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Biogrammar Summary of The Ubiquitin–Proteasome System and the Autophagic–Lysosomal System in Alzheimer Disease 1.0.0

Table of Contents

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

Contradictory Statements 3

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
bp(GO:"lysosomal protein catabolic process") decreases, increases a(CHEBI:"amyloid-beta")
p(HGNC:RAB5A) decreases, increases bp(GO:endocytosis)
bp(GO:autophagy) decreases, increases path(HBP:neurotoxicity)

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
Chaotic p(MESH:Proteins, pmod(Ub)) p(MESH:Proteins, pmod(Ub))
Dampened p(HBP:"UBB+1", pmod(UbPoly)) p(HBP:"UBB+1", pmod(UbPoly))

Contradictory Triplets 19

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
Mutual bp(GO:"lysosomal protein catabolic process") bp(GO:endocytosis) path(MESH:"Alzheimer Disease")
Jens a(CHEBI:"amyloid-beta") a(CHEBI:sirolimus) bp(GO:autophagy)
Jens a(CHEBI:"amyloid-beta") bp(GO:"lysosomal protein catabolic process") bp(GO:memory)
Jens bp(GO:endocytosis) p(HBP:"APP C-terminally truncated carboxyl-terminal fragments") p(HGNC:APP)
Jens a(CHEBI:"amyloid-beta polypeptide 42") a(CHEBI:"amyloid-beta") g(HBP:"APOE e4")
Jens a(MESH:Proteins) bp(GO:endocytosis) p(HGNC:RAB5A)
Jens a(CHEBI:"amyloid-beta polypeptide 42") a(CHEBI:"amyloid-beta") bp(GO:endocytosis)
Jens bp(GO:endocytosis) g(HBP:"APOE e4") p(HBP:"APP C-terminally truncated carboxyl-terminal fragments")
Jens a(CHEBI:"amyloid-beta") bp(GO:"lysosomal protein catabolic process") bp(GO:autophagy)
Jens p(HBP:"UBB+1", pmod(UbPoly)) p(HBP:"UBB+1", pmod(UbPoly)) p(HBP:"UBB+1", pmod(UbPoly))
Jens a(CHEBI:"amyloid-beta") bp(GO:endocytosis) g(HBP:"APOE e4")
Jens p(MESH:Proteins, pmod(Ub)) p(MESH:Proteins, pmod(Ub)) p(MESH:Proteins, pmod(Ub))
Jens a(CHEBI:"amyloid-beta") a(GO:synapse) bp(GO:endocytosis)
Jens a(CHEBI:"amyloid-beta") bp(GO:endocytosis) bp(GO:memory)
Jens bp(GO:endocytosis) p(HBP:"APP C-terminally truncated carboxyl-terminal fragments") p(HGNC:RAB5A)
Jens a(CHEBI:"amyloid-beta") bp(GO:endocytosis) p(HGNC:RAB5A)
Jens a(CHEBI:cholesterol) bp(GO:endocytosis) p(HBP:"APP C-terminally truncated carboxyl-terminal fragments")
Jens a(CHEBI:lipid) bp(GO:endocytosis) p(HGNC:RAB5A)
Jens a(CHEBI:"amyloid-beta polypeptide 42") bp(GO:endocytosis) g(HBP:"APOE e4")

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.