Table of Contents

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(RGD:Irf1) p(RGD:Stat1)
Dampened p(RGD:Nfkbia) p(RGD:Nfkbia)

Contradictory Triplets 7

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 bp(GOBP:"megakaryocyte differentiation") p(RGD:Gata1) p(RGD:Tubb1)
Jens bp(GOBP:"megakaryocyte differentiation") p(RGD:Fli1) p(RGD:Tesc)
Jens p(RGD:Nfkbia) p(RGD:Nfkbia) p(RGD:Nfkbia)
Jens complex(SCOMP:"IkappaB Kinase Complex") p(HGNC:NFKBIA, pmod(Ph, Ser, 36)) p(RGD:Nfkbia)
Jens bp(GOBP:"megakaryocyte differentiation") p(RGD:Gata1) p(RGD:Pf4)
Jens complex(SCOMP:"IkappaB Kinase Complex") p(HGNC:NFKBIA, pmod(Ph, Ser, 32)) p(RGD:Nfkbia)
Jens bp(GOBP:"megakaryocyte differentiation") p(RGD:Gata1) p(RGD:Nfe2)

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.