Table of Contents

Regulatory Pairs 2

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

Node A Node B
a(CHEBI:"5-fluorouracil") p(HGNC:HSPA1A)
bp(MESHPP:"DNA Damage") p(HGNC:RAD18)

Contradictory Statements 18

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:HDAC2) increases, decreases, association p(HGNC:ABCB1)
p(HGNC:HDAC2) increases, decreases, association a(SCHEM:Doxorubicin)
a(CHEMBLID:CHEMBL77517) increases, decreases a(SCHEM:"SN 38")
p(HGNC:DAPK1) decreases, causesNoChange, association bp(GOBP:"cell migration")
p(HGNC:SPARC) increases, decreases bp(GOBP:"cell growth")
a(CHEBI:bortezomib) increases, decreases bp(GOBP:"apoptotic process")
p(HGNC:E2F1) increases, causesNoChange bp(GOBP:"apoptotic process")
a(CHEMBLID:CHEMBL79140) increases, decreases a(SCHEM:"SN 38")
p(HGNC:TRAP1) increases, decreases, association p(HGNC:BRAF)
a(CHEBI:thapsigargin) increases, decreases bp(GOBP:"apoptotic process")
a(PH:placeholder) increases, decreases p(HGNC:HDAC2)
a(PH:placeholder) increases, decreases a(SCHEM:Oxaliplatin)
p(MGI:Gstp1) increases, decreases bp(MESHPP:"Drug Resistance, Multiple")
p(HGNC:KDM5B) increases, decreases, positiveCorrelation bp(GOBP:"cell growth")
p(HGNC:KAT5) increases, decreases bp(GOBP:"cell growth")
p(HGNC:KAT5) increases, decreases p(HGNC:AKT1, pmod(Ph, Ser, 473))
p(HGNC:BRD8) increases, decreases bp(GOBP:"cell growth")
p(HGNC:GSN) decreases, directlyIncreases p(HGNC:PLAU)

Unstable Pairs 6

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 p(HGNC:HEXA, pmod(Glyco)) p(HGNC:HEXA, pmod(Glyco))
Chaotic p(HGNC:KRAS) p(HGNC:YAP1)
Chaotic p(HGNC:HIF1A) p(HGNC:LOX)
Chaotic p(HGNC:HIF1A) p(HGNC:KRAS)
Dampened p(HGNC:HEXA) p(HGNC:HEXA)
Dampened p(MGI:Gstp1) p(MGI:Gstp1)

Contradictory Triplets 19

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(CHEMBLID:CHEMBL77517) a(SCHEM:"SN 38") p(HGNC:TOP2A)
Jens p(HGNC:HEXA) p(HGNC:HEXA) p(HGNC:HEXA)
Jens p(HGNC:HEXA, pmod(Glyco)) p(HGNC:HEXA, pmod(Glyco)) p(HGNC:HEXA, pmod(Glyco))
Jens bp(MESHPP:"Drug Resistance, Multiple") p(MGI:Gstp1) p(MGI:Gstp1)
Jens a(SCHEM:Oxaliplatin) a(SCHEM:Resveratrol) p(HGNC:BCL2)
Jens a(CHEBI:"serotonin uptake inhibitor") bp(GOBP:"apoptotic process") p(HGNC:BCL2)
Jens a(SCHEM:Oxaliplatin) bp(GOBP:"apoptotic process") p(HGNC:BCL2)
Jens a(SCHEM:Oxaliplatin) a(SCHEM:Resveratrol) p(HGNC:CASP3)
Jens path(MESHD:"Neoplasm Invasiveness") p(HGNC:GSN) p(HGNC:PLAU)
Jens a(CHEBI:paclitaxel) bp(GOBP:"cell growth") p(HGNC:BRD8)
Jens a(CHEBI:piperazine) bp(GOBP:"apoptotic process") p(HGNC:BCL2)
Jens a(CHEBI:oxaliplatin) a(SCHEM:Luteolin) p(HGNC:NFE2L2)
Jens p(MGI:Gstp1) p(MGI:Gstp1) p(MGI:Gstp1)
Jens bp(GOBP:"cell growth") p(HGNC:HIF1A) p(HGNC:LOX)
Jens a(CHEBI:"serotonin uptake inhibitor") bp(GOBP:"MAPK cascade") bp(GOBP:"cell proliferation")
Jens bp(GOBP:"phosphatidylinositol 3-kinase signaling") p(HGNC:HIF1A) p(HGNC:LOX)
Increase Mismatch p(HGNC:IL6) bp(MESHPP:"Drug Resistance") p(HGNC:STAT3)
Increase Mismatch p(HGNC:HIF1A) bp(GOBP:"cell growth") p(HGNC:LOX)
Decrease Mismatch a(SCHEM:Doxorubicin) p(HGNC:EGFR) bp(MESHPP:"Drug Resistance")

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
Chaotic bp(GOBP:"phosphatidylinositol 3-kinase signaling") p(HGNC:HIF1A) p(HGNC:LOX)

Causal Pathologies 2

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(MESHD:"Gastrointestinal Neoplasms") decreases p(HGNC:MT1A)
path(MESHD:Anoxia) increases p(HGNC:KRAS, var(p.Gly12Val))

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