1. Catalog
  2. Networks
  3. mTOR-Related Brain Dysfunctions in Neuropsychiatric Disorders v1.0.0
  4. Biogrammar

Biogrammar Summary of mTOR-Related Brain Dysfunctions in Neuropsychiatric Disorders 1.0.0

Table of Contents

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

Contradictory Statements 1

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
a(CHEBI:methamphetamine) association, decreases, increases a(CHEBI:dopamine)

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 a(CHEBI:methamphetamine) p(HGNC:MTOR)
Dampened a(CHEBI:methamphetamine) bp(GO:autophagy)

Contradictory Triplets 15

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:autophagy) p(HGNC:MTOR) path(MESH:Schizophrenia)
Jens a(CHEBI:dopamine) a(CHEBI:methamphetamine) bp(GO:autophagy)
Jens a(CHEBI:sirolimus) bp(GO:autophagy) p(HGNC:MTOR)
Jens a(CHEBI:methamphetamine) a(CHEBI:sirolimus) bp(GO:autophagy)
Jens p(HGNC:CDK5) p(HGNC:DRD1) path(MESH:Schizophrenia)
Jens a(CHEBI:methamphetamine) bp(GO:autophagy) p(HGNC:DRD1)
Jens a(CHEBI:methamphetamine) bp(GO:autophagy) p(HGNC:MTOR)
Jens bp(GO:autophagy) p(HGNC:MTOR) path(MESH:"Neurodegenerative Diseases")
Jens a(CHEBI:chlorpromazine) bp(GO:autophagy) p(HGNC:MTOR)
Jens a(CHEBI:dopamine) p(HGNC:DISC1, var("?")) path(MESH:Schizophrenia)
Jens p(HGNC:CDK5) p(HGNC:MAPT, pmod(HBP:hyperphosphorylation)) path(MESH:Schizophrenia)
Jens p(FPLX:AKT) p(HGNC:DRD1) path(MESH:Schizophrenia)
Increase Mismatch p(HGNC:DISC1, var("?")) path(MESH:Schizophrenia) p(HGNC:MTOR)
Decrease Mismatch a(CHEBI:"lithium(1+)") path(MESH:Schizophrenia) p(HGNC:MTOR)
Decrease Mismatch a(CHEBI:sirolimus) p(HGNC:MTOR) path(MESH:Schizophrenia)

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
Dampened a(CHEBI:methamphetamine) bp(GO:autophagy) p(HGNC:DRD1)

Causal Pathologies 11

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(MESH:Schizophrenia) increases a(CHEBI:dopamine)
path(MESH:Schizophrenia) decreases a(GO:dendrite)
path(MESH:Schizophrenia) decreases p(FPLX:AKT)
path(MESH:Schizophrenia) decreases p(HGNC:ADNP)
path(MESH:Schizophrenia) decreases p(HGNC:ADNP2)
path(MESH:Schizophrenia) decreases p(HGNC:ATG3)
path(MESH:Schizophrenia) decreases p(HGNC:BECN1)
path(MESH:Schizophrenia) decreases p(HGNC:MAP2)
path(MESH:Schizophrenia) increases p(HGNC:MAPT)
path(MESH:Schizophrenia) decreases p(HGNC:SLC6A3)
path(MESH:Schizophrenia) decreases p(HGNC:ULK2)

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.