Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

Table 1

Listing of the refinement rules, involving any nested combination of the three types of regulation: positive regulation (Pos), negative regulation (Neg) and unspecified regulation (Reg). Each parent event has a regulatory (T)heme argument and an optional (C)ause. The nested regulations are all regulations without a Cause and their detailed structure is omitted for brevity. In full, the first structure would read Pos(C:geneA, T:Pos(T:geneB)) which is rewritten to Pos(C:geneA, T:geneB) with geneA and geneB being any two genes.

Original	Result	Example
Pos(C, T:Pos)	Pos(C, T)	BRs induce accumulation of BZR1 protein
Pos(C, T:Reg)	Pos(C, T)	PKS5 mediates PM H +- ATPase regulation
Reg(C, T:Pos)	Pos(C, T)	CaM regulates activation of HSFs
Neg(C, T:Neg)	Pos(C, T)	E2 prevented downregulation of p21
Reg(C, T:Reg)	Reg(C, T)	PDK1 is involved in the regulation of S6K
Neg(C, T:Reg)	Neg(C, T)	GW5074 prevents this effect on ENT1 mRNA
Neg(C, T:Pos)	Neg(C, T)	BIN2 negatively regulates BZR1 accumulation
Reg(C, T:Neg)	Neg(C, T)	The effect of hCG in downregulating ER beta
Pos(C, T:Neg)	Neg(C, T)	DtRE is required for repression of CAB2