1. Catalog
  2. Networks
  3. Nuclear Factor Kappa-light-chain-enhancer of Activated B Cells (NF-κB) - a Friend, a Foe, or a Bystander - in the Neurodegenerative Cascade and Pathogenesis of Alzheimer's Disease v1.0.0
  4. Biogrammar

Biogrammar Summary of Nuclear Factor Kappa-light-chain-enhancer of Activated B Cells (NF-κB) - a Friend, a Foe, or a Bystander - in the Neurodegenerative Cascade and Pathogenesis of Alzheimer's Disease 1.0.0

Table of Contents

  1. Regulatory Pairs
  2. Contradictory Pairs
  3. Unstable Pairs
  4. Contradictory Triplets
  5. Unstable Triplets
  6. Causal Pathologies

Regulatory Pairs 3

These pairs of nodes represent motifs like A increases B and B decreases A.

Node A Node B
p(HGNC:RELA) bp(GO:"long-term synaptic potentiation")
p(HGNC:NFKB1) bp(GO:"long-term synaptic potentiation")
bp(GO:"calcium ion homeostasis") complex(GO:"NF-kappaB complex")

Contradictory Statements 2

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
complex(GO:"NF-kappaB complex") decreases, increases p(HGNC:BCL2L1)
complex(p(HGNC:BACE1), p(HGNC:NFKB2), p(HGNC:RELA)) hasComponent, decreases, increases p(HGNC:BACE1)

Unstable Pairs 5

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") complex(GO:"NF-kappaB complex")
Chaotic complex(GO:"NF-kappaB complex") p(HGNC:CNTF)
Chaotic complex(GO:"NF-kappaB complex") p(HGNC:IL6)
Chaotic complex(GO:"NF-kappaB complex") p(HGNC:TNF)
Chaotic complex(GO:"NF-kappaB complex") p(HGNC:LIF)

Contradictory Triplets 14

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(GO:"JNK cascade") complex(GO:"NF-kappaB complex")
Jens bp(GO:"neuron death") complex(GO:"NF-kappaB complex") p(HGNC:IL1B)
Jens bp(GO:"neuron death") complex(GO:"NF-kappaB complex") p(HGNC:TNF)
Jens a(PUBCHEM:16057918) complex(GO:"NF-kappaB complex") p(HGNC:BCL2L1)
Jens a(CHEBI:"amyloid-beta") bp(GO:"Fas signaling pathway") complex(GO:"NF-kappaB complex")
Jens bp(GO:"neuron death") complex(GO:"NF-kappaB complex") p(HGNC:CXCL8)
Jens a(CHEBI:"amyloid-beta") bp(MESH:"Oxidative Stress") complex(GO:"NF-kappaB complex")
Jens a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") complex(a(GO:"membrane attack complex"), p(HGNC:C5))
Jens a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") p(HGNC:TNF)
Jens bp(GO:"neuron death") complex(GO:"NF-kappaB complex") p(HGNC:IL6)
Jens a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") complex(GO:"calcium- and calmodulin-dependent protein kinase complex")
Jens a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") p(HGNC:BCL2L1)
Jens a(CHEBI:"amyloid-beta") bp(GO:"apoptotic process") complex(GO:"NF-kappaB complex")
Jens a(CHEBI:"amyloid-beta") bp(GO:"apoptotic process") p(HGNC:BCL2L1)

Unstable Triplets 6

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(GO:"JNK cascade") complex(GO:"NF-kappaB complex")
Chaotic a(CHEBI:"amyloid-beta") bp(GO:"Fas signaling pathway") complex(GO:"NF-kappaB complex")
Chaotic a(CHEBI:"amyloid-beta") bp(MESH:"Oxidative Stress") complex(GO:"NF-kappaB complex")
Chaotic a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") complex(a(GO:"membrane attack complex"), p(HGNC:C5))
Chaotic a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") p(HGNC:TNF)
Chaotic a(CHEBI:"amyloid-beta") complex(GO:"NF-kappaB complex") complex(GO:"calcium- and calmodulin-dependent protein kinase complex")

Causal Pathologies 5

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(HP:"Ischemic stroke") increases complex(GO:"NF-kappaB complex")
path(HP:Seizures) increases complex(GO:"NF-kappaB complex")
path(MESH:"Brain Injuries, Traumatic") increases complex(GO:"NF-kappaB complex")
path(MESH:"Cerebral Infarction") increases complex(GO:"NF-kappaB complex")
path(MESH:Hypoxia) increases complex(GO:"NF-kappaB complex")

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.