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Heme Curation 0.0.1-dev

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charles.hoyt@scai.fraunhofer.de at 2019-09-10 13:50:40.134319
Authors
Daniel Domingo-Fernández, Farah Humayun
Contact
daniel.domingo.fernandez@scai.fraunhofer.de
Description
Mechanistic knowledge surrounding heme
License
MIT License
Number Nodes
763
Number Edges
3004
Number Components
10
Network Density
0.00516678534449249
Average Degree
3.93709043250328
Number Citations
46
Number BEL Errors
0

Content Statistics

Network Overlap

The node-based overlap between this network and other networks is calculated as the Szymkiewicz-Simpson coefficient of their respective nodes. Up to the top 10 are shown below.

Network Overlap
Anti-inflammatory activity of anatabine via inhibition of STAT3 phosphorylation v1.0.0 28%
Posiphen as a candidate drug to lower CSF amyloid precursor protein, amyloid-b peptide and s levels: target engagement, tolerability and pharmacokinetics in humans v0.1.0 27%
Tau protein aggregation is associated with cellular senescence in the brain v1.0.0 22%
Inflammasome Involvement in Alzheimer’s Disease v1.0.0 22%
The role of inflammasome in Alzheimer’s disease v1.0.3 21%
Amelioration of Experimental Autoimmune Encephalomyelitis by Anatabine v1.0.0 21%
Molecular chaperones and proteostasis regulation during redox imbalance v1.0.0 20%
In Vivo and In Vitro Characterization of Antalarmin, a Nonpeptide Corticotropin-Releasing Hormone (CRH) Receptor Antagonist: Suppression of Pituitary ACTH Release and Peripheral Inflammation v1.0.0 20%
Significance of NF-κB as a pivotal therapeutic target in the neurodegenerative pathologies of Alzheimer's disease and multiple sclerosis v1.0.0 18%
Inflammasome activation and innate immunity in Alzheimer’s disease v1.0.2 17%

Sample Edges

p(HGNC:SYK) hasVariant p(HGNC:SYK, pmod(Ph)) View Subject | View Object

a(CHEBI:"2-(2-amino-3-methoxyphenyl)chromen-4-one") decreases bp(GO:"cell proliferation") View Subject | View Object

In VSMC pretreated with the ERK-2 inhibitor PD98059 (10 mM), migration induced by heme was partially inhibited (Fig. 3A) and heme proliferative effect on VSMC was impaired (Fig. 3B). PubMed:22954673

Annotations
Cell Ontology (CL)
neutrophil
MeSH
Muscle, Smooth, Vascular
Text Location
Results

a(CHEBI:"2-(2-amino-3-methoxyphenyl)chromen-4-one") decreases bp(GO:"cell migration") View Subject | View Object

In VSMC pretreated with the ERK-2 inhibitor PD98059 (10 mM), migration induced by heme was partially inhibited (Fig. 3A) and heme proliferative effect on VSMC was impaired (Fig. 3B). PubMed:22954673

Annotations
Cell Ontology (CL)
neutrophil
MeSH
Muscle, Smooth, Vascular
Text Location
Results

a(CHEBI:"3',5'-cyclic GMP") increases bp(GO:vasodilation) View Subject | View Object

As such, it nitrosylates the haem-moiety of guanylate cyclase, thereby stimulating formation of cyclic guanine monophosphate (cGMP), which then initiates calcium-dependent vasodilation (Olson et al, 2004). PubMed:25307023

Annotations
Cell Ontology (CL)
erythrocyte
MeSH
Plasma
MeSH
Urine
MeSH
Anemia, Hemolytic, Autoimmune
Text Location
Review

a(CHEBI:"3',5'-cyclic GMP") decreases bp(MESH:"Platelet Aggregation") View Subject | View Object

NO inhibits platelet aggregation mediated by guanylate cyclase activation with a subsequent rise in cGMP (Faint et al, 1991). PubMed:25307023

Annotations
Cell Ontology (CL)
macrophage
MeSH
Plasma
MeSH
Urine
MeSH
Anemia, Hemolytic, Autoimmune
Text Location
Review

Sample Nodes

a(MESH:Monocytes)

In-Edges: 4 | Out-Edges: 7 | Explore Neighborhood | Download JSON

bp(GO:"cellular respiration")

In-Edges: 6 | Out-Edges: 3 | Explore Neighborhood | Download JSON

bp(GO:"inflammatory response")

In-Edges: 55 | Out-Edges: 24 | Explore Neighborhood | Download JSON

bp(GO:aging)

In-Edges: 27 | Out-Edges: 61 | Explore Neighborhood | Download JSON

bp(GO:phagocytosis)

In-Edges: 12 | Out-Edges: 10 | Explore Neighborhood | Download JSON

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.