1. Catalog
  2. Networks
  3. M1 muscarinic acetylcholine receptor in Alzheimer’s disease v1.0.0
  4. Biogrammar

Biogrammar Summary of M1 muscarinic acetylcholine receptor in Alzheimer’s disease 1.0.0

Table of Contents

  1. Contradictory Pairs
  2. Unstable Pairs
  3. Contradictory Triplets
  4. Causal Pathologies

Contradictory Statements 1

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:CHRM1) causesNoChange, increases bp(GO:"ERK1 and ERK2 cascade")

Unstable Pairs 2

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
Dampened a(CHEBI:"amyloid-beta") p(HGNC:CHRM1)
Dampened a(CHEBI:"amyloid-beta") complex(p(FPLX:"G_protein"), p(HGNC:CHRM1))

Contradictory Triplets 1

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
Jens a(CHEBI:"amyloid-beta") a(MESH:"1-(1'-(2-methylbenzyl)-1,4'-bipiperidin-4-yl)-1H-benzo(d)imidazol-2-(3H)-one") p(HGNC:CHRM1)

Causal Pathologies 4

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(MESH:"Alzheimer Disease") decreases a(MESH:"Cholinergic Neurons")
path(MESH:"Alzheimer Disease") decreases p(HGNC:CHAT)
path(MESH:"Alzheimer Disease") decreases p(HGNCGENEFAMILY:"Cholinergic receptors nicotinic subunits")
path(MESH:"Parkinson Disease") decreases a(MESH:"Dopaminergic Neurons")

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.