Table 2

List of predefined interaction types

Interaction type

Gene

Ligand

Acts on upstream signaling pathway

•

Competitive inhibition

•

•

Genetic

•

•

Indirect

•

•

Multimerization

•

•

Not specified

•

•

Physical: deacetylation

•

•

Physical: dephosphorylation

•

•

Physical: desumoylation

•

•

Physical: deubiqiutination

•

•

Physical: enzyme modification: acetylation

•

•

Physical: enzyme modification: methylation

•

•

Physical: enzyme modification: phosphorylation

•

•

Physical: enzyme modification: protein cleavage

•

•

Physical: enzyme modification: sumoylation

•

•

Physical: indirect altering posttranslational modifications

•

•

Physical: sequestering

•

•

Physical: translocation

•

•

Physical: ubiquitination

•

•

Physical: undefined direct interaction

•

•

Physical: with another TF

•

Physical: with another TF: complex binds DNA

•

Physical: with co-activator affecting recruitment

•

•

Physical: with co-repressor affecting recruitment

•

•

Regulatory: decreases expression of this TF

•

•

Regulatory: increases expression of this TF

•

•

Unknown

•

•

When a protein-to-protein or protein-to-ligand is added to a TFe article either by the author or automatically from BioGRID, the author of that article has the option to define the interaction type if this information is known. To promote a standardized vocabulary for describing interaction types, a list of possible interaction types between proteins and ligands is provided to the author. This list continues to be adjusted and expanded based on need and author feedback.

Yusuf et al. Genome Biology 2012 13:R24   doi:10.1186/gb-2012-13-3-r24