotype POSITIVE platelet activation_phenotype
ERN1 POSITIVE ERN1:Unfolded protein_complex
Unfolded protein_Endoplasmic Reticulum POSITIVE ERN1:Unfolded protein_complex
TRAF2:ERN1_complex POSITIVE ERN1:Unfolded protein_complex
ERN1:BCL2L11_complex POSITIVE ERN1
ERN1:BBC3_complex POSITIVE ERN1
Persistant ER Stress_phenotype POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
TRIM13 POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
Apoptosis_phenotype POSITIVE CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex
TRAF2:ERN1_complex NEGATIVE Persistant ER Stress_phenotype
EIF2AK3:EIF2AK3_complex POSITIVE Persistant ER Stress_phenotype
ERN1:BCL2L11_complex NEGATIVE Persistant ER Stress_phenotype
ERN1:BBC3_complex NEGATIVE Persistant ER Stress_phenotype
DDIT3_rna POSITIVE Persistant ER Stress_phenotype
ER Stress_phenotype POSITIVE Persistant ER Stress_phenotype
BAK1:ERN1_complex POSITIVE TRAF2:ERN1_complex
BAX:ERN1_complex POSITIVE TRAF2:ERN1_complex
BCL2 NEGATIVE TRAF2:ERN1_complex
BCL2L1 NEGATIVE TRAF2:ERN1_complex
BAX POSITIVE TRAF2:ERN1_complex
BAK1 POSITIVE TRAF2:ERN1_complex
UPR_phenotype POSITIVE TRAF2:ERN1_complex
TRAF2_Cytoplasm POSITIVE TRAF2:ERN1_complex
MAP3K5_phosphorylated POSITIVE TRAF2:ERN1_complex
XBP1_rna POSITIVE TRAF2:ERN1_complex
EIF2AK3 POSITIVE EIF2AK3:EIF2AK3_complex
Unfolded protein_Endoplasmic Reticulum POSITIVE EIF2AK3:EIF2AK3_complex
retrograde transport from ER to cytosol_phenotype POSITIVE EIF2AK3:EIF2AK3_complex
UPR_phenotype POSITIVE EIF2AK3:EIF2AK3_complex
EIF2S1_phosphorylated POSITIVE EIF2AK3:EIF2AK3_complex
ATF6_Endoplasmic Reticulum POSITIVE Unfolded protein_Endoplasmic Reticulum
HSPA5 POSITIVE Unfolded protein_Endoplasmic Reticulum
accumulation of misfolded protein in ER_phenotype POSITIVE Unfolded protein_Endoplasmic Reticulum
EIF2:GDP:Met-tRNA_complex POSITIVE Ternary Complex_complex
EIF2B*_complex POSITIVE Ternary Complex_complex
Translation initiation_phenotype POSITIVE Ternary Complex_complex
EIF2S2 POSITIVE EIF2:GDP:Met-tRNA_complex
EIF2S3:GDP_complex POSITIVE EIF2:GDP:Met-tRNA_complex
EIF2-P:GDP_complex POSITIVE EIF2S2
EIF2S1_phosphorylated POSITIVE EIF2-P:GDP_complex
ATF4_rna POSITIVE EIF2-P:GDP_complex
EIF2S1 POSITIVE EIF2S1_phosphorylated
GCN2:ATP_complex POSITIVE EIF2S1_phosphorylated
EIF2AK2 POSITIVE EIF2S1_phosphorylated
DNAJC3 NEGATIVE EIF2S1_phosphorylated
BCL2L11_Endoplasmic Reticulum POSITIVE ERN1:BCL2L11_complex
XBP1_rna POSITIVE ERN1:BCL2L11_complex
BBC3 POSITIVE ERN1:BBC3_complex
XBP1_rna POSITIVE ERN1:BBC3_complex
CAPN1 POSITIVE CAPN1:Ca2+_complex
Ca2+_ion_Cytoplasm POSITIVE CAPN1:Ca2+_complex
high Ca2+ cytosolic concentration_phenotype POSITIVE CAPN1:Ca2+_complex
cleaved~CASP4 POSITIVE CAPN1:Ca2+_complex
TMBIM6_Endoplasmic Reticulum POSITIVE Ca2+_ion_Cytoplasm
RYR1 POSITIVE Ca2+_ion_Cytoplasm
ITPR POSITIVE Ca2+_ion_Cytoplasm
high Ca2+ cytosolic concentration_phenotype POSITIVE Ca2+_ion_Cytoplasm
release of ER Ca2+_phenotype POSITIVE high Ca2+ cytosolic concentration_phenotype
ATF6:HSPA5_complex POSITIVE ATF6_Endoplasmic Reticulum
retrograde transport from ER to cytosol_phenotype POSITIVE ATF6_Endoplasmic Reticulum
ATF6_Golgi POSITIVE ATF6_Endoplasmic Reticulum
HSPA5 POSITIVE ATF6:HSPA5_complex
UPR_phenotype POSITIVE accumulation of misfolded protein in ER_phenotype
ER Stress_phenotype POSITIVE accumulation of misfolded protein in ER_phenotype
ERAD_phenotype POSITIVE accumulation of misfolded protein in ER_phenotype
protein ubiquitination and destruction_phenotype POSITIVE retrograde transport from ER to cytosol_phenotype
ATF6_Golgi NEGATIVE retrograde transport from ER to cytosol_phenotype
XBP1_rna POSITIVE XBP1
UPR_phenotype POSITIVE XBP1
ERAD_phenotype POSITIVE XBP1
DDIT3_rna POSITIVE XBP1
ATF6_Nucleus POSITIVE XBP1_rna
ATF6_Golgi POSITIVE UPR_phenotype
ATF6_Golgi POSITIVE ATF6_Golgi
MBTPS2 POSITIVE ATF6_Golgi
ATF6_Nucleus POSITIVE ATF6_Golgi
MAP3K4_phosphorylated POSITIVE MAPK8_phosphorylated
MAP3K5_phosphorylated POSITIVE MAPK8_phosphorylated
BAX_phosphorylated POSITIVE MAPK8_phosphorylated
AP-1_phosphorylated_phosphorylated POSITIVE MAPK8_phosphorylated
BCL2L11_phosphorylated POSITIVE MAPK8_phosphorylated
BID_phosphorylated POSITIVE MAPK8_phosphorylated
CDK5 POSITIVE MAP3K4_phosphorylated
MAPK14_phosphorylated POSITIVE MAP3K5_phosphorylated
TRAF2_Cytoplasm POSITIVE MAP3K5_phosphorylated
Apoptosis_phenotype POSITIVE MAPK14_phosphorylated
DDIT3_phosphorylated POSITIVE MAPK14_phosphorylated
BAX_phosphorylated POSITIVE MAPK14_phosphorylated
DDIT3_phosphorylated POSITIVE Apoptosis_phenotype
BAX_phosphorylated POSITIVE Apoptosis_phenotype
BCL2L11_phosphorylated POSITIVE Apoptosis_phenotype
BID_phosphorylated POSITIVE Apoptosis_phenotype
cleaved~CASP3 POSITIVE Apoptosis_phenotype
cleaved~CASP9 POSITIVE Apoptosis_phenotype
Cell death_phenotype POSITIVE Apoptosis_phenotype
DDIT3 POSITIVE DDIT3_phosphorylated
BCL2_rna NEGATIVE DDIT3_phosphorylated
release of ER Ca2+_phenotype POSITIVE BAX_phosphorylated
BCL2L11_Cytoplasm POSITIVE BCL2L11_phosphorylated
CASP3 POSITIVE cleaved~CASP3
cleaved~CASP4 POSITIVE cleaved~CASP3
CASP9 POSITIVE cleaved~CASP9
cleaved~CASP4 POSITIVE cleaved~CASP9
DDIT3_rna POSITIVE DDIT3
PPP1R15A_rna POSITIVE DDIT3
ERO1A_rna POSITIVE DDIT3
AP-1_phosphorylated_phosphorylated POSITIVE DDIT3
TRIB3_rna POSITIVE DDIT3
ER Stress_phenotype POSITIVE ATF6_Golgi
ATF6_Golgi POSITIVE ATF6_Golgi
CDK5 POSITIVE ER Stress_phenotype
MBTPS1 POSITIVE ATF6_Golgi
DDIT3_rna POSITIVE ATF6_Nucleus
ERO1A_rna POSITIVE ATF6_Nucleus
DNAJC3_rna POSITIVE ATF6_Nucleus
HYOU1_rna POSITIVE ATF6_Nucleus
ATF4 POSITIVE DDIT3_rna
ATF4_rna POSITIVE ATF4
PPP1R15A_rna POSITIVE ATF4
PPP1R15A POSITIVE EIF2S1
EIF2AK1 POSITIVE EIF2S1
presence of dsRNA_phenotype POSITIVE EIF2AK2
DNAJC3 NEGATIVE EIF2AK2
DNAJC3_rna POSITIVE DNAJC3
PPP1R15A_rna POSITIVE PPP1R15A
ERO1A_rna POSITIVE ERO1A_Cytoplasm
ERO1A_Endoplasmic Reticulum POSITIVE ERO1A_Cytoplasm
ITPR POSITIVE ERO1A_Cytoplasm
Ca2+_ion_Mitochondrial inner membrane POSITIVE release of ER Ca2+_phenotype
Cell death_phenotype POSITIVE Cell survival_phenotype
TRIB3 POSITIVE Cell death_phenotype
ITPR POSITIVE Ca2+_ion_Mitochondrial inner membrane
MAM_phenotype POSITIVE Ca2+_ion_Mitochondrial inner membrane
s619_complex POSITIVE Ca2+_ion_Mitochondrial inner membrane
TMBIM6_Endoplasmic Reticulum POSITIVE ITPR
TRIB3_rna POSITIVE TRIB3
ERO1A_Endoplasmic Reticulum POSITIVE hyperoxidation_phenotype
PPP2CA POSITIVE BCL2L11_Cytoplasm
CASP4 POSITIVE cleaved~CASP4
HYOU1 POSITIVE HYOU1_rna
OXPHOS factors_complex POSITIVE Complex 1_complex
complex 2_complex_mitochondrial matrix POSITIVE Complex 1_complex
complex 3_complex POSITIVE Complex 1_complex
NAD+_simple_molecule POSITIVE Complex 1_complex
H+_ion_Intermembrane space POSITIVE Complex 1_complex
paraquat_simple_molecule POSITIVE Complex 1_complex
complex 2_complex_mitochondrial matrix POSITIVE OXPHOS factors_complex
complex 3_complex POSITIVE OXPHOS factors_complex
complex 4_complex POSITIVE OXPHOS factors_complex
mt mRNA_rna POSITIVE mtDNA encoded OXPHOS units_complex_mitochondrial matrix
Mt translation_complex POSITIVE mtDNA encoded OXPHOS units_complex_mitochondrial matrix
Mt ribosomal proteins_complex POSITIVE mtDNA encoded OXPHOS units_complex_mitochondrial matrix
Nsp8-affected Mt ribosomal proteins_complex POSITIVE mtDNA encoded OXPHOS units_complex_mitochondrial matrix
mt DNA_gene POSITIVE mt mRNA_rna
TFAM POSITIVE mt mRNA_rna
MT transcription_complex POSITIVE mt mRNA_rna
damaged mt DNA_gene NEGATIVE mt mRNA_rna
Nsp8 NEGATIVE Nsp8-affected Mt ribosomal proteins_complex
SIRT3_mitochondrial matrix POSITIVE complex 2_complex_mitochondrial matrix
complex 2_complex_mitochondrial matrix POSITIVE complex 2_complex_mitochondrial matrix
TCA_phenotype POSITIVE complex 2_complex_mitochondrial matrix
Q_simple_molecule_mitochondrial matrix POSITIVE complex 3_complex
complex 4_complex POSITIVE complex 3_complex
O^_2-_endsuper__simple_molecule POSITIVE complex 3_complex
H+_ion_Intermembrane space POSITIVE complex 3_complex
H+_ion_Intermembrane space POSITIVE ATP Synthase_complex
H+_ion_Intermembrane space POSITIVE ATP Synthase_complex
H+_ion_Intermembrane space POSITIVE ATP Synthase_complex
Nsp6 NEGATIVE ATP Synthase_complex
ATP_simple_molecule POSITIVE ATP Synthase_complex
H+_ion_mitochondrial matrix POSITIVE ATP Synthase_complex
Cyt C_mitochondrial matrix POSITIVE complex 4_complex
paraquat_simple_molecule POSITIVE paraquat dication_complex
superoxide_simple_molecule_mitochondrial matrix POSITIVE paraquat_simple_molecule
mt DNA_gene POSITIVE MT tRNAs_complex
Mt-tRNA synthetase_complex POSITIVE MT tRNAs_complex
TRMT1 POSITIVE MT tRNAs_complex
mt DNA damage_phenotype NEGATIVE mt DNA_gene
mt DNA replication_phenotype POSITIVE mt DNA_gene
damaged mt DNA_gene POSITIVE mt DNA_gene
TFAM POSITIVE mt DNA_gene
Mt-DNA repair_complex POSITIVE mt DNA_gene
Mt-dNTP pool_complex POSITIVE mt DNA_gene
NSP4 NEGATIVE TIM22 complex_complex
precursor protein N-terminus binding POSITIVE TIM22 complex_complex
TIM9-TIM10 complex_complex NEGATIVE NSP4
precursor protein N-terminus binding POSITIVE TIM9-TIM10 complex_complex
NADH_simple_molecule POSITIVE NAD+_simple_molecule
O_2__simple_molecule_mitochondrial matrix POSITIVE O^_2-_endsuper__simple_molecule
ADP_simple_molecule POSITIVE ATP_simple_molecule
Pi_simple_molecule POSITIVE ATP_simple_molecule
H+_ion_mitochondrial matrix POSITIVE ATP_simple_molecule
H_2_O_2__simple_molecule POSITIVE superoxide_simple_molecule_mitochondrial matrix
O_2__simple_molecule_mitochondrial matrix POSITIVE superoxide_simple_molecule_mitochondrial matrix
ROS_simple_molecule POSITIVE superoxide_simple_molecule_mitochondrial matrix
SOD1 POSITIVE H_2_O_2__simple_molecule
superoxide_simple_molecule_mitochondrial matrix POSITIVE H_2_O_2__simple_molecule
SOD2 POSITIVE H_2_O_2__simple_molecule
H_2_O_simple_molecule_mitochondrial matrix POSITIVE H_2_O_2__simple_molecule
ROS_simple_molecule POSITIVE H_2_O_2__simple_molecule
HO_simple_molecule POSITIVE H_2_O_2__simple_molecule
O_2__simple_molecule_mitochondrial matrix POSITIVE superoxide_simple_molecule_mitochondrial matrix
ROS_simple_molecule POSITIVE superoxide_simple_molecule_mitochondrial matrix
SIRT3_mitochondrial matrix POSITIVE SOD2
PRDX_complex POSITIVE H_2_O_simple_molecule_mitochondrial matrix
GPX4 POSITIVE H_2_O_simple_molecule_mitochondrial matrix
GPX1 POSITIVE H_2_O_simple_molecule_mitochondrial matrix
CAT POSITIVE H_2_O_simple_molecule_mitochondrial matrix
hydroxide_simple_molecule POSITIVE ROS_simple_molecule
HO_simple_molecule POSITIVE hydroxide_simple_molecule
glutathione disulfide_simple_molecule POSITIVE glutathione_simple_molecule
GSR POSITIVE glutathione_simple_molecule
TXNRD2 POSITIVE TXN2
mt DNA replication_phenotype POSITIVE TFAM
mt DNA damage_phenotype POSITIVE damaged mt DNA_gene
Mt replication_complex POSITIVE mt DNA replication_phenotype
Mt-dNTP pool_complex POSITIVE mt DNA replication_phenotype
Orf9c NEGATIVE NDUFB9
NDUFA1 NEGATIVE Orf9c
ECSIT NEGATIVE Orf9c
ACAD9 NEGATIVE Orf9c
Nsp7 NEGATIVE NDUFAF7
TOM complex_complex POSITIVE precursor protein N-terminus binding
TIM23 complex_complex POSITIVE precursor protein N-terminus binding
histone_complex_Nucleus POSITIVE histone_complex_Nucleus
BRD4 POSITIVE histone_complex_Nucleus
BRD2 POSITIVE histone_complex_Nucleus
Chromatin organization_phenotype POSITIVE histone_complex_Nucleus
H4C14 POSITIVE histone_complex_Nucleus
P-TEFb_complex POSITIVE BRD4
E_Nucleus NEGATIVE BRD4
TBP POSITIVE BRD2
E_Nucleus NEGATIVE BRD2
JQ1 NEGATIVE BRD2
PALS1_Cytoplasm POSITIVE CRB3:PALS1:PATJ complex_complex
PALS1_Cytoplasm POSITIVE PALS1_Cytoplasm
E_Cytoplasm NEGATIVE ASIC1 trimer:H+:STOML3_complex
ASIC1 trimer POSITIVE ASIC1 trimer:H+:STOML3_complex
ATP1A:ATP1B:FXYDs_complex NEGATIVE E_Cytoplasm
K+_ion POSITIVE ATP1A:ATP1B:FXYDs_complex
E_Cytoplasm POSITIVE E-PALS1_complex
PALS1_Cytoplasm POSITIVE E-PALS1_complex
CDK9 POSITIVE P-TEFb_complex
CCNT1 POSITIVE P-TEFb_complex
RNA Polymerase II-dependent Transcription _phenotype POSITIVE P-TEFb_complex
JNK_complex_Cytoplasm POSITIVE JNK_complex_Cytoplasm
MAP2K4_phosphorylated POSITIVE JNK_complex_Cytoplasm
MAP2K7_phosphorylated POSITIVE JNK_complex_Cytoplasm
7a POSITIVE JNK_complex_Cytoplasm
3a POSITIVE JNK_complex_Cytoplasm
S POSITIVE JNK_complex_Cytoplasm
AP-1_complex POSITIVE JNK_complex_Cytoplasm
BCL2_phosphorylated POSITIVE JNK_complex_Cytoplasm
ATF2_phosphorylated POSITIVE JNK_complex_Cytoplasm
TP53_phosphorylated POSITIVE JNK_complex_Cytoplasm
MEKK1/4_complex POSITIVE MAP2K4_phosphorylated
SARS-CoV-1 proteins_complex POSITIVE MAP2K4_phosphorylated
MLK1/2/3_complex POSITIVE MAP2K7_phosphorylated
SARS-CoV-1 proteins_complex POSITIVE MAP2K7_phosphorylated
SARS-CoV-1 proteins_complex POSITIVE MLK1/2/3_complex
MEKK1/4_complex POSITIVE SARS-CoV-1 proteins_complex
3b POSITIVE AP-1_complex
Innate Immunity_phenotype POSITIVE AP-1_complex
Apoptosis_phenotype POSITIVE BCL2_phosphorylated
Autophagy_phenotype POSITIVE BCL2_phosphorylated
TP53 signalling_phenotype POSITIVE TP53_phosphorylated
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