- 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.

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`

.

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 | p(FPLX:ERK) | p(FPLX:NFkappaB) | p(HGNC:TNF) | |

Chaotic | p(FPLX:NFkappaB) | p(FPLX:NFkappaB) | p(HGNC:IL1B) | |

Chaotic | p(FPLX:NFkappaB) | p(FPLX:NFkappaB) | p(HGNC:TNF) |

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.