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Biogrammar Summary of Protein phosphatase 2A dysfunction in Alzheimer’s disease 1.0.0

Table of Contents

  1. Regulatory Pairs
  2. Contradictory Pairs
  3. Contradictory Triplets
  4. Causal Pathologies

Regulatory Pairs 1

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

Node A Node B
complex(GO:"protein phosphatase type 2A complex") p(HGNC:GSK3B)

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
p(HGNC:PPP2CA, pmod(Ph, Tyr, 307)) decreases, increases complex(GO:"protein phosphatase type 2A complex")
p(HGNC:PPP2CB, pmod(Ph, Tyr, 307)) decreases, increases complex(GO:"protein phosphatase type 2A complex")

Contradictory Triplets 8

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
Separate path(MESH:"Alzheimer Disease") complex(GO:"protein phosphatase type 2A complex") p(HGNC:SET)
Separate path(MESH:"Alzheimer Disease") complex(GO:"protein phosphatase type 2A complex") p(HGNC:SET, frag("?"))
Separate path(MESH:"Alzheimer Disease") complex(GO:"protein phosphatase type 2A complex") p(HGNC:ANP32A)
Jens complex(GO:"protein phosphatase type 2A complex") p(HGNC:SET) path(MESH:"Alzheimer Disease")
Jens complex(GO:"protein phosphatase type 2A complex") p(FPLX:PPP2, pmod(Ph, Tyr, 307)) p(HGNC:PTPA)
Jens a(CHEBI:"okadaic acid") complex(GO:"protein phosphatase type 2A complex") p(HGNC:MAPT, pmod(Ph))
Jens complex(GO:"protein phosphatase type 2A complex") p(HGNC:MAPT, pmod(Ph)) path(MESH:"Alzheimer Disease")
Jens complex(GO:"protein phosphatase type 2A complex") p(HGNC:ANP32A) path(MESH:"Alzheimer Disease")

Causal Pathologies 3

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:"Vitamin B Deficiency") decreases p(FPLX:PPP2, pmod(Me))
path(MESH:"Vitamin B Deficiency") increases p(HGNC:APP, pmod(Ph))
path(MESH:"Vitamin B Deficiency") increases p(HGNC:MAPT, pmod(Ph))

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.