### Regulatory Pairs 1

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

Node A Node B

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:"methylene blue") decreases, increases p(HGNC:MARK4)
p(HGNC:TTBK2, var("p.Tyr448*")) decreases, increases p(HGNC:TTBK2)
p(HGNC:TTBK2, var("p.Glu450*")) decreases, increases p(HGNC:TTBK2)
p(HGNC:TTBK2, var("p.Asp449*")) decreases, increases p(HGNC:TTBK2)

### Unstable Pairs 1

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 complex(p(HGNC:CDK5), p(HGNC:CDK5R1)) p(HGNC:CDK5)

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`.
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 p(HGNC:MAPT, pmod(Ac, Lys, 280)) p(HGNC:MAPT, pmod(Ph, Ser, 262)) path(MESH:"Alzheimer Disease")
Jens a(HBP:"Tau aggregates") a(HBP:"Tau aggregates") a(HBP:"Tau aggregates")
Jens a(CHEBI:"D-ribose") a(CHEBI:"advanced glycation end-product") p(MGI:Mapt, pmod(Ph, Ser, 214))
Jens a(CHEBI:rolipram) complex(GO:"proteasome complex") p(FPLX:PKA)
Jens a(CHEBI:"D-ribose") a(HBP:"advanced glycation end product") p(HGNC:MAPT, pmod(Ph, Ser, 396))
Jens bp(GO:"microtubule polymerization") p(HGNC:DAPK1) p(HGNC:MAPT)
Jens a(CHEBI:"okadaic acid") p(HGNC:MAPT, pmod(Ph, Ser, 202)) p(HGNC:MAPT, pmod(Sumo, Lys, 340))
Jens a(CHEBI:resveratrol) p(HGNC:MID1) p(HGNC:PPP2CA)
Jens a(GO:mitochondrion) bp(MESH:"Oxidative Stress") p(HGNC:GLP1R)
Jens a(CHEBI:"D-ribose") a(HBP:"advanced glycation end product") p(HGNC:MAPT, pmod(Ph, Thr, 181))
Jens a(CHEBI:"D-ribose") a(HBP:"advanced glycation end product") p(HGNC:MAPT, pmod(Ph, Ser, 214))
Jens a(CHEBI:"trichostatin A") p(FPLX:HDAC) p(HGNC:MAPT, pmod(Ac))
Jens a(HBP:"Tau aggregates") a(HBP:"Tau aggregates") p(MGI:Crhr1)
Jens p(HGNC:DAPK1) p(HGNC:MAPT) p(HGNC:PIN1, pmod(Ph, Ser, 71))
Jens a(HBP:"Tau epitope, PHF1") p(HGNC:GSK3B) p(HGNC:MAPT, pmod(Ph, Ser, 396))
Jens p(HBP:"CDK5R1 p25") p(HBP:"Tau epitope, AT8") p(MGI:Cdk5)
Jens a(HBP:"granulovacuolar degeneration") p(HGNC:MAPT, pmod(Ph, Ser, 262)) p(HGNC:MARK4, pmod(Ph))
Jens a(CHEBI:"D-ribose") a(CHEBI:"advanced glycation end-product") p(MGI:Mapt, pmod(Ph, Ser, 396))
Jens p(FPLX:CALM) p(HBP:"DAPK, basic loop (BL) motif") p(HGNC:DAPK2)
Jens p(HGNC:GSK3B) p(HGNC:GSK3B, pmod(Ph, Ser, 9)) p(HGNC:PPP1CA)
Increase Mismatch p(HBP:"APOE e4") p(MGI:Cdk5) p(MGI:Cdk5r1)
Increase Mismatch p(HGNC:DAPK1) p(HGNC:MAPT, pmod(Ph, Ser, 262)) bp(GO:"apoptotic process")
Increase Mismatch p(HGNC:DAPK1) bp(GO:"apoptotic process") p(HGNC:MAPT, pmod(Ph, Ser, 396))
Increase Mismatch p(HGNC:DAPK1) bp(GO:"apoptotic process") p(HGNC:MAPT, pmod(Ph, Thr, 231))

### Causal Pathologies 14

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:"Alzheimer Disease") increases p(ECCODE:"3.1.1.89")
path(MESH:"Alzheimer Disease") increases p(HGNC:ITPKB)
path(MESH:"Alzheimer Disease") decreases p(HGNC:LCMT1)
path(MESH:"Alzheimer Disease") increases p(HGNC:MAPK1)
path(MESH:"Alzheimer Disease") increases p(HGNC:PRKCB)
path(MESH:"Alzheimer Disease") increases p(HGNC:TGM2)
path(MESH:"Supranuclear Palsy, Progressive") increases p(ECCODE:"3.1.1.89")
path(MESH:"Supranuclear Palsy, Progressive") decreases p(HGNC:LCMT1)
path(MESH:"Supranuclear Palsy, Progressive") increases p(HGNC:TGM1)
path(MESH:"Supranuclear Palsy, Progressive") increases r(HBP:"TGM2 Isoform 3 (349 aa)")
path(MESH:"Supranuclear Palsy, Progressive") increases r(HGNC:TGM1)
path(MESH:"Supranuclear Palsy, Progressive") increases r(HGNC:TGM2)
path(MESH:Fasting) decreases p(MGI:Mapt, pmod(HBP:"O-GlcNAcylation"))
path(MESH:Fasting) increases p(MGI:Mapt, pmod(Ph))