Advances in Bioinformatics / 2012 / Article / Tab 1

Research Article

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

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