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Table of Contents

Unstable Pairs 1

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(CHEBI:"amyloid-beta") bp(GOBP:"non-canonical Wnt signaling pathway")

Contradictory Triplets 2

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") bp(GOBP:"non-canonical Wnt signaling pathway") p(HGNC:DKK1)
Jens a(CHEBI:"amyloid-beta") path(MESHD:"Cognitive Dysfunction") p(HGNC:DKK1)

Unstable Triplets 1

Like unstable pairs, unstable triplets require additional context to understand their mechanisms of regulation.

Chaotic Triplets
A triplet of nodes that mutually increase each other, such as when A increases B, B increases C, and C increases A.
Dampened Triplets
A triplet of nodes that mutually decreases each other, such as when A decreases B, B decreases C, and C decreases A.
Type Node A Node B Node C
Chaotic a(CHEBI:"amyloid-beta") bp(GOBP:"non-canonical Wnt signaling pathway") p(HGNC:DKK1)

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(MESHD:"Alzheimer Disease") increases a(CHEBI:"amyloid-beta")

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 the open source project, PyBEL. Please feel free to contact us here to give us feedback or report any issues.