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  3. Heme Curation v0.0.1-dev
  4. Biogrammar

Biogrammar Summary of Heme Curation 0.0.1-dev

Table of Contents

  1. Regulatory Pairs
  2. Contradictory Pairs
  3. Unstable Pairs
  4. Contradictory Triplets
  5. Unstable Triplets
  6. Causal Pathologies

Regulatory Pairs 2

These pairs of nodes represent motifs like A increases B and B decreases A.

Node A Node B
a(CHEBI:heme) p(HGNC:FTH1)
a(CHEBI:heme) p(MGI:Hmox1)

Contradictory Statements 11

These pairs of nodes have a contradiction in their causal relationships, meaning they have more than one of INCREASES, DECREASES, or CAUSES NO CHANGE. This may be due to different experimental conditions, so these statements need to be carefully considered in analyses.

Source Relations Target
p(HGNC:AMBP) decreases, increases a(CHEBI:Catalase)
p(HGNC:LRP1) decreases, increases complex(a(CHEBI:heme), p(HGNC:HPX))
a(HM:"stored erythrocytes") decreases, increases bp(MESH:"Erythrocyte Deformability")
p(MGI:Hmox1) negativeCorrelation, decreases, increases a(CHEBI:heme)
bp(MESH:"Erythrocyte Aggregation") decreases, increases bp(MESH:"Blood Viscosity")
p(HGNC:ALB) decreases, causesNoChange bp(MESH:"Erythrocyte Aggregation")
p(HGNC:AMBP) positiveCorrelation, decreases, increases a(CHEBI:heme)
p(HGNC:CD163) decreases, increases a(MESH:"haptoglobin-hemoglobin complex")
p(MGI:Bach1) decreases, increases p(MGI:Spic)
path(MESH:Anemia) decreases, causesNoChange a(MESH:"Partial Pressure")
path(MESH:Anemia) causesNoChange, increases r(MGI:Epo)

Unstable Pairs 3

Chaotic Pairs
Nodes that mutually increase each other, such as when both A increases B and B increases A.
Dampened Pairs
Nodes that mutually decrease each other, such as when both A decreases B and B decreases A.

While neither chaotic nor dampened pairs are biologically invalid, they require additional context to understand their regulation.

Type Node A Node B
Chaotic a(CHEBI:heme) p(HGNC:HMOX1)
Chaotic a(CHEBI:heme) p(MGI:Hmox1)
Dampened a(CHEBI:"nitric oxide") bp(GO:"endothelial cell activation")

Contradictory Triplets 349

Analysis of triple stability comes from a deep graph theoretic background. It identifies triangles within the graph that have logically inconsistent relations.

Separately Unstable Triplet
When both A positiveCorrelation B, B negativeCorrelation C, but C positiveCorrelation A.
Mutually Unstable Triplets
When both A negativeCorrelation B, B negativeCorrelation C, and C negativeCorrelation A.
Jens Contradictory Triplet
When A increases B, A decreases C, and C positiveCorrelation A.
Increase Mismatch Triplet
When A increases B, A increases C, and C negativeCorrelation A.
Decrease Mismatch Triplet
When A decreases B, A decreases C, and C negativeCorrelation A.
Type Node A Node B Node C
Separate a(HM:"stored erythrocytes") a(CHEBI:methemoglobin) p(MGI:Prdx2)
Separate bp(MESH:"Platelet Activation") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate p(HGNC:HBB) bp(MESH:"Erythrocyte Deformability") bp(MESH:"Oxidative Stress")
Separate a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(MESH:"Erythrocyte Deformability")
Separate path(MESH:Inflammation) a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate a(CHEBI:"carbon monoxide") a(CHEBI:heme) p(MGI:Hpx)
Separate bp(MESH:"Erythrocyte Deformability") a(CHEBI:heme) p(MGI:Prdx2)
Separate a(HM:"stored erythrocytes") a(CHEBI:heme) p(MGI:Prdx2)
Separate a(CHEBI:"iron(2+)") a(CHEBI:lipopolysaccharide) p(MGI:Slc40a1)
Separate path(MESH:"Vascular Diseases") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate p(MGI:Slc40a1) a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate a(CHEBI:heme) p(HGNC:HP) path(MESH:"Pre-Eclampsia")
Separate p(HGNC:ARG1) p(HGNC:HPX) path(MESH:Hemolysis)
Separate a(HM:"stored erythrocytes") p(MGI:Prdx2) path(MESH:Hemolysis)
Separate a(HM:"nitrite oxidation") a(CHEBI:heme) p(MGI:Prdx2)
Separate p(PFAM:Proteasome) a(CHEBI:heme) bp(GO:"cellular homeostasis")
Separate a(MESH:"haptoglobin-hemoglobin complex") p(HGNC:HP) path(MESH:"Pre-Eclampsia")
Separate a(CHEBI:"iron(2+)") a(CHEBI:heme) complex(a(MESH:"Blood Transfusion"), p(MGI:Hpx))
Separate a(HM:"stored erythrocytes") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate a(CHEBI:heme) a(CHEBI:"carbon monoxide") path(HM:"vaso-occlusive crisis")
Separate bp(GO:"inflammatory response") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate a(HM:"stored erythrocytes") bp(MESH:"Oxidative Stress") p(MGI:Prdx2)
Separate path(MESH:Thrombosis) a(CHEBI:"iron(2+)") a(CHEBI:heme)
Separate a(CHEBI:lactate) p(HGNC:HBB) p(HGNC:HP)
Separate a(CHEBI:"carbon monoxide") a(CHEBI:antioxidant) a(CHEBI:heme)
Separate a(CHEBI:heme) p(HGNC:HP) path(MESH:Thrombosis)
Separate a(CHEBI:heme) bp(MESH:"Erythrocyte Deformability") bp(MESH:"Oxidative Stress")
Separate a(CHEBI:heme) p(HGNC:HP) path(MESH:Hemolysis)
Separate p(MGI:Cdc42) bp(MESH:Phagocytosis) p(MGI:Dock8)
Separate a(CHEBI:heme) bp(MESH:"Erythrocyte Deformability") path(MESH:Thrombosis)
Separate p(HGNC:HBB) bp(MESH:"Erythrocyte Deformability") path(MESH:Thrombosis)
Separate a(HM:"nitrite oxidation") bp(MESH:"Oxidative Stress") p(MGI:Prdx2)
Separate bp(MESH:"Oxidative Stress") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Mutual p(HGNC:HBB) p(HGNC:HP) path(HP:"Elevated mean arterial pressure")
Mutual complex(a(CHEBI:"tin atom"), a(CHEBI:protoporphyrin)) p(MGI:Hp) p(MGI:Nfkb1)
Mutual complex(a(CHEBI:"tin atom"), a(CHEBI:protoporphyrin)) p(MGI:Hpx) p(MGI:Nfkb1)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") p(HGNC:AMBP)
Jens a(HM:erythrophagocytosis) p(HGNC:CD163) p(HGNC:HMOX1)
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:"Vascular Diseases")
Jens bp(GO:"inflammatory response") p(HGNC:IL1B) path(MESH:Inflammation)
Jens bp(MESH:"Platelet Activation") p(HGNC:HBB) path(HP:"Paroxysmal nocturnal hemoglobinuria")
Jens a(MESH:"Cell-Derived Microparticles") path(HM:"endothelial lesions") path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(HGNC:ARG1) path(MESH:Hemolysis)
Jens a(CHEBI:heme) path(MESH:"Acute Kidney Injury") path(MESH:Hemolysis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) a(MESH:"Blood Transfusion")
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") bp(MESH:"Oxidative Stress") p(HGNC:HBB)
Jens a(CHEBI:heme) p(HGNC:HP) path(MESH:Inflammation)
Jens a(CHEBI:heme) bp(MESH:"Platelet Activation") p(HGNC:SELP)
Jens a(CHEBI:heme) bp(MESH:"Platelet Activation") p(HGNC:HBB)
Jens a(MESH:ferrylhemoglobin) p(HGNC:CXCL8) path(MESH:Inflammation)
Jens a(MESH:"Cell-Derived Microparticles") bp(MESH:Hemostasis) path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(HGNC:F3) path(HM:"endothelial lesions")
Jens p(HGNC:AMBP) p(HGNC:HBB) path(HM:"Oxidative damage")
Jens p(MGI:Il1b) p(MGI:Nlrp3) p(MGI:P2rx4)
Jens path(HP:"Paroxysmal nocturnal hemoglobinuria") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) bp(MESH:"Platelet Activation")
Jens a(CHEBI:methemoglobin) a(CHEBI:oxyhemoglobin) a(HM:"stored erythrocytes")
Jens a(CHEBI:heme) bp(GO:"inflammatory response") p(HGNC:IL1B)
Jens bp(MESH:"Platelet Aggregation") p(HGNC:HBB) path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") path(MESH:Thrombosis)
Jens a(MESH:"Erythrocytes, Abnormal") p(HGNC:HBB) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") path(MESH:Thrombosis)
Jens path(HP:"Hemolytic-uremic syndrome") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(GO:"protein oxidation") bp(MESH:"Oxidative Stress")
Jens a(CHEBI:heme) p(HGNC:TNF) path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(HGNC:HP) path(MESH:"Anemia, Sickle Cell")
Jens a(CHEBI:heme) bp(GO:vasoconstriction) p(HGNC:HBB)
Jens complex(a(MESH:"Blood Transfusion"), p(MGI:Hpx)) p(MGI:Hmox1) p(MGI:Hpx)
Jens a(CHEBI:"iron trichloride") p(HGNC:HBB) path(HM:"Endothelial dysfunction")
Jens a(CHEBI:methemoglobin) a(MESH:"Blood Transfusion") path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(MGI:Hpx) p(MGI:Tfrc)
Jens a(CHEBI:heme) a(MESH:Cytokines) p(HGNC:AMBP)
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") bp(MESH:"Bacterial Load")
Jens a(CHEBI:heme) a(HM:"oxidative reactions") p(HGNC:HP)
Jens a(CHEBI:"iron(2+)") a(HM:"stored erythrocytes") path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(HM:"stored erythrocytes") p(HGNC:HBB)
Jens a(CHEBI:heme) path(MESH:"Vascular System Injuries") path(MESH:Hemolysis)
Jens p(MGI:Il1b) p(MGI:Nlrp3) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(MGI:Casp1) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:CD55) path(MESH:Hemolysis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) path(MESH:Inflammation)
Jens a(CHEBI:heme) path(MESH:"Thrombotic Microangiopathies") path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(HGNC:HPX) p(HGNC:IL10)
Jens a(CHEBI:"nitric oxide") a(HM:"stored erythrocytes") path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") path(MESH:Inflammation)
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) bp(GO:"inflammatory response")
Jens a(CHEBI:"nitric oxide") p(HGNC:HBB) path(MESH:"Platelet Aggregation")
Jens a(HM:"stored erythrocytes") p(HGNC:HBB) path(MESH:Inflammation)
Jens a(CHEBI:heme) a(MESH:Cytokines) bp(MESH:"Platelet Activation")
Jens a(CHEBI:heme) path(HM:"endothelial lesions") path(MESH:Thrombosis)
Jens p(HGNC:HBB) path(HP:"Paroxysmal nocturnal hemoglobinuria") path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(HGNC:TNF) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:HBB) path(HM:"endothelial lesions")
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") path(MESH:"Reperfusion Injury")
Jens a(CHEBI:heme) p(MGI:Il1b) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:AMBP) p(HGNC:HBB)
Jens a(CHEBI:"nitric oxide") path(MESH:Hemolysis) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") p(HGNC:HBB) path(MESH:"Vascular Diseases")
Jens a(CHEBI:"iron(2+)") a(CHEBI:"nitric oxide") a(MESH:"Cell Adhesion Molecules")
Jens a(CHEBI:heme) bp(MESH:"Oxidative Stress") p(HGNC:HBB)
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) p(MGI:Hpx)
Jens a(CHEBI:"lipid hydroperoxide") a(HM:"Erythrocytes, lysed") bp(HM:"Atheromatous lesions")
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") p(MGI:Slc40a1)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") path(MESH:Inflammation)
Jens a(MESH:"Cell-Derived Microparticles") path(HP:Hypercoagulability) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") p(HGNC:HBB) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(MESH:"Blood Transfusion") p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") a(HM:"stored erythrocytes") bp(MESH:"Oxidative Stress")
Jens a(MESH:"Reactive Oxygen Species") bp(GO:"inflammatory response") path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) path(MESH:"Vascular Diseases")
Jens p(HGNC:HBB) path(MESH:"Vascular Diseases") path(MESH:Hemolysis)
Jens bp(MESH:"Oxidative Stress") p(HGNC:AMBP) p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") bp(MESH:"Platelet Activation") p(HGNC:HBB)
Jens p(HGNC:ARG1) path(MESH:"Pulmonary Embolism") path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") p(MGI:Slc40a1)
Jens a(CHEBI:heme) p(MGI:Hmox1) p(MGI:Sqstm1)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) p(MGI:Slc40a1)
Jens a(CHEBI:"desferrioxamine B") p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:heme) bp(GO:"inflammatory response") bp(HM:"macrophage M1 polarization")
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) p(MGI:Hmox1)
Jens a(CHEBI:heme) a(MESH:Cytokines) p(HGNC:TLR9)
Jens a(CHEBI:"hydrogen peroxide") a(CHEBI:heme) a(CHEBI:methemoglobin)
Jens a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") bp(MESH:Eryptosis)
Jens a(CHEBI:"phosphatidyl-L-serine") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(MESH:ferrylhemoglobin) path(MESH:Inflammation)
Jens path(MESH:"Pulmonary Embolism") path(MESH:"beta-Thalassemia") path(MESH:Hemolysis)
Jens a(MESH:"Cell-Derived Microparticles") path(HP:"Paroxysmal nocturnal hemoglobinuria") path(MESH:Thrombosis)
Jens a(CHEBI:Thrombin) path(MESH:"Disseminated Intravascular Coagulation") path(MESH:Hemolysis)
Jens a(HM:erythrophagocytosis) p(HGNC:CD163) path(MESH:Hematoma)
Jens a(CHEBI:heme) path(MESH:"Vascular Diseases") path(MESH:Hemolysis)
Jens a(CHEBI:heme) path(MESH:Hemolysis) path(MESH:Inflammation)
Jens a(CHEBI:heme) path(HM:"endothelial lesions") path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:Cytokines) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") bp(MESH:"Cytotoxicity, Immunologic")
Jens a(MESH:"Reactive Oxygen Species") a(MESH:Cytokines) p(HGNC:AMBP)
Jens a(CHEBI:heme) p(MGI:Il1b) p(MGI:P2rx4)
Jens a(MESH:"haptoglobin-hemoglobin complex") p(HGNC:CD163) path(MESH:"Pre-Eclampsia")
Jens a(HM:"ABO-incompatible erythrocytes") path(MESH:"Transfusion Reaction") path(MESH:Death)
Jens a(CHEBI:"nitric oxide") bp(MESH:"Platelet Aggregation") p(HGNC:HBB)
Jens p(HGNC:HBB) path(HP:"Paroxysmal nocturnal hemoglobinuria") path(MESH:Thrombosis)
Jens a(CHEBI:methemoglobin) p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") path(MESH:Inflammation)
Jens p(HGNC:HBB) path(MESH:"Anemia, Sickle Cell") path(MESH:Hemolysis)
Jens a(CHEBI:heme) path(MESH:"Thrombotic Microangiopathies") path(MESH:Hemolysis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) a(MESH:"Cell Adhesion Molecules")
Jens a(CHEBI:heme) a(MESH:"Complement Membrane Attack Complex") path(MESH:Hemolysis)
Jens a(HM:"stored erythrocytes") bp(MESH:"Oxidative Stress") p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") bp(GO:"inflammatory response") path(MESH:Inflammation)
Jens a(CHEBI:"4-hydroxynon-2-enal") a(MESH:"Blood Transfusion") p(HGNC:HP)
Jens a(HM:"stored erythrocytes") bp(MESH:"Erythrocyte Deformability") p(MGI:Prdx2)
Jens a(MESH:"Reactive Oxygen Species") bp(MESH:"Oxidative Stress") p(HGNC:AMBP)
Jens a(CHEBI:heme) a(MESH:"Cell Adhesion Molecules") p(HGNC:HMOX1)
Jens a(CHEBI:heme) p(HGNC:HBB) path(HM:"vaso-occlusive crisis")
Jens a(CHEBI:heme) p(HGNC:IL1B) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:"nitric oxide") path(MESH:Inflammation)
Jens a(CHEBI:heme) a(MESH:"Blood Transfusion") p(HGNC:HP)
Jens a(CHEBI:heme) p(MGI:Hmox1) p(MGI:Hspa2)
Jens a(CHEBI:ATP) a(CHEBI:heme) p(HGNC:HPX)
Jens a(CHEBI:heme) path(MESH:Hemolysis) path(MESH:Malaria)
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(MGI:Il1b) p(MGI:P2rx7)
Jens p(HGNC:HBB) path(HM:"Endothelial dysfunction") path(MESH:Thrombosis)
Jens a(MESH:"Adenosine Diphosphate") bp(MESH:"Platelet Activation") path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(MGI:Hmox1) p(PFAM:ubiquitin)
Jens a(CHEBI:heme) a(HM:"oxidative reactions") p(HGNC:HBB)
Jens a(CHEBI:heme) bp(MESH:"Oxidative Stress") p(MGI:Hmox1)
Jens a(CHEBI:methemoglobin) a(HM:"stored erythrocytes") path(MESH:Hemolysis)
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) a(MESH:"Cell Adhesion Molecules")
Jens a(MESH:"Cell-Derived Microparticles") bp(MESH:Hemostasis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(HGNC:HPX) p(HGNC:MRC1)
Jens p(MGI:Casp1) p(MGI:Il1b) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(CHEBI:"nitric oxide") bp(MESH:"Platelet Activation")
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) a(MESH:"Reactive Oxygen Species")
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") a(MESH:"Blood Transfusion") bp(MESH:"Platelet Activation")
Jens a(CHEBI:heme) bp(MESH:"Erythrocyte Count") bp(MESH:"Erythrocyte Deformability")
Jens p(HGNC:AMBP) path(HM:"Oxidative damage") path(MESH:Hemorrhage)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(GO:"endothelial cell activation")
Jens a(CHEBI:heme) p(HGNC:AMBP) path(MESH:"Pre-Eclampsia")
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:"Anemia, Sickle Cell")
Jens a(CHEBI:"oxidised LDL") a(CHEBI:heme) p(HGNC:HMOX1)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) bp(HM:"macrophage M1 polarization")
Jens a(CHEBI:heme) bp(GO:"inflammatory response") path(MESH:"Knee Injuries")
Jens a(CHEBI:heme) path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(MESH:"Oxidative Stress")
Jens a(CHEBI:heme) bp(GO:"complement activation") path(MESH:Hemolysis)
Jens p(HGNC:HBB) path(MESH:Hemolysis) path(MESH:Thrombophilia)
Jens a(HM:"fibrin deposition") a(MESH:"Extracellular Traps") path(MESH:Hemolysis)
Jens p(HGNC:CD59, var("p.Cys89Tyr")) p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:"iron(2+)") complex(a(MESH:"Blood Transfusion"), p(MGI:Hp)) p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") p(MGI:Slc40a1) path(MESH:"Porphyria, Erythropoietic")
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(MESH:Apoptosis)
Jens a(CHEBI:heme) a(CHEBI:methemoglobin) a(HM:"stored erythrocytes")
Jens a(CHEBI:heme) p(HGNC:CXCL8) path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(HM:"nitrite oxidation") bp(MESH:"Oxidative Stress")
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") bp(MESH:"Oxidative Stress")
Jens a(CHEBI:heme) p(HGNC:AMBP) path(HM:"Oxidative damage")
Jens a(CHEBI:heme) a(CHEBI:methemoglobin) path(MESH:Hemolysis)
Jens a(CHEBI:"nitric oxide") bp(MESH:"Erythrocyte Aggregation") path(MESH:Thrombosis)
Jens a(CHEBI:"phosphatidyl-L-serine") a(HM:"stored erythrocytes") path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(MGI:Il1b) p(MGI:Nlrp3)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") a(MESH:Cytokines)
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") path(MESH:Inflammation)
Jens a(MESH:"Cell-Derived Microparticles") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens p(HGNC:CD59, var("p.Cys89Tyr")) p(HGNC:HBB) path(MESH:Thrombosis)
Jens bp(GO:"complement activation") path(MESH:Hemolysis) path(MESH:Inflammation)
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) bp(GO:"endothelial cell activation")
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") bp(MESH:"Erythrocyte Deformability")
Jens a(CHEBI:"hydrogen peroxide") a(CHEBI:heme) bp(MESH:"Oxidative Stress")
Jens a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") path(MESH:Hemolysis)
Jens a(HM:erythrophagocytosis) p(HGNC:HMOX1) path(MESH:Hematoma)
Jens a(CHEBI:"iron(2+)") p(HGNC:HBB) path(MESH:Thrombosis)
Jens bp(MESH:"Platelet Activation") path(HP:"Paroxysmal nocturnal hemoglobinuria") path(MESH:Thrombosis)
Jens a(HM:"stored erythrocytes") path(MESH:Hemolysis) path(MESH:Inflammation)
Jens p(HGNC:TNF) path(MESH:Hemolysis) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) a(HM:"stored erythrocytes")
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") p(MGI:Hmgb1)
Jens a(CHEBI:"nitric oxide") p(HGNC:HBB) path(MESH:Inflammation)
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") bp(MESH:"Platelet Activation")
Jens p(HGNC:HBB) path(HM:"endothelial lesions") path(MESH:Thrombosis)
Jens a(CHEBI:"phosphatidyl-L-serine") a(CHEBI:Thrombin) path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(MESH:"Platelet Activation")
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") bp(GO:"inflammatory response")
Jens a(HM:"stored erythrocytes") bp(MESH:"Oxidative Stress") p(MGI:Prdx2)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) bp(GO:"inflammatory response")
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:"Vascular System Injuries")
Jens a(HM:"stored erythrocytes") bp(MESH:"Erythrocyte Deformability") p(HGNC:HBB)
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) bp(MESH:Vasodilation)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") a(MESH:"Reactive Oxygen Species") bp(GO:"inflammatory response")
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(MGI:Bach1) p(MGI:Spic)
Jens a(CHEBI:lactate) p(HGNC:HBB) p(HGNC:HP)
Jens a(MESH:"Complement Membrane Attack Complex") p(HGNC:CD59, var("p.Cys89Tyr")) path(MESH:Hemolysis)
Jens a(CHEBI:"nitric oxide") complex(p(HGNC:F13A1), p(HGNC:F13B)) path(MESH:"Clot Retraction")
Jens a(CHEBI:"nitric oxide") p(HGNC:HBB) path(MESH:Thrombosis)
Jens p(HGNC:TNF) path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) path(MESH:"Anemia, Sickle Cell") path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:Cytokines) p(HGNC:TLR2)
Jens a(MESH:"Cell-Derived Microparticles") bp(MESH:"Platelet Activation") path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(MESH:"Complement C3a") path(MESH:Hemolysis)
Jens a(CHEBI:"carbon monoxide") a(CHEBI:antioxidant) a(CHEBI:heme)
Jens a(CHEBI:heme) a(MESH:"Complement C5a") path(MESH:Hemolysis)
Jens a(CHEBI:methemoglobin) a(HM:"stored erythrocytes") p(HGNC:HBB)
Jens a(HM:"Glucose-6-phosphate dehydrogenase deficiency") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:"iron trichloride") p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(HGNC:ARG1) p(HGNC:HPX)
Jens p(MGI:Il1b) p(MGI:Nlrp3) p(MGI:P2rx7)
Jens a(CHEBI:"nitric oxide") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(GO:"complement activation") path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:HMOX1) path(MESH:Atherosclerosis)
Jens a(CHEBI:heme) p(HGNC:VWF) path(MESH:Thrombosis)
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) path(MESH:Thrombosis)
Jens a(CHEBI:"iron trichloride") p(HGNC:HBB) path(MESH:"Vascular System Injuries")
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) bp(MESH:"Platelet Aggregation")
Jens a(CHEBI:"nitric oxide") a(CHEBI:heme) bp(MESH:"Platelet Activation")
Jens a(MESH:"Blood Transfusion") p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:heme) p(HGNC:CXCL8) path(MESH:Inflammation)
Jens a(CHEBI:"phosphatidyl-L-serine") path(HP:Hypercoagulability) path(MESH:Thrombosis)
Jens a(CHEBI:"nitric oxide") a(CHEBI:"phosphatidyl-L-serine") path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(MESH:"Platelet Aggregation") path(MESH:Thrombosis)
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") path(MESH:Hemolysis)
Jens path(MESH:"Disseminated Intravascular Coagulation") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens bp(MESH:Hemostasis) path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(MESH:"Oxidative Stress") p(HGNC:AMBP)
Jens a(CHEBI:"iron(2+)") bp(MESH:"Platelet Activation") path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(MGI:Hmox1) path(MESH:Inflammation)
Jens bp(MESH:"Platelet Activation") p(HGNC:HBB) path(MESH:Thrombosis)
Jens a(MESH:"Blood Transfusion") p(HGNC:HBB) p(HGNC:HP)
Jens a(CHEBI:heme) bp(MESH:"Platelet Activation") path(MESH:Thrombosis)
Jens p(HGNC:HBB) p(HGNC:HP) path(MESH:"Anemia, Sickle Cell")
Jens a(CHEBI:"carbon monoxide") a(CHEBI:heme) bp(GO:"cell proliferation")
Jens bp(MESH:"Erythrocyte Volume") bp(MESH:Hemostasis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(MESH:"Lipid Peroxidation") p(HGNC:HP)
Jens a(CHEBI:heme) p(MGI:Nlrp3) path(MESH:Inflammation)
Jens a(CHEBI:heme) a(MESH:Cytokines) p(HGNC:NOD1)
Jens a(CHEBI:heme) a(MESH:"Reactive Oxygen Species") path(MESH:Atherosclerosis)
Jens a(CHEBI:heme) p(MGI:Nlrp3) p(MGI:P2rx7)
Jens a(CHEBI:heme) bp(GO:"inflammatory response") path(MESH:Inflammation)
Jens a(CHEBI:heme) a(HM:"stored erythrocytes") bp(MESH:"Oxidative Stress")
Jens a(MESH:"Cell-Derived Microparticles") p(HGNC:VWF) path(MESH:Thrombosis)
Jens a(CHEBI:heme) p(HGNC:HBB) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(MESH:"Erythrocyte Deformability") p(HGNC:HBB)
Jens a(CHEBI:"lead nitrate") path(MESH:"Hematopoiesis, Extramedullary") path(MESH:Anemia)
Jens a(CHEBI:"hydrogen peroxide") a(CHEBI:methemoglobin) path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:"Blood Transfusion") path(MESH:Hemolysis)
Jens a(CHEBI:heme) a(MESH:Cytokines) p(HGNC:NFKB1)
Jens p(HGNC:HBB) path(MESH:Hemolysis) path(MESH:Inflammation)
Jens a(CHEBI:heme) p(HGNC:IL1B) path(MESH:Inflammation)
Jens p(HGNC:HBB) path(HM:"endothelial lesions") path(MESH:Hemolysis)
Jens p(HGNC:CD163) p(HGNC:HMOX1) path(MESH:Hematoma)
Jens a(CHEBI:"iron(2+)") a(CHEBI:lipopolysaccharide) p(HGNC:HBB)
Jens a(CHEBI:methemoglobin) a(MESH:"Blood Transfusion") p(HGNC:HBB)
Jens a(MESH:"Blood Transfusion") bp(MESH:"Platelet Activation") p(HGNC:HBB)
Jens a(CHEBI:"nitric oxide") bp(MESH:"Platelet Activation") p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") a(CHEBI:"nitric oxide") path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(GO:vasoconstriction) path(MESH:Hemolysis)
Jens p(HGNC:HBB) p(HGNC:HP) path(HP:"Paroxysmal nocturnal hemoglobinuria")
Jens a(CHEBI:"L-arginine") bp(MESH:"Platelet Aggregation") p(HGNC:HBB)
Jens p(HGNC:CD59, var("p.Cys89Tyr")) path(HP:Hypercoagulability) path(MESH:Thrombosis)
Jens p(HGNC:HBB) path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:"iron(2+)") bp(GO:"inflammatory response") bp(HM:"macrophage M1 polarization")
Jens path(MESH:"Thrombotic Microangiopathies") path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens bp(HM:"Atheromatous lesions") p(HGNC:HMOX1) path(MESH:Hematoma)
Jens a(CHEBI:heme) bp(MESH:"Erythrocyte Deformability") path(MESH:Thrombosis)
Jens bp(MESH:"Erythrocyte Deformability") p(HGNC:HBB) path(MESH:Thrombosis)
Jens a(MESH:"Cell-Derived Microparticles") path(MESH:Hemolysis) path(MESH:Thrombophilia)
Jens a(HM:"nitrite oxidation") bp(MESH:"Oxidative Stress") p(MGI:Prdx2)
Jens a(CHEBI:heme) path(MESH:"beta-Thalassemia") path(MESH:Hemolysis)
Jens p(HGNC:HBB) path(MESH:"Vascular System Injuries") path(MESH:Hemolysis)
Jens a(CHEBI:"lead nitrate") a(MESH:Reticulocytes) bp(MESH:Erythropoiesis)
Jens a(HM:"stored erythrocytes") p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(CHEBI:"iron(2+)") a(CHEBI:"lead nitrate") a(CHEBI:heme)
Jens a(CHEBI:"nitric oxide") bp(GO:"endothelial cell activation") p(HGNC:HBB)
Jens p(HGNC:AMBP) path(MESH:"Knee Injuries") path(MESH:"Osteoarthritis, Knee")
Jens a(MESH:"Cell-Derived Microparticles") p(HGNC:CD59, var("p.Cys89Tyr")) path(MESH:Thrombosis)
Jens a(CHEBI:"iron trichloride") path(MESH:"Vascular System Injuries") path(MESH:Hemolysis)
Jens a(CHEBI:heme) bp(GO:"necroptotic process") p(HGNC:HMOX1)
Jens bp(GO:vasoconstriction) p(HGNC:HBB) path(MESH:Hemolysis)
Jens a(MESH:"Erythrocytes, Abnormal") bp(MESH:"Oxidative Stress") p(HGNC:HBB)
Jens a(CHEBI:"iron(2+)") a(CHEBI:heme) bp(MESH:"Oxidative Stress")
Jens a(CHEBI:heme) p(MGI:Nlrp3) p(MGI:P2rx4)
Jens a(CHEBI:heme) path(HM:"Endothelial dysfunction") path(MESH:Thrombosis)
Jens p(HGNC:CD59, var("p.Cys89Tyr")) path(MESH:Hemolysis) path(MESH:Thrombosis)
Jens a(CHEBI:heme) bp(GO:"inflammatory response") p(HGNC:TLR4)
Jens a(CHEBI:"hydrogen peroxide") a(CHEBI:heme) path(MESH:Hemolysis)
Jens a(MESH:"Cell-Derived Microparticles") path(HM:"endothelial lesions") path(MESH:Hemolysis)
Increase Mismatch a(CHEBI:heme) path(MESH:"Acute Kidney Injury") p(MGI:Hmox1)
Increase Mismatch a(CHEBI:heme) p(MGI:Hmox1) path(MESH:"Vascular System Injuries")
Increase Mismatch a(CHEBI:heme) p(MGI:Hmox1) p(MGI:Il1b)
Increase Mismatch a(CHEBI:heme) p(MGI:Hmox1) path(HM:"vaso-occlusive crisis")
Increase Mismatch a(CHEBI:heme) p(HGNC:HMOX1) path(MESH:Atherosclerosis)
Increase Mismatch a(CHEBI:methemoglobin) a(CHEBI:heme) p(MGI:Hmox1)
Increase Mismatch a(CHEBI:protoporphyrin) p(MGI:Hmox1) p(MGI:Il1b)
Increase Mismatch a(MESH:"Blood Transfusion") a(CHEBI:"iron(2+)") a(CHEBI:heme)
Increase Mismatch a(MESH:ferrylhemoglobin) a(CHEBI:heme) p(MGI:Hmox1)
Increase Mismatch p(HGNC:HBB) a(CHEBI:"iron(2+)") a(CHEBI:heme)
Increase Mismatch p(HGNC:HBB) a(CHEBI:heme) p(MGI:Hmox1)
Increase Mismatch p(HGNC:HBB) p(MGI:Hmox1) path(MESH:"Vascular System Injuries")
Decrease Mismatch a(MESH:"haptoglobin-hemoglobin complex") p(HGNC:HP) p(HGNC:HBB)
Decrease Mismatch p(MGI:Hpx) a(CHEBI:heme) p(MGI:Hmox1)
Decrease Mismatch p(MGI:Hpx) p(MGI:Hmox1) path(HM:"vaso-occlusive crisis")
Decrease Mismatch p(MGI:Hp) path(MESH:"Acute Kidney Injury") p(MGI:Hmox1)
Decrease Mismatch p(MGI:Hp) path(HM:"vaso-occlusive crisis") p(MGI:Hmox1)
Decrease Mismatch p(HGNC:AMBP) bp(MESH:Phagocytosis) a(CHEBI:heme)
Decrease Mismatch p(HGNC:FTH1) a(CHEBI:"iron(2+)") a(CHEBI:heme)
Decrease Mismatch p(MGI:Hmox1) p(MGI:Sqstm1) a(CHEBI:heme)

Unstable Triplets 3

Like unstable pairs, unstable triplets require additional context to understand their mechanisms of regulation.

Chaotic Triplets
A triplet of nodes that mutually increase each other, such as when A increases B, B increases C, and C increases A.
Dampened Triplets
A triplet of nodes that mutually decreases each other, such as when A decreases B, B decreases C, and C decreases A.
Type Node A Node B Node C
Chaotic a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") bp(MESH:Eryptosis)
Chaotic a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") path(MESH:Inflammation)
Chaotic a(MESH:"Cell-Derived Microparticles") bp(GO:"complement activation") path(MESH:Hemolysis)

Causal Pathologies 24

Pathologies are more dogmatically the result of molecular and physical processes, and do not necessarily make sense as the subject of causal statements.

Source Relation Target
path(HP:"Paroxysmal nocturnal hemoglobinuria") increases a(MESH:"Cell-Derived Microparticles")
path(HP:"Paroxysmal nocturnal hemoglobinuria") increases p(HGNC:HBB)
path(HP:"Paroxysmal nocturnal hemoglobinuria") decreases p(HGNC:HP)
path(MESH:"Anemia, Sickle Cell") increases p(HGNC:HBB)
path(MESH:"Anemia, Sickle Cell") decreases p(HGNC:HP)
path(MESH:"Blood Loss, Surgical") decreases a(CHEBI:nitrate)
path(MESH:"Blood Loss, Surgical") decreases a(CHEBI:nitrite)
path(MESH:"Knee Injuries") increases a(CHEBI:heme)
path(MESH:"Knee Injuries") increases p(HGNC:AMBP)
path(MESH:"Knee Injuries") increases p(HGNC:HBB)
path(MESH:Anemia) increases a(MESH:"Blood Gas Monitoring, Transcutaneous")
path(MESH:Anemia) increases a(MESH:"Carotid Artery, Internal")
path(MESH:Anemia) decreases a(MESH:"Partial Pressure")
path(MESH:Anemia) increases complex(a(MESH:Luciferases), p(MGI:Hif1a))
path(MESH:Anemia) decreases p(HGNC:HBB)
path(MESH:Anemia) increases r(MGI:Epo)
path(MESH:Anemia) increases r(MGI:Gapdh)
path(MESH:Anemia) increases r(MGI:Hmox1)
path(MESH:Hemolysis) decreases a(CHEBI:"nitric oxide")
path(MESH:Hemolysis) increases a(MESH:"Cell-Derived Microparticles")
path(MESH:Hemolysis) increases p(HGNC:HBB)
path(MESH:Hemolysis) increases p(HGNC:TNF)
path(MESH:Hyperlipidemias) decreases a(MESH:"Nitric Oxide Synthase")
path(MESH:Inflammation) increases a(MESH:"Cell-Derived Microparticles")

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of PyBEL, an open source project. Please feel free to contact us here to give us feedback or report any issues. Also, see our Publishing Notes and Data Protection information.

If you find BEL Commons useful in your work, please consider citing: Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.