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  3. Autophagy and the ubiquitin-proteasome system: collaborators in neuroprotection v1.0.0
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Biogrammar Summary of Autophagy and the ubiquitin-proteasome system: collaborators in neuroprotection 1.0.0

Table of Contents

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

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(GO:lysosome) a(GO:lysosome)
Chaotic a(MESH:Proteins) a(MESH:Proteins)
Dampened p(HGNC:SNCA, var("?")) p(HGNC:SNCA, var("?"))

Contradictory Triplets 4

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(GO:lysosome) a(GO:lysosome) a(GO:lysosome)
Jens a(MESH:Proteins) a(MESH:Proteins) a(MESH:Proteins)
Jens p(HGNC:SNCA, var("?")) p(HGNC:SNCA, var("?")) p(HGNC:SNCA, var("?"))
Increase Mismatch p(HGNC:SQSTM1) bp(GO:"proteasome-mediated ubiquitin-dependent protein catabolic process") bp(GO:autophagy)

Causal Pathologies 1

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:Starvation) increases p(HGNC:WDFY3)

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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.