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Structural and functional properties of prefibrillar α-synuclein oligomers 1.0.0

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charles.hoyt@scai.fraunhofer.de at 2019-02-27 16:21:28.587610
Authors
Esther Wollert and Charles Tapley Hoyt
Contact
charles.hoyt@scai.fraunhofer.de
License
CC BY 4.0
Copyright
Copyright © 2018 Fraunhofer Institute SCAI, All rights reserved
Number Nodes
13
Number Edges
19
Number Components
1
Network Density
0.121794871794872
Average Degree
1.46153846153846
Number Citations
1
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
Alpha-synuclein oligomers: a new hope v1.0.0 54%
Promoting the clearance of neurotoxic proteins in neurodegenerative disorders of ageing v1.0.0 38%
Tau Modifications v1.9.5 38%
Nicotinic Acetylcholine Receptors and Nicotinic Cholinergic Mechanisms of the Central Nervous System v1.0.0 38%
albuquerque2009 v1.0.0 31%
Nicotinic acetylcholine receptor signalling: roles in Alzheimer's disease and amyloid neuroprotection. v1.0.0 31%
Tau clearance mechanisms and their possible role in the pathogenesis of Alzheimer disease v1.0.0 23%
The Ubiquitin–Proteasome System and the Autophagic–Lysosomal System in Alzheimer Disease v1.0.0 23%
New insights into the role of microRNAs and long noncoding RNAs in most common neurodegenerative diseases v1.0.0 23%
Nuclear Factor Kappa-light-chain-enhancer of Activated B Cells (NF-κB) - a Friend, a Foe, or a Bystander - in the Neurodegenerative Cascade and Pathogenesis of Alzheimer's Disease v1.0.0 23%

Sample Edges

a(CHEBI:dopamine) increases a(HBP:HBP00093) View Subject | View Object

The neurotransmitter dopamine (DA) has been shown to promote the formation of stable, SDS-resistant α -syn oligomers both in vitro and in neurons30–32 by different mechanisms, including the formation of stable α -syn-DA-quinone adducts, methionine oxidation, or non-covalent interactions33. PubMed:27075649

Annotations
Cell Ontology (CL)
neuron
Confidence
High
MeSH
Lewy Bodies

a(CHEBI:dopamine) increases a(HBP:HBP00093) View Subject | View Object

DA-mediated α -syn oligomers constitute a range of SDS-resistant species with apparent molecular weights ranging from over 2200 to 200 kDa as determined by SEC (Fig. 4a). PubMed:27075649

Annotations
MeSH
Intracellular Space
Cell Ontology (CL)
neuron
Confidence
High
MeSH
Lewy Bodies

a(CHEBI:glutaraldehyde) increases a(HBP:HBP00093) View Subject | View Object

GA-cross-linked α -syn oligomers are also a heterogeneous set of SDS-resistant oligomeric species (Fig. 4b). PubMed:27075649

Annotations
MeSH
Intracellular Space
Cell Ontology (CL)
neuron
Confidence
High
MeSH
Lewy Bodies

a(HBP:HBP00016) positiveCorrelation path(MESH:"Parkinson Disease") View Subject | View Object

Parkinson’s disease (PD), Multiple System Atrophy (MSA) and Dementia with Lewy Bodies (DLB) are devastating synucleinopathies. The deposition of filamentous insoluble protein inclusions termed Lewy bodies and Lewy neurites whose main constituent is aggregated α -synuclein (α -syn) characterizes synucleinopathies. PubMed:27075649

Annotations
Confidence
High
MeSH
Lewy Bodies

a(HBP:HBP00016) positiveCorrelation path(MESH:"Multiple System Atrophy") View Subject | View Object

Parkinson’s disease (PD), Multiple System Atrophy (MSA) and Dementia with Lewy Bodies (DLB) are devastating synucleinopathies. The deposition of filamentous insoluble protein inclusions termed Lewy bodies and Lewy neurites whose main constituent is aggregated α -synuclein (α -syn) characterizes synucleinopathies. PubMed:27075649

Annotations
Confidence
High
MeSH
Lewy Bodies

Sample Nodes

path(MESH:"Parkinson Disease")

In-Edges: 68 | Out-Edges: 53 | Explore Neighborhood | Download JSON

a(CHEBI:"calcium(2+)")

In-Edges: 56 | Out-Edges: 30 | Explore Neighborhood | Download JSON

bp(GO:"neuron death")

In-Edges: 77 | Out-Edges: 17 | Explore Neighborhood | Download JSON

bp(GO:"apoptotic process")

In-Edges: 94 | Out-Edges: 13 | Explore Neighborhood | Download JSON

a(CHEBI:dopamine)

In-Edges: 46 | Out-Edges: 13 | 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.